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Mechanisms of membrane deformation. Curvature in a lipid bilayer membrane is created in five important ways: (a) lipid composition; (b) protein inclusions; (c) cytoskeleton and motor proteins; (d) scaffolding; (e) helix insertion into one leaflet.
Source: McMahon and Gallop; Membrane curvature and mechanisms of dynamic cell membrane remodelling, Nature, Dec 2005; 438(7068):590.
- The poster session will be on Wed. March 8th from 3-6 pm in Winnett Lounge. Pizza is on the menu! :D
- Our final class will be held at 9 am on Thursday, March 9th
- Physical Biology of the Cell
by Phillips, Kondev and Theriot
Click here to download book chapters
- Essential Cell Biology
by Alberts et al.
- Mechanics of Motor Proteins and the Cytoskeleton
by Howard
- Mechanics of the Cell
by Boal
- HW 1 (problems, solutions)
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- Whitman, Coleman and Wiebe; Prokaryotes: the unseen majority, Proc Nat Acad Sci, Jun 1998; 95(12):6578.
- Zimmerman and Trach; Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli, J Mol Biol, Dec 1991; 222(3):599.
- Barnett; Beginnings of microbiology and biochemistry: the contribution of yeast research, Microbiology, Mar 2003; 149(pt 3):557.
- HW 2 (problems, solutions)
Links
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- Theriot; The Polymerization Motor, Traffic, Jan 2000; 1(1):19-28.
- Theriot, Mitchison, Tilney and Portnoy; The rate of actin-based motility of intracellular Listeria monocytogenes equals the rate of actin polymerization, Nature, May 1992; 357:257.
- Bonner; A note on the number of cells in a slug of Dictyostelium discoideum
"This paper will help you estimate the size of a Dictyostelium cell for use in estimating the number of cells associated with a fruiting body."
- HW 3 (problems, solutions)
Links
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- HW 4 (problems, solutions)
Related articles
- Ellis; Macromolecular crowding: obvious but underappreciated, Trends Biochem Sci, Oct 2001; 26(10):597.
Hall and Minton; Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges, Biochim Biophys Acta, Jul 2003; 1649(2):127.
"These papers emphasize the importance of crowding in altering equilibria and kinetics in the cell."
- HW 5 (problems, solutions)
- HW 6 (problems, solutions)
- HW 7 (problems, solutions)
Links
Related articles
- Fisher and Kolomeisky; Simple mechanochemistry describes the dynamics of kinesin molecules, Proc Natl Acad Sci USA, 3 Jul 2001; 98(14):7748.
- Statistical Mechanics
- Lecture #1 (ppt, pdf) 1/5/06
Helpful links
Suggested reading
- Pedersen, Bloch, Reeh and Neidhardt; Patterns of Protein Synthesis in E. coli: a Catalog of the Amount of 140 Individual Proteins at Different Growth Rates, Cell, May 1978; 14(1):179.
"This paper attempts to take a molecular census of an E. coli cell and was the quantitative inspiration for the famous cartoons of Goodsell."
- Hall-Stoodley, Costerton and Stoodley; Bacterial biofilms: from the natural environment to infectious diseases, Nat Rev Microbiol, Feb 2004; 2(2):95.
"This paper is a review of the ways in which bacteria form films in a wide range of settings, including within humans."
- Lecture #2 (ppt, pdf) 1/10/06
Helpful links
Suggested reading
- Lučić, Förster and Baumeister; Structural studies by electron tomography: from cells to molecules, Annu Rev Biochem, 2005; 74:833.
"This paper shows how cryo-electron tomography allows for a structural determination of the contents of cells."
- Kürner, Medalia, Linaroudis and Baumeister; New insights into the structural organization of eukaryotic and prokaryotic cytoskeletons using cryo-electron tomography, Exp Cell Res, Nov 2004; 301(1):38.
"This is a short review that gives a sense of the power of cryo-electron microscopy to spy on cells."
- Neidhardt; Bacterial Growth: Constant Obsession with dN/dt, J Bacteriol, Dec 1999; 181(24):7405.
"This personal account describes the views of a microbiologist about the interest of studying dN/dt in cell cultures."
- Nurse; The Incredible Life and Times of Biological Cells, Science, Sep 2000; 289(5485):1711.
"This paper gives a beautiful introduction to the origins of cell theory and subsequent thinking on the cell cycle."
- Nurse; A Long Twentieth Century of the Cell Cycle and Beyond, Cell, Jan 2000; 100(1):71.
"A description of the key events of the cell cycle and the cell cycle engines that mediate it."
- Monod; The Growth of Bacterial Cultures, Annual Review of Microbiology, 1949; 3(1):371.
"This paper by Monod describes quantitative studies of bacterial growth. The final figure illustrates the kind of growth curves that led to the elucidation of the operon concept.
- Wu and Pollard; Counting cytokinesis proteins globally and locally in fission yeast, Science, Oct 2005; 310(5746):310.
- Lecture #3 (ppt, pdf) 1/12/06
Helpful links
- Lecture #4 (ppt, pdf) 1/17/06
Suggested reading
- Bintu, Buchler, Garcia, Gerland, Hwa, Kondev and Phillips; Transcriptional regulation by the numbers: models, Curr Opin Genet Dev, Apr 2005; 15(2):116.
Bintu, Buchler, Garcia, Gerland, Hwa, Kondev and Phillips; Transcriptional regulation by the numbers: applications, Curr Opin Genet Dev, Apr 2005; 15(2):125.
"These papers review the use of statistical mechanics to compute promoter occupancy as we have done in class."
- Shea and Ackers; The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation, J Mol Biol, 20 Jan 1985; 181(2):211.
"This paper pioneered the use of 'thermodynamics models' (statistical mechanics) of gene regulation. Their work centered on the case of the genetic switch in phage lambda."
- Lectures #5 and #6 (ppt, pdf) 1/19/06 & 1/24/06
Suggested reading
- Elowitz and Leibler; A synthetic oscillatory network of transcriptional regulators, Nature, Jan 2000; 403(6767):335.
- Oppenheim, Kobiler, Stavans, Court and Adhya; Switches in Bacteriophage Lambda Development, Annu Rev Genet, 2005; 39:409.
"This paper reviews the status of the genetic switch in phage lambda."
- Gardner, Cantor and Collins; Construction of a genetic toggle switch in Escherichia coli, Nature, 20 Jan 2000; 403(6767):339.
"This paper shows how the tools of synthetic biology can be used to construct an artificial genetic switch in bacteria."
- Cherry and Adler; How to make a biological switch, J Theor Biol, Mar 2000; 203(2):117.
"This paper gives an analysis of the conditions under which a genetic circuit will exhibit switching behavior."
- Barnard, Wolfe and Busby; Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes, Curr Opin Microbiol, Apr 2004; 7(2):102.
Browning and Busby; The regulation of bacterial transcription initiation, Nat Rev Microbiol, Jan 2004; 2(1):57.
Ptashne; Regulation of transcription: from lambda to eukaryotes, Trends Biochem Sci, Jun 2005; 30(6):275.
Lev Bar-Or, Maya, Segel, Alon, Levine and Oren; Generation of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study, Proc Natl Acad Sci USA, Oct 10 2000; 97(21):11250.
Greive and von Hippel; Thinking quantitatively about transcriptional regulation, Nat Rev Mol Cell Biol, Mar 2005; 6(3):221.
Yildirim and Mackey; Feedback regulation in the lactose operon: a mathematical modeling study and comparison with experimental data, Biophys J, May 2003; 84(5):2841.
"Here are some other articles that will give you an impression of current thinking about modeling gene expression. One of my ideas here is to show you several distinct styles of thinking for these problems."
- Lecture #7 (ppt, pdf) 1/26/06
Suggested reading
- Dill, Bromberg, Yue, Fiebig, Yee, Thomas and Chan; Principles of protein folding--A perspective from simple exact models, Protein Sci, Apr 1995; 4(4):561.
"This review by Dill reviews a decade of progress in applying the hydrophobic/polar (HP) model of protein folding."
- Hecht, Das, Go, Bradley, Wei; De novo proteins from designed combinatorial libraries., Protein Sci, Jul 2004; 13(7):1711.
"This paper shows how the Hecht group has used the HP model as the basis of a protein design philosophy."
- Hopfield; Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity, Proc Natl Acad Sci USA, Oct 1974; 71(10):4135.
Ninio; Kinetic amplification of enzyme discrimination, Biochimie, 1975; 57(5):587.
"The Hopfield and Ninio papers introduced the idea that biological accuracy could be increased beyond the thermodynamic limit via a dynamic scheme known as kinetic proofreading."
- Ninio; Contributions to the Kinetic Theory of Accuracy
"This interesting essay gives the personal perspective of Jacques Ninio on the development of the proofreading concept."
- Gromadski and Rodnina; Kinetic determinants of high-fidelity tRNA discrimination on the ribosome, Mol Cell, Jan 2004; 13(2):191.
"This paper will give you an impression of some of the experimental efforts surrounding the question of fiidelity in translation."
- Lecture #8 (no slides) 1/30/06
Suggested reading
- Berg, Winter and von Hippel; Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory, Biochemistry, Nov 1981; 20(24):6929.
Winter and von Hippel; Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli Repressor-Operator Interaction: Equilibrium Measurements, Biochemistry, Nov 1981; 20(24):6948.
Winter, Berg and von Hippel; Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions, Biochemistry, Nov 1981; 20(24):6961.
"These papers are classics in the analysis of the way in which DNA-binding proteins find their DNA target sites."
- Blanchard, Gonzalez, Kim, Chu and Puglisi; tRNA selection and kinetic proofreading in translation, Nat Struct Mol Biol, Oct 2004; 11(10):1008.
- Lecture #9 (ppt, pdf) 1/31/06
Suggested reading
- Hu, Grosberg and Shklovskii; How do proteins search for their specific sites on coiled or globular DNA, http://arxiv.org/abs/q-bio/0510043.
"This paper is a thorough theoretical analysis of the protein search problem and includes the role of DNA conformation."
- Halford and Marko; How do site-specific DNA-binding proteins find their targets?, Nucleic Acids Res, Jun 2004; 32(10):3040.
"A review on the status of the problem of the search by DNA-binding proteins for their specific target sites."
- Halford and Szczelkun; How to get from A to B: strategies for analysing protein motion on DNA, Eur Biophys J, Jul 2002; 31(4):257.
"This paper gives an overview of the experimental study of how DNA-binding proteins find their targets on DNA."
- Gowers, Wilson and Halford; Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA, Proc Natl Acad Sci USA, Nov 2005; 102(44):15883.
"This paper explores the relative importance of one-dimensional and three-dimensional diffusion during target search of DNA-binding proteins"
- Stanford, Szczelkun, Marko and Halford; One- and three-dimensional pathways for proteins to reach specific DNA sites, EMBO J, Dec 1 2000; 19(23):6546.
"This is the paper that obtained the data using restriction enzymes discussed in class."
- Lecture #10 (no slides) 2/7/06
Suggested reading
- Bruinsma; Physics of protein-DNA interaction, Physica A, 2002; 313(1):211.
- Verkman; Solute and macromolecule diffusion in cellular aqueous compartments, Trends Biochem Sci, Jan 2002; 27(1):27.
- Ellis; Macromolecular crowding: obvious but underappreciated, Trends Biochem Sci, Oct 2001; 26(10):597.
- Wang, Austin and Cox; Single molecule measurements of repressor protein 1-D diffusion on DNA, preprint, to appear in PRL; do not distribute.
- Lecture #11 (ppt, pdf) 2/9/06
Helpful links
Suggested reading
- Garner, Campbell and Mullins; Dynamic instability in a DNA-segregating prokaryotic actin homolog, Science, 5 Nov 2004; 306(5698):1021.
"This paper does single molecule measurements demonstrating dynamic instability in the polymerization of ParM."
- Flyvbjerg, Holy and Leibler; Microtubule dynamics: Caps, catastrophes, and coupled hydrolysis, Phys Rev E, Nov 1996; 54(5):5538.
"This paper has a beautiful model of the dynamics of the hydrolysis cap in microtubules."
- Errington; Dynamic proteins and a cytoskeleton in bacteria, Nat Cell Biol, Mar 2003; 5:175.
"A nice review of the emerging picture of the bacterial cytoskeleton."
- Dogterom and Leibler, Physical Aspects of the Growth and Regulation of Microtubule Structures, Phys Rev Lett, 1 Mar 1993; 70(9):1347.
"A simple phenomenological model of the steady-state distribution of microtubule lengths."
- Fygenson, Braun and Libchaber, Phase diagram of microtubules, Phys Rev E, Aug 1994; 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, Holy and Leibler, Stochastic Dynamics of Microtubules: A Model for Caps and Catastrophes, Phys Rev Lett, 24 Oct 1994; 73(17):2372.
"This model treats the dynamics of the cap of GTP tubulin in microtubules."
- Abraham, Krishnamurthi, Taylor and Lanni, The Actin-Based Nanomachine at the Leading Edge of Migrating Cells, Biophys J, Sep 1999; 77:1721.
- Borisy and Svitkina, Actin machinery: pushing the envelope, Curr Op Cell Biol, 2000; 12:104.
- Fletcher and Theriot, An introduction to cell motility for the physical scientist, Phys Biol, 2004; 1:T1.
- Pollard, The cytoskeleton, cellular motility and the reductionist agenda, Nature, 17 Apr 2003; 422:741.
- Rafelski and Theriot, Crawling Toward a Unified Model of Cell Motility: Spatial and Temporal Regulation of Actin Dynamics, Annu Rev Biochem, 2004; 73:209.
- Mitchison and Kirschner, Dynamic instability of microtubule growth, Nature, 15 Nov 1984; 312:237.
- Carlier and Pantaloni, Control of Actin Dynamics in Cell Motility, J Mol Biol, 1997; 269:459.
- Pollard, Rate Constants for the Reactions of ATP- and ADP-Actin with the Ends of Actin Filaments, J Cell Biol, Dec 1986; 103(2):2747.
- Lecture #12 (see slides for previous lecture) 2/14/06
Suggested reading
- Hill and Kirschner; Bioenergetics and kinetics of microtubule and actin filament assembly-disassembly, Int Rev Cytol, 1982; 78:1.
"This article is a detailed exposition on cytoskeletal polymerization by two of the leading figures in the field."
- Mitchison and Kirschner, Dynamic instability of microtubule growth, Nature, 15-21 Nov 1984; 312(5991):237.
"This paper reports the discovery of dynamic instability in microtubules."
- Lecture #13 (ppt, pdf) 2/16/06
- Lecture #14 2/23/06
Suggested reading
- Theriot; The Polymerization Motor, Traffic, Jan 2000; 1(1):19-28.
- Lecture #15 (no slides) 2/28/06
Suggested reading
- Thomas, Imafuku and Tawada, Molecular motors: thermodynamics and the random walk, Proc Biol Sci, 22 Oct 2001; 268(1481):2113.
"This paper shows how simple random walk arguments can be used to write down evolution equations for motors."
- Lecture #16 (ppt, pdf) 3/2/06
Suggested reading
- Kirchhausen, Three ways to make a vesicle, Nat Rev Mol Cell Biol, Dec 2000; 1(3):187.
- Tzlil, Deserno, Gelbart and Ben-Shaul, A statistical-thermodynamic model of viral budding, Biophys J, Apr 2004; 86(4):2037.
- Gao, Shi and Freund, Mechanics of receptor-mediated endocytosis, Proc Natl Acad Sci USA, 5 Jul 2005; 102(27):9469.
- Engelman; Membranes are more mosaic than fluid, Nature, 1 Dec 2005; 438(7068):578.
"This article shows that cell membranes are much more complex than simple lipid bilayers."
- McMahon and Gallop; Membrane curvature and mechanisms of dynamic cell membrane remodelling, Nature, 1 Dec 2005; 438(7068):590.
"This excellent paper illustrates the many ways in which membrane curvature plays a role in cell biology."
- Lecture #17 (ppt, pdf) 3/7/06
Suggested reading
- Bialek; Physical limits to sensation and perception, Annu Rev Biophys Biophys Chem, 1987; 16:455.
- Rob Phillips
159 Broad
x3374
phillips AT pboc.caltech.edu
- Jen Barnet
122 Braun
x6015
jbarnet AT caltech.edu
- Eric Peterson
155 Broad
x5876
eric AT caltech.edu
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