Statistical Physics of Biomolecules : An Introduction

Content: 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