Statistical Physics of Biomolecules: An Introduction, 1st Edition (Hardback) book cover

Statistical Physics of Biomolecules

An Introduction, 1st Edition

By Daniel M. Zuckerman

CRC Press

356 pages | 98 B/W Illus.

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pub: 2010-06-02
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Description

From the hydrophobic effect to protein-ligand binding, statistical physics is relevant in almost all areas of molecular biophysics and biochemistry, making it essential for modern students of molecular behavior. But traditional presentations of this material are often difficult to penetrate. Statistical Physics of Biomolecules: An Introduction brings "down to earth" some of the most intimidating but important theories of molecular biophysics.

With an accessible writing style, the book unifies statistical, dynamic, and thermodynamic descriptions of molecular behavior using probability ideas as a common basis. Numerous examples illustrate how the twin perspectives of dynamics and equilibrium deepen our understanding of essential ideas such as entropy, free energy, and the meaning of rate constants. The author builds on the general principles with specific discussions of water, binding phenomena, and protein conformational changes/folding. The same probabilistic framework used in the introductory chapters is also applied to non-equilibrium phenomena and to computations in later chapters. The book emphasizes basic concepts rather than cataloguing a broad range of phenomena.

Focuses on what students need to know now

Students build a foundational understanding by initially focusing on probability theory, low-dimensional models, and the simplest molecular systems. The basics are then directly developed for biophysical phenomena, such as water behavior, protein binding, and conformational changes. The book’s accessible development of equilibrium and dynamical statistical physics makes this a valuable text for students with limited physics and chemistry backgrounds.

Table of Contents

Proteins Don’t Know Biology

Prologue: Statistical Physics of Candy, Dirt, and Biology

Guiding Principles

About This Book

Molecular Prologue: A Day in the Life of Butane

What Does Equilibrium Mean to a Protein?

A Word on Experiments

Making Movies: Basic Molecular Dynamics Simulation

Basic Protein Geometry

A Note on the Chapters

The Heart of It All: Probability Theory

Introduction

Basics of One-Dimensional Distributions

Fluctuations and Error

Two+ Dimensions: Projection and Correlation

Simple Statistics Help Reveal a Motor Protein’s Mechanism

Additional Problems: Trajectory Analysis

Big Lessons from Simple Systems: Equilibrium Statistical Mechanics in One Dimension

Introduction

Energy Landscapes Are Probability Distributions

States, Not Configurations

Free Energy: It’s Just Common Sense If You Believe in Probability

Entropy: It’s Just a Name

Summing Up

Molecular Intuition from Simple Systems

Loose Ends: Proper Dimensions, Kinetic Energy

Nature Doesn’t Calculate Partition Functions: Elementary Dynamics and Equilibrium

Introduction

Newtonian Dynamics: Deterministic but Not Predictable

Barrier Crossing—Activated Processes

Flux Balance: The Definition of Equilibrium

Simple Diffusion, Again

More on Stochastic Dynamics: The Langevin Equation

Key Tools: The Correlation Time and Function

Tying It All Together

So Many Ways to ERR: Dynamics in Molecular Simulation

Mini-Project: Double-Well Dynamics

Molecules Are Correlated! Multidimensional Statistical Mechanics

Introduction

A More-Than-Two-Dimensional Prelude

Coordinates and Force Fields

The Single-Molecule Partition Function

Multimolecular Systems

The Free Energy Still Gives the Probability

Summary

From Complexity to Simplicity: The Potential of Mean Force

Introduction: PMFs Are Everywhere

The Potential of Mean Force Is Like a Free Energy

The PMF May Not Yield the Reaction Rate or Transition State

The Radial Distribution Function

PMFs Are the Typical Basis for "Knowledge-Based" ("Statistical") Potentials

Summary: The Meaning, Uses, and Limitations of the PMF

What’s Free about "Free" Energy? Essential Thermodynamics

Introduction

Statistical Thermodynamics: Can You Take a Derivative?

You Love the Ideal Gas

Boring but True: The First Law Describes Energy Conservation

G vs. F: Other Free Energies and Why They (Sort of ) Matter

Overview of Free Energies and Derivatives

The Second Law and (Sometimes) Free Energy Minimization

Calorimetry: A Key Thermodynamic Technique

The Bare-Bones Essentials of Thermodynamics

Key Topics Omitted from This Chapter

The Most Important Molecule: Electro-Statistics of Water

Basics of Water Structure

Water Molecules Are Structural Elements in Many Crystal Structures

The pH of Water and Acid–Base Ideas

Hydrophobic Effect

Water Is a Strong Dielectric

Charges in Water + Salt = Screening

A Brief Word on Solubility

Summary

Additional Problem: Understanding Differential Electrostatics

Basics of Binding and Allostery

A Dynamical View of Binding: On- and Off-Rates

Macroscopic Equilibrium and the Binding Constant

A Structural-Thermodynamic View of Binding

Understanding Relative Affinities: ∆∆G and Thermodynamic Cycles

Energy Storage in "Fuels" Like ATP

Direct Statistical Mechanics Description of Binding

Allostery and Cooperativity

Elementary Enzymatic Catalysis

pH AND pKa

Summary

Kinetics of Conformational Change and Protein Folding

Introduction: Basins, Substates, and States

Kinetic Analysis of Multistate Systems

Conformational and Allosteric Changes in Proteins

Protein Folding

Summary

Ensemble Dynamics: From Trajectories to Diffusion and Kinetics

Introduction: Back to Trajectories and Ensembles

One-Dimensional Ensemble Dynamics

Four Key Trajectory Ensembles

From Trajectory Ensembles to Observables

Diffusion and Beyond: Evolving Probability Distributions

The Jarzynski Relation and Single-Molecule Phenomena

Summary

A Statistical Perspective on Biomolecular Simulation

Introduction: Ideas, Not Recipes

First, Choose Your Model: Detailed or Simplified

"Basic" Simulations Emulate Dynamics

Metropolis Monte Carlo: A Basic Method and Variations

Another Basic Method: Reweighting and Its Variations

Discrete-State Simulations

How to Judge Equilibrium Simulation Quality

Free Energy and PMF Calculations

Path Ensembles: Sampling Trajectories

Protein Folding: Dynamics and Structure Prediction

Summary

Index

Subject Categories

BISAC Subject Codes/Headings:
MAT029000
MATHEMATICS / Probability & Statistics / General
SCI008000
SCIENCE / Life Sciences / Biology / General
SCI055000
SCIENCE / Physics