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S1812 Sigma

Structure and Mechanism in Protein Science

  •  ISBN-10 0-7167-3268-8

  •  ISBN-13 978-0-7167-3268-6

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publication info   A. Fersht, ed., W.H. Freeman, 1999, 650 pp., hard cover
mfr. no.   Freeman

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General description

There is a new era of protein design, sparked by the convergence of protein folding and enzymology. This book is a depiction of the principles of protein structure, activity, and mechanism today. It takes a more general look at mechanisms in protein science, emphasizing the unity of concepts in folding and catalysis and the importance of the relationships between basic chemistry, kinetics, thermodynamics, and structure. It makes protein engineering easier to understand and apply.

Table of Contents

1. The Three-Dimensional Structure of Proteins
A. The primary structure of proteins
B. Methods for determination of three-dimensional structure
1. Structures of crystalline proteins by x-ray diffraction methods
2. Neutron diffraction
3. Structure of proteins in solution from NMR methods
C. The three-dimensional structure of proteins
1. The structural building blocks
2. The Ramachandran diagram
3. Motifs or supersecondary structures
4. Assembly of proteins from the building blocks
D. Protein diversity
1. Introns, exons, and inteins and exteins
2. Divergent evolution of families of proteins
3. Convergent evolution
4. Convergence or divergence?
5. Alpha/Beta Barrel (or TIM barrel) proteins
6. Dehydrogenases and domains
7. Evolution of proteins by fusion of gene fragments
8. Homology, sequence identity, and structural similarity
E. Higher levels of organization: Multienzyme complexes
F. The structure of enzyme - substrate complexes
G. Flexibility and conformational mobility of proteins
2. Chemical Catalysis
A. Transition state theory
B. Principles of catalysis
C. Covalent catalysis
D. Structure - activity relationships
E. The principle of microscopic reversibility or detailed balance
F. The principle of kinetic equivalence
G. Kinetic isotope effects
H. Summary of classical factors of enzyme catalysis
3. The Basic Equations of Enzyme Kinetics
A. Steady state kinetics
B. The significance of the Michaelis-Menten parameters
C. Graphical representation of data
D. Inhibition
E. Nonproductive binding
F. k(cat)/K(M) = k(2)/K(s)
G. Competing substrates
H. Reversibility: The Haldane equation
I. Breakdown of the Michaelis-Menten equation
J. Multisubstrate systems
K. Useful kinetic shortcuts
L. Thermodynamic cycles
4. Measurement and Magnitude of Individual Rate Constants
Part 1 Methods for measurement: An introduction to pre-steady state kinetics
A. Rapid mixing and sampling techniques
B. Flash photolysis
C. Relaxation methods
D . Analysis of pre - steady state and relaxation kinetics
E. The absolute concentration of enzymes
Part 2 The magnitude of rate constants for enzymatic processes
A. Upper limits on rate constants
B. Enzymatic rate constants and rate-determining processes
5. The pH Dependence of Enzyme Catalysis
A. Ionization of simple acids and bases: The basic equations
B. The effect of ionizations of groups in enzymes on kinetics
C. Modifications and breakdown of the simple theory
D. The influence of surface charge on pK(a)′s of groups in enzymes
E. Graphical representation of data
F. Illustrative examples and experimental evidence
G. Direct titration of groups in enzymes
H. The effect of temperature, polarity of solvent, and ionic strength on pK(a)′s of groups in enzymes and in solution
I. Highly perturbed pK(a)′s in enzymes
6. Practical Methods for Kinetics and Equilibria
A. Spectrometry and methods for kinetics
B. Plotting kinetic data
C. Determination of protein-ligand dissociation constant
D. Plotting binding data
E. Computer fitting of data
F. Statistics, errors of observation, and accuracy

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