Enzymes A Practical Introduction to Structure, Mechanism, and Data Analysis

by Copeland, Robert A.

• ISBN13: 9781119793250
• ISBN10: 1119793254
• Edition: 3rd
• Format: Hardcover
• Copyright: 2023-03-01
• Publisher: Wiley

Summary

ENZYMES

A complete and approachable introduction to the study of enzymes, from theory to practice

Enzymes catalyze the bulk of important biological processes, both metabolic and biochemical. They are specialized proteins whose function is determined by their structure, understanding which is therefore a key focus of biological, pharmacological, and agrarian research, among many others. A thorough knowledge of enzyme structure, pathways, and mechanisms is a fundamental building block of the life sciences and all others connected to them.

Enzymes offers a detailed introduction to this critical subject. It analyzes enzyme proteins at the structural level and details the mechanisms by which they perform their catalyzing functions. The book’s in-depth engagement with primary literature and up-to-date research allows it to continuously deploy illustrative examples and connect readers with further research on key subjects. Fully updated after decades as the standard text, this book unlocks a thriving field of biological and biochemical research.

Readers of the third edition of Enzymes will also find:

• Expanded chapters on steady-state and transient-state enzyme kinetics, structural components of enzymes, and more
• New chapters on enzyme regulation, enzyme-macromolecule interactions, enzyme evolution, and enzymes in human health
• Key Learning Points at the beginning of each chapter to assist students and instructors

Enzymes promises to continue as the standard reference on this subject for practitioners of the life sciences and related fields in both academia and industry.

Author Biography

Robert A. Copeland, PhD, is founder, President, and Chief Scientific Officer (CSO) of Accent Therapeutics, Inc. and the President of Ki Consultant, LLC. Previously, he was President of Research and CSO of Enzyme, Inc., and Vice President for Cancer Biology at the Oncology Center of Excellence in Drug Discovery for GlaxoSmithKline. He is a fellow of the American Association for the Advancement of Science and the Royal Society of Chemistry, and has published very widely on enzymes and related subjects.

Table of Contents

Preface to the Third Edition        

Acknowledgments

Preface to the Second Edition    

Preface to the First Edition          

1 A Brief History of Enzymology

Key Learning Points

1.1 Enzymes in Antiquity

1.2 Early Enzymology

1.3 The Development of Mechanistic Enzymology

1.4 Studies of Enzyme Structure

1.5 Enzymology Today

1.6 Summary

References and Further Reading

 

2 Chemical Bonds and Reactions in Biochemistry              

Key Learning Points

2.1 Atomic and Molecular Orbitals

2.2 Thermodynamics of Chemical Reactions

2.3 Acid-Base Chemistry

2.4 Noncovalent Interactions in Reversible Binding

2.5 Rates of Chemical Reactions

2.6 Summary

References and Further Reading

 

3 Structural Components of Enzymes     

Key Learning Points

3.1 The Amino Acids

3.2 The Peptide Bond

3.3 Amino Acid Sequence or Primary Structure

3.4 Secondary Structure

3.5 Tertiary Structure

3.6 Subunits and Quaternary Structure

3.7 Cofactors in Enzymes

3.8  Conformational Dynamics & Enzyme Function

3.9 Methods of Protein Structure Determination

3.10 Summary

References and Further Reading

 

4 Protein–Ligand Binding Equilibria          

Key Learning Points

4.1 The Equilibrium Dissociation Constant, Kd

4.2 The Kinetic Approach to Equilibrium

4.3 Binding Measurements at Equilibrium

4.4 Graphic Analysis of Equilibrium Ligand Binding Data

4.5 Equilibrium Binding with Ligand Depletion (Tight Binding Interactions)

4.6 Competition Among Ligands for a Common Binding Site

4.7 Protein Dynamics in Protein-Ligand Binding

4.8 Orthosteric and Allosteric Ligand Binding Sites

4.9 Experimental Methods for Measuring Ligand Binding

4.10 Summary

References and Further Reading

 

5 Steady State Kinetics of Single-Substrate Enzyme Reactions     

Key Learning Points

5.1 The Time Course of Enzymatic Reactions

5.2 Effects of Substrate Concentration on Velocity

5.3 The Rapid Equilibrium Model of Enzyme Kinetics

5.4 The Steady State Model of Enzyme Kinetics

5.5 The Significance of kcal and Km

5.6 Experimental Measurement of kcat and Km

5.7 Other Linear Transformations of Enzyme Kinetic Data

5.8 Measurements at Low Substrate Concentrations

5.9 Deviations from Hyperbolic Kinetics

5.10 Summary

References and Further Reading

 

6 Chemical Mechanisms in Enzyme Catalysis

Key Learning Points

6.1 Substrate-Active Site Complementarity

6.2 Rate Enhancement Through Transition State Stabilization

6.3 Chemical Mechanisms for Transition State Stabilization

6.4 The Serine Proteases: An Illustrative Example

6.5 Enzymatic Reaction Nomenclature

6.6 Summary

References and Further Reading

 

7 Experimental Measures of Steady State Enzyme Activity            

Key Learning Points

7.1 Initial Velocity Measurements

7.2 Detection Methods

7.3 Separation Methods in Enzyme Assays

7.4 Factors Affecting the Velocity of Enzymatic Reactions

7.5 Reporting Enzyme Activity Data

7.6 Enzyme Stability

7.7 Summary

References and Further Reading

 

8  Transient-State Kinetics

Key Learning Points

8.1 Timescale of Pre-Steady State Turnover

8.2 Instrumentation for Transient Kinetic Measurements

8.3 Estimating Initial Conditions for Transient Kinetic Measurements

8.4 Examples of Some Common Transient Kinetic Reaction Mechanisms

8.5 Examples of Transient Kinetic Studies from the Literature

8.6 Summary

 

9.  Enzyme Regulation

Key Learning Points

9.1 Active and Inactive Conformational States   

9.2 Post-Translational Modifications

9.3 Enzyme Regulation Through Protein-Protein Interactions

9.4 Small Molecule Allosteric Ligands

     9.5  Quantitative Measurements of Enzyme Activation and Inhibition

9.6 Regulation of Protein Kinases

9.7 Summary

References and Further Reading

 

10 Reversible Inhibitors

Key Learning Points

10.1 Equilibrium Treatment of Reversible Inhibition

10.2 Thermodynamic Modes of Reversible Inhibition

10.3 Effects of Inhibitors on Steady State Parameters

10.4 Concentration-Response Plots of Enzyme Inhibition

10.5 Effects of Substrate Concentration on Inhibitor Concentration-Response Curves

10.6 Mutually Exclusive Binding of Two Inhibitors

10.7 Structure-Activity Relationships and Inhibitor Design

10.8 Summary

References and Further Reading

 

11 Tight Binding Inhibitors          

Key Learning Points

11.1 Identifying Tight Binding Inhibition

11.2 Distinguishing Inhibitor Type for Tight Binding Inhibitors

11.3 Determining Ki for Tight Binding Inhibitors

11.4 Use of Tight Binding Inhibitors to Determine Active Enzyme Concentration

11.5 Summary

References and Further Reading

 

12 Time-Dependent Inhibition  

Key Learning Points

12.1 Progress Curves for Slow Binding Inhibitors

12.2 Distinguishing Between Slow Binding Schemes

12.3 Distinguishing Between Modes of Inhibitor Interaction with Enzyme

12.4 Determining Reversibility

12.5 Examples of Slow Binding Enzyme Inhibitors

12.6 Summary

References and Further Reading

 

13 Enzyme Reactions with Multiple Substrates  

Key Learning Points

13.1 Reaction Nomenclature

13.2 Bi Bi Reaction Mechanisms

13.3 Distinguishing Between Random and Compulsory Ordered Mechanisms by Inhibition Pattern

13.4 Isotope Exchange Studies for Distinguishing Reaction Mechanisms

13.5 Using the King -Altman Method to Determine Velocity Equations

13.6 Cleland’s Net Rate Constant Method for Determining Vmax and Vmax/Km

13.7 Summary

References and Further Reading

 

14 Enzyme-Macromolecule Interactions

    Key Learning Points

14.1 Multiprotein Enzyme Complexes

    14.2 Enzymes Reactions on Macromolecular Substrates

14.3 Summary

References and Further Reading

 

15 Cooperativity in Enzyme Catalysis      

Key Learning Points

15.1 Historic Examples of Cooperativity and Allostery in Proteins

15.2 Models of Allosteric Behavior

15.3 Effects of Cooperativity on Velocity Curves

15.4 Sigmoidal Kinetics for Nonallosteric Enzymes

15.5 Summary

References and Further Reading

 

16  Evolution of Enzymes

Key Learning Points

16.1 Early Earth Conditions

16.2 Natural Selection

16.3 Genetic Alternations

16.4 Enzyme Families and Superfamilies

16.5 Enzyme Promiscuity as a Springboard of Evolution

16.6 Protein Dynamics and Conformational Selection in Evolution of Neofunctionality

16.7 Ancestral Enzyme Reconstruction

16.8 Contemporary Enzyme Evolution

16.9 Summary

References and Further Reading

 

17  Enzymes in Human Health

    Key Learning Points

17.1 Enzymes as Therapeutic Agents

    17.2 Enzyme Inhibitors as Therapeutic Agents

    17.3 Properties of Small Molecule Drugs

17.4 Enzyme-Mediated Target Protein Degradation

17.5 The Role of Enzymology in Drug Discovery & Development

17.6 Summary

References and Further Reading