Note: Cover -- Half-title -- Title -- Copyright -- Contents -- Preface -- Acknowledgements -- Global transitions in proteins -- 1.1 Defining a global state -- 1.2 Equilibrium between two global states -- 1.3 Global transitions induced by temperature -- 1.4 Lysozyme unfolding -- 1.5 Steepness and enthalpy -- 1.6 Cooperativity and thermal transitions -- 1.7 Transitions induced by other variables -- 1.8 Transitions induced by voltage -- 1.9 The voltage sensor of voltage-gated channels -- 1.10 Gating current -- 1.11 Cooperativity and voltage-induced transitions -- 1.12 Compliance of a global state -- Problems for Chapter 1 -- Chapter 2 Molecular forces in biological structures -- 2.1 The Coulomb potential -- 2.2 Electrostatic self-energy -- 2.3 Image forces -- 2.4 Charge-dipole interactions -- 2.5 Induced dipoles -- 2.6 Cation-phi interactions -- 2.7 Dispersion forces -- 2.8 Hydrophobic forces -- 2.9 Hydration forces -- 2.10 Hydrogen bonds -- 2.11 Steric repulsions -- 2.12 Bond flexing and harmonic potentials -- 2.13 Stabilizing forces in proteins -- 2.14 Protein force fields -- 2.15 Stabilizing forces in nucleic acids -- 2.16 Lipid bilayers and membrane proteins -- Problems for Chapter 2 -- Chapter 3 Conformations of macromolecules -- 3.1 n-Butane -- 3.2 Configurational partition functions and polymer chains -- 3.3 Statistics of random coils -- 3.4 Effective segment length -- 3.5 Nonideal polymer chains and theta solvents -- 3.6 Probability distributions -- 3.7 Loop formation -- 3.8 Stretching a random coil -- 3.9 When do molecules act like random coils? -- 3.10 Backbone rotations in proteins: secondary structure -- 3.11 The entropy of protein denaturation -- 3.12 The helix-coil transition -- 3.13 Mathematical analysis of the helix-coil transition -- 3.14 Results of helix-coil theory -- 3.15 Helical propensities -- 3.16 Protein folding. , 3.17 Cooperativity in protein folding -- Problems for Chapter 3 -- Chapter 4 Molecular associations -- 4.1 Association equilibrium in solution -- 4.2 Cooperativity -- 4.2.1 Concerted binding -- 4.2.2 Sequential binding -- 4.2.3 Nearest neighbor interactions -- 4.3 Thermodynamics of associations -- 4.4 Contact formation -- 4.5 Statistical mechanics of association -- 4.6 Translational free energy -- 4.7 Rotational free energy -- 4.8 Vibrational free energy -- 4.9 Solvation effects -- 4.10 Configurational free energy -- 4.11 Protein association in membranes - reduction of dimensionality -- 4.12 Binding to membranes -- Problems for Chapter 4 -- Chapter 5 Allosteric interactions -- 5.1 The allosteric transition -- 5.2 The simplest caseone binding site and one allosteric transition -- 5.3 Binding and response -- 5.4 Energy balance in the one-site model -- 5.5 G-protein coupled receptors -- 5.6 Binding site interactions -- 5.7 The Monod-Wyman-Changeux (MWC) model -- 5.8 Hemoglobin -- 5.9 Energetics of the MWC model -- 5.10 Macroscopic and microscopic additivity -- 5.11 Phosphofructokinase -- 5.12 Ligand-gated channels -- 5.13 Subunit-subunit interactions: the Koshland-Nemethy-Filmer (KNF) model -- 5.14 The Szabo-Karplus (SK) model -- Problems for Chapter 5 -- Chapter 6 Diffusion and Brownian motion -- 6.1 Macroscopic diffusion: Fick's laws -- 6.2 Solving the diffusion equation -- 6.2.1 One-dimensional diffusion from a point -- 6.2.2 Three-dimensional diffusion from a point -- 6.2.3 Diffusion across an interface -- 6.2.4 Diffusion with boundary conditions -- 6.3 Diffusion at steady state -- 6.3.1 A long pipe -- 6.3.2 A small hole -- 6.3.3 A porous membrane -- 6.4 Microscopic diffusion - random walks -- 6.5 Random walks and the Gaussian distribution -- 6.6 The diffusion equation from microscopic theory -- 6.7 Friction -- 6.8 Stokes' law. , 6.9 Diffusion constants of macromolecules -- 6.10 Lateral diffusion in membranes -- Problems for Chapter 6 -- Chapter 7 Fundamental rate processes -- 7.1 Exponential relaxations -- 7.2 Activation energies -- 7.3 The reaction coordinate and detailed balance -- 7.4 Linear free energy relations -- 7.5 Voltage-dependent rate constants -- 7.6 The Marcus free energy relation -- 7.7 Eyring theory -- 7.8 Diffusion over a barrier - Kramers' theory -- 7.9 Single-channel kinetics -- 7.10 The reaction coordinate for a global transition -- Problems for Chapter 7 -- Chapter 8 Association kinetics -- 8.1 Bimolecular association -- 8.2 Small perturbations -- 8.3 Diffusion-limited association -- 8.4 Diffusion-limited dissociation -- 8.5 Site binding -- 8.6 Protein-ligand association rates -- 8.6.1 Evolution of speed -- 8.6.2 Acetylcholinesterase -- 8.6.3 Horseradish peroxidase -- 8.7 Proton transfer -- 8.8 Binding to membrane receptors -- 8.9 Reduction in dimensionality -- 8.10 Binding to DNA -- Problems for Chapter 8 -- Chapter 9 Multi-state kinetics -- 9.1 The three-state model -- 9.2 Initial conditions -- 9.3 Separation of timescales -- 9.4 General solution to multi-state systems -- 9.5 The three-state model in matrix notation -- 9.6 Stationarity, conservation, and detailed balance -- 9.7 Single-channel kinetics: the three-state model -- 9.8 Separation of timescales in single channels: burst analysis -- 9.9 General treatment of single-channel kinetics: state counting -- 9.10 Relation between single-channel and macroscopic kinetics -- 9.11 Loss of stationarity, conservation, and detailed balance -- 9.12 Single-channel correlations: pathway counting -- 9.13 Multisubunit kinetics -- 9.14 Random walks and "stretched kinetics -- Problems for Chapter 9 -- Chapter 10 Enzyme catalysis -- 10.1 Basic mechanisms - serine proteases -- 10.2 Michaelis-Menten kinetics. , 10.3 Steady-state approximations -- 10.4 Pre-steady-state kinetics -- 10.5 Allosteric enzymes -- 10.6 Utilization of binding energy -- 10.7 Kramers' rate theory and catalysis -- 10.8 Proximity and translational entropy -- 10.9 Rotational entropy -- 10.10 Reducing E: transition state complementarity -- 10.11 Friction in an enzyme-substrate complex -- 10.12 General-acid-base catalysis and Brønsted slopes -- 10.13 Acid-base catalysis in Beta-galactosidase -- 10.14 Catalysis in serine proteases and strong H-bonds -- 10.15 Marcus' theory and proton transfer in carbonic anhydrase -- Problems for Chapter 10 -- Chapter 11 Ions and counterions -- 11.1 The Poisson-Boltzmann equation and the Debye length -- 11.2 Activity coefficient of an ion -- 11.3 Ionization of proteins -- 11.4 Gouy-Chapman theory and membrane surface charge -- 11.5 Stern's improvements of Gouy-Chapman theory -- 11.6 Surface charge and channel conductance -- 11.7 Surface charge and voltage gating -- 11.8 Electrophoretic mobility -- 11.9 Polyelectrolyte solutions I. Debye-Hückel screening -- 11.10 Polyelectrolyte solutions II. Counterion-condensation -- 11.11 DNA melting -- Problems for Chapter 11 -- Chapter 12 Fluctuations -- 12.1 Deviations from the mean -- 12.2 Number fluctuations and the Poisson distribution -- 12.3 The statistics of light detection by the eye -- 12.4 Equipartition of energy -- 12.5 Energy fluctuations in a macromolecule -- 12.6 Fluctuations in protein ionization -- 12.7 Fluctuations in a two-state system -- 12.8 Single-channel current -- 12.9 The correlation function of a two-state system -- 12.10 The Wiener-Khintchine theorem -- 12.11 Channel noise -- 12.12 Circuit noise -- 12.13 Fluorescence correlation spectroscopy -- 12.14 Friction and the fluctuation-dissipation theorem -- Problems for Chapter 12 -- Chapter 13 Ion permeation and membrane potential. , 13.1 Nernst potentials -- 13.2 Donnan potentials -- 13.3 Membrane potentials of cells -- 13.3.1 Neurons -- 13.3.2 Vertebrate skeletal muscle -- 13.4 A membrane permeable to Na+ and K+ -- 13.5 Membrane potentials of neurons again -- 13.6 The Ussing flux ratio and active transport -- 13.7 The Goldman-Hodgkin-Katz voltage equation -- 13.8 Membrane pumps and potentials -- 13.9 Transporters and potentials -- 13.10 The Goldman-Hodgkin-Katz current equation -- 13.11 Divalent ions -- 13.12 Surface charge and membrane potentials -- 13.13 Rate theory and membrane potentials -- Problems for Chapter 13 -- Chapter 14 Ion permeation and channel structure -- 14.1 Permeation without channels -- 14.2 The Ohmic channel -- 14.3 Energy barriers and channel properties -- 14.4 Eisenman selectivity sequences -- 14.5 Forces inside an ion channel -- 14.6 Gramicidin A -- 14.7 Rate theory for multibarrier channels -- 14.8 Single-ion channels -- 14.9 Single-file channels -- 14.10 The KcsA channel -- Problems for Chapter 14 -- Chapter 15 Cable theory -- 15.1 Current through membranes and cytoplasm -- 15.2 The cable equation -- 15.3 Steady state in a finite cable -- 15.4 Voltage steps in a finite cable -- 15.5 Current steps in a finite cable -- 15.6 Branches and equivalent cylinder representations -- 15.6.1 Steady state -- 15.6.2 Time constants -- 15.7 Cable analysis of a neuron -- 15.8 Synaptic integration in dendrites: analytical models -- 15.8.1 Impulse responses -- 15.8.2 Realistic synaptic inputs -- 15.9 Compartmental models and cable theory -- 15.10 Synaptic integration in dendrites: compartmental models -- Problems for Chapter 15 -- Chapter 16 Action potentials -- 16.1 The action potential -- 16.2 The voltage clamp and the properties of Na+ and K+ channels -- 16.3 The Hodgkin-Huxley equations -- 16.4 Current-voltage curves and thresholds -- 16.5 Propagation -- 16.6 Myelin. , 16.7 Axon geometry and conduction.