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Biomolecular Thermodynamics

From Theory to Application

Edition:
1st
Author(s):
Douglas Barrick
ISBN:
9781439800195
Format:
Paperback
Publication Date:
September 14, 2017
Content Details:
524 pages
Language:
English

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  • About the Book

    Book Summary

    "an impressive text that addresses a glaring gap in the teaching of physical chemistry, being specifically focused on biologically-relevant systems along with a practical focus…. the ample problems and tutorials throughout are much appreciated."
    –Tobin R. Sosnick, Professor and Chair of Biochemistry and Molecular Biology, University of Chicago

    "Presents both the concepts and equations associated with statistical thermodynamics in a unique way that is at visual, intuitive, and rigorous. This approach will greatly benefit students at all levels."
    –Vijay S. Pande, Henry Dreyfus Professor of Chemistry, Stanford University

    "a masterful tour de force…. Barrick's rigor and scholarship come through in every chapter."
    –Rohit V. Pappu, Edwin H. Murty Professor of Engineering, Washington University in St. Louis

    This book provides a comprehensive, contemporary introduction to developing a quantitative understanding of how biological macromolecules behave using classical and statistical thermodynamics. The author focuses on practical skills needed to apply the underlying equations in real life examples. The text develops mechanistic models, showing how they connect to thermodynamic observables, presenting simulations of thermodynamic behavior, and analyzing experimental data. The reader is presented with plenty of exercises and problems to facilitate hands-on learning through mathematical simulation.

     

    Douglas E. Barrick is a professor in the Department of Biophysics at Johns Hopkins University. He earned his Ph.D. in biochemistry from Stanford University, and a Ph.D. in biophysics and structural biology from the University of Oregon.

    Features

      • Emphasizes problem solving using both real and simulated data
      • Develops multiple skill sets, including data analysis and mathematical simulation
      • Covers various biochemical problems, including conformational equilibria, ligand binding, chemical denaturation, proton titration, helix-coil transition theory, allostery, and catalysis
      • Offers a concise yet thorough and novel approach to understanding the essential aspects of physical chemistry without dry theoretical discussion
      • Shows how to apply classical and statistical thermodynamics to complicated biochemical processes, such as ligand binding, cooperativity, and assembly

    Reviews

      "Presents both the concepts and equations associated with statistical thermodynamics in a unique way that is at visual, intuitive, and rigorous. This approach will greatly benefit students at all levels."
      –Vijay S. Pande, Henry Dreyfus Professor of Chemistry, Stanford University

      "a masterful tour de force…. Barrick's rigor and scholarship come through in every chapter. The focus on biomolecules combined with the detailed demonstrations of how concepts apply to practical aspects of biophysics make this a truly unique contribution. Everyone, from the purported expert to the true novice will gain immensely from this carefully crafted, well motivated, and deeply thought out contribution. This book should live on all of our bookshelves and be consulted routinely as a quick reference or as material for in depth study and training."
      —Rohit V. Pappu, Edwin H. Murty Professor of Engineering, Washington University in St. Louis

      "The author has created an impressive text that addresses a glaring gap in the teaching of physical chemistry, being specifically focused on biologically-relevant systems along with a practical focus. It starts by bringing students up to speed on probability theory, multi-variate calculus and data fitting, the necessary tools for tackling the advanced topics covered in the remaining dozen chapters and for conducting rigorous interdisciplinary research…. the ample problems and tutorials throughout are much appreciated."
      —Tobin R. Sosnick, Professor and Chair, Dept of Biochemistry and Molecular Biology, University of Chicago

  • Contents

    Probabilities and Statistics in Chemical and Biothermodynamics

    Elementary Events.

    How Probabilities Combine.

    Permutation versus composition.

    Discrete Probability Distributions

    Continuous Distributions

    Mathematical Tools in Thermodynamics

    Calculus in Thermodynamics.

    Fitting continuous curves to discrete data.

    Determining the covariance matrix in least-squares fitting.

    Model testing with the 2 and f-ratio probability distributions.

    The Framework of Thermodynamics and the First Law

    What is Thermodynamics and What Does it Treat?

    Dividing up the Universe: System and Surroundings

    Equilibrium, Changes of State, and Reversibility

    Thermodynamic Variables and Equations of State

    The First law of Thermodynamics

    Work

    The reversible work associated with four fundamental changes of state.

    The heat flow associated with the four fundamental changes in an ideal gas.

    The work associated with the irreversible expansion of an ideal gas.

    The connection between heat capacities and state functions.

    A non-ideal model: the van der Walls equation of state

    The Second Law and Entropy

    Some familiar examples of spontaneous change.

    Spontaneous change and statistics

    The directionality of heat flow at the macroscopic (classical) level

    Free Energy as a Potential for the Laboratory and Biology

    Internal energy as a potential--combining the first and second laws.

    Contributions of different chemical species to thermodynamic state functions—molar quantities.

    Partial pressures of mixtures of gases.

    Legendre transforms of a single variable.

    Using Chemical Potentials to Describe Phase Transitions

     

     

    Phases and their transformations.

    The condition for equilibrium between two phases.

    How chemical potentials of different phases depend on temperature and pressure: deriving a T-p phase diagram for water.

    Additional restrictions from the phase diagram: the Clausius-Clapeyron equation and Gibbs' phase rule.

    The Concentration Dependence of Chemical Potential, Mixing, and Reactions

    The dependence of chemical potential on concentration.

    A simple lattice model for nonideal solution behavior.

    Chemical reactions

    Similarities (and differences) between free energies of reaction and mixing.

    How chemical equilibrium depends on temperature

    How chemical equilibrium depends on pressure

    Conformational Equilibrium

    Macromolecular structure.

    A simple two-state model for conformational transitions.

    Simultaneous visualization of N and D.

    The thermal unfolding transition as a way to determine Kfold and G°.

    A simple geometric way to connect Yobs to Kfold.

    Fitting conformational transitions to analyze the thermodynamics of unfolding.

    A more realistic model thermal unfolding of proteins: the constant heat capacity model.

    Measurement of thermal denaturation by differential scanning calorimetry.

    Chemical denaturation of proteins.

    APPENDIX 1: Differential Scanning Calorimetry

    Ensembles that Interact with their Surroundings

    Heat exchange and the canonical ensemble.

    The canonical partition function.

    A canonical ensemble representing a three particle isothermal system.

    The isothermal isobaric ensemble and Gibbs free energy.

    Partition Functions for Single Molecules and Chemical Reactions

    A canonical partition function for a system with one molecule.

    The relationship between the molecular and canonical partition functions.

    An isothermal-isobaric molecular partition function.

    A statistical thermodynamic approach to chemical reaction.

    The Helix-Coil Transition

    The noncooperative homopolymer model.

    The noncooperative heteropolymer model.

    Coupling between the sites and the basis for cooperativity

    Coupling between residues through "nearest-neighbor" models

    Ligand Binding Equilibria from a Macroscopic Perspective

    Ligand Binding to a single site

    Practical issues in measuring and analyzing binding curves

    Binding of multiple ligands

    A macroscopic representation of multiple ligand binding.

    The binding polynomial P: a partition function for ligand binding.

    An example—the macroscopic binding of two ligands.

    Binding to multiple different ligands: "heterotropic" binding

    A general framework to represent thermodynamic linkage between multiple independent ligands.

    Ligand Binding Equilibria from a Microscopic Perspective.

    An example of general microscopic binding: three ligand binding sites.

    Simplifications to microscopic binding models.

    Binding to s identical, independent sites.

    Binding to two classes of independent sites.

    Binding to identical coupled sites

    Explicit structural models for coupling among between binding sites

    Allostery in ligand binding