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E-grāmata: Equilibria and Kinetics of Biological Macromolecules

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  • Formāts: PDF+DRM
  • Izdošanas datums: 25-Nov-2013
  • Izdevniecība: John Wiley & Sons Inc
  • Valoda: eng
  • ISBN-13: 9781118733769
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Equilibria and Kinetics of Biological MacromoleculesPalielināt
  • Formāts: PDF+DRM
  • Izdošanas datums: 25-Nov-2013
  • Izdevniecība: John Wiley & Sons Inc
  • Valoda: eng
  • ISBN-13: 9781118733769
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Progressively builds a deep understanding of macromolecular behavior

Based on each of the authors' roughly forty years of biophysics research and teaching experience, this text instills readers with a deep understanding of the biophysics of macromolecules. It sets a solid foundation in the basics by beginning with core physical concepts such as thermodynamics, quantum chemical models, molecular structure and interactions, and water and the hydrophobic effect. Next, the book examines statistical mechanics, protein-ligand binding, and conformational stability. Finally, the authors address kinetics and equilibria, exploring underlying theory, protein folding, and stochastic models.

With its strong emphasis on molecular interactions, Equilibria and Kinetics of Biological Macromolecules offers new insights and perspectives on proteins and other macromolecules. The text features coverage of:

  • Basic theory, applications, and new research findings
  • Related topics in thermodynamics, quantum mechanics, statistical mechanics, and molecular simulations
  • Principles and applications of molecular simulations in a dedicated chapter and interspersed throughout the text
  • Macromolecular binding equilibria from the perspective of statistical mechanics
  • Stochastic processes related to macromolecules

Suggested readings at the end of each chapter include original research papers, reviews and monographs, enabling readers to explore individual topics in greater depth. At the end of the text, ten appendices offer refreshers on mathematical treatments, including probability, computational methods, Poisson equations, and defining molecular boundaries.

With its classroom-tested pedagogical approach, Equilibria and Kinetics of Biological Macromolecules is recommended as a graduate-level textbook for biophysics courses and as a reference for researchers who want to strengthen their understanding of macromolecular behavior.

Preface xix
Acknowledgments xxi
PART 1 BASIC PRINCIPLES
1(90)
1 Thermodynamics
3(32)
1.1 Introduction
3(1)
1.2 The fundamental postulates or Laws of thermodynamics
4(10)
1.3 Other useful quantities and concepts
14(5)
1.4 Thermodynamics of the ideal gas
19(1)
1.5 Thermodynamics of solutions
20(5)
1.6 Phase equilibria
25(4)
1.7 Chemical equilibria
29(2)
1.8 Temperature dependence of chemical equilibria: The van't Hoff equation
31(1)
1.9 Microcalorimetry
31(4)
Notes
33(2)
2 Four Basic Quantum Mechanical Models of Nuclear and Electronic Motion: A Synopsis
35(16)
2.1 Introduction
35(1)
2.2 Fundamental hypotheses of quantum theory
36(2)
2.3 Three simple models of nuclear motion
38(6)
2.4 Hydrogen atomic orbitals: A simple model of electronic motion in atoms
44(3)
2.5 Many electron atoms
47(4)
Notes
49(1)
Suggested reading
49(2)
3 Molecular Structure and Interactions
51(26)
3.1 Introduction
51(1)
3.2 Chemical bonding: Electronic structure of molecules
51(7)
3.3 Empirical classical energy expressions
58(4)
3.4 Noncovalent forces between atoms and molecules
62(8)
3.5 Molecular mechanics
70(7)
Notes
75(1)
Suggested reading
76(1)
4 Water and the Hydrophobic Effect
77(14)
4.1 Introduction
77(1)
4.2 Structure of liquid water
78(6)
4.3 The hydrophobic effect
84(7)
Notes
89(1)
Suggested reading
89(2)
PART 2 STATISTICAL MECHANICS: THE MOLECULAR BASIS OF THERMODYNAMICS
91(70)
5 The Molecular Partition Function
93(18)
5.1 Introduction
93(1)
5.2 The Maxwell--Boltzmann distribution
93(6)
5.3 The molecular partition function and thermodynamic functions
99(2)
5.4 Application to macromolecules
101(10)
Notes
108(2)
Suggested reading
110(1)
6 System Ensembles and Partition Functions
111(26)
6.1 Introduction
111(1)
6.2 Closed systems: The canonical ensemble
112(7)
6.3 The canonical partition function of systems with continuous energy distributions: The phase-space integral
119(4)
6.4 Application: Relation between binding and molecular interaction energy
123(2)
6.5 Application: Binding of ligand to a macromolecule
125(2)
6.6 Open systems: The grand canonical ensemble or grand ensemble
127(4)
6.7 Fluctuations
131(3)
6.8 Application: Light scattering as a measure of fluctuations of concentration
134(3)
Notes
135(1)
Suggested reading
136(1)
7 Sampling Molecular Systems with Simulations
137(24)
7.1 Introduction
137(1)
7.2 Background
138(1)
7.3 Molecular dynamics
139(3)
7.4 Metropolis Monte Carlo
142(1)
7.5 Simulation of a condensed system
143(1)
7.6 Connecting microscopic and macroscopic system properties
144(2)
7.7 An example: Dynamics of Ace-Ala-Nme in solution
146(3)
7.8 Forced transitions
149(3)
7.9 Potential of mean force for changes of chemistry: "Computer Alchemy"
152(5)
7.10 The potential of mean force and the association equilibrium constant of methane
157(4)
Notes
158(1)
Suggested reading
159(2)
PART 3 BINDING TO MACROMOLECULES
161(116)
8 Binding Equilibria
163(22)
8.1 Introduction
163(1)
8.2 Single-site model
163(3)
8.3 Measuring ligand activity and saturation
166(7)
8.4 Multiple sites for a single ligand
173(9)
8.5 A few practical recommendations
182(3)
Notes
183(1)
Suggested reading
184(1)
9 Thermodynamics of Molecular Interactions
185(12)
9.1 Introduction
185(1)
9.2 Relation between binding and chemical potential: Unified formulation of binding and "exclusion"
186(1)
9.3 Free energy of binding
187(1)
9.4 Mutual response
188(1)
9.5 Volume exclusion
189(4)
9.6 Accounting for interactions of macromolecule and solvent components
193(4)
Notes
196(1)
Suggested reading
196(1)
10 Elements of Statistical Mechanics of Liquids and Solutions
197(16)
10.1 Introduction
197(1)
10.2 Partition function of ideal solution from thermodynamics
198(2)
10.3 Statistical mechanics of the ideal solution
200(2)
10.4 Formulation of molecular binding interactions in terms of a partition function: Empirical approach based on thermodynamics
202(2)
10.5 A purely statistical mechanical formulation of molecular binding interactions
204(4)
10.6 Statistical mechanical models of nonideal solutions and liquids
208(5)
Notes
211(1)
Suggested reading
211(2)
11 Analysis of Binding Equilibria in Terms of Partition Functions
213(10)
11.1 Alternate equivalent representations of the partition function
213(2)
11.2 General implications
215(1)
11.3 Site-specific binding: General formulation
216(2)
11.4 Use of single-site binding constants
218(2)
11.5 Partition function for site binding: One type of ligand, independent multiple sites
220(1)
11.6 Site binding to interdependent or coupled sites
221(2)
Suggested reading
222(1)
12 Coupled Equilibria
223(16)
12.1 Introduction
223(1)
12.2 Simple case: Coupling of binding (one site) and conformation change
224(1)
12.3 Coupling of binding to multiple sites and conformation change
225(5)
12.4 Free energy of binding can "drive" conformation change
230(2)
12.5 Formation of oligomers and polymers
232(5)
12.6 Coupled polymerization and ligand binding
237(2)
Notes
238(1)
Suggested reading
238(1)
13 Allosteric Function
239(16)
13.1 Introduction
239(1)
13.2 Background on hemoglobin
240(1)
13.3 The allosteric or induced-fit model of hemoglobin
241(1)
13.4 Simplified allosteric models: Concerted and sequential
242(2)
13.5 Numeric example
244(1)
13.6 Comparison of oxygen binding curves
245(1)
13.7 Separating oxygen binding and conformation change of hemoglobin
246(2)
13.8 Experiments with hybrid hemoglobins
248(1)
13.9 Two-site proteins, half-the-sites reactivity, and negative cooperativity
248(1)
13.10 Allosteric effects in protein function
249(1)
13.11 Sickle cell hemoglobin
250(1)
13.12 Hill plot
250(5)
Notes
252(1)
Suggested reading
253(2)
14 Charged Groups: Binding of Hydrogen Ions, Solvation, and Charge--Charge Interactions
255(22)
14.1 Introduction
255(1)
14.2 Ionizable groups in peptides
256(1)
14.3 pH titration of a protein: Ribonuclease---normal and abnormal ionizable groups
257(3)
14.4 Local interactions cause pKaS to be abnormal
260(1)
14.5 Internal charge--charge interactions: Ion pairs or salt bridges
260(1)
14.6 Measuring stability of salt bridges from double mutant cycles
261(1)
14.7 Salt bridges stabilize proteins from thermophilic organisms
262(1)
14.8 Charged side chains in enzyme catalysis and protein solubility
263(1)
14.9 Accounting for charge--charge and charge--solvent interactions
263(1)
14.10 The continuum dielectric model
264(2)
14.11 Application to a charged spherical particle
266(1)
14.12 Accounting for ionic strength: The Poisson--Boltzmann equation and Debye--Huckel theory
267(1)
14.13 Numerical treatment via finite differences
268(1)
14.14 Strengths and limitations of the continuum dielectric model
269(1)
14.15 Applications of the continuum dielectric model to macromolecules
270(7)
Notes
273(2)
Suggested reading
275(2)
PART 4 CONFORMATIONAL STABILITY AND CONFORMATION CHANGE
277(80)
15 Some Elements of Polymer Physics
279(12)
15.1 Introduction
279(1)
15.2 Conformational variation in small molecules
280(1)
15.3 Conformational variation in chain molecules
280(1)
15.4 The ideal random coil and the characteristic ratio
281(1)
15.5 The persistence length as a measure of chain flexibility
282(1)
15.6 Conformation of self-avoiding chains
283(1)
15.7 Dependence of chain conformation on solvent conditions; "Theta" conditions
284(2)
15.8 Relating chain statistics to molecular structure
286(1)
15.9 Polyelectrolytes
287(4)
Notes
288(1)
Suggested reading
289(2)
16 Helix-Coil Equilibria
291(20)
16.1 Introduction: Multistate transitions of helical polymers
291(1)
16.2 Single-stranded poly (A): A completely non-cooperative transition
291(1)
16.3 Synthetic polypeptides
292(3)
16.4 Zimm--Bragg, Gibbs--DiMarzio, and Lifson--Roig analyses
295(2)
16.5 Solution of the partition function
297(2)
16.6 Experiments on synthetic homo-polypeptides and protein fragments
299(1)
16.7 Experimental determination of helix propensities in synthetic peptides
299(2)
16.8 Helix stabilization by salt bridges in oligomers containing Glu and Lys
301(2)
16.9 Helix stabilization by charged groups interacting with the helix dipole
303(1)
16.10 Helix-coil equilibria of nucleic acids
303(3)
16.11 Melting transition of DNA
306(5)
Notes
309(2)
17 Protein Unfolding Equilibria
311(36)
17.1 Introduction
311(1)
17.2 The two-state approximation
312(2)
17.3 Working with the two-state model
314(2)
17.4 Calorimetric measurements of the thermodynamics of protein unfolding
316(2)
17.5 Unfolding thermodynamics of ribonuclease
318(4)
17.6 Cold denaturation
322(1)
17.7 Solvent-induced unfolding: Guanidine hydrochloride and urea
322(2)
17.8 Mixed solvents: Denaturants and stabilizers
324(4)
17.9 Unfolding is not two-state under native conditions: Hydrogen exchange
328(4)
17.10 Nature of the two states
332(4)
17.11 A third state: The molten globule
336(2)
17.12 Range of stability
338(2)
17.13 Decomposition of the thermodynamic parameters for unfolding
340(7)
Notes
342(3)
Suggested reading
345(2)
18 Elasticity of Biological Materials
347(10)
18.1 Background
341(7)
18.2 Rubber-like elasticity of polymer networks
348(1)
18.3 Theory of rubber elasticity
349(2)
18.4 Rubber-like elasticity of elastin
351(1)
18.5 Titin and tenascin: Elasticity based on transitions between conformation states
352(2)
18.6 Single-molecule force-extension measurement
354(3)
Notes
355(2)
PART 5 KINETICS AND IRREVERSIBLE PROCESSES
357(80)
19 Kinetics
359(30)
19.1 Introduction
359(1)
19.2 Measuring fast kinetics by rapid perturbation
360(2)
19.3 Fast rates from spectroscopic line shape and relaxation times
362(2)
19.4 Relaxation time in a unimolecular reaction
364(1)
19.5 Relaxation time in a bimolecular reaction
365(2)
19.6 Multiple reactions
367(1)
19.7 Numeric integration of the master equation
367(1)
19.8 Consecutive reactions cause delays
368(1)
19.9 Steady state assumption: Michaelis--Menten model, microscopic reversibility, and cyclic processes
369(3)
19.10 Nucleation and growth mechanisms in phase transitions and biopolymer folding reactions
372(1)
19.11 Kinetic theory and the transition state
373(2)
19.12 Transition state in catalysis
375(2)
19.13 Inhibitor design: Transition state analogs
377(2)
19.14 The diffusion-limited reaction
379(2)
19.15 Estimating reaction rates from simulations
381(8)
Notes
386(1)
Suggested reading
387(2)
20 Kinetics of Protein Folding
389(26)
20.1 Introduction
389(1)
20.2 Slow folding: Misfolding
390(1)
20.3 Slow folding: Cis-trans isomerization of proline
391(1)
20.4 Slow folding: Disulfide bond formation
392(1)
20.5 Two-state folding kinetics
393(2)
20.6 Folding rates of some peptides and proteins
395(3)
20.7 Probing the transition state: Tanford's β value and Fersht's φ value
398(2)
20.8 Early events in folding
400(2)
20.9 (Free) energy landscape for folding
402(1)
20.10 The "Levinthal Paradox" and the folding funnel
403(1)
20.11 Transition state(s), pathway(s), reaction coordinate(s)
404(1)
20.12 Computer simulations of protein folding and unfolding
405(5)
20.13 Conclusion
410(5)
Notes
410(2)
Suggested reading
412(1)
General references
413(2)
21 Irreversible and Stochastic Processes
415(22)
21.1 Introduction
415(1)
21.2 Macroscopic treatment of diffusion
416(1)
21.3 Friction force opposes motion
417(1)
21.4 Random walk as a model diffusive process
418(1)
21.5 Equation of motion for stochastic processes: The Langevin equation
419(1)
21.6 Fluctuation--dissipation theorem
420(1)
21.7 Specific examples of fluctuating force
421(1)
21.8 Alternative form of the fluctuation--dissipation theorem
422(2)
21.9 Diffusive motion and the Langevin equation
424(1)
21.10 Smoluchowski and Fokker--Planck equations
425(4)
21.11 Transition state theory revisited
429(3)
21.12 Kramers' theory of reaction rates
432(5)
Notes
435(1)
Suggested reading
436(1)
APPENDICES
437(54)
A Probability
439(6)
A.1 Introduction
439(1)
A.2 Sample statistics
440(1)
A.3 Probability distributions
440(2)
A.4 A few comments
442(1)
A.5 Fitting theory to data: Computer-facilitated "Least Squares"
442(3)
B Random Walk and Central Limit Theorem
445(4)
B.1 Introduction
445(1)
B.2 Random selection
445(1)
B.3 The central limit theorem
446(1)
B.4 Simple random walk
447(2)
C The Grand Partition Function: Derivation and Relation to Other Types of Partition Functions
449(8)
C.1 Introduction
449(1)
C.2 Derivation
450(1)
C.3 Connection with thermodynamic functions
451(2)
C.4 Relation to other types of partition functions
453(4)
D Methods to Compute a Potential of Mean Force
457(6)
D.1 Introduction
457(1)
D.2 Thermodynamic integration
458(1)
D.3 Slow growth
458(1)
D.4 Thermodynamic perturbation
459(1)
D.5 Umbrella sampling
460(1)
D.6 Conclusion
461(2)
E Theory of the Helix-Coil Transition
463(6)
E.1 Introduction
463(1)
E.2 Maximum term solution
464(2)
E.3 Solution via matrix algebra
466(3)
F Laplace Transform
469(8)
F.1 Solving linear differential equations with the Laplace transform
469(1)
F.2 The Laplace transform
469(1)
F.3 Two key properties of the Laplace transform
470(1)
F.4 Example 1: The Poisson process (or consecutive reactions)
471(1)
F.5 Example 2: General case of linear kinetic equations
472(2)
F.6 Example 3: Coupled harmonic oscillators'normal modes
474(2)
F.7 Table of inverse Laplace transforms
476(1)
G Poisson Equation
477(6)
G.1 Formulation
477(1)
G.2 Exact solution for a simple case: The Born model
478(2)
G.3 Accounting for ionic strength: Poisson--Boltzmann equation and Debye--Huckel theory
480(3)
H Defining Molecular Boundaries
483(2)
I Equations
485(6)
I.1 Stirling's formula and combinatorials
485(1)
I.2 Integrals of Gaussian distributions
486(1)
I.3 Cartesian and spherical polar coordinates
486(1)
I.4 Laplace operator in three-dimensional cartesian, polar, and cylindrical coordinates
487(1)
I.5 Sums of geometric series
487(1)
I.6 The Kronecker and Dirac delta functions
488(1)
I.7 Useful relations between differential quotients
488(1)
I.8 Random numbers
489(2)
Index 491
JAN HERMANS, PhD, is Emeritus Professor in the Department of Biochemistry and Biophysics at the University of North Carolina at Chapel Hill. He is the author of over 130 papers in the field of protein and macromolecular biophysics.

BARRY LENTZ, PhD, is Professor in the Department of Biochemistry and Biophysics at the University of North Carolina at Chapel Hill and Director of the UNC Molecular & Cellular Biophysics Program. He has authored roughly 130 original research publications in the field of biophysics, focusing on biomembrane microstructure and cell function.
Biežāk uzdotie jautājumi par e-grāmatām Biežāk uzdotie jautājumi par e-grāmatām
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