Michel Daune: Molecular Biophysics: Structures in motion. 1999. Oxford University Press, Oxford.

Instructors' Note: This book has no problems to assign; however, some of its worked examples would make good problems. Although on the surface this book appeared promising in its selection of topics covered and level of mathematical difficulty, it soon proved to be inadequate as a stand-alone text. Derivations were not well-explained and, on occasion, contained mistakes. The organization of chapters is bizarre, and subsections within each chapter are often completely uninformative. The most useful feature turned out to be the list of additional readings at the end of each major section.

Peter R. Bergethon. The Physical Basis of Biochemistry. The foundations of molecular biophysics. 1998. Springer-Verlag, New York.

Instructors' Note: The first third of this book is essentially a summary of all of physics and was inappropriate for our course. We did assign the chapters on water, ionic solutions, and diffusion as supplementary reading. There are a few problems at the end of each chapter, but they are generally conceptual in nature. Few or none of the problems give students practice in actually using the equations that are presented in the chapters.

J.O.M. Bockris and A.K.M. Reddy. Modern Electrochemistry; an introduction to an interdisciplinary area. Volume 1. 1970. Plenum Press, New York, NY.

Instructors' Note: Although somewhat old, this book provided some very useful readings on water, solvation, and ionic solutions. Lots of nice figures and clear derivations. The use of Gaussian units in Maxwell's equations makes it a bit confusing to those students who have only taken a standard introductory physics course, since most texts now use mks units. No problems, unfortunately.

R.K. Hobbie. Intermediate Physics for Medicine and Biology. 1997. Springer: AIP Press, New York, NY.

Instructors' Note: This was very good for diffusion and for membrane potentials. It contains quite a few problems, a few of which we did use.

I. Tinoco, J. Sauer, and K.C. Wang. Physical Chemistry: Principles and Applications in the Biological Sciences, 3^rd edition. 1995. Prentice Hall, Englewood Cliffs, NJ.

Note: Good for readings and problems on membrane potentials, random walks, diffusion, and statistical definition of entropy.

K.E. van Holde, W.C. Johnson, and P.S. Ho. Principles of Physical Biochemistry. 1998. Prentice Hall, Upper Saddle River, NJ.

Note: more readings on diffusion and random walks; also, some protein folding readings. Contains some problems, though we didn't use any.

A.Y. Grusberg and A.R. Khokhlov. 1997. Giant Molecules: Here, There, and Everywhere. 1997. Academic Press, San Diego, CA.

Note: a fun-to-read book on polymers, with good discussions of things like persistence length, entropic elasticity, etc.

Note: a * in front of the reference indicates this was assigned reading or used in a student presentation.

Chapter 1 from Intermolecular Forces: Their Origin and Determination by Maitlland, Rigby, Smith, and Wakeham. 1981. Clarendon Press, Oxford.

McLaughlin S. 1989. The electrostatic properties of membranes. Annu. Rev. Biophys. Biophys. Chem. 18: 113-36.

Parsegian VA. 1973. Long-range physical forces in the biological milieu. ??

*Chapter 4 from The Structure and Properties of Water by Eisenberg and Kauzmann.

*Yang DSC, Sax M, Chakrabartty A, and Hew CL. 1988. Crystal structure of an antifreeze polypeptide and its mechanistic implications. Nature 333: 232.

*Jorgensen WL, Chandrasekhar J, and Madura JD. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79: 926-935.

*Kusalik PG and Svishchev IM. 1994. The spatial structure of water. Science 265: 1219-1221.

Silverstein KAT, Haymet ADJ and Dill KA. 1998. A simple model of water and the hydrophobic effect. J. Am. Chem. Soc. 120: 3166-3175.

*Muller N. 1990. Search for a realistic view of hydrophobic effects. Acc. Chem. Res. 23: 23-28.

*Eisenberg D and McLachlan AD. 1986. Solvation energy in protein folding and binding. Nature 319: 199-203.

Silverstein KAT, Haymet ADJ, and Dill KA. 1999. Molecular model of hydrophobic solvation. J. Chem. Phys. 111: 8000-8009.

Kauzmann. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14: 1-63.

*Mehler EL and Eichele G. 1984. Electrostatic effects in water-accessible regions of proteins. Biochemistry 23: 3887-3891.

Richards FM. 1977. Areas, volumes, packing, and protein structure. Ann. Rev. Biophys. Bioeng. 6: 151-176.

*Honig B and Nicholls A. 1995. Classical electrostatics in biology and chemistry. Science 268: 1144-1149.

*Honig B, Hubbell WL, and Flewelling RF. 1986. Electrostatic interactions in membranes and proteins. Annu. Rev. Biophys. Biophys. Chem. 15: 163-193.

Leopold PE, Montal M, and Onuchic JN. 1992. Protein folding funnels: a kinetic relationship to the sequence-structure relationship. Proc. Natl. Acad. Sci. USA 89: 8721-8725.

Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, and Chan HS. 1995. Principles of protein folding - a perspective from simple exact models. Protein Sci. 4: 561-602.

Saxton MJ and Jacobson K. 1997. Single-particle tracking: applications to membrane dynamics. Annu. Rev. Biophys. Biomol. Struct. 26: 373-399.

*von Hippel PH and Berg OG. 1989. Facilitated target location in biological systems. J. Biol. Chem. 264: 675-78.

*Harada Y, Funatsu T, Murakami K, Nonoyama Y, Ishihama A, and Yanagida T. 1999. Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophys. J. 76: 709-715.

Eyring H, Lin SH, and Lin SM. Basic Chemical Kinetics. 1980. Wiley, New York, NY. (pp. 376-385, derivation of diffusion-limited association rate)

*Singer P and Wu C-W. 1987. Promoter search by Escherichia coli RNA polymerase on a circular DNA template. J. Biol. Chem. 262: 14178-14189.

Berg OG and von Hippel PH. 1985. Diffusion-controlled macromolecular interactions. Ann. Rev. Biophys. Biophys. Chem. 14: 131-160.

*Zhou H-X, Wong K-Y, and Vijayakumar M. 1997. Design of fast enzymes by optimizing interaction potential in active site. Proc. Natl. Acad. Sci. USA 94: 12372-12377.

Camacho CJ, Weng Z, Vajda S, and DeLisi C. 1999. Free energy landscapes of encounter complexes in protein-protein association. Biophys. J. 76: 1166-1178.

Adzuma K. 1998. No sliding during homology search by RecA protien. J. Biol. Chem. 273: 31565-31573.

Jeltsch A and Pingoud A. 1998. Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA. Biochemistry 37: 2160-2169.

Lieberman BA and Nordeen SK. 1997. DNA intersegment transfer, how steroid receptors search for a target site. J. Biol. Chem. 272: 1061-1068.

Bustamante C, Guthold M, Zhu X, and Yang G. 1999. Facilitated target location on DNA by individual Escherichia coli RNA polymerase molecules observed with the scanning force microscope operating in liquid. J. Biol. Chem. 274: 16665-16668.

Shimamoto N. 1999. One-dimensional diffusion of proteins along DNA. J. Biol. Chem. 274: 15293-15296.

Gonda DK and Radding CM. 1986. The mechanism of the search for homology promoted by recA protein. Facilitated diffusion within nucleoprotein networks. J. Biol. Chem. 261: 13087-13096.

Kohler JJ , Metallo SJ, Schneider TL, and Schepartz A. 1999. DNA specificity enhanced by sequential binding of protein monomers. Proc. Natl. Acad. Sci. USA 96: 11735-11739.

Hannon R, Richards EG, and Gould HJ. 1986. Facilitated diffusion of a DNA binding protein on chromatin. EMBO J. 5: 3313-3319.

*D.J. Aidley and P.R. Stanfield. Ion Channels: Molecules in action. 1996. Cambridge University Press, Cambridge. Chapter 5.

*D.J. Aidley. The Physiology of Excitable Cells, 4^th ed., 1998. Cambridge University Press, Cambridge. Chapters 5 and 6.

*Eisenman G and Dani JA. 1987. An introduction to molecular architecture and permeability of ion channels. Ann. Rev. Biophys. Biophys. Chem. 16: 205-226.

*Chung S-H, Allen TW, Hoyles M, and Kuyucak S. 1999. Permeation of ions across the potassium channel: Brownian dynamics studies. Biophys. J. 77: 2517-2533.

*Doyle DA, Cabral JM, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, and MacKinnon R. 1998. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280: 69-77.

Moy G, Corry B, Kuyucak S, and Chung S-H. 2000. Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics. Biophys. J. 78: 2349-2363.

Corry B, Kuyucak S, and Chung S-H. 2000. Tests of continuum theories as models of ion channels. II. Poisson-Nernst-Planck theory versus Brownian dynamics. Biophys. J. 78: 2364-2381.

*Peskin CS, Odell GM, and Oster GF. 1993. Cellular motions and thermal fluctuations: The Brownian ratchet. Biophys. J. 65: 316-324.

Olbris DJ and Herzfeld J. 1999. An analysis of actin delivery in the acrosomal process of Thyone. Biophys. J. 77: 3407-3423.

Inoue S and Salmon ED. 1995. Force generation by microtubule assembly/disassembly in mitosis and related movements. Mol. Biol. Cell 6: 1619-1640.

*Zlotnick A. 1994. To build a virus capsid. An equilibrium model of the self assembly of polyhedral protein complexes. J. Mol. Biol. 241: 59-67.

*Luger K, Mader AW, Richmond RK, Sargent DF, and Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389: 251-260.

*Cate JH, Yusupov MM, Yusupova GZ, Earnest TN, and Noller HF. 1999. X-ray crystal structures of 70S ribosome functional complexes. Science 285: 2095-2104.