Molecular and Cellular Biophysics

ISBN-10: 0521624703

ISBN-13: 9780521624701

Edition: 2005

Authors: Meyer B. Jackson

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Description:

Molecular and Cellular Biophysics provides 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. Conformational transitions of proteins are studied first using thermodynamics, and subsequently with kinetics. Allosteric theory is developed as the synthesis of conformational transitions and association reactions. Basic ideas of thermodynamics and kinetics are applied to topics such as protein folding, enzyme catalysis and ion channel permeation. These concepts are then used as the building blocks in a treatment of membrane excitability. Through these examples, students will gain an understanding of the general importance and broad applicability of biophysical principles to biological problems.
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Book details

List price: $82.00
Copyright year: 2005
Publisher: Cambridge University Press
Publication date: 1/12/2006
Binding: Paperback
Pages: 528
Size: 7.25" wide x 9.25" long x 0.75" tall
Weight: 0.990
Language: English

MEYER B. JACKSON is Professor of Physiology at the University of Wisconsin Medical School. He has been teaching graduate level biophysics for nearly 25 years.

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