APh161 - Physics of Biological Structure and Function
Rob
Phillips
Myosin V (blue), a biomolecular motor that moves in nanometer-size steps on actin (red), transports cargo within cells
Source:
http://www.news.uiuc.edu/scitips/03/0605selvin.html
[ Announcements | Class Schedule | Course Outline and Bibliography | Lecture Notes | Assignments | Contact ]
Announcements
Class Schedule
- Tuesday & Thursday -- 8:30 am to 10:00 am, 104 Watson
Course Outline and Bibliography
Interdisciplinary research:
- Ares M. Jr, Interdisciplinary research and the undergraduate biology student, Nat Struct Mol Biol.
2004 Dec;11(12):1170-2.
- Cech TR, Rubin GM, Nurturing interdisciplinary research, Nat Struct Mol Biol. 2004 Dec;11(12):1166-9.
- Cohen JE, Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better,
PLoS Biology, 2004 Dec;2(12):e439.
Reading Material
Lecture 1:
- Whitman WB, Coleman DC, Wiebe WJ, Prokaryotes: the unseen majority, Proc Nat Acad Sci, 1998 Jun 9;95(12):6578.
- Zimmerman SB, Trach SO, Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli, J Mol Biol. 1991 Dec 5;222(3):599.
- Kinosita K, Yasuda R, Noji H, Adachi K, A rotary molecular motor that can work at near 100% efficiency, Proc. R. Soc. Lond. B 2000; 268:473.
- Alberts B, The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists, Cell 1998; 92:291.
- Molecular Machinery:
A Tour of the Protein Data Bank.
Lecture 2 :
- Davenport RJ, Wuite GJL, Landick R, Bustamante C, Single-Molecule Study of Transcriptional Pausing and Arrest by E. coli RNA Polymerase, Science, 2000 March 31;287:2497.
Transcription speed single molecule experiment.
- Wuite GJL, Smith SB, Young M, Keller D, Bustamante C, Single-molecule studies of the effect of template tension on T7 DNA polymerase activity, Nature, 2000 March 2;404:103.
DNA duplication speed single molecule experiment.
- Blanchard SC, Kim HD, Gonzalez RL, Puglisi JD, Chu S, tRNA dynamics on the ribosome during translation, PNAS, 2004 August 31;101(35):12893.
- Vanzi F, Vladimirov S, Knudsen CR, Goldman YE, Cooperman BS, Protein synthesis by single ribosomes, RNA, 2003;9:1174.
Lecture 3:
- Mogilner A, Oster G, Polymer Motors: Pushing out the Front and Pulling up the Back, Curr.
Biol., 2003 September 16;13:R721.
- Tilney LG, Portnoy DA, Actin Filaments and the Growth, Movement, and Spread of the Intracellular Bacterial Parasite, Listeria monocytogenes, J. Cell Biol., 1989 October;109:1597.
See figs.
14-17 for images of Listeria in infected cells.
- Theriot JA, Mitchison TJ, Tilney LG, Portnoy DA, The rate of actin-based motility of intracellular Listeria monocytogenes equals the rate of actin polymerization, Nature, 1992 May 21;357:257.
This paper is the basis of the estimate we did in class of the rate of actin polymerization using observed speeds of Listeria.
Lecture 4:
- Sheperd N, Dennis P, Bremer H, Cytoplasmic RNA Polymerase in Escherichia coli, J. Bacteriol.,
2001 April;183(8):2527.
This paper discusses the census of RNAP in the cell.
- Dove SL, Joung JK, Hochschild A, Activation of prokaryotik transcription through arbitrary protein-protein contacts, Nature,
1997 April 10;386:627.
This paper is an example of the use of the beta galactosidase activity as a measure of gene expression.
- Ackers GK, Johnson AD, Shea MA, Quantitative model for gene regulation by lambda phage repressor, PNAS, 1982;79:1129.
This paper pioneered the use of the so-called thermodynamic models to examine gene expression.
Lecture 5:
- Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R, Transcriptional Regulation by the Numbers 1: Models, Curr. Op. Gen. and Dev, 2005, in press.
Review on statistical mechanics models of transcriptional regulation.
- Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R, Transcriptional Regulation by the Numbers 2: Applications, Curr. Op. Gen. and Dev, 2005, in press.
Applications of statistical mechanics models of transcriptional regulation.
- Dayton CJ, Prosen DE, Parker KL, Cech CL, Kinetic Measurements of Escherichia coli RNA Polymerase Association with Bacteriophage
T7 Early Promoters, J. of Biol. Chem., 1984 February 10;259(3):1616.
- Liu M, Gupte G, Roy S, Bandwar RP, Patel SS, Garges S, Kinetics of Transcription Initiation at lacP1, J. of Biol. Chem.,
2003 October 10;278(41):39755.
- Record MT, Reznikoff WS, Craig ML, McQuade KL, Schlax PJ , Escherichia coli RNA Plymerase (Esigma70), Promoters, and the Kinetics of the Steps of Transcription Initiation, in "Escherichia coli and Salmonella : cellular and molecular biology", 1996;ASM Press, Washington DC.
- Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH, Structural Basis of Transcription Activation: The CAP-alphaCTD-DNA Complex, Science, 2002 August 30;297:1562.
This paper shows from a structural perspective how activators recruit RNAP to the promoter.
Lecture 6:
- Oehler S, Amouyal M, Kolkhof P, von Wilcken-Bergmann B, Mueller-Hill B , Quality and position of the three lac operators of E. Coli define efficiency of repression, EMBO J., 1994;13(14):3348.
DNA looping in the lac operon by mutating binding sites.
- Mueller J, Oehler S, Mueller-Hill B , Repression of lac Promoter as a Function of Distance, Phase and Quality of an Auxiliary lac Operator, JMB, 1996;257:21.
DNA looping in the lac operon as a function of the distance between operators.
This paper is a beautiful experiment which shows how repression depends upon the distance between the two operators.
- Vilar JMG, Leibler S , DNA Looping and Physical Constraints on Transcription Regulation, JMB, 2003;331:981.
Modeling of the experiment in Oehler et al. (1994) using a thermodynamic model.
- Buchler NE, Gerland U, Hwa T , On schemes of combinatorial transcription logic, PNAS,
2003 April 29;100(9):5136.
- Bruinsma RF , Physics of protein-DNA interaction, Physica A, 2002;313:211.
- T. Cremer and C. Cremer, Chromosomes territories, nuclear architecture, and gene regulation in mammalian cells, Nature Reviews: Genetics, 2001 April;2:292-301.
Lecture 7:
- Richmond TJ, Davey CA , The structure of DNA in the nucleosome core, Nature, 2003 May 8;423:145.
- Polach KJ, Widom J , Mechanism of Protein Access to Specific DNA Sequences in Chromatin: A Dynamic Equilibrium Model for Gene Regulation, JMB, 1995;254:130.
- Polach KJ, Widom J , A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target Sites, JMB,1996;258:800.
- Nancy L. Marky and Gerald S. Manning, A theory of DNA dissociation from the nucleosome, J. Mol. Biol, 1995; 254:50-61.
- Li G, Levitus M, Bustamante C, Widom J , Rapid spontaneous accessibility of nucleosomal DNA, Nat. Struc. Biol.,
2005 January;12(1):46.
- Roger D. Kornberg and Yahli Lorch, Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome Cell, 1999 August 6;98:285-294.
-
Thomas D. Yager, Cynthia T. McMurray, and K. E. van Holde , Salt-Induced Release of DNA from Nucleosome Core Particles, Biochemistry, 1989;28:2271-2281.
Lecture 8:
- Adam M. Breier and Nicholas R.
Cozzarelli, Linear ordering and dynamic segregation of the bacterial chromosomes, PNAS, 2004 June 22;101:9175-6.
-
Patrick H. Viollier, Martin Thanbichler, Patrick T. McGrath, Lisandra West, Maliwan Meewan, Harley H. McAdams, and Lucy Shapiro, Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication, PNAS, 2004 June 22;101(25):9257-62.
Lecture 9:
- Rau DV, Lee B, Parsegian VA , Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: Hydration forces between parallel DNA double helices, PNAS, 1984 May;81:2621.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
-
Alan A. Simpson, Yizhi Tao, Petr G. Leiman, Mohammed O. Badasso, Yongning He, Paul J. Jardinek, Norman H. Olson, Marc C. Morais, Shelley Grimes, Dwight L. Anderson, Timothy S. Baker & Michael G. Rossmann, Structure of the bacteriophage Phi29 DNA packaging motor, Nature, 2000 December 7;408:745-750.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
- Rizal Hariadi , Interaction Energy in Helical Array of DNA strands.
- Baker TS, Olson NH, Fuller SD, Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral
Viruses from Cryo-Electron Micrographs, Microb. Mol. Biol. Rev., 1999 December; 63(4):862.
- Mario E. Cerritelli, Naiqian Cheng, Alan H. Rosenberg, Catherine E. McPherson, Frank P. Booy, and Alasdair C. Steven, Encapsidated Conformation of Bacteriophage T7 DNA, Cell, 1997 October 17;91:271.
- Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, Solvent Mediated Interactions in the Structure of the Nucleosome Core
Particle at 1.9 A Resolution, J. Mol. Biol., 2002;319:1097.
- Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ, Crystal structure of the nucleosome core particle at 2.8A resolution,
Nature, 1997 September 18;389:251.
- Earnshaw WC, Harrison SC, DNA arrangement in isometric phage heads,
Nature, 1977 August 18;268:598.
Lecture 10:
- R. John Ellis, Macromolecular crowding: an important but neglected aspect of the intracellular environment, Current Opinion in Structural Biology, 2001;11:114–119.
- R. John Ellis, Macromolecular crowding: obvious but underappreciated, Trends in Biochemical Sciences, 2001 October;26(10):567.
- Michael B. Elowitz, Michael G.
Surette, Pierre-Etiene Wolf, Jeffry B. Stock, and Stanislas Leibler, Protein Mobility in the Cytoplasm of Escherichia coli, Journal of Bacteriology, 1999 January;181(1):197-203.
- Karine A. Gibbs, Daniel D. Isaac, Jun Xu, Roger W. Hendrix, Thomas J. Silhavy and Julie A. Theriot, Complex spatial distribution and dynamics of an abundant Escherichia coli outer membrane protein, LamB, Molecular Microbiology, 2004;53(6):1771.
-
Katherine Luby-Phelps,
Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular, surface area, International Review of Cytology, 2000;192:189-221.
- Allen P. Minton, The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media, J. Biol. Chem., 2001 April 6;276(14),10577-80.
-
Alan S.Verkman, Solute and macromolecule diffusion in cellular aqueous compartments, Trends in Biochemical Sciences, 2002 January 1;27(1):27-33.
- Einstein A, On the movement of small particles suspended in a stationary liquid demanded by the molecular-kinetic theory of heat, 1905.
- Reits EAJ, Neefjes JJ, From fixed to FRAP: measuring protein mobility and activity in living cells, Nat. Cell Biol., 2001 June;
3:E145.
- Zimmerman SB, Minton AP, Macromolecular Crowding: Biochemical, Biophysical, and Physiological Consequences,
Annu. Rev. Biophys. Biomol. Struct., 1993;22:27.
- Rivetti C, Guthold M, Bustamante C, Scanning Force Microscopy of DNA Deposited onto Mica: Equilibration versus Kinetic Trapping
Studied by Statistical Polymer Chain Analysis, J. Mol. Biol., 1996;264:919.
- Goodsell DS, Molecular Art - Molecular Science.
- Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W, Macromolecular Architecture in Eukaryotic Cells
Visualized by Cryoelectron Tomography, Science, 2002 November 8;298:1209.
Lecture 11:
- Mitosis World, Stunning movies which reveal the activities of the cytoskeleton during cell division.
Lecture 14:
- Abraham VC, Krishnamurthi V, Taylor DL, Lanni F, The Actin-Based Nanomachine at the Leading Edge of Migrating Cells,
Biophysical Journal, 1999 September;77:1721.
- Borisy GG, Svitkina TM, Actin machinery: pushing the envelope,
Curr. Op. Cell Biol., 2000;12:104.
- Errington J, Dynamic proteins and a cytoskeleton in bacteria,
Nat. Cell Biol., 2003 March;5:175.
A nice review of the emerging picture of the bacterial cytoskeleton.
- Fletcher DA, Theriot JA, An introduction to cell motility for the physical scientist,
Phys. Biol., 2004;1:T1.
- Garner EC, Campbell CS, Mullins RD, Dynamic Instability in a DNA-Segregating Prokaryotic Actin Homolog,
Phys. Biol., 2004;1:T1.
- Pollard TD, The cytoskeleton, cellular motility and the reductionist agenda,
Nature, 2003 April 17;422:741.
- Rafelski SM, Theriot JA, Crawling Toward a Unified Model of Cell Motility: Spatial and Temporal Regulation of Actin Dynamics,
Annu. Rev. Biochem., 2004;73:209.
- Mitchison T, Kirschner M, Dynamic instability of microtubule growth,
Nature, 1984 November 15;312:237.
- Waterman-Storer Laboratory Movies
- Salmon Lab Movies
Lecture 15:
- Dogterom M, Leibler S, Physical Aspects of the Growth and Regulation of Microtubule Structures,
Phys. Rev. Lett., 1993 March 1;70(9):1347.
A simple phenomenological model of the steady-state distribution of microtubule lengths.
- Kuchnir Fygenson D, Braun E, Libchaber A, Phase diagram of microtubules,
Phys. Rev. E, 1994 August;50(2):1579.
Fig. 1 shows an experimental time series for the length of microtubules as a function of time, fig. 6
shows the distribution of microtubule lengths.
- Flyvbjerg H, Holy TE, Leibler S, Stochastic Dynamics of Microtubules:
A Model cor Caps and Catastrophes, Phys. Rev. Lett., 1994 October 24;73(17):2372.
This model treats the dynamics of the cap of GTP tubulin in microtubules.
- Flyvbjerg H, Holy TE, Leibler S, Microtubule dynamics: Caps, catastrophes, and coupled hydrolysis
, Phys. Rev. E, 1996 November;54(5):5538.
- Carlier MF, Pantaloni D, Control of Actin Dynamics in Cell Motility
, J. Mol. Biol., 1997;269:459.
- Pollard TD, Rate Constants for the Reactions of ATP- and ADP-Actin
with the Ends of Actin Filaments, J. Cell Biol., 1986 December;103(2):2747.
Lecture 16:
- Thomas N, Imafuku Y, Tawada K, Molecular motors: thermodynamics and the random walk, Proc R Soc Lond B Biol Sci. 2001 Oct 22;268(1481):2113.
- Fisher ME, Kolomeisky AB, The force exerted by a molecular motor,
PNAS, 1999 June;96:6597.
- Gross SP, Hither and yon: a review of bi-directional microtubule-based transport,
Phys. Biol., 2004;1:R1.
- Fisher ME, Kolomeisky AB, Simple mechanochemistry describes the dynamics of kinesin molecules,
PNAS, 2001 July 3;98(14):7748.
- Huxley HE, Fifty years of muscle and the sliding filament hypothesis,
Eur. J. Biochem., 2004;271:1403.
- Mahadevan L, Matsudaira P, Motility Powered by Supramolecular Springs and Ratchets,
Science, 2000 April 7;288:95.
This paper describes classes of motors other than the translational motors described in class.
- Schliwa M, Woehlke G, Molecular motors,
Nature, 2003 April 17;422:759.
- Schnitzer MJ, Block SM, Kinesin hydrolyses one ATP per 8-nm step,
Nature, 1997 July 24;388:386.
- Vale RD, Milligan RA, The Way Things Move: Looking Under the Hood of Molecular Motor Proteins,
Nature, 2000 April 7;288:88.
- Vale RD, The Molecular Motor Toolbox for Intracellular Transport,
Cell, 2003 February 21;112:467.
- Woehlke G, Schliwa M, Walking on two heads: the many talents of kinesin,
Nature Reviews, 2000 October;1:50.
- Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR, Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with
1.5-nm Localization, Science, 2003 June 27 ;300:2061.
- Kinosita Lab Movies, cool single molecule movies of the action of molecular motors.
- Heuser Lab Galleries, this site includes some of the classic electron micrographs of
muscle and muscle proteins.
Lecture 17:
- Rief M, Rock RS, Mehta AD, Mooseker MS, Cheney RE, Spudich JA,
Myosin-V stepping kinetics: A molecular model for processivity,
PNAS, 2000 Aug 15;97(17):9482.
- Simon SM, Peskin CS, Oster GF,
What drives the translocation of proteins?,
PNAS, 1992 May;89:3770.
Lecture 18:
- Gillespie PG, Walker RG,
Molecular basis of mechanosensory transduction,
Nature, 2001 Sep 13;413:194.
- Miyazawa A, Fujiyoshi Y, Unwin N,
Structure and gating mechanism of the acetylcholine receptor pore,
Nature, 2003 Jun 26;423:949.
Lecture 19:
- Nilsson DE, Pelger S,
A Pessimistic Estimate of the Time Required for an Eye to Evolve,
Proc. Roy. Soc Lond., 1994 Apr 22;256(1345):53.
- Sens P, Turnery MS,
Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations,
Biophysical Journal, 2004 Apr;86:2049.
Homeworks
- HW1, Due on Tuesday,
January 18
- HW2, Due on Thursday,
January 27
- HW3, Due on Thursday,
February 3
- HW4, Due on Thursday,
February 10
- HW5, Due on Tuesday,
February 22
- HW6, Due on Tuesday,
March 1
- HW7, Due on Tuesday,
March 8
- HW8, Due on Friday,
March 11
Solutions
Lecture notes
- Lecture 1 slides
- Lecture 2 slides
- Stat. Mech. lecture slides
- Lecture 3 slides
- Lecture 4 slides
- Lectures 6 and 7 slides
- Lecture 8 slides
- Lecture 10 slides
- Lectures 12, 13 and 14 slides
- Lecture 16 slides
- Lecture 18 slides
- Lecture 19 slides
Contact Information
Rob
Phillips
221 Steele
x3374
phillips AT pboc.caltech
Hernan Garcia
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Rizal Hariadi
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Mandar M. Inamdar
226 Steele
x3106
mandar AT caltech
Office hours: TBA
- Whitman WB, Coleman DC, Wiebe WJ, Prokaryotes: the unseen majority, Proc Nat Acad Sci, 1998 Jun 9;95(12):6578.
- Zimmerman SB, Trach SO, Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli, J Mol Biol. 1991 Dec 5;222(3):599.
- Kinosita K, Yasuda R, Noji H, Adachi K, A rotary molecular motor that can work at near 100% efficiency, Proc. R. Soc. Lond. B 2000; 268:473.
- Alberts B, The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists, Cell 1998; 92:291.
- Molecular Machinery: A Tour of the Protein Data Bank.
Lecture 2 :
- Davenport RJ, Wuite GJL, Landick R, Bustamante C, Single-Molecule Study of Transcriptional Pausing and Arrest by E. coli RNA Polymerase, Science, 2000 March 31;287:2497.
Transcription speed single molecule experiment.
- Wuite GJL, Smith SB, Young M, Keller D, Bustamante C, Single-molecule studies of the effect of template tension on T7 DNA polymerase activity, Nature, 2000 March 2;404:103.
DNA duplication speed single molecule experiment.
- Blanchard SC, Kim HD, Gonzalez RL, Puglisi JD, Chu S, tRNA dynamics on the ribosome during translation, PNAS, 2004 August 31;101(35):12893.
- Vanzi F, Vladimirov S, Knudsen CR, Goldman YE, Cooperman BS, Protein synthesis by single ribosomes, RNA, 2003;9:1174.
Lecture 3:
- Mogilner A, Oster G, Polymer Motors: Pushing out the Front and Pulling up the Back, Curr.
Biol., 2003 September 16;13:R721.
- Tilney LG, Portnoy DA, Actin Filaments and the Growth, Movement, and Spread of the Intracellular Bacterial Parasite, Listeria monocytogenes, J. Cell Biol., 1989 October;109:1597.
See figs.
14-17 for images of Listeria in infected cells.
- Theriot JA, Mitchison TJ, Tilney LG, Portnoy DA, The rate of actin-based motility of intracellular Listeria monocytogenes equals the rate of actin polymerization, Nature, 1992 May 21;357:257.
This paper is the basis of the estimate we did in class of the rate of actin polymerization using observed speeds of Listeria.
Lecture 4:
- Sheperd N, Dennis P, Bremer H, Cytoplasmic RNA Polymerase in Escherichia coli, J. Bacteriol.,
2001 April;183(8):2527.
This paper discusses the census of RNAP in the cell.
- Dove SL, Joung JK, Hochschild A, Activation of prokaryotik transcription through arbitrary protein-protein contacts, Nature,
1997 April 10;386:627.
This paper is an example of the use of the beta galactosidase activity as a measure of gene expression.
- Ackers GK, Johnson AD, Shea MA, Quantitative model for gene regulation by lambda phage repressor, PNAS, 1982;79:1129.
This paper pioneered the use of the so-called thermodynamic models to examine gene expression.
Lecture 5:
- Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R, Transcriptional Regulation by the Numbers 1: Models, Curr. Op. Gen. and Dev, 2005, in press.
Review on statistical mechanics models of transcriptional regulation.
- Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R, Transcriptional Regulation by the Numbers 2: Applications, Curr. Op. Gen. and Dev, 2005, in press.
Applications of statistical mechanics models of transcriptional regulation.
- Dayton CJ, Prosen DE, Parker KL, Cech CL, Kinetic Measurements of Escherichia coli RNA Polymerase Association with Bacteriophage
T7 Early Promoters, J. of Biol. Chem., 1984 February 10;259(3):1616.
- Liu M, Gupte G, Roy S, Bandwar RP, Patel SS, Garges S, Kinetics of Transcription Initiation at lacP1, J. of Biol. Chem.,
2003 October 10;278(41):39755.
- Record MT, Reznikoff WS, Craig ML, McQuade KL, Schlax PJ , Escherichia coli RNA Plymerase (Esigma70), Promoters, and the Kinetics of the Steps of Transcription Initiation, in "Escherichia coli and Salmonella : cellular and molecular biology", 1996;ASM Press, Washington DC.
- Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH, Structural Basis of Transcription Activation: The CAP-alphaCTD-DNA Complex, Science, 2002 August 30;297:1562.
This paper shows from a structural perspective how activators recruit RNAP to the promoter.
Lecture 6:
- Oehler S, Amouyal M, Kolkhof P, von Wilcken-Bergmann B, Mueller-Hill B , Quality and position of the three lac operators of E. Coli define efficiency of repression, EMBO J., 1994;13(14):3348.
DNA looping in the lac operon by mutating binding sites.
- Mueller J, Oehler S, Mueller-Hill B , Repression of lac Promoter as a Function of Distance, Phase and Quality of an Auxiliary lac Operator, JMB, 1996;257:21.
DNA looping in the lac operon as a function of the distance between operators.
This paper is a beautiful experiment which shows how repression depends upon the distance between the two operators.
- Vilar JMG, Leibler S , DNA Looping and Physical Constraints on Transcription Regulation, JMB, 2003;331:981.
Modeling of the experiment in Oehler et al. (1994) using a thermodynamic model.
- Buchler NE, Gerland U, Hwa T , On schemes of combinatorial transcription logic, PNAS,
2003 April 29;100(9):5136.
- Bruinsma RF , Physics of protein-DNA interaction, Physica A, 2002;313:211.
- T. Cremer and C. Cremer, Chromosomes territories, nuclear architecture, and gene regulation in mammalian cells, Nature Reviews: Genetics, 2001 April;2:292-301.
Lecture 7:
- Richmond TJ, Davey CA , The structure of DNA in the nucleosome core, Nature, 2003 May 8;423:145.
- Polach KJ, Widom J , Mechanism of Protein Access to Specific DNA Sequences in Chromatin: A Dynamic Equilibrium Model for Gene Regulation, JMB, 1995;254:130.
- Polach KJ, Widom J , A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target Sites, JMB,1996;258:800.
- Nancy L. Marky and Gerald S. Manning, A theory of DNA dissociation from the nucleosome, J. Mol. Biol, 1995; 254:50-61.
- Li G, Levitus M, Bustamante C, Widom J , Rapid spontaneous accessibility of nucleosomal DNA, Nat. Struc. Biol.,
2005 January;12(1):46.
- Roger D. Kornberg and Yahli Lorch, Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome Cell, 1999 August 6;98:285-294.
-
Thomas D. Yager, Cynthia T. McMurray, and K. E. van Holde , Salt-Induced Release of DNA from Nucleosome Core Particles, Biochemistry, 1989;28:2271-2281.
Lecture 8:
- Adam M. Breier and Nicholas R.
Cozzarelli, Linear ordering and dynamic segregation of the bacterial chromosomes, PNAS, 2004 June 22;101:9175-6.
-
Patrick H. Viollier, Martin Thanbichler, Patrick T. McGrath, Lisandra West, Maliwan Meewan, Harley H. McAdams, and Lucy Shapiro, Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication, PNAS, 2004 June 22;101(25):9257-62.
Lecture 9:
- Rau DV, Lee B, Parsegian VA , Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: Hydration forces between parallel DNA double helices, PNAS, 1984 May;81:2621.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
-
Alan A. Simpson, Yizhi Tao, Petr G. Leiman, Mohammed O. Badasso, Yongning He, Paul J. Jardinek, Norman H. Olson, Marc C. Morais, Shelley Grimes, Dwight L. Anderson, Timothy S. Baker & Michael G. Rossmann, Structure of the bacteriophage Phi29 DNA packaging motor, Nature, 2000 December 7;408:745-750.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
- Rizal Hariadi , Interaction Energy in Helical Array of DNA strands.
- Baker TS, Olson NH, Fuller SD, Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral
Viruses from Cryo-Electron Micrographs, Microb. Mol. Biol. Rev., 1999 December; 63(4):862.
- Mario E. Cerritelli, Naiqian Cheng, Alan H. Rosenberg, Catherine E. McPherson, Frank P. Booy, and Alasdair C. Steven, Encapsidated Conformation of Bacteriophage T7 DNA, Cell, 1997 October 17;91:271.
- Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, Solvent Mediated Interactions in the Structure of the Nucleosome Core
Particle at 1.9 A Resolution, J. Mol. Biol., 2002;319:1097.
- Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ, Crystal structure of the nucleosome core particle at 2.8A resolution,
Nature, 1997 September 18;389:251.
- Earnshaw WC, Harrison SC, DNA arrangement in isometric phage heads,
Nature, 1977 August 18;268:598.
Lecture 10:
- R. John Ellis, Macromolecular crowding: an important but neglected aspect of the intracellular environment, Current Opinion in Structural Biology, 2001;11:114–119.
- R. John Ellis, Macromolecular crowding: obvious but underappreciated, Trends in Biochemical Sciences, 2001 October;26(10):567.
- Michael B. Elowitz, Michael G.
Surette, Pierre-Etiene Wolf, Jeffry B. Stock, and Stanislas Leibler, Protein Mobility in the Cytoplasm of Escherichia coli, Journal of Bacteriology, 1999 January;181(1):197-203.
- Karine A. Gibbs, Daniel D. Isaac, Jun Xu, Roger W. Hendrix, Thomas J. Silhavy and Julie A. Theriot, Complex spatial distribution and dynamics of an abundant Escherichia coli outer membrane protein, LamB, Molecular Microbiology, 2004;53(6):1771.
-
Katherine Luby-Phelps,
Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular, surface area, International Review of Cytology, 2000;192:189-221.
- Allen P. Minton, The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media, J. Biol. Chem., 2001 April 6;276(14),10577-80.
-
Alan S.Verkman, Solute and macromolecule diffusion in cellular aqueous compartments, Trends in Biochemical Sciences, 2002 January 1;27(1):27-33.
- Einstein A, On the movement of small particles suspended in a stationary liquid demanded by the molecular-kinetic theory of heat, 1905.
- Reits EAJ, Neefjes JJ, From fixed to FRAP: measuring protein mobility and activity in living cells, Nat. Cell Biol., 2001 June;
3:E145.
- Zimmerman SB, Minton AP, Macromolecular Crowding: Biochemical, Biophysical, and Physiological Consequences,
Annu. Rev. Biophys. Biomol. Struct., 1993;22:27.
- Rivetti C, Guthold M, Bustamante C, Scanning Force Microscopy of DNA Deposited onto Mica: Equilibration versus Kinetic Trapping
Studied by Statistical Polymer Chain Analysis, J. Mol. Biol., 1996;264:919.
- Goodsell DS, Molecular Art - Molecular Science.
- Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W, Macromolecular Architecture in Eukaryotic Cells
Visualized by Cryoelectron Tomography, Science, 2002 November 8;298:1209.
Lecture 11:
- Mitosis World, Stunning movies which reveal the activities of the cytoskeleton during cell division.
Lecture 14:
- Abraham VC, Krishnamurthi V, Taylor DL, Lanni F, The Actin-Based Nanomachine at the Leading Edge of Migrating Cells,
Biophysical Journal, 1999 September;77:1721.
- Borisy GG, Svitkina TM, Actin machinery: pushing the envelope,
Curr. Op. Cell Biol., 2000;12:104.
- Errington J, Dynamic proteins and a cytoskeleton in bacteria,
Nat. Cell Biol., 2003 March;5:175.
A nice review of the emerging picture of the bacterial cytoskeleton.
- Fletcher DA, Theriot JA, An introduction to cell motility for the physical scientist,
Phys. Biol., 2004;1:T1.
- Garner EC, Campbell CS, Mullins RD, Dynamic Instability in a DNA-Segregating Prokaryotic Actin Homolog,
Phys. Biol., 2004;1:T1.
- Pollard TD, The cytoskeleton, cellular motility and the reductionist agenda,
Nature, 2003 April 17;422:741.
- Rafelski SM, Theriot JA, Crawling Toward a Unified Model of Cell Motility: Spatial and Temporal Regulation of Actin Dynamics,
Annu. Rev. Biochem., 2004;73:209.
- Mitchison T, Kirschner M, Dynamic instability of microtubule growth,
Nature, 1984 November 15;312:237.
- Waterman-Storer Laboratory Movies
- Salmon Lab Movies
Lecture 15:
- Dogterom M, Leibler S, Physical Aspects of the Growth and Regulation of Microtubule Structures,
Phys. Rev. Lett., 1993 March 1;70(9):1347.
A simple phenomenological model of the steady-state distribution of microtubule lengths.
- Kuchnir Fygenson D, Braun E, Libchaber A, Phase diagram of microtubules,
Phys. Rev. E, 1994 August;50(2):1579.
Fig. 1 shows an experimental time series for the length of microtubules as a function of time, fig. 6
shows the distribution of microtubule lengths.
- Flyvbjerg H, Holy TE, Leibler S, Stochastic Dynamics of Microtubules:
A Model cor Caps and Catastrophes, Phys. Rev. Lett., 1994 October 24;73(17):2372.
This model treats the dynamics of the cap of GTP tubulin in microtubules.
- Flyvbjerg H, Holy TE, Leibler S, Microtubule dynamics: Caps, catastrophes, and coupled hydrolysis
, Phys. Rev. E, 1996 November;54(5):5538.
- Carlier MF, Pantaloni D, Control of Actin Dynamics in Cell Motility
, J. Mol. Biol., 1997;269:459.
- Pollard TD, Rate Constants for the Reactions of ATP- and ADP-Actin
with the Ends of Actin Filaments, J. Cell Biol., 1986 December;103(2):2747.
Lecture 16:
- Thomas N, Imafuku Y, Tawada K, Molecular motors: thermodynamics and the random walk, Proc R Soc Lond B Biol Sci. 2001 Oct 22;268(1481):2113.
- Fisher ME, Kolomeisky AB, The force exerted by a molecular motor,
PNAS, 1999 June;96:6597.
- Gross SP, Hither and yon: a review of bi-directional microtubule-based transport,
Phys. Biol., 2004;1:R1.
- Fisher ME, Kolomeisky AB, Simple mechanochemistry describes the dynamics of kinesin molecules,
PNAS, 2001 July 3;98(14):7748.
- Huxley HE, Fifty years of muscle and the sliding filament hypothesis,
Eur. J. Biochem., 2004;271:1403.
- Mahadevan L, Matsudaira P, Motility Powered by Supramolecular Springs and Ratchets,
Science, 2000 April 7;288:95.
This paper describes classes of motors other than the translational motors described in class.
- Schliwa M, Woehlke G, Molecular motors,
Nature, 2003 April 17;422:759.
- Schnitzer MJ, Block SM, Kinesin hydrolyses one ATP per 8-nm step,
Nature, 1997 July 24;388:386.
- Vale RD, Milligan RA, The Way Things Move: Looking Under the Hood of Molecular Motor Proteins,
Nature, 2000 April 7;288:88.
- Vale RD, The Molecular Motor Toolbox for Intracellular Transport,
Cell, 2003 February 21;112:467.
- Woehlke G, Schliwa M, Walking on two heads: the many talents of kinesin,
Nature Reviews, 2000 October;1:50.
- Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR, Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with
1.5-nm Localization, Science, 2003 June 27 ;300:2061.
- Kinosita Lab Movies, cool single molecule movies of the action of molecular motors.
- Heuser Lab Galleries, this site includes some of the classic electron micrographs of
muscle and muscle proteins.
Lecture 17:
- Rief M, Rock RS, Mehta AD, Mooseker MS, Cheney RE, Spudich JA,
Myosin-V stepping kinetics: A molecular model for processivity,
PNAS, 2000 Aug 15;97(17):9482.
- Simon SM, Peskin CS, Oster GF,
What drives the translocation of proteins?,
PNAS, 1992 May;89:3770.
Lecture 18:
- Gillespie PG, Walker RG,
Molecular basis of mechanosensory transduction,
Nature, 2001 Sep 13;413:194.
- Miyazawa A, Fujiyoshi Y, Unwin N,
Structure and gating mechanism of the acetylcholine receptor pore,
Nature, 2003 Jun 26;423:949.
Lecture 19:
- Nilsson DE, Pelger S,
A Pessimistic Estimate of the Time Required for an Eye to Evolve,
Proc. Roy. Soc Lond., 1994 Apr 22;256(1345):53.
- Sens P, Turnery MS,
Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations,
Biophysical Journal, 2004 Apr;86:2049.
Homeworks
- HW1, Due on Tuesday,
January 18
- HW2, Due on Thursday,
January 27
- HW3, Due on Thursday,
February 3
- HW4, Due on Thursday,
February 10
- HW5, Due on Tuesday,
February 22
- HW6, Due on Tuesday,
March 1
- HW7, Due on Tuesday,
March 8
- HW8, Due on Friday,
March 11
Solutions
Lecture notes
- Lecture 1 slides
- Lecture 2 slides
- Stat. Mech. lecture slides
- Lecture 3 slides
- Lecture 4 slides
- Lectures 6 and 7 slides
- Lecture 8 slides
- Lecture 10 slides
- Lectures 12, 13 and 14 slides
- Lecture 16 slides
- Lecture 18 slides
- Lecture 19 slides
Contact Information
Rob
Phillips
221 Steele
x3374
phillips AT pboc.caltech
Hernan Garcia
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Rizal Hariadi
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Mandar M. Inamdar
226 Steele
x3106
mandar AT caltech
Office hours: TBA
Transcription speed single molecule experiment.
DNA duplication speed single molecule experiment.
- Mogilner A, Oster G, Polymer Motors: Pushing out the Front and Pulling up the Back, Curr. Biol., 2003 September 16;13:R721.
- Tilney LG, Portnoy DA, Actin Filaments and the Growth, Movement, and Spread of the Intracellular Bacterial Parasite, Listeria monocytogenes, J. Cell Biol., 1989 October;109:1597.
See figs. 14-17 for images of Listeria in infected cells. - Theriot JA, Mitchison TJ, Tilney LG, Portnoy DA, The rate of actin-based motility of intracellular Listeria monocytogenes equals the rate of actin polymerization, Nature, 1992 May 21;357:257.
This paper is the basis of the estimate we did in class of the rate of actin polymerization using observed speeds of Listeria.
Lecture 4:
- Sheperd N, Dennis P, Bremer H, Cytoplasmic RNA Polymerase in Escherichia coli, J. Bacteriol.,
2001 April;183(8):2527.
This paper discusses the census of RNAP in the cell.
- Dove SL, Joung JK, Hochschild A, Activation of prokaryotik transcription through arbitrary protein-protein contacts, Nature,
1997 April 10;386:627.
This paper is an example of the use of the beta galactosidase activity as a measure of gene expression.
- Ackers GK, Johnson AD, Shea MA, Quantitative model for gene regulation by lambda phage repressor, PNAS, 1982;79:1129.
This paper pioneered the use of the so-called thermodynamic models to examine gene expression.
Lecture 5:
- Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R, Transcriptional Regulation by the Numbers 1: Models, Curr. Op. Gen. and Dev, 2005, in press.
Review on statistical mechanics models of transcriptional regulation.
- Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R, Transcriptional Regulation by the Numbers 2: Applications, Curr. Op. Gen. and Dev, 2005, in press.
Applications of statistical mechanics models of transcriptional regulation.
- Dayton CJ, Prosen DE, Parker KL, Cech CL, Kinetic Measurements of Escherichia coli RNA Polymerase Association with Bacteriophage
T7 Early Promoters, J. of Biol. Chem., 1984 February 10;259(3):1616.
- Liu M, Gupte G, Roy S, Bandwar RP, Patel SS, Garges S, Kinetics of Transcription Initiation at lacP1, J. of Biol. Chem.,
2003 October 10;278(41):39755.
- Record MT, Reznikoff WS, Craig ML, McQuade KL, Schlax PJ , Escherichia coli RNA Plymerase (Esigma70), Promoters, and the Kinetics of the Steps of Transcription Initiation, in "Escherichia coli and Salmonella : cellular and molecular biology", 1996;ASM Press, Washington DC.
- Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH, Structural Basis of Transcription Activation: The CAP-alphaCTD-DNA Complex, Science, 2002 August 30;297:1562.
This paper shows from a structural perspective how activators recruit RNAP to the promoter.
Lecture 6:
- Oehler S, Amouyal M, Kolkhof P, von Wilcken-Bergmann B, Mueller-Hill B , Quality and position of the three lac operators of E. Coli define efficiency of repression, EMBO J., 1994;13(14):3348.
DNA looping in the lac operon by mutating binding sites.
- Mueller J, Oehler S, Mueller-Hill B , Repression of lac Promoter as a Function of Distance, Phase and Quality of an Auxiliary lac Operator, JMB, 1996;257:21.
DNA looping in the lac operon as a function of the distance between operators.
This paper is a beautiful experiment which shows how repression depends upon the distance between the two operators.
- Vilar JMG, Leibler S , DNA Looping and Physical Constraints on Transcription Regulation, JMB, 2003;331:981.
Modeling of the experiment in Oehler et al. (1994) using a thermodynamic model.
- Buchler NE, Gerland U, Hwa T , On schemes of combinatorial transcription logic, PNAS,
2003 April 29;100(9):5136.
- Bruinsma RF , Physics of protein-DNA interaction, Physica A, 2002;313:211.
- T. Cremer and C. Cremer, Chromosomes territories, nuclear architecture, and gene regulation in mammalian cells, Nature Reviews: Genetics, 2001 April;2:292-301.
Lecture 7:
- Richmond TJ, Davey CA , The structure of DNA in the nucleosome core, Nature, 2003 May 8;423:145.
- Polach KJ, Widom J , Mechanism of Protein Access to Specific DNA Sequences in Chromatin: A Dynamic Equilibrium Model for Gene Regulation, JMB, 1995;254:130.
- Polach KJ, Widom J , A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target Sites, JMB,1996;258:800.
- Nancy L. Marky and Gerald S. Manning, A theory of DNA dissociation from the nucleosome, J. Mol. Biol, 1995; 254:50-61.
- Li G, Levitus M, Bustamante C, Widom J , Rapid spontaneous accessibility of nucleosomal DNA, Nat. Struc. Biol.,
2005 January;12(1):46.
- Roger D. Kornberg and Yahli Lorch, Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome Cell, 1999 August 6;98:285-294.
-
Thomas D. Yager, Cynthia T. McMurray, and K. E. van Holde , Salt-Induced Release of DNA from Nucleosome Core Particles, Biochemistry, 1989;28:2271-2281.
Lecture 8:
- Adam M. Breier and Nicholas R.
Cozzarelli, Linear ordering and dynamic segregation of the bacterial chromosomes, PNAS, 2004 June 22;101:9175-6.
-
Patrick H. Viollier, Martin Thanbichler, Patrick T. McGrath, Lisandra West, Maliwan Meewan, Harley H. McAdams, and Lucy Shapiro, Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication, PNAS, 2004 June 22;101(25):9257-62.
Lecture 9:
- Rau DV, Lee B, Parsegian VA , Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: Hydration forces between parallel DNA double helices, PNAS, 1984 May;81:2621.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
-
Alan A. Simpson, Yizhi Tao, Petr G. Leiman, Mohammed O. Badasso, Yongning He, Paul J. Jardinek, Norman H. Olson, Marc C. Morais, Shelley Grimes, Dwight L. Anderson, Timothy S. Baker & Michael G. Rossmann, Structure of the bacteriophage Phi29 DNA packaging motor, Nature, 2000 December 7;408:745-750.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
- Rizal Hariadi , Interaction Energy in Helical Array of DNA strands.
- Baker TS, Olson NH, Fuller SD, Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral
Viruses from Cryo-Electron Micrographs, Microb. Mol. Biol. Rev., 1999 December; 63(4):862.
- Mario E. Cerritelli, Naiqian Cheng, Alan H. Rosenberg, Catherine E. McPherson, Frank P. Booy, and Alasdair C. Steven, Encapsidated Conformation of Bacteriophage T7 DNA, Cell, 1997 October 17;91:271.
- Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, Solvent Mediated Interactions in the Structure of the Nucleosome Core
Particle at 1.9 A Resolution, J. Mol. Biol., 2002;319:1097.
- Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ, Crystal structure of the nucleosome core particle at 2.8A resolution,
Nature, 1997 September 18;389:251.
- Earnshaw WC, Harrison SC, DNA arrangement in isometric phage heads,
Nature, 1977 August 18;268:598.
Lecture 10:
- R. John Ellis, Macromolecular crowding: an important but neglected aspect of the intracellular environment, Current Opinion in Structural Biology, 2001;11:114–119.
- R. John Ellis, Macromolecular crowding: obvious but underappreciated, Trends in Biochemical Sciences, 2001 October;26(10):567.
- Michael B. Elowitz, Michael G.
Surette, Pierre-Etiene Wolf, Jeffry B. Stock, and Stanislas Leibler, Protein Mobility in the Cytoplasm of Escherichia coli, Journal of Bacteriology, 1999 January;181(1):197-203.
- Karine A. Gibbs, Daniel D. Isaac, Jun Xu, Roger W. Hendrix, Thomas J. Silhavy and Julie A. Theriot, Complex spatial distribution and dynamics of an abundant Escherichia coli outer membrane protein, LamB, Molecular Microbiology, 2004;53(6):1771.
-
Katherine Luby-Phelps,
Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular, surface area, International Review of Cytology, 2000;192:189-221.
- Allen P. Minton, The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media, J. Biol. Chem., 2001 April 6;276(14),10577-80.
-
Alan S.Verkman, Solute and macromolecule diffusion in cellular aqueous compartments, Trends in Biochemical Sciences, 2002 January 1;27(1):27-33.
- Einstein A, On the movement of small particles suspended in a stationary liquid demanded by the molecular-kinetic theory of heat, 1905.
- Reits EAJ, Neefjes JJ, From fixed to FRAP: measuring protein mobility and activity in living cells, Nat. Cell Biol., 2001 June;
3:E145.
- Zimmerman SB, Minton AP, Macromolecular Crowding: Biochemical, Biophysical, and Physiological Consequences,
Annu. Rev. Biophys. Biomol. Struct., 1993;22:27.
- Rivetti C, Guthold M, Bustamante C, Scanning Force Microscopy of DNA Deposited onto Mica: Equilibration versus Kinetic Trapping
Studied by Statistical Polymer Chain Analysis, J. Mol. Biol., 1996;264:919.
- Goodsell DS, Molecular Art - Molecular Science.
- Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W, Macromolecular Architecture in Eukaryotic Cells
Visualized by Cryoelectron Tomography, Science, 2002 November 8;298:1209.
Lecture 11:
- Mitosis World, Stunning movies which reveal the activities of the cytoskeleton during cell division.
Lecture 14:
- Abraham VC, Krishnamurthi V, Taylor DL, Lanni F, The Actin-Based Nanomachine at the Leading Edge of Migrating Cells,
Biophysical Journal, 1999 September;77:1721.
- Borisy GG, Svitkina TM, Actin machinery: pushing the envelope,
Curr. Op. Cell Biol., 2000;12:104.
- Errington J, Dynamic proteins and a cytoskeleton in bacteria,
Nat. Cell Biol., 2003 March;5:175.
A nice review of the emerging picture of the bacterial cytoskeleton.
- Fletcher DA, Theriot JA, An introduction to cell motility for the physical scientist,
Phys. Biol., 2004;1:T1.
- Garner EC, Campbell CS, Mullins RD, Dynamic Instability in a DNA-Segregating Prokaryotic Actin Homolog,
Phys. Biol., 2004;1:T1.
- Pollard TD, The cytoskeleton, cellular motility and the reductionist agenda,
Nature, 2003 April 17;422:741.
- Rafelski SM, Theriot JA, Crawling Toward a Unified Model of Cell Motility: Spatial and Temporal Regulation of Actin Dynamics,
Annu. Rev. Biochem., 2004;73:209.
- Mitchison T, Kirschner M, Dynamic instability of microtubule growth,
Nature, 1984 November 15;312:237.
- Waterman-Storer Laboratory Movies
- Salmon Lab Movies
Lecture 15:
- Dogterom M, Leibler S, Physical Aspects of the Growth and Regulation of Microtubule Structures,
Phys. Rev. Lett., 1993 March 1;70(9):1347.
A simple phenomenological model of the steady-state distribution of microtubule lengths.
- Kuchnir Fygenson D, Braun E, Libchaber A, Phase diagram of microtubules,
Phys. Rev. E, 1994 August;50(2):1579.
Fig. 1 shows an experimental time series for the length of microtubules as a function of time, fig. 6
shows the distribution of microtubule lengths.
- Flyvbjerg H, Holy TE, Leibler S, Stochastic Dynamics of Microtubules:
A Model cor Caps and Catastrophes, Phys. Rev. Lett., 1994 October 24;73(17):2372.
This model treats the dynamics of the cap of GTP tubulin in microtubules.
- Flyvbjerg H, Holy TE, Leibler S, Microtubule dynamics: Caps, catastrophes, and coupled hydrolysis
, Phys. Rev. E, 1996 November;54(5):5538.
- Carlier MF, Pantaloni D, Control of Actin Dynamics in Cell Motility
, J. Mol. Biol., 1997;269:459.
- Pollard TD, Rate Constants for the Reactions of ATP- and ADP-Actin
with the Ends of Actin Filaments, J. Cell Biol., 1986 December;103(2):2747.
Lecture 16:
- Thomas N, Imafuku Y, Tawada K, Molecular motors: thermodynamics and the random walk, Proc R Soc Lond B Biol Sci. 2001 Oct 22;268(1481):2113.
- Fisher ME, Kolomeisky AB, The force exerted by a molecular motor,
PNAS, 1999 June;96:6597.
- Gross SP, Hither and yon: a review of bi-directional microtubule-based transport,
Phys. Biol., 2004;1:R1.
- Fisher ME, Kolomeisky AB, Simple mechanochemistry describes the dynamics of kinesin molecules,
PNAS, 2001 July 3;98(14):7748.
- Huxley HE, Fifty years of muscle and the sliding filament hypothesis,
Eur. J. Biochem., 2004;271:1403.
- Mahadevan L, Matsudaira P, Motility Powered by Supramolecular Springs and Ratchets,
Science, 2000 April 7;288:95.
This paper describes classes of motors other than the translational motors described in class.
- Schliwa M, Woehlke G, Molecular motors,
Nature, 2003 April 17;422:759.
- Schnitzer MJ, Block SM, Kinesin hydrolyses one ATP per 8-nm step,
Nature, 1997 July 24;388:386.
- Vale RD, Milligan RA, The Way Things Move: Looking Under the Hood of Molecular Motor Proteins,
Nature, 2000 April 7;288:88.
- Vale RD, The Molecular Motor Toolbox for Intracellular Transport,
Cell, 2003 February 21;112:467.
- Woehlke G, Schliwa M, Walking on two heads: the many talents of kinesin,
Nature Reviews, 2000 October;1:50.
- Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR, Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with
1.5-nm Localization, Science, 2003 June 27 ;300:2061.
- Kinosita Lab Movies, cool single molecule movies of the action of molecular motors.
- Heuser Lab Galleries, this site includes some of the classic electron micrographs of
muscle and muscle proteins.
Lecture 17:
- Rief M, Rock RS, Mehta AD, Mooseker MS, Cheney RE, Spudich JA,
Myosin-V stepping kinetics: A molecular model for processivity,
PNAS, 2000 Aug 15;97(17):9482.
- Simon SM, Peskin CS, Oster GF,
What drives the translocation of proteins?,
PNAS, 1992 May;89:3770.
Lecture 18:
- Gillespie PG, Walker RG,
Molecular basis of mechanosensory transduction,
Nature, 2001 Sep 13;413:194.
- Miyazawa A, Fujiyoshi Y, Unwin N,
Structure and gating mechanism of the acetylcholine receptor pore,
Nature, 2003 Jun 26;423:949.
Lecture 19:
- Nilsson DE, Pelger S,
A Pessimistic Estimate of the Time Required for an Eye to Evolve,
Proc. Roy. Soc Lond., 1994 Apr 22;256(1345):53.
- Sens P, Turnery MS,
Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations,
Biophysical Journal, 2004 Apr;86:2049.
Homeworks
- HW1, Due on Tuesday,
January 18
- HW2, Due on Thursday,
January 27
- HW3, Due on Thursday,
February 3
- HW4, Due on Thursday,
February 10
- HW5, Due on Tuesday,
February 22
- HW6, Due on Tuesday,
March 1
- HW7, Due on Tuesday,
March 8
- HW8, Due on Friday,
March 11
Solutions
Lecture notes
- Lecture 1 slides
- Lecture 2 slides
- Stat. Mech. lecture slides
- Lecture 3 slides
- Lecture 4 slides
- Lectures 6 and 7 slides
- Lecture 8 slides
- Lecture 10 slides
- Lectures 12, 13 and 14 slides
- Lecture 16 slides
- Lecture 18 slides
- Lecture 19 slides
Contact Information
Rob
Phillips
221 Steele
x3374
phillips AT pboc.caltech
Hernan Garcia
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Rizal Hariadi
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Mandar M. Inamdar
226 Steele
x3106
mandar AT caltech
Office hours: TBA
This paper discusses the census of RNAP in the cell.
This paper is an example of the use of the beta galactosidase activity as a measure of gene expression.
This paper pioneered the use of the so-called thermodynamic models to examine gene expression.
- Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R, Transcriptional Regulation by the Numbers 1: Models, Curr. Op. Gen. and Dev, 2005, in press.
Review on statistical mechanics models of transcriptional regulation. - Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R, Transcriptional Regulation by the Numbers 2: Applications, Curr. Op. Gen. and Dev, 2005, in press.
Applications of statistical mechanics models of transcriptional regulation. - Dayton CJ, Prosen DE, Parker KL, Cech CL, Kinetic Measurements of Escherichia coli RNA Polymerase Association with Bacteriophage T7 Early Promoters, J. of Biol. Chem., 1984 February 10;259(3):1616.
- Liu M, Gupte G, Roy S, Bandwar RP, Patel SS, Garges S, Kinetics of Transcription Initiation at lacP1, J. of Biol. Chem., 2003 October 10;278(41):39755.
- Record MT, Reznikoff WS, Craig ML, McQuade KL, Schlax PJ , Escherichia coli RNA Plymerase (Esigma70), Promoters, and the Kinetics of the Steps of Transcription Initiation, in "Escherichia coli and Salmonella : cellular and molecular biology", 1996;ASM Press, Washington DC.
- Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH, Structural Basis of Transcription Activation: The CAP-alphaCTD-DNA Complex, Science, 2002 August 30;297:1562.
This paper shows from a structural perspective how activators recruit RNAP to the promoter.
Lecture 6:
- Oehler S, Amouyal M, Kolkhof P, von Wilcken-Bergmann B, Mueller-Hill B , Quality and position of the three lac operators of E. Coli define efficiency of repression, EMBO J., 1994;13(14):3348.
DNA looping in the lac operon by mutating binding sites.
- Mueller J, Oehler S, Mueller-Hill B , Repression of lac Promoter as a Function of Distance, Phase and Quality of an Auxiliary lac Operator, JMB, 1996;257:21.
DNA looping in the lac operon as a function of the distance between operators.
This paper is a beautiful experiment which shows how repression depends upon the distance between the two operators.
- Vilar JMG, Leibler S , DNA Looping and Physical Constraints on Transcription Regulation, JMB, 2003;331:981.
Modeling of the experiment in Oehler et al. (1994) using a thermodynamic model.
- Buchler NE, Gerland U, Hwa T , On schemes of combinatorial transcription logic, PNAS,
2003 April 29;100(9):5136.
- Bruinsma RF , Physics of protein-DNA interaction, Physica A, 2002;313:211.
- T. Cremer and C. Cremer, Chromosomes territories, nuclear architecture, and gene regulation in mammalian cells, Nature Reviews: Genetics, 2001 April;2:292-301.
Lecture 7:
- Richmond TJ, Davey CA , The structure of DNA in the nucleosome core, Nature, 2003 May 8;423:145.
- Polach KJ, Widom J , Mechanism of Protein Access to Specific DNA Sequences in Chromatin: A Dynamic Equilibrium Model for Gene Regulation, JMB, 1995;254:130.
- Polach KJ, Widom J , A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target Sites, JMB,1996;258:800.
- Nancy L. Marky and Gerald S. Manning, A theory of DNA dissociation from the nucleosome, J. Mol. Biol, 1995; 254:50-61.
- Li G, Levitus M, Bustamante C, Widom J , Rapid spontaneous accessibility of nucleosomal DNA, Nat. Struc. Biol.,
2005 January;12(1):46.
- Roger D. Kornberg and Yahli Lorch, Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome Cell, 1999 August 6;98:285-294.
-
Thomas D. Yager, Cynthia T. McMurray, and K. E. van Holde , Salt-Induced Release of DNA from Nucleosome Core Particles, Biochemistry, 1989;28:2271-2281.
Lecture 8:
- Adam M. Breier and Nicholas R.
Cozzarelli, Linear ordering and dynamic segregation of the bacterial chromosomes, PNAS, 2004 June 22;101:9175-6.
-
Patrick H. Viollier, Martin Thanbichler, Patrick T. McGrath, Lisandra West, Maliwan Meewan, Harley H. McAdams, and Lucy Shapiro, Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication, PNAS, 2004 June 22;101(25):9257-62.
Lecture 9:
- Rau DV, Lee B, Parsegian VA , Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: Hydration forces between parallel DNA double helices, PNAS, 1984 May;81:2621.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
-
Alan A. Simpson, Yizhi Tao, Petr G. Leiman, Mohammed O. Badasso, Yongning He, Paul J. Jardinek, Norman H. Olson, Marc C. Morais, Shelley Grimes, Dwight L. Anderson, Timothy S. Baker & Michael G. Rossmann, Structure of the bacteriophage Phi29 DNA packaging motor, Nature, 2000 December 7;408:745-750.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
- Rizal Hariadi , Interaction Energy in Helical Array of DNA strands.
- Baker TS, Olson NH, Fuller SD, Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral
Viruses from Cryo-Electron Micrographs, Microb. Mol. Biol. Rev., 1999 December; 63(4):862.
- Mario E. Cerritelli, Naiqian Cheng, Alan H. Rosenberg, Catherine E. McPherson, Frank P. Booy, and Alasdair C. Steven, Encapsidated Conformation of Bacteriophage T7 DNA, Cell, 1997 October 17;91:271.
- Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, Solvent Mediated Interactions in the Structure of the Nucleosome Core
Particle at 1.9 A Resolution, J. Mol. Biol., 2002;319:1097.
- Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ, Crystal structure of the nucleosome core particle at 2.8A resolution,
Nature, 1997 September 18;389:251.
- Earnshaw WC, Harrison SC, DNA arrangement in isometric phage heads,
Nature, 1977 August 18;268:598.
Lecture 10:
- R. John Ellis, Macromolecular crowding: an important but neglected aspect of the intracellular environment, Current Opinion in Structural Biology, 2001;11:114–119.
- R. John Ellis, Macromolecular crowding: obvious but underappreciated, Trends in Biochemical Sciences, 2001 October;26(10):567.
- Michael B. Elowitz, Michael G.
Surette, Pierre-Etiene Wolf, Jeffry B. Stock, and Stanislas Leibler, Protein Mobility in the Cytoplasm of Escherichia coli, Journal of Bacteriology, 1999 January;181(1):197-203.
- Karine A. Gibbs, Daniel D. Isaac, Jun Xu, Roger W. Hendrix, Thomas J. Silhavy and Julie A. Theriot, Complex spatial distribution and dynamics of an abundant Escherichia coli outer membrane protein, LamB, Molecular Microbiology, 2004;53(6):1771.
-
Katherine Luby-Phelps,
Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular, surface area, International Review of Cytology, 2000;192:189-221.
- Allen P. Minton, The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media, J. Biol. Chem., 2001 April 6;276(14),10577-80.
-
Alan S.Verkman, Solute and macromolecule diffusion in cellular aqueous compartments, Trends in Biochemical Sciences, 2002 January 1;27(1):27-33.
- Einstein A, On the movement of small particles suspended in a stationary liquid demanded by the molecular-kinetic theory of heat, 1905.
- Reits EAJ, Neefjes JJ, From fixed to FRAP: measuring protein mobility and activity in living cells, Nat. Cell Biol., 2001 June;
3:E145.
- Zimmerman SB, Minton AP, Macromolecular Crowding: Biochemical, Biophysical, and Physiological Consequences,
Annu. Rev. Biophys. Biomol. Struct., 1993;22:27.
- Rivetti C, Guthold M, Bustamante C, Scanning Force Microscopy of DNA Deposited onto Mica: Equilibration versus Kinetic Trapping
Studied by Statistical Polymer Chain Analysis, J. Mol. Biol., 1996;264:919.
- Goodsell DS, Molecular Art - Molecular Science.
- Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W, Macromolecular Architecture in Eukaryotic Cells
Visualized by Cryoelectron Tomography, Science, 2002 November 8;298:1209.
Lecture 11:
- Mitosis World, Stunning movies which reveal the activities of the cytoskeleton during cell division.
Lecture 14:
- Abraham VC, Krishnamurthi V, Taylor DL, Lanni F, The Actin-Based Nanomachine at the Leading Edge of Migrating Cells,
Biophysical Journal, 1999 September;77:1721.
- Borisy GG, Svitkina TM, Actin machinery: pushing the envelope,
Curr. Op. Cell Biol., 2000;12:104.
- Errington J, Dynamic proteins and a cytoskeleton in bacteria,
Nat. Cell Biol., 2003 March;5:175.
A nice review of the emerging picture of the bacterial cytoskeleton.
- Fletcher DA, Theriot JA, An introduction to cell motility for the physical scientist,
Phys. Biol., 2004;1:T1.
- Garner EC, Campbell CS, Mullins RD, Dynamic Instability in a DNA-Segregating Prokaryotic Actin Homolog,
Phys. Biol., 2004;1:T1.
- Pollard TD, The cytoskeleton, cellular motility and the reductionist agenda,
Nature, 2003 April 17;422:741.
- Rafelski SM, Theriot JA, Crawling Toward a Unified Model of Cell Motility: Spatial and Temporal Regulation of Actin Dynamics,
Annu. Rev. Biochem., 2004;73:209.
- Mitchison T, Kirschner M, Dynamic instability of microtubule growth,
Nature, 1984 November 15;312:237.
- Waterman-Storer Laboratory Movies
- Salmon Lab Movies
Lecture 15:
- Dogterom M, Leibler S, Physical Aspects of the Growth and Regulation of Microtubule Structures,
Phys. Rev. Lett., 1993 March 1;70(9):1347.
A simple phenomenological model of the steady-state distribution of microtubule lengths.
- Kuchnir Fygenson D, Braun E, Libchaber A, Phase diagram of microtubules,
Phys. Rev. E, 1994 August;50(2):1579.
Fig. 1 shows an experimental time series for the length of microtubules as a function of time, fig. 6
shows the distribution of microtubule lengths.
- Flyvbjerg H, Holy TE, Leibler S, Stochastic Dynamics of Microtubules:
A Model cor Caps and Catastrophes, Phys. Rev. Lett., 1994 October 24;73(17):2372.
This model treats the dynamics of the cap of GTP tubulin in microtubules.
- Flyvbjerg H, Holy TE, Leibler S, Microtubule dynamics: Caps, catastrophes, and coupled hydrolysis
, Phys. Rev. E, 1996 November;54(5):5538.
- Carlier MF, Pantaloni D, Control of Actin Dynamics in Cell Motility
, J. Mol. Biol., 1997;269:459.
- Pollard TD, Rate Constants for the Reactions of ATP- and ADP-Actin
with the Ends of Actin Filaments, J. Cell Biol., 1986 December;103(2):2747.
Lecture 16:
- Thomas N, Imafuku Y, Tawada K, Molecular motors: thermodynamics and the random walk, Proc R Soc Lond B Biol Sci. 2001 Oct 22;268(1481):2113.
- Fisher ME, Kolomeisky AB, The force exerted by a molecular motor,
PNAS, 1999 June;96:6597.
- Gross SP, Hither and yon: a review of bi-directional microtubule-based transport,
Phys. Biol., 2004;1:R1.
- Fisher ME, Kolomeisky AB, Simple mechanochemistry describes the dynamics of kinesin molecules,
PNAS, 2001 July 3;98(14):7748.
- Huxley HE, Fifty years of muscle and the sliding filament hypothesis,
Eur. J. Biochem., 2004;271:1403.
- Mahadevan L, Matsudaira P, Motility Powered by Supramolecular Springs and Ratchets,
Science, 2000 April 7;288:95.
This paper describes classes of motors other than the translational motors described in class.
- Schliwa M, Woehlke G, Molecular motors,
Nature, 2003 April 17;422:759.
- Schnitzer MJ, Block SM, Kinesin hydrolyses one ATP per 8-nm step,
Nature, 1997 July 24;388:386.
- Vale RD, Milligan RA, The Way Things Move: Looking Under the Hood of Molecular Motor Proteins,
Nature, 2000 April 7;288:88.
- Vale RD, The Molecular Motor Toolbox for Intracellular Transport,
Cell, 2003 February 21;112:467.
- Woehlke G, Schliwa M, Walking on two heads: the many talents of kinesin,
Nature Reviews, 2000 October;1:50.
- Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR, Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with
1.5-nm Localization, Science, 2003 June 27 ;300:2061.
- Kinosita Lab Movies, cool single molecule movies of the action of molecular motors.
- Heuser Lab Galleries, this site includes some of the classic electron micrographs of
muscle and muscle proteins.
Lecture 17:
- Rief M, Rock RS, Mehta AD, Mooseker MS, Cheney RE, Spudich JA,
Myosin-V stepping kinetics: A molecular model for processivity,
PNAS, 2000 Aug 15;97(17):9482.
- Simon SM, Peskin CS, Oster GF,
What drives the translocation of proteins?,
PNAS, 1992 May;89:3770.
Lecture 18:
- Gillespie PG, Walker RG,
Molecular basis of mechanosensory transduction,
Nature, 2001 Sep 13;413:194.
- Miyazawa A, Fujiyoshi Y, Unwin N,
Structure and gating mechanism of the acetylcholine receptor pore,
Nature, 2003 Jun 26;423:949.
Lecture 19:
- Nilsson DE, Pelger S,
A Pessimistic Estimate of the Time Required for an Eye to Evolve,
Proc. Roy. Soc Lond., 1994 Apr 22;256(1345):53.
- Sens P, Turnery MS,
Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations,
Biophysical Journal, 2004 Apr;86:2049.
Homeworks
- HW1, Due on Tuesday,
January 18
- HW2, Due on Thursday,
January 27
- HW3, Due on Thursday,
February 3
- HW4, Due on Thursday,
February 10
- HW5, Due on Tuesday,
February 22
- HW6, Due on Tuesday,
March 1
- HW7, Due on Tuesday,
March 8
- HW8, Due on Friday,
March 11
Solutions
Lecture notes
- Lecture 1 slides
- Lecture 2 slides
- Stat. Mech. lecture slides
- Lecture 3 slides
- Lecture 4 slides
- Lectures 6 and 7 slides
- Lecture 8 slides
- Lecture 10 slides
- Lectures 12, 13 and 14 slides
- Lecture 16 slides
- Lecture 18 slides
- Lecture 19 slides
Contact Information
Rob
Phillips
221 Steele
x3374
phillips AT pboc.caltech
Hernan Garcia
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Rizal Hariadi
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Mandar M. Inamdar
226 Steele
x3106
mandar AT caltech
Office hours: TBA
DNA looping in the lac operon by mutating binding sites.
DNA looping in the lac operon as a function of the distance between operators.
This paper is a beautiful experiment which shows how repression depends upon the distance between the two operators.
Modeling of the experiment in Oehler et al. (1994) using a thermodynamic model.
- Richmond TJ, Davey CA , The structure of DNA in the nucleosome core, Nature, 2003 May 8;423:145.
- Polach KJ, Widom J , Mechanism of Protein Access to Specific DNA Sequences in Chromatin: A Dynamic Equilibrium Model for Gene Regulation, JMB, 1995;254:130.
- Polach KJ, Widom J , A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target Sites, JMB,1996;258:800.
- Nancy L. Marky and Gerald S. Manning, A theory of DNA dissociation from the nucleosome, J. Mol. Biol, 1995; 254:50-61.
- Li G, Levitus M, Bustamante C, Widom J , Rapid spontaneous accessibility of nucleosomal DNA, Nat. Struc. Biol., 2005 January;12(1):46.
- Roger D. Kornberg and Yahli Lorch, Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome Cell, 1999 August 6;98:285-294.
- Thomas D. Yager, Cynthia T. McMurray, and K. E. van Holde , Salt-Induced Release of DNA from Nucleosome Core Particles, Biochemistry, 1989;28:2271-2281.
Lecture 8:
- Adam M. Breier and Nicholas R.
Cozzarelli, Linear ordering and dynamic segregation of the bacterial chromosomes, PNAS, 2004 June 22;101:9175-6.
-
Patrick H. Viollier, Martin Thanbichler, Patrick T. McGrath, Lisandra West, Maliwan Meewan, Harley H. McAdams, and Lucy Shapiro, Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication, PNAS, 2004 June 22;101(25):9257-62.
Lecture 9:
- Rau DV, Lee B, Parsegian VA , Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: Hydration forces between parallel DNA double helices, PNAS, 1984 May;81:2621.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
-
Alan A. Simpson, Yizhi Tao, Petr G. Leiman, Mohammed O. Badasso, Yongning He, Paul J. Jardinek, Norman H. Olson, Marc C. Morais, Shelley Grimes, Dwight L. Anderson, Timothy S. Baker & Michael G. Rossmann, Structure of the bacteriophage Phi29 DNA packaging motor, Nature, 2000 December 7;408:745-750.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
- Rizal Hariadi , Interaction Energy in Helical Array of DNA strands.
- Baker TS, Olson NH, Fuller SD, Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral
Viruses from Cryo-Electron Micrographs, Microb. Mol. Biol. Rev., 1999 December; 63(4):862.
- Mario E. Cerritelli, Naiqian Cheng, Alan H. Rosenberg, Catherine E. McPherson, Frank P. Booy, and Alasdair C. Steven, Encapsidated Conformation of Bacteriophage T7 DNA, Cell, 1997 October 17;91:271.
- Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, Solvent Mediated Interactions in the Structure of the Nucleosome Core
Particle at 1.9 A Resolution, J. Mol. Biol., 2002;319:1097.
- Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ, Crystal structure of the nucleosome core particle at 2.8A resolution,
Nature, 1997 September 18;389:251.
- Earnshaw WC, Harrison SC, DNA arrangement in isometric phage heads,
Nature, 1977 August 18;268:598.
Lecture 10:
- R. John Ellis, Macromolecular crowding: an important but neglected aspect of the intracellular environment, Current Opinion in Structural Biology, 2001;11:114–119.
- R. John Ellis, Macromolecular crowding: obvious but underappreciated, Trends in Biochemical Sciences, 2001 October;26(10):567.
- Michael B. Elowitz, Michael G.
Surette, Pierre-Etiene Wolf, Jeffry B. Stock, and Stanislas Leibler, Protein Mobility in the Cytoplasm of Escherichia coli, Journal of Bacteriology, 1999 January;181(1):197-203.
- Karine A. Gibbs, Daniel D. Isaac, Jun Xu, Roger W. Hendrix, Thomas J. Silhavy and Julie A. Theriot, Complex spatial distribution and dynamics of an abundant Escherichia coli outer membrane protein, LamB, Molecular Microbiology, 2004;53(6):1771.
-
Katherine Luby-Phelps,
Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular, surface area, International Review of Cytology, 2000;192:189-221.
- Allen P. Minton, The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media, J. Biol. Chem., 2001 April 6;276(14),10577-80.
-
Alan S.Verkman, Solute and macromolecule diffusion in cellular aqueous compartments, Trends in Biochemical Sciences, 2002 January 1;27(1):27-33.
- Einstein A, On the movement of small particles suspended in a stationary liquid demanded by the molecular-kinetic theory of heat, 1905.
- Reits EAJ, Neefjes JJ, From fixed to FRAP: measuring protein mobility and activity in living cells, Nat. Cell Biol., 2001 June;
3:E145.
- Zimmerman SB, Minton AP, Macromolecular Crowding: Biochemical, Biophysical, and Physiological Consequences,
Annu. Rev. Biophys. Biomol. Struct., 1993;22:27.
- Rivetti C, Guthold M, Bustamante C, Scanning Force Microscopy of DNA Deposited onto Mica: Equilibration versus Kinetic Trapping
Studied by Statistical Polymer Chain Analysis, J. Mol. Biol., 1996;264:919.
- Goodsell DS, Molecular Art - Molecular Science.
- Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W, Macromolecular Architecture in Eukaryotic Cells
Visualized by Cryoelectron Tomography, Science, 2002 November 8;298:1209.
Lecture 11:
- Mitosis World, Stunning movies which reveal the activities of the cytoskeleton during cell division.
Lecture 14:
- Abraham VC, Krishnamurthi V, Taylor DL, Lanni F, The Actin-Based Nanomachine at the Leading Edge of Migrating Cells,
Biophysical Journal, 1999 September;77:1721.
- Borisy GG, Svitkina TM, Actin machinery: pushing the envelope,
Curr. Op. Cell Biol., 2000;12:104.
- Errington J, Dynamic proteins and a cytoskeleton in bacteria,
Nat. Cell Biol., 2003 March;5:175.
A nice review of the emerging picture of the bacterial cytoskeleton.
- Fletcher DA, Theriot JA, An introduction to cell motility for the physical scientist,
Phys. Biol., 2004;1:T1.
- Garner EC, Campbell CS, Mullins RD, Dynamic Instability in a DNA-Segregating Prokaryotic Actin Homolog,
Phys. Biol., 2004;1:T1.
- Pollard TD, The cytoskeleton, cellular motility and the reductionist agenda,
Nature, 2003 April 17;422:741.
- Rafelski SM, Theriot JA, Crawling Toward a Unified Model of Cell Motility: Spatial and Temporal Regulation of Actin Dynamics,
Annu. Rev. Biochem., 2004;73:209.
- Mitchison T, Kirschner M, Dynamic instability of microtubule growth,
Nature, 1984 November 15;312:237.
- Waterman-Storer Laboratory Movies
- Salmon Lab Movies
Lecture 15:
- Dogterom M, Leibler S, Physical Aspects of the Growth and Regulation of Microtubule Structures,
Phys. Rev. Lett., 1993 March 1;70(9):1347.
A simple phenomenological model of the steady-state distribution of microtubule lengths.
- Kuchnir Fygenson D, Braun E, Libchaber A, Phase diagram of microtubules,
Phys. Rev. E, 1994 August;50(2):1579.
Fig. 1 shows an experimental time series for the length of microtubules as a function of time, fig. 6
shows the distribution of microtubule lengths.
- Flyvbjerg H, Holy TE, Leibler S, Stochastic Dynamics of Microtubules:
A Model cor Caps and Catastrophes, Phys. Rev. Lett., 1994 October 24;73(17):2372.
This model treats the dynamics of the cap of GTP tubulin in microtubules.
- Flyvbjerg H, Holy TE, Leibler S, Microtubule dynamics: Caps, catastrophes, and coupled hydrolysis
, Phys. Rev. E, 1996 November;54(5):5538.
- Carlier MF, Pantaloni D, Control of Actin Dynamics in Cell Motility
, J. Mol. Biol., 1997;269:459.
- Pollard TD, Rate Constants for the Reactions of ATP- and ADP-Actin
with the Ends of Actin Filaments, J. Cell Biol., 1986 December;103(2):2747.
Lecture 16:
- Thomas N, Imafuku Y, Tawada K, Molecular motors: thermodynamics and the random walk, Proc R Soc Lond B Biol Sci. 2001 Oct 22;268(1481):2113.
- Fisher ME, Kolomeisky AB, The force exerted by a molecular motor,
PNAS, 1999 June;96:6597.
- Gross SP, Hither and yon: a review of bi-directional microtubule-based transport,
Phys. Biol., 2004;1:R1.
- Fisher ME, Kolomeisky AB, Simple mechanochemistry describes the dynamics of kinesin molecules,
PNAS, 2001 July 3;98(14):7748.
- Huxley HE, Fifty years of muscle and the sliding filament hypothesis,
Eur. J. Biochem., 2004;271:1403.
- Mahadevan L, Matsudaira P, Motility Powered by Supramolecular Springs and Ratchets,
Science, 2000 April 7;288:95.
This paper describes classes of motors other than the translational motors described in class.
- Schliwa M, Woehlke G, Molecular motors,
Nature, 2003 April 17;422:759.
- Schnitzer MJ, Block SM, Kinesin hydrolyses one ATP per 8-nm step,
Nature, 1997 July 24;388:386.
- Vale RD, Milligan RA, The Way Things Move: Looking Under the Hood of Molecular Motor Proteins,
Nature, 2000 April 7;288:88.
- Vale RD, The Molecular Motor Toolbox for Intracellular Transport,
Cell, 2003 February 21;112:467.
- Woehlke G, Schliwa M, Walking on two heads: the many talents of kinesin,
Nature Reviews, 2000 October;1:50.
- Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR, Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with
1.5-nm Localization, Science, 2003 June 27 ;300:2061.
- Kinosita Lab Movies, cool single molecule movies of the action of molecular motors.
- Heuser Lab Galleries, this site includes some of the classic electron micrographs of
muscle and muscle proteins.
Lecture 17:
- Rief M, Rock RS, Mehta AD, Mooseker MS, Cheney RE, Spudich JA,
Myosin-V stepping kinetics: A molecular model for processivity,
PNAS, 2000 Aug 15;97(17):9482.
- Simon SM, Peskin CS, Oster GF,
What drives the translocation of proteins?,
PNAS, 1992 May;89:3770.
Lecture 18:
- Gillespie PG, Walker RG,
Molecular basis of mechanosensory transduction,
Nature, 2001 Sep 13;413:194.
- Miyazawa A, Fujiyoshi Y, Unwin N,
Structure and gating mechanism of the acetylcholine receptor pore,
Nature, 2003 Jun 26;423:949.
Lecture 19:
- Nilsson DE, Pelger S,
A Pessimistic Estimate of the Time Required for an Eye to Evolve,
Proc. Roy. Soc Lond., 1994 Apr 22;256(1345):53.
- Sens P, Turnery MS,
Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations,
Biophysical Journal, 2004 Apr;86:2049.
Homeworks
- HW1, Due on Tuesday,
January 18
- HW2, Due on Thursday,
January 27
- HW3, Due on Thursday,
February 3
- HW4, Due on Thursday,
February 10
- HW5, Due on Tuesday,
February 22
- HW6, Due on Tuesday,
March 1
- HW7, Due on Tuesday,
March 8
- HW8, Due on Friday,
March 11
Solutions
Lecture notes
- Lecture 1 slides
- Lecture 2 slides
- Stat. Mech. lecture slides
- Lecture 3 slides
- Lecture 4 slides
- Lectures 6 and 7 slides
- Lecture 8 slides
- Lecture 10 slides
- Lectures 12, 13 and 14 slides
- Lecture 16 slides
- Lecture 18 slides
- Lecture 19 slides
Contact Information
Rob
Phillips
221 Steele
x3374
phillips AT pboc.caltech
Hernan Garcia
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Rizal Hariadi
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Mandar M. Inamdar
226 Steele
x3106
mandar AT caltech
Office hours: TBA
- Rau DV, Lee B, Parsegian VA , Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: Hydration forces between parallel DNA double helices, PNAS, 1984 May;81:2621.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
- Alan A. Simpson, Yizhi Tao, Petr G. Leiman, Mohammed O. Badasso, Yongning He, Paul J. Jardinek, Norman H. Olson, Marc C. Morais, Shelley Grimes, Dwight L. Anderson, Timothy S. Baker & Michael G. Rossmann, Structure of the bacteriophage Phi29 DNA packaging motor, Nature, 2000 December 7;408:745-750.
- Carlos Bustamante Data
- Douglas E. Smith, Sander J. Tans, Steven B. Smith, Shelley Grimes, Dwight L. Anderson & Carlos Bustamante, The bacteriophage Phi29 portal motor can package DNA againts a large internal force, Nature, 2001 October 18; 413:748-752.
- Rizal Hariadi , Interaction Energy in Helical Array of DNA strands.
- Baker TS, Olson NH, Fuller SD, Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs, Microb. Mol. Biol. Rev., 1999 December; 63(4):862.
- Mario E. Cerritelli, Naiqian Cheng, Alan H. Rosenberg, Catherine E. McPherson, Frank P. Booy, and Alasdair C. Steven, Encapsidated Conformation of Bacteriophage T7 DNA, Cell, 1997 October 17;91:271.
- Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution, J. Mol. Biol., 2002;319:1097.
- Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ, Crystal structure of the nucleosome core particle at 2.8A resolution, Nature, 1997 September 18;389:251.
- Earnshaw WC, Harrison SC, DNA arrangement in isometric phage heads, Nature, 1977 August 18;268:598.
Lecture 10:
- R. John Ellis, Macromolecular crowding: an important but neglected aspect of the intracellular environment, Current Opinion in Structural Biology, 2001;11:114–119.
- R. John Ellis, Macromolecular crowding: obvious but underappreciated, Trends in Biochemical Sciences, 2001 October;26(10):567.
- Michael B. Elowitz, Michael G.
Surette, Pierre-Etiene Wolf, Jeffry B. Stock, and Stanislas Leibler, Protein Mobility in the Cytoplasm of Escherichia coli, Journal of Bacteriology, 1999 January;181(1):197-203.
- Karine A. Gibbs, Daniel D. Isaac, Jun Xu, Roger W. Hendrix, Thomas J. Silhavy and Julie A. Theriot, Complex spatial distribution and dynamics of an abundant Escherichia coli outer membrane protein, LamB, Molecular Microbiology, 2004;53(6):1771.
-
Katherine Luby-Phelps,
Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular, surface area, International Review of Cytology, 2000;192:189-221.
- Allen P. Minton, The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media, J. Biol. Chem., 2001 April 6;276(14),10577-80.
-
Alan S.Verkman, Solute and macromolecule diffusion in cellular aqueous compartments, Trends in Biochemical Sciences, 2002 January 1;27(1):27-33.
- Einstein A, On the movement of small particles suspended in a stationary liquid demanded by the molecular-kinetic theory of heat, 1905.
- Reits EAJ, Neefjes JJ, From fixed to FRAP: measuring protein mobility and activity in living cells, Nat. Cell Biol., 2001 June;
3:E145.
- Zimmerman SB, Minton AP, Macromolecular Crowding: Biochemical, Biophysical, and Physiological Consequences,
Annu. Rev. Biophys. Biomol. Struct., 1993;22:27.
- Rivetti C, Guthold M, Bustamante C, Scanning Force Microscopy of DNA Deposited onto Mica: Equilibration versus Kinetic Trapping
Studied by Statistical Polymer Chain Analysis, J. Mol. Biol., 1996;264:919.
- Goodsell DS, Molecular Art - Molecular Science.
- Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W, Macromolecular Architecture in Eukaryotic Cells
Visualized by Cryoelectron Tomography, Science, 2002 November 8;298:1209.
Lecture 11:
- Mitosis World, Stunning movies which reveal the activities of the cytoskeleton during cell division.
Lecture 14:
- Abraham VC, Krishnamurthi V, Taylor DL, Lanni F, The Actin-Based Nanomachine at the Leading Edge of Migrating Cells,
Biophysical Journal, 1999 September;77:1721.
- Borisy GG, Svitkina TM, Actin machinery: pushing the envelope,
Curr. Op. Cell Biol., 2000;12:104.
- Errington J, Dynamic proteins and a cytoskeleton in bacteria,
Nat. Cell Biol., 2003 March;5:175.
A nice review of the emerging picture of the bacterial cytoskeleton.
- Fletcher DA, Theriot JA, An introduction to cell motility for the physical scientist,
Phys. Biol., 2004;1:T1.
- Garner EC, Campbell CS, Mullins RD, Dynamic Instability in a DNA-Segregating Prokaryotic Actin Homolog,
Phys. Biol., 2004;1:T1.
- Pollard TD, The cytoskeleton, cellular motility and the reductionist agenda,
Nature, 2003 April 17;422:741.
- Rafelski SM, Theriot JA, Crawling Toward a Unified Model of Cell Motility: Spatial and Temporal Regulation of Actin Dynamics,
Annu. Rev. Biochem., 2004;73:209.
- Mitchison T, Kirschner M, Dynamic instability of microtubule growth,
Nature, 1984 November 15;312:237.
- Waterman-Storer Laboratory Movies
- Salmon Lab Movies
Lecture 15:
- Dogterom M, Leibler S, Physical Aspects of the Growth and Regulation of Microtubule Structures,
Phys. Rev. Lett., 1993 March 1;70(9):1347.
A simple phenomenological model of the steady-state distribution of microtubule lengths.
- Kuchnir Fygenson D, Braun E, Libchaber A, Phase diagram of microtubules,
Phys. Rev. E, 1994 August;50(2):1579.
Fig. 1 shows an experimental time series for the length of microtubules as a function of time, fig. 6
shows the distribution of microtubule lengths.
- Flyvbjerg H, Holy TE, Leibler S, Stochastic Dynamics of Microtubules:
A Model cor Caps and Catastrophes, Phys. Rev. Lett., 1994 October 24;73(17):2372.
This model treats the dynamics of the cap of GTP tubulin in microtubules.
- Flyvbjerg H, Holy TE, Leibler S, Microtubule dynamics: Caps, catastrophes, and coupled hydrolysis
, Phys. Rev. E, 1996 November;54(5):5538.
- Carlier MF, Pantaloni D, Control of Actin Dynamics in Cell Motility
, J. Mol. Biol., 1997;269:459.
- Pollard TD, Rate Constants for the Reactions of ATP- and ADP-Actin
with the Ends of Actin Filaments, J. Cell Biol., 1986 December;103(2):2747.
Lecture 16:
- Thomas N, Imafuku Y, Tawada K, Molecular motors: thermodynamics and the random walk, Proc R Soc Lond B Biol Sci. 2001 Oct 22;268(1481):2113.
- Fisher ME, Kolomeisky AB, The force exerted by a molecular motor,
PNAS, 1999 June;96:6597.
- Gross SP, Hither and yon: a review of bi-directional microtubule-based transport,
Phys. Biol., 2004;1:R1.
- Fisher ME, Kolomeisky AB, Simple mechanochemistry describes the dynamics of kinesin molecules,
PNAS, 2001 July 3;98(14):7748.
- Huxley HE, Fifty years of muscle and the sliding filament hypothesis,
Eur. J. Biochem., 2004;271:1403.
- Mahadevan L, Matsudaira P, Motility Powered by Supramolecular Springs and Ratchets,
Science, 2000 April 7;288:95.
This paper describes classes of motors other than the translational motors described in class.
- Schliwa M, Woehlke G, Molecular motors,
Nature, 2003 April 17;422:759.
- Schnitzer MJ, Block SM, Kinesin hydrolyses one ATP per 8-nm step,
Nature, 1997 July 24;388:386.
- Vale RD, Milligan RA, The Way Things Move: Looking Under the Hood of Molecular Motor Proteins,
Nature, 2000 April 7;288:88.
- Vale RD, The Molecular Motor Toolbox for Intracellular Transport,
Cell, 2003 February 21;112:467.
- Woehlke G, Schliwa M, Walking on two heads: the many talents of kinesin,
Nature Reviews, 2000 October;1:50.
- Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR, Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with
1.5-nm Localization, Science, 2003 June 27 ;300:2061.
- Kinosita Lab Movies, cool single molecule movies of the action of molecular motors.
- Heuser Lab Galleries, this site includes some of the classic electron micrographs of
muscle and muscle proteins.
Lecture 17:
- Rief M, Rock RS, Mehta AD, Mooseker MS, Cheney RE, Spudich JA,
Myosin-V stepping kinetics: A molecular model for processivity,
PNAS, 2000 Aug 15;97(17):9482.
- Simon SM, Peskin CS, Oster GF,
What drives the translocation of proteins?,
PNAS, 1992 May;89:3770.
Lecture 18:
- Gillespie PG, Walker RG,
Molecular basis of mechanosensory transduction,
Nature, 2001 Sep 13;413:194.
- Miyazawa A, Fujiyoshi Y, Unwin N,
Structure and gating mechanism of the acetylcholine receptor pore,
Nature, 2003 Jun 26;423:949.
Lecture 19:
- Nilsson DE, Pelger S,
A Pessimistic Estimate of the Time Required for an Eye to Evolve,
Proc. Roy. Soc Lond., 1994 Apr 22;256(1345):53.
- Sens P, Turnery MS,
Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations,
Biophysical Journal, 2004 Apr;86:2049.
Homeworks
- HW1, Due on Tuesday,
January 18
- HW2, Due on Thursday,
January 27
- HW3, Due on Thursday,
February 3
- HW4, Due on Thursday,
February 10
- HW5, Due on Tuesday,
February 22
- HW6, Due on Tuesday,
March 1
- HW7, Due on Tuesday,
March 8
- HW8, Due on Friday,
March 11
Solutions
Lecture notes
- Lecture 1 slides
- Lecture 2 slides
- Stat. Mech. lecture slides
- Lecture 3 slides
- Lecture 4 slides
- Lectures 6 and 7 slides
- Lecture 8 slides
- Lecture 10 slides
- Lectures 12, 13 and 14 slides
- Lecture 16 slides
- Lecture 18 slides
- Lecture 19 slides
Contact Information
Rob
Phillips
221 Steele
x3374
phillips AT pboc.caltech
Hernan Garcia
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Rizal Hariadi
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Mandar M. Inamdar
226 Steele
x3106
mandar AT caltech
Office hours: TBA
- Mitosis World, Stunning movies which reveal the activities of the cytoskeleton during cell division.
Lecture 14:
- Abraham VC, Krishnamurthi V, Taylor DL, Lanni F, The Actin-Based Nanomachine at the Leading Edge of Migrating Cells,
Biophysical Journal, 1999 September;77:1721.
- Borisy GG, Svitkina TM, Actin machinery: pushing the envelope,
Curr. Op. Cell Biol., 2000;12:104.
- Errington J, Dynamic proteins and a cytoskeleton in bacteria,
Nat. Cell Biol., 2003 March;5:175.
A nice review of the emerging picture of the bacterial cytoskeleton.
- Fletcher DA, Theriot JA, An introduction to cell motility for the physical scientist,
Phys. Biol., 2004;1:T1.
- Garner EC, Campbell CS, Mullins RD, Dynamic Instability in a DNA-Segregating Prokaryotic Actin Homolog,
Phys. Biol., 2004;1:T1.
- Pollard TD, The cytoskeleton, cellular motility and the reductionist agenda,
Nature, 2003 April 17;422:741.
- Rafelski SM, Theriot JA, Crawling Toward a Unified Model of Cell Motility: Spatial and Temporal Regulation of Actin Dynamics,
Annu. Rev. Biochem., 2004;73:209.
- Mitchison T, Kirschner M, Dynamic instability of microtubule growth,
Nature, 1984 November 15;312:237.
- Waterman-Storer Laboratory Movies
- Salmon Lab Movies
Lecture 15:
- Dogterom M, Leibler S, Physical Aspects of the Growth and Regulation of Microtubule Structures,
Phys. Rev. Lett., 1993 March 1;70(9):1347.
A simple phenomenological model of the steady-state distribution of microtubule lengths.
- Kuchnir Fygenson D, Braun E, Libchaber A, Phase diagram of microtubules,
Phys. Rev. E, 1994 August;50(2):1579.
Fig. 1 shows an experimental time series for the length of microtubules as a function of time, fig. 6
shows the distribution of microtubule lengths.
- Flyvbjerg H, Holy TE, Leibler S, Stochastic Dynamics of Microtubules:
A Model cor Caps and Catastrophes, Phys. Rev. Lett., 1994 October 24;73(17):2372.
This model treats the dynamics of the cap of GTP tubulin in microtubules.
- Flyvbjerg H, Holy TE, Leibler S, Microtubule dynamics: Caps, catastrophes, and coupled hydrolysis
, Phys. Rev. E, 1996 November;54(5):5538.
- Carlier MF, Pantaloni D, Control of Actin Dynamics in Cell Motility
, J. Mol. Biol., 1997;269:459.
- Pollard TD, Rate Constants for the Reactions of ATP- and ADP-Actin
with the Ends of Actin Filaments, J. Cell Biol., 1986 December;103(2):2747.
Lecture 16:
- Thomas N, Imafuku Y, Tawada K, Molecular motors: thermodynamics and the random walk, Proc R Soc Lond B Biol Sci. 2001 Oct 22;268(1481):2113.
- Fisher ME, Kolomeisky AB, The force exerted by a molecular motor,
PNAS, 1999 June;96:6597.
- Gross SP, Hither and yon: a review of bi-directional microtubule-based transport,
Phys. Biol., 2004;1:R1.
- Fisher ME, Kolomeisky AB, Simple mechanochemistry describes the dynamics of kinesin molecules,
PNAS, 2001 July 3;98(14):7748.
- Huxley HE, Fifty years of muscle and the sliding filament hypothesis,
Eur. J. Biochem., 2004;271:1403.
- Mahadevan L, Matsudaira P, Motility Powered by Supramolecular Springs and Ratchets,
Science, 2000 April 7;288:95.
This paper describes classes of motors other than the translational motors described in class.
- Schliwa M, Woehlke G, Molecular motors,
Nature, 2003 April 17;422:759.
- Schnitzer MJ, Block SM, Kinesin hydrolyses one ATP per 8-nm step,
Nature, 1997 July 24;388:386.
- Vale RD, Milligan RA, The Way Things Move: Looking Under the Hood of Molecular Motor Proteins,
Nature, 2000 April 7;288:88.
- Vale RD, The Molecular Motor Toolbox for Intracellular Transport,
Cell, 2003 February 21;112:467.
- Woehlke G, Schliwa M, Walking on two heads: the many talents of kinesin,
Nature Reviews, 2000 October;1:50.
- Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR, Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with
1.5-nm Localization, Science, 2003 June 27 ;300:2061.
- Kinosita Lab Movies, cool single molecule movies of the action of molecular motors.
- Heuser Lab Galleries, this site includes some of the classic electron micrographs of
muscle and muscle proteins.
Lecture 17:
- Rief M, Rock RS, Mehta AD, Mooseker MS, Cheney RE, Spudich JA,
Myosin-V stepping kinetics: A molecular model for processivity,
PNAS, 2000 Aug 15;97(17):9482.
- Simon SM, Peskin CS, Oster GF,
What drives the translocation of proteins?,
PNAS, 1992 May;89:3770.
Lecture 18:
- Gillespie PG, Walker RG,
Molecular basis of mechanosensory transduction,
Nature, 2001 Sep 13;413:194.
- Miyazawa A, Fujiyoshi Y, Unwin N,
Structure and gating mechanism of the acetylcholine receptor pore,
Nature, 2003 Jun 26;423:949.
Lecture 19:
- Nilsson DE, Pelger S,
A Pessimistic Estimate of the Time Required for an Eye to Evolve,
Proc. Roy. Soc Lond., 1994 Apr 22;256(1345):53.
- Sens P, Turnery MS,
Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations,
Biophysical Journal, 2004 Apr;86:2049.
Homeworks
- HW1, Due on Tuesday,
January 18
- HW2, Due on Thursday,
January 27
- HW3, Due on Thursday,
February 3
- HW4, Due on Thursday,
February 10
- HW5, Due on Tuesday,
February 22
- HW6, Due on Tuesday,
March 1
- HW7, Due on Tuesday,
March 8
- HW8, Due on Friday,
March 11
Solutions
Lecture notes
- Lecture 1 slides
- Lecture 2 slides
- Stat. Mech. lecture slides
- Lecture 3 slides
- Lecture 4 slides
- Lectures 6 and 7 slides
- Lecture 8 slides
- Lecture 10 slides
- Lectures 12, 13 and 14 slides
- Lecture 16 slides
- Lecture 18 slides
- Lecture 19 slides
Contact Information
Rob
Phillips
221 Steele
x3374
phillips AT pboc.caltech
Hernan Garcia
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Rizal Hariadi
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Mandar M. Inamdar
226 Steele
x3106
mandar AT caltech
Office hours: TBA
A nice review of the emerging picture of the bacterial cytoskeleton.
- Dogterom M, Leibler S, Physical Aspects of the Growth and Regulation of Microtubule Structures,
Phys. Rev. Lett., 1993 March 1;70(9):1347.
A simple phenomenological model of the steady-state distribution of microtubule lengths. - Kuchnir Fygenson D, Braun E, Libchaber A, Phase diagram of microtubules,
Phys. Rev. E, 1994 August;50(2):1579.
Fig. 1 shows an experimental time series for the length of microtubules as a function of time, fig. 6 shows the distribution of microtubule lengths. - Flyvbjerg H, Holy TE, Leibler S, Stochastic Dynamics of Microtubules:
A Model cor Caps and Catastrophes, Phys. Rev. Lett., 1994 October 24;73(17):2372.
This model treats the dynamics of the cap of GTP tubulin in microtubules. - Flyvbjerg H, Holy TE, Leibler S, Microtubule dynamics: Caps, catastrophes, and coupled hydrolysis , Phys. Rev. E, 1996 November;54(5):5538.
- Carlier MF, Pantaloni D, Control of Actin Dynamics in Cell Motility , J. Mol. Biol., 1997;269:459.
- Pollard TD, Rate Constants for the Reactions of ATP- and ADP-Actin with the Ends of Actin Filaments, J. Cell Biol., 1986 December;103(2):2747.
Lecture 16:
- Thomas N, Imafuku Y, Tawada K, Molecular motors: thermodynamics and the random walk, Proc R Soc Lond B Biol Sci. 2001 Oct 22;268(1481):2113.
- Fisher ME, Kolomeisky AB, The force exerted by a molecular motor,
PNAS, 1999 June;96:6597.
- Gross SP, Hither and yon: a review of bi-directional microtubule-based transport,
Phys. Biol., 2004;1:R1.
- Fisher ME, Kolomeisky AB, Simple mechanochemistry describes the dynamics of kinesin molecules,
PNAS, 2001 July 3;98(14):7748.
- Huxley HE, Fifty years of muscle and the sliding filament hypothesis,
Eur. J. Biochem., 2004;271:1403.
- Mahadevan L, Matsudaira P, Motility Powered by Supramolecular Springs and Ratchets,
Science, 2000 April 7;288:95.
This paper describes classes of motors other than the translational motors described in class.
- Schliwa M, Woehlke G, Molecular motors,
Nature, 2003 April 17;422:759.
- Schnitzer MJ, Block SM, Kinesin hydrolyses one ATP per 8-nm step,
Nature, 1997 July 24;388:386.
- Vale RD, Milligan RA, The Way Things Move: Looking Under the Hood of Molecular Motor Proteins,
Nature, 2000 April 7;288:88.
- Vale RD, The Molecular Motor Toolbox for Intracellular Transport,
Cell, 2003 February 21;112:467.
- Woehlke G, Schliwa M, Walking on two heads: the many talents of kinesin,
Nature Reviews, 2000 October;1:50.
- Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR, Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with
1.5-nm Localization, Science, 2003 June 27 ;300:2061.
- Kinosita Lab Movies, cool single molecule movies of the action of molecular motors.
- Heuser Lab Galleries, this site includes some of the classic electron micrographs of
muscle and muscle proteins.
Lecture 17:
- Rief M, Rock RS, Mehta AD, Mooseker MS, Cheney RE, Spudich JA,
Myosin-V stepping kinetics: A molecular model for processivity,
PNAS, 2000 Aug 15;97(17):9482.
- Simon SM, Peskin CS, Oster GF,
What drives the translocation of proteins?,
PNAS, 1992 May;89:3770.
Lecture 18:
- Gillespie PG, Walker RG,
Molecular basis of mechanosensory transduction,
Nature, 2001 Sep 13;413:194.
- Miyazawa A, Fujiyoshi Y, Unwin N,
Structure and gating mechanism of the acetylcholine receptor pore,
Nature, 2003 Jun 26;423:949.
Lecture 19:
- Nilsson DE, Pelger S,
A Pessimistic Estimate of the Time Required for an Eye to Evolve,
Proc. Roy. Soc Lond., 1994 Apr 22;256(1345):53.
- Sens P, Turnery MS,
Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations,
Biophysical Journal, 2004 Apr;86:2049.
Homeworks
- HW1, Due on Tuesday,
January 18
- HW2, Due on Thursday,
January 27
- HW3, Due on Thursday,
February 3
- HW4, Due on Thursday,
February 10
- HW5, Due on Tuesday,
February 22
- HW6, Due on Tuesday,
March 1
- HW7, Due on Tuesday,
March 8
- HW8, Due on Friday,
March 11
Solutions
Lecture notes
- Lecture 1 slides
- Lecture 2 slides
- Stat. Mech. lecture slides
- Lecture 3 slides
- Lecture 4 slides
- Lectures 6 and 7 slides
- Lecture 8 slides
- Lecture 10 slides
- Lectures 12, 13 and 14 slides
- Lecture 16 slides
- Lecture 18 slides
- Lecture 19 slides
Contact Information
Rob
Phillips
221 Steele
x3374
phillips AT pboc.caltech
Hernan Garcia
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Rizal Hariadi
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Mandar M. Inamdar
226 Steele
x3106
mandar AT caltech
Office hours: TBA
This paper describes classes of motors other than the translational motors described in class.
- Rief M, Rock RS, Mehta AD, Mooseker MS, Cheney RE, Spudich JA, Myosin-V stepping kinetics: A molecular model for processivity, PNAS, 2000 Aug 15;97(17):9482.
- Simon SM, Peskin CS, Oster GF, What drives the translocation of proteins?, PNAS, 1992 May;89:3770.
Lecture 18:
- Gillespie PG, Walker RG,
Molecular basis of mechanosensory transduction,
Nature, 2001 Sep 13;413:194.
- Miyazawa A, Fujiyoshi Y, Unwin N,
Structure and gating mechanism of the acetylcholine receptor pore,
Nature, 2003 Jun 26;423:949.
Lecture 19:
- Nilsson DE, Pelger S,
A Pessimistic Estimate of the Time Required for an Eye to Evolve,
Proc. Roy. Soc Lond., 1994 Apr 22;256(1345):53.
- Sens P, Turnery MS,
Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations,
Biophysical Journal, 2004 Apr;86:2049.
Homeworks
- HW1, Due on Tuesday,
January 18
- HW2, Due on Thursday,
January 27
- HW3, Due on Thursday,
February 3
- HW4, Due on Thursday,
February 10
- HW5, Due on Tuesday,
February 22
- HW6, Due on Tuesday,
March 1
- HW7, Due on Tuesday,
March 8
- HW8, Due on Friday,
March 11
Solutions
Lecture notes
- Lecture 1 slides
- Lecture 2 slides
- Stat. Mech. lecture slides
- Lecture 3 slides
- Lecture 4 slides
- Lectures 6 and 7 slides
- Lecture 8 slides
- Lecture 10 slides
- Lectures 12, 13 and 14 slides
- Lecture 16 slides
- Lecture 18 slides
- Lecture 19 slides
Contact Information
Rob
Phillips
221 Steele
x3374
phillips AT pboc.caltech
Hernan Garcia
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Rizal Hariadi
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Mandar M. Inamdar
226 Steele
x3106
mandar AT caltech
Office hours: TBA
- Nilsson DE, Pelger S, A Pessimistic Estimate of the Time Required for an Eye to Evolve, Proc. Roy. Soc Lond., 1994 Apr 22;256(1345):53.
- Sens P, Turnery MS, Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations, Biophysical Journal, 2004 Apr;86:2049.
Homeworks
- HW1, Due on Tuesday, January 18
- HW2, Due on Thursday, January 27
- HW3, Due on Thursday, February 3
- HW4, Due on Thursday, February 10
- HW5, Due on Tuesday, February 22
- HW6, Due on Tuesday, March 1
- HW7, Due on Tuesday, March 8
- HW8, Due on Friday, March 11
Solutions
Lecture notes
- Lecture 1 slides
- Lecture 2 slides
- Stat. Mech. lecture slides
- Lecture 3 slides
- Lecture 4 slides
- Lectures 6 and 7 slides
- Lecture 8 slides
- Lecture 10 slides
- Lectures 12, 13 and 14 slides
- Lecture 16 slides
- Lecture 18 slides
- Lecture 19 slides
Contact Information
Rob
Phillips
221 Steele
x3374
phillips AT pboc.caltech
Hernan Garcia
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Rizal Hariadi
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
Mandar M. Inamdar
226 Steele
x3106
mandar AT caltech
Office hours: TBA
230 Steele
x5876
hgarcia AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
210A Moore
x6994
reez AT caltech
Office hours: Mondays 3-5pm @ 230 Steele
226 Steele
x3106
mandar AT caltech
Office hours: TBA
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