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| Preface | |
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| Acknowledgements | |
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| Global transitions in proteins | |
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| Defining a global state | |
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| Equilibrium between two global states | |
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| Global transitions induced by temperature | |
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| Lysozyme unfolding | |
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| Steepness and enthalpy | |
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| Cooperativity and thermal transitions | |
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| Transitions induced by other variables | |
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| Transitions induced by voltage | |
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| The voltage sensor of voltage-gated channels | |
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| Gating current | |
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| Cooperativity and voltage-induced transitions | |
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| Compliance of a global state | |
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| Molecular forces in biological structures | |
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| The Coulomb potential | |
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| Electrostatic self-energy | |
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| Image forces | |
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| Charge-dipole interactions | |
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| Induced dipoles | |
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| Cation-[pi] interactions | |
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| Dispersion forces | |
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| Hydrophobic forces | |
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| Hydration forces | |
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| Hydrogen bonds | |
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| Steric repulsions | |
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| Bond flexing and harmonic potentials | |
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| Stabilizing forces in proteins | |
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| Protein force fields | |
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| Stabilizing forces in nucleic acids | |
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| Lipid bilayers and membrane proteins | |
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| Conformations of macromolecules | |
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| n-Butane | |
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| Configurational partition functions and polymer chains | |
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| Statistics of random coils | |
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| Effective segment length | |
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| Nonideal polymer chains and theta solvents | |
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| Probability distributions | |
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| Loop formation | |
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| Stretching a random coil | |
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| When do molecules act like random coils? | |
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| Backbone rotations in proteins: secondary structure | |
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| The entropy of protein denaturation | |
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| The helix-coil transition | |
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| Mathematical analysis of the helix-coil transition | |
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| Results of helix-coil theory | |
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| Helical propensities | |
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| Protein folding | |
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| Cooperativity in protein folding | |
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| Molecular associations | |
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| Association equilibrium in solution | |
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| Cooperativity | |
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| Concerted binding | |
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| Sequential binding | |
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| Nearest neighbor interactions | |
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| Thermodynamics of associations | |
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| Contact formation | |
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| Statistical mechanics of association | |
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| Translational free energy | |
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| Rotational free energy | |
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| Vibrational free energy | |
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| Solvation effects | |
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| Configurational free energy | |
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| Protein association in membranes - reduction of dimensionality | |
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| Binding to membranes | |
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| Allosteric interactions | |
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| The allosteric transition | |
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| The simplest case: one binding site and one allosteric transition | |
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| Binding and response | |
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| Energy balance in the one-site model | |
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| G-protein coupled receptors | |
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| Binding site interactions | |
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| The Monod-Wyman-Changeux (MWC) model | |
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| Hemoglobin | |
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| Energetics of the MWC model | |
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| Macroscopic and microscopic additivity | |
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| Phosphofructokinase | |
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| Ligand-gated channels | |
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| Subunit-subunit interactions: the Koshland-Nemethy-Filmer (KNF) model | |
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| The Szabo-Karplus (SK) model | |
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| Diffusion and Brownian motion | |
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| Macroscopic diffusion: Fick's laws | |
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| Solving the diffusion equation | |
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| One-dimensional diffusion from a point | |
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| Three-dimensional diffusion from a point | |
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| Diffusion across an interface | |
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| Diffusion with boundary conditions | |
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| Diffusion at steady state | |
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| A long pipe | |
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| A small hole | |
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| A porous membrane | |
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| Microscopic diffusion - random walks | |
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| Random walks and the Gaussian distribution | |
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| The diffusion equation from microscopic theory | |
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| Friction | |
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| Stokes' law | |
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| Diffusion constants of macromolecules | |
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| Lateral diffusion in membranes | |
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| Fundamental rate processes | |
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| Exponential relaxations | |
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| Activation energies | |
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| The reaction coordinate and detailed balance | |
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| Linear free energy relations | |
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| Voltage-dependent rate constants | |
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| The Marcus free energy relation | |
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| Eyring theory | |
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| Diffusion over a barrier - Kramers' theory | |
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| Single-channel kinetics | |
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| The reaction coordinate for a global transition | |
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| Association kinetics | |
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| Bimolecular association | |
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| Small perturbations | |
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| Diffusion-limited association | |
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| Diffusion-limited dissociation | |
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| Site binding | |
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| Protein-ligand association rates | |
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| Evolution of speed | |
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| Acetylcholinesterase | |
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| Horseradish peroxidase | |
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| Proton transfer | |
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| Binding to membrane receptors | |
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| Reduction in dimensionality | |
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| Binding to DNA | |
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| Multi-state kinetics | |
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| The three-state model | |
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| Initial conditions | |
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| Separation of timescales | |
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| General solution to multi-state systems | |
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| The three-state model in matrix notation | |
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| Stationarity, conservation, and detailed balance | |
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| Single-channel kinetics: the three-state model | |
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| Separation of timescales in single channels: burst analysis | |
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| General treatment of single-channel kinetics: state counting | |
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| Relation between single-channel and macroscopic kinetics | |
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| Loss of stationarity, conservation, and detailed balance | |
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| Single-channel correlations: pathway counting | |
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| Multisubunit kinetics | |
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| Random walks and "stretched kinetics" | |
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| Enzyme catalysis | |
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| Basic mechanisms - serine proteases | |
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| Michaelis-Menten kinetics | |
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| Steady-state approximations | |
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| Pre-steady-state kinetics | |
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| Allosteric enzymes | |
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| Utilization of binding energy | |
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| Kramers' rate theory and catalysis | |
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| Proximity and translational entropy | |
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| Rotational entropy | |
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| Reducing E[superscript dagger]: transition state complementarity | |
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| Friction in an enzyme-substrate complex | |
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| General-acid-base catalysis and Bronsted slopes | |
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| Acid-base catalysis in [beta]-galactosidase | |
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| Catalysis in serine proteases and strong H-bonds | |
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| Marcus' theory and proton transfer in carbonic anhydrase | |
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| Ions and counterions | |
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| The Poisson-Boltzmann equation and the Debye length | |
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| Activity coefficient of an ion | |
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| Ionization of proteins | |
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| Gouy-Chapman theory and membrane surface charge | |
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| Stern's improvements of Gouy-Chapman theory | |
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| Surface charge and channel conductance | |
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| Surface charge and voltage gating | |
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| Electrophoretic mobility | |
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| Polyelectrolyte solutions I. Debye-Huckel screening | |
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| Polyelectrolyte solutions II. Counterion-condensation | |
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| DNA melting | |
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| Fluctuations | |
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| Deviations from the mean | |
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| Number fluctuations and the Poisson distribution | |
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| The statistics of light detection by the eye | |
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| Equipartition of energy | |
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| Energy fluctuations in a macromolecule | |
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| Fluctuations in protein ionization | |
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| Fluctuations in a two-state system | |
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| Single-channel current | |
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| The correlation function of a two-state system | |
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| The Wiener-Khintchine theorem | |
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| Channel noise | |
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| Circuit noise | |
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| Fluorescence correlation spectroscopy | |
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| Friction and the fluctuation-dissipation theorem | |
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| Ion permeation and membrane potential | |
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| Nernst potentials | |
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| Donnan potentials | |
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| Membrane potentials of cells | |
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| Neurons | |
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| Vertebrate skeletal muscle | |
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| A membrane permeable to Na[superscript +] and K[superscript +] | |
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| Membrane potentials of neurons again | |
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| The Ussing flux ratio and active transport | |
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| The Goldman-Hodgkin-Katz voltage equation | |
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| Membrane pumps and potentials | |
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| Transporters and potentials | |
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| The Goldman-Hodgkin-Katz current equation | |
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| Divalent ions | |
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| Surface charge and membrane potentials | |
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| Rate theory and membrane potentials | |
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| Ion permeation and channel structure | |
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| Permeation without channels | |
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| The Ohmic channel | |
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| Energy barriers and channel properties | |
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| Eisenman selectivity sequences | |
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| Forces inside an ion channel | |
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| Gramicidin A | |
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| Rate theory for multibarrier channels | |
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| Single-ion channels | |
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| Single-file channels | |
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| The KcsA channel | |
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| Cable theory | |
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| Current through membranes and cytoplasm | |
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| The cable equation | |
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| Steady state in a finite cable | |
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| Voltage steps in a finite cable | |
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| Current steps in a finite cable | |
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| Branches and equivalent cylinder representations | |
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| Steady state | |
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| Time constants | |
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| Cable analysis of a neuron | |
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| Synaptic integration in dendrites: analytical models | |
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| Impulse responses | |
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| Realistic synaptic inputs | |
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| Compartmental models and cable theory | |
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| Synaptic integration in dendrites: compartmental models | |
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| Action potentials | |
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| The action potential | |
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| The voltage clamp and the properties of Na[superscript +] and K[superscript +] channels | |
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| The Hodgkin-Huxley equations | |
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| Current-voltage curves and thresholds | |
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| Propagation | |
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| Myelin | |
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| Axon geometry and conduction | |
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| Channel diversity | |
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| Repetitive activity and the A-current | |
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| Oscillations | |
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| Dendritic integration | |
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| Expansions and series | |
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| Taylor series | |
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| The binomial expansion | |
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| Geometric series | |
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| Matrix algebra | |
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| Linear transforms | |
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| Determinants | |
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| Eigenvalues, eigenvectors, and diagonalization | |
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| Fourier analysis | |
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| Gaussian integrals | |
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| Hyperbolic functions | |
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| Polar and spherical coordinates | |
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| References | |
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| Index | |