Molecular And Cellular Biophysics

by Meyer B. Jackson

• ISBN13: 9780521624411
• ISBN10: 052162441X
• Format: Hardcover
• Copyright: 2006-03-20
• Publisher: Cambridge University Press

Summary

Providing advanced undergraduate and graduate students with a foundation in the basic concepts of biophysics, students who have taken physical chemistry and calculus courses will find this book an accessible and valuable aid in learning how these concepts can be used in biological research. The text provides a rigorous treatment of the fundamental theories in biophysics and illustrates their application with examples including protein folding, enzyme catalysis and ion channel permeation. Through these examples, students will gain an understanding of the general importance and broad applicability of biophysical principles to biological problems.

Author Biography

Meyer B. Jackson is the Kenneth Cole Professor of Physiology at the University of Wisconsin Medical School

Table of Contents

Preface	xii
Acknowledgements	xiv
Global transitions in proteins	1	(24)
Defining a global state	2	(2)
Equilibrium between two global states	4	(1)
Global transitions induced by temperature	5	(2)
Lysozyme unfolding	7	(2)
Steepness and enthalpy	9	(2)
Cooperativity and thermal transitions	11	(1)
Transitions induced by other variables	12	(2)
Transitions induced by voltage	14	(3)
The voltage sensor of voltage-gated channels	17	(1)
Gating current	18	(1)
Cooperativity and voltage-induced transitions	19	(2)
Compliance of a global state	21	(4)
Molecular forces in biological structures	25	(31)
The Coulomb potential	25	(2)
Electrostatic self-energy	27	(2)
Image forces	29	(2)
Charge-dipole interactions	31	(1)
Induced dipoles	32	(1)
Cation-π interactions	33	(2)
Dispersion forces	35	(1)
Hydrophobic forces	36	(3)
Hydration forces	39	(1)
Hydrogen bonds	39	(4)
Steric repulsions	43	(1)
Bond flexing and harmonic potentials	44	(2)
Stabilizing forces in proteins	46	(4)
Protein force fields	50	(2)
Stabilizing forces in nucleic acids	52	(1)
Lipid bilayers and membrane proteins	53	(3)
Conformations of macromolecules	56	(33)
n-Butane	56	(2)
Configurational partition functions and polymer chains	58	(2)
Statistics of random coils	60	(2)
Effective segment length	62	(1)
Nonideal polymer chains and theta solvents	63	(2)
Probability distributions	65	(1)
Loop formation	66	(1)
Stretching a random coil	67	(1)
When do molecules act like random coils?	68	(1)
Backbone rotations in proteins: secondary structure The entropy of protein denaturation	68	(3)
The helix-coil transition	71	(3)
Mathematical analysis of the helix-coil transition	74	(4)
Results of helix-coil theory	78	(2)
Helical propensities	80	(2)
Protein folding	82	(4)
Cooperativity in protein folding	86	(3)
Molecular associations	89	(22)
Association equilibrium in solution	89	(2)
Cooperativity	91	(3)
Concerted binding	91	(2)
Sequential binding	93	(1)
Nearest neighbor interactions	94	(1)
Thermodynamics of associations	94	(1)
Contact formation	95	(1)
Statistical mechanics of association	96	(2)
Translational free energy	98	(3)
Rotational free energy	101	(1)
Vibrational free energy	102	(3)
Solvation effects	105	(1)
Configurational free energy	106	(1)
Protein association in membranes-reduction of dimensionality	107	(1)
Binding to membranes	108	(3)
Allosteric interactions	111	(31)
The allosteric transition	112	(1)
The simplest case: one binding site and one allosteric transition	112	(3)
Binding and response	115	(1)
Energy balance in the one-site model	116	(1)
G-protein coupled receptors	117	(4)
Binding site interactions	121	(2)
The Monod-Wyman-Changeux (MWC) model	123	(3)
Hemoglobin	126	(1)
Energetics of the MWC model	127	(1)
Macroscopic and microscopic additivity	128	(2)
Phosphofructokinase	130	(2)
Ligand-gated channels	132	(2)
Subunit-subunit interactions: the Koshland-Nemethy-Filmer (KNF) model	134	(3)
The Szabo-Karplus (SK) model	137	(5)
Diffusion and Brownian motion	142	(25)
Macroscopic diffusion: Fick's laws	142	(1)
Solving the diffusion equation	143	(7)
One-dimensional diffusion from a point	144	(2)
Three-dimensional diffusion from a point	146	(1)
Diffusion across an interface	146	(2)
Diffusion with boundary conditions	148	(2)
Diffusion at steady state	150	(4)
A long pipe	151	(1)
A small hole	152	(1)
A porous membrane	153	(1)
Microscopic diffusion-random walks	154	(2)
Random walks and the Gaussian distribution	156	(3)
The diffusion equation from microscopic theory	159	(1)
Friction	160	(2)
Stokes' law	162	(1)
Diffusion constants of macromolecules	163	(1)
Lateral diffusion in membranes	164	(3)
Fundamental rate processes	167	(27)
Exponential relaxations	167	(2)
Activation energies	169	(1)
The reaction coordinate and detailed balance	170	(2)
Linear free energy relations	172	(3)
Voltage-dependent rate constants	175	(2)
The Marcus free energy relation	177	(2)
Eyring theory	179	(1)
Diffusion over a barrier-Kramers' theory	180	(3)
Single-channel kinetics	183	(3)
The reaction coordinate for a global transition	186	(8)
Association kinetics	194	(22)
Bimolecular association	194	(1)
Small perturbations	195	(2)
Diffusion-limited association	197	(3)
Diffusion-limited dissociation	200	(1)
Site binding	201	(2)
Protein-ligand association rates	203	(4)
Evolution of speed	205	(1)
Acetylcholinesterase	205	(1)
Horseradish peroxidase	206	(1)
Proton transfer	207	(1)
Binding to membrane receptors	208	(4)
Reduction in dimensionality	212	(2)
Binding to DNA	214	(2)
Multi-state kinetics	216	(32)
The three-state model	216	(3)
Initial conditions	219	(1)
Separation of timescales	220	(1)
General solution to multi-state systems	221	(4)
The three-state model in matrix notation	225	(1)
Stationarity, conservation, and detailed balance	226	(3)
Single-channel kinetics: the three-state model	229	(3)
Separation of timescales in single channels: burst analysis	232	(3)
General treatment of single-channel kinetics: state counting	235	(1)
Relation between single-channel and macroscopic kinetics	236	(1)
Loss of stationarity, conservation, and detailed balance	237	(3)
Single-channel correlations: pathway counting	240	(2)
Multisubunit kinetics	242	(2)
Random walks and ``stretched kinetics''	244	(4)
Enzyme catalysis	248	(28)
Basic mechanisms-serine proteases	248	(3)
Michaelis-Menten kinetics	251	(3)
Steady-state approximations	254	(2)
Pre-steady-state kinetics	256	(1)
Allosteric enzymes	257	(1)
Utilization of binding energy	258	(1)
Kramers' rate theory and catalysis	259	(1)
Proximity and translational entropy	260	(3)
Rotational entropy	263	(1)
Reducing E: transition state complementarity	264	(3)
Friction in an enzyme-substrate complex	267	(1)
General-acid-base catalysis and Bronsted slopes	268	(2)
Acid-base catalysis in β-galactosidase	270	(2)
Catalysis in serine proteases and strong H-bonds	272	(1)
Marcus' theory and proton transfer in carbonic anhydrase	273	(3)
Ions and counterions	276	(31)
The Poisson-Boltzmann equation and the Debye length	277	(2)
Activity coefficient of an ion	279	(4)
Ionization of proteins	283	(2)
Gouy-Chapman theory and membrane surface charge	285	(3)
Stern's improvements of Gouy-Chapman theory	288	(3)
Surface charge and channel conductance	291	(2)
Surface charge and voltage gating	293	(1)
Electrophoretic mobility	294	(3)
Polyelectrolyte solutions I. Debye-Huckel screening	297	(3)
Polyelectrolyte solutions II. Counterion-condensation	300	(2)
DNA melting	302	(5)
Fluctuations	307	(32)
Deviations from the mean	307	(2)
Number fluctuations and the Poisson distribution	309	(2)
The statistics of light detection by the eye	311	(2)
Equipartition of energy	313	(2)
Energy fluctuations in a macromolecule	315	(2)
Fluctuations in protein ionization	317	(2)
Fluctuations in a two-state system	319	(1)
Single-channel current	320	(2)
The correlation function of a two-state system	322	(2)
The Wiener-Khintchine theorem	324	(3)
Channel noise	327	(2)
Circuit noise	329	(3)
Fluorescence correlation spectroscopy	332	(4)
Friction and the fluctuation-dissipation theorem	336	(3)
Ion permeation and membrane potential	339	(28)
Nernst potentials	339	(2)
Donnan potentials	341	(2)
Membrane potentials of cells	343	(4)
Neurons	345	(1)
Vertebrate skeletal muscle	345	(2)
A membrane permeable to Na+ and K+	347	(3)
Membrane potentials of neurons again	350	(1)
The Ussing flux ratio and active transport	351	(1)
The Goldman-Hodgkin-Katz voltage equation	352	(2)
Membrane pumps and potentials	354	(1)
Transporters and potentials	355	(2)
The Goldman-Hodgkin-Katz current equation	357	(3)
Divalent ions	360	(1)
Surface charge and membrane potentials	361	(1)
Rate theory and membrane potentials	362	(5)
Ion permeation and channel structure	367	(33)
Permeation without channels	367	(3)
The Ohmic channel	370	(1)
Energy barriers and channel properties	371	(3)
Eisenman selectivity sequences	374	(2)
Forces inside an ion channel	376	(2)
Gramicidin A	378	(2)
Rate theory for multibarrier channels	380	(4)
Single-ion channels	384	(6)
Single-file channels	390	(4)
The KcsA channel	394	(6)
Cable theory	400	(34)
Current through membranes and cytoplasm	401	(2)
The cable equation	403	(3)
Steady state in a finite cable	406	(2)
Voltage steps in a finite cable	408	(3)
Current steps in a finite cable	411	(1)
Branches and equivalent cylinder representations	412	(6)
Steady state	413	(2)
Time constants	415	(3)
Cable analysis of a neuron	418	(4)
Synaptic integration in dendrites: analytical models	422	(6)
Impulse responses	423	(2)
Realistic synaptic inputs	425	(3)
Compartmental models and cable theory	428	(2)
Synaptic integration in dendrites: compartmental models	430	(4)
Action potentials	434	(36)
The action potential	434	(5)
The voltage clamp and the properties of Na+ and K+ channels	439	(3)
The Hodgkin-Huxley equations	442	(5)
Current-voltage curves and thresholds	447	(3)
Propagation	450	(3)
Myelin	453	(2)
Axon geometry and conduction	455	(2)
Channel diversity	457	(1)
Repetitive activity and the A-current	458	(3)
Oscillations	461	(5)
Dendritic integration	466	(4)
Appendix I Expansions and series	470	(2)
Taylor series	470	(1)
The binomial expansion	471	(1)
Geometric series	471	(1)
Appendix 2 Matrix algebra	472	(5)
Linear transforms	472	(1)
Determinants	473	(1)
Eigenvalues, eigenvectors, and diagonalization	474	(3)
Appendix 3 Fourier analysis	477	(4)
Appendix 4 Gaussian integrals	481	(2)
Appendix 5 Hyperbolic functions	483	(1)
Appendix 6 Polar and spherical coordinates	484	(2)
References	486	(18)
Index	504