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Enzymes catalysis, kinetics and mechanisms
Punekar, N. S
Cataloging brief
Enzymes catalysis, kinetics and mechanisms
Author :
Punekar, N. S
Publisher :
Springer
Pub. Year :
[2018]
Subjects :
Enzymes chemistry Catalysis Kinetics
Call Number :
QP 601 .P86 2018
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Preface
(6)
Purpose of This Book
(6)
Audience and Their Background
(7)
Organization
(8)
How to Use This Book
(9)
Useful Constants and Conversion Factors
(10)
Acknowledgments
(12)
Contents
(14)
About the Author
(22)
Part I: Enzyme Catalysis - A Perspective
(23)
1: Enzymes: Their Place in Biology
(24)
Suggested Reading
(25)
2: Enzymes: Historical Aspects
(26)
2.1 Biocatalysis: The Beginnings
(26)
2.2 ``Enzyme´´: Conceptual Origin
(28)
2.3 Key Developments in Enzymology
(29)
Reference
(34)
Suggested Reading
(34)
3: Exploiting Enzymes: Technology and Applications
(35)
3.1 Exploiting Natural Diversity
(36)
3.2 Modifying Enzymes to Suit Requirements
(42)
3.3 Genetic Engineering and Enzymes
(47)
3.4 Summing Up
(50)
References
(50)
Suggested Reading
(51)
4: On Enzyme Nomenclature and Classification
(52)
4.1 What Is in the Name?
(52)
4.2 Enzyme Diversity and Need for Systematics
(53)
4.3 Enzyme Commission: Recommendations
(54)
4.4 Some Concerns
(58)
References
(60)
5: Hallmarks of an Enzyme Catalyst
(61)
5.1 Catalysis
(61)
5.2 Specificity
(64)
5.3 Regulation
(67)
References
(69)
6: Origins of Enzyme Catalytic Power
(70)
6.1 Proximity and Orientation Effects
(70)
6.2 Contribution by Electrostatics
(74)
6.3 Metal Ions in Catalysis
(77)
6.4 General Acid-Base Catalysis
(79)
6.5 Covalent Catalysis
(81)
6.6 Transition State Binding and Stabilization
(82)
References
(86)
Suggested Reading
(87)
7: Which Enzyme Uses What Tricks?
(88)
References
(91)
8: Structure and Catalysis: Conformational Flexibility and Protein Motion
(92)
References
(99)
Suggested Reading
(99)
Part II: Enzyme Kinetic Practice and Measurements
(100)
9: Chemical Kinetics: Fundamentals
(101)
9.1 Measurement of Reaction Rates
(101)
9.2 Factors that Influence Chemical Reaction Rates
(103)
9.3 Reaction Progress and Its Concentration Dependence
(103)
9.4 Temperature Dependence of Reaction Rates
(107)
9.5 Catalysis
(110)
9.6 Purpose of Kinetic Studies: Reaction Mechanism
(110)
Reference
(112)
Suggested Reading
(112)
10: Concepts of Equilibrium and Steady State
(113)
10.1 Chemical Reaction Equilibrium
(114)
10.2 Binding Equilibrium
(118)
10.3 Complex Reactions Involving Intermediates
(119)
References
(122)
Suggested Reading
(122)
11: ES Complex and Pre-steady-state Kinetics
(123)
11.1 ES Complex, Intermediates, and Transient Species
(124)
11.2 Kinetic Competence of an Intermediate
(126)
11.3 Pre-steady-state Kinetics
(126)
References
(130)
12: Principles of Enzyme Assays
(131)
12.1 Detection and Estimation Methods
(131)
12.2 Enzyme Reaction Time Course
(136)
12.3 Precautions and Practical Considerations
(139)
12.4 Summing Up
(143)
References
(145)
Suggested Reading
(145)
13: Good Kinetic Practices
(146)
13.1 How to Assemble Enzyme Assay Mixtures
(146)
13.2 pH and Ionic Strength Considerations
(152)
13.3 Temperature Effects
(154)
13.4 Summing Up
(156)
References
(157)
14: Quantification of Catalysis and Measures of Enzyme Purity
(158)
14.1 Enzyme Units, Specific Activity, and Turnover Number
(158)
14.2 Enzyme Purification and Characterization
(161)
14.3 Interpreting a Purification Table: Criteria of Enzyme Purity
(163)
14.4 Unity of the Enzyme
(165)
14.5 Summing Up
(168)
References
(168)
15: Henri-Michaelis-Menten Equation
(169)
15.1 Derivation of the Michaelis-Menten Equation
(169)
15.2 Salient Features of Michaelis-Menten Equation
(173)
Calculating [S]0.9/[S]0.1
(176)
h and r: The Two Cooperativity Indices
(178)
15.3 Significance of KM, Vmax, and kcat/KM
(179)
The Tradeoff Between kcat and KM
(183)
15.4 Haldane Relationship: Equilibrium Constant Meets Kinetic Constants
(185)
Haldane Relationship and Isozymes
(187)
15.5 Use and Misuse of Michaelis-Menten Equation
(189)
References
(189)
Suggested Reading
(190)
16: More Complex Rate Expressions
(191)
16.1 Investigating Enzyme Mechanisms Through Kinetics
(191)
Mechanism Building: The Process
(191)
16.2 Notations and Nomenclature in Enzyme Kinetics
(193)
16.3 Deriving Rate Equations for Complex Equilibria
(196)
16.3.1 Algebraic Method
(196)
Rate Equation for the Equilibria Involving Two Enzyme Forms
(196)
16.3.2 King-Altman Procedure
(198)
King-Altman Procedure for Equilibria with Two Enzyme Forms
(199)
16.3.3 Net Rate Constant Method
(201)
Net Rate Constant Method for Linear Equilibria
(201)
16.3.4 Other Methods
(204)
16.4 Enzyme Kinetics and Common Sense
(204)
References
(205)
17: Enzyme Kinetic Data: Collection and Analysis
(206)
17.1 Obtaining Primary Data: Practical Aspects
(206)
17.1.1 Reductionism in Experimental Design
(206)
17.1.2 Choice of Substrate Concentrations
(207)
17.1.3 Pilot Experiments and Iteration
(208)
17.1.4 Importance of Measuring Initial Velocities
(209)
Monitoring NADP-Glutamate Dehydrogenase Reaction Progress
(209)
17.1.5 Utility of the Integrated Form of Michaelis-Menten Equation
(210)
17.2 Analyzing Data: The Basics
(211)
17.2.1 Variation, Errors, and Statistics
(211)
17.3 Plotting v Versus [S] Data
(212)
17.3.1 The v Versus [S] Plot
(212)
17.3.2 Direct Linear Plot
(213)
17.3.3 v Versus log[S] Plot
(214)
17.3.4 Hill Plot
(216)
17.4 Linear Transforms of Michaelis-Menten Equation
(217)
17.4.1 Lineweaver-Burk Plot
(218)
Practical Aspects of Double-Reciprocal Analysis
(219)
17.4.2 Eadie-Hofstee Plot
(221)
17.4.3 Woolf-Hanes Plot
(222)
17.5 Summing Up
(224)
References
(224)
Part III: Elucidation of Kinetic Mechanisms
(225)
18: Approaches to Kinetic Mechanism: An Overview
(226)
18.1 Which Study Gives What Kind of Information?
(227)
18.2 Two Thumb Rules
(228)
19: Analysis of Initial Velocity Patterns
(231)
19.1 Intersecting Patterns
(232)
19.1.1 Determination/Evaluation of Kinetic Constants and Replots
(232)
19.1.2 Interpretation
(234)
19.2 Parallel Patterns
(235)
19.2.1 Determination/Evaluation of Kinetic Constants and Replots
(236)
19.2.2 Interpretation
(236)
19.3 Few Unique Variations
(238)
Appendix
(239)
References
(240)
20: Enzyme Inhibition Analyses
(241)
20.1 Reversible Versus Irreversible Inhibition
(241)
20.2 Partial Versus Complete Inhibition
(243)
20.3 Other Inhibitor Types
(244)
References
(246)
21: Irreversible Inhibitions
(247)
21.1 Chemical Modification Agents
(247)
21.2 Affinity Labels
(251)
21.3 Suicide Substrates
(252)
21.4 Tight-Binding Inhibitors
(253)
References
(254)
22: Reversible Inhibitions
(255)
22.1 Competitive Inhibition
(256)
22.1.1 Determination/Evaluation of Kinetic Constants and Replots
(257)
22.1.2 Interpretation
(258)
22.2 Uncompetitive Inhibition
(258)
22.2.1 Determination/Evaluation of Kinetic Constants and Replots
(259)
22.2.2 Interpretation
(260)
22.3 Noncompetitive Inhibition
(260)
22.3.1 Determination/Evaluation of Kinetic Constants and Replots
(261)
22.3.2 Interpretation
(262)
22.4 Reversible Inhibition Equilibria: Another Viewpoint
(263)
22.4.1 Significance of α and β Values
(264)
22.5 IC50 and Its Relation to KI of an Inhibitor
(264)
Appendix
(266)
References
(267)
23: Alternate Substrate (Product) Interactions
(268)
23.1 Substrate Inhibition
(268)
23.1.1 Determination of Kinetic Constants and Their Significance
(269)
23.2 Use of Alternate Substrates in Enzyme Studies
(270)
23.2.1 Information About the Active Site Shape, Geometry, and Interactions
(271)
23.2.2 Understanding Kinetic Mechanism
(275)
Reference
(275)
24: pH Studies with Enzymes
(276)
24.1 Enzyme pH Optimum
(277)
24.2 pH Kinetic Profiles
(278)
24.3 Identifying Groups Seen in pH Profiles
(281)
Reference
(283)
25: Isotopes in Enzymology
(284)
25.1 Enzyme Assays with a Radiolabeled Substrate
(285)
25.2 Isotope Partitioning
(286)
References
(288)
26: Isotope Exchanges at Equilibrium
(289)
26.1 Partial Reactions and Ping-Pong Mechanism
(290)
26.2 Sequential Mechanisms
(291)
References
(294)
27: Isotope Effects in Enzymology
(295)
27.1 Magnitude of the Observed Isotope Effect
(297)
27.2 Experimental Approaches to Measure Isotope Effects
(300)
27.2.1 Direct Comparison
(300)
27.2.2 Equilibrium Perturbation
(301)
27.2.3 Internal Competition Method
(301)
27.3 Applications of KIEs in Enzymology:
(302)
27.3.1 Elucidating Kinetic Mechanism
(302)
27.3.2 Deciding Chemical Mechanism
(302)
27.3.3 Understanding Enzyme Transition State
(305)
References
(307)
Suggested Reading
(307)
28: From Kinetic Data to Mechanism and Back
(308)
28.1 How to Relate Mechanisms with Steady-State Kinetic Data
(308)
28.1.1 Ordered Mechanism
(309)
28.1.2 Random Mechanism
(309)
28.1.3 Ping-Pong Mechanism
(312)
28.2 Assigning Kinetic Mechanisms: An Action Plan
(313)
28.3 Practical Relevance of Enzyme Kinetics
(314)
28.3.1 Affinity Chromatography and Protein Purification
(314)
28.3.2 Dissection of Metabolism
(315)
28.3.3 Enzyme-Targeted Drugs in Medicine
(315)
References
(317)
Part IV: Chemical Mechanisms and Catalysis
(318)
29: Chemical Reactivity and Molecular Interactions
(319)
29.1 Atoms, Molecules, and Chemical Bonding
(319)
29.1.1 Covalent Bonds
(320)
29.1.2 Directional Property of Covalent Bonds
(322)
29.1.3 Non-covalent Interactions and Intermolecular Forces
(324)
29.2 Chemical Reaction Mechanisms
(326)
29.2.1 Cleaving and Forming Covalent Bonds
(326)
29.2.2 Logic of Pushing Electrons and Moving Bonds
(328)
Guidelines to a Chemical Mechanism
(329)
29.3 Stereochemical Course of Reaction
(330)
29.4 Common Organic Reaction Types
(331)
29.4.1 Nucleophilic Displacements
(332)
29.4.2 Elimination Reactions
(333)
29.4.3 Carbon-Carbon Bond Formation
(334)
29.5 Summing Up
(336)
Reference
(336)
Suggested Reading
(336)
30: Acid-Base Chemistry and Catalysis
(337)
30.1 Acids and Bases
(337)
Acid Dissociation Constant
(338)
30.2 General Acid-Base Catalysis
(344)
Contributions of Specific and General Acid Catalysis
(345)
30.3 Summing Up
(348)
References
(349)
31: Nucleophilic Catalysis and Covalent Reaction Intermediates
(350)
31.1 Nucleophiles and Electrophiles Available on the Enzyme
(350)
31.2 Nucleophilic (Covalent) Catalysis
(355)
Criteria for Nucleophilic Catalysis
(356)
Catalysis by Nucleophile or Base?
(357)
31.3 Covalent Reaction Intermediates
(360)
How Covalent Reaction Intermediates Are Formed?
(361)
31.4 Detecting Intermediates and Establishing Their Catalytic Competence
(362)
31.5 Summing Up
(369)
References
(370)
32: Phosphoryl Group Chemistry and Importance of ATP
(371)
32.1 Why Nature Chose Phosphates
(371)
32.2 Chemical Mechanisms at the Phosphoryl Group
(372)
Phosphoryl Transfer Mechanism: Single or Double Displacement?
(376)
32.3 Adenosine Triphosphate: Structure Relates to Function
(377)
32.4 Investing Group Transfer Potential to Create Good Leaving Groups
(384)
32.5 Summing Up
(386)
References
(387)
33: Enzymatic Oxidation-Reduction Reactions
(388)
33.1 What Are Oxidation-Reduction Reactions?
(388)
Redox Chemistry of Lactate Dehydrogenase Reaction
(391)
33.2 How Enzymes Influence Redox Reaction Rates
(393)
33.3 Mechanisms and Modes of Electron Transfer
(395)
33.4 Pterine and Folate Cofactors
(396)
33.5 Nicotinamide Cofactors
(397)
33.6 Flavins and Flavoenzymes
(399)
33.7 Reactions Involving Molecular Oxygen
(401)
33.8 Summing Up
(404)
References
(405)
34: Carboxylations and Decarboxylations
(406)
34.1 Reactions and Reactivity of CO2
(406)
34.2 Carboxylation Chemistry with Pyruvate and Phosphoenolpyruvate
(408)
Enzymes That Carboxylate PEP
(409)
34.3 Cofactor-Assisted Carboxylations
(410)
Exchange Reactions Observed with Acetyl-CoA Carboxylase
(412)
34.4 Decarboxylation Reactions
(415)
34.5 Thiamine Pyrophosphate and α-Keto Acid Decarboxylations
(418)
Partial Reactions of Pyruvate Dehydrogenase Complex
(421)
34.6 Summing Up
(422)
References
(423)
35: Electrophilic Catalysis and Amino Acid Transformations
(424)
35.1 Protein Electrophiles
(426)
35.2 Reactions Involving Pyridoxal Phosphate (PLP)
(431)
35.3 Summing Up
(436)
References
(439)
Suggested Reading
(439)
36: Integrating Kinetic and Chemical Mechanisms: A Synthesis
(440)
36.1 Competence of the Proposed Reaction Intermediate
(440)
36.2 Glutamine Synthetase
(442)
36.3 Glutamate Dehydrogenase
(445)
36.4 Disaccharide Phosphorylases
(446)
36.5 Acyl Transferases
(449)
36.6 Chymotrypsin
(451)
36.7 Aldolases and Transaldolase
(453)
36.8 Ribonuclease A
(457)
36.9 Interdependence of Kinetic and Chemical Mechanisms: A Summary
(458)
References
(460)
Part V: Frontiers in Enzymology
(461)
37: Regulation of Enzyme Activity
(462)
37.1 Control of Enzyme Concentration
(464)
37.2 Control of Enzyme Activity: Inhibition
(466)
37.3 Control of Enzyme Activity: Cooperativity and Allostery
(469)
Oligomeric State, Subunit Cooperativity, and Metabolic Switch Behavior
(470)
37.4 Isozymes and Regulation
(476)
37.5 Covalent Modifications and Control
(480)
37.6 Protein-Protein Interactions and Enzyme Control
(485)
37.7 Compartmental Regulation and Membrane Transport
(486)
37.8 Glutamine Synthetase: An Anthology of Control Mechanisms
(489)
37.9 Summing Up
(491)
References
(493)
Suggested Reading
(493)
38: In Vitro Versus In Vivo: Concepts and Consequences
(494)
38.1 Why Michaelis-Menten Formalism Is Not Suitable In Vivo
(495)
38.2 Concentration of Enzymes, Substrates, and Their Equilibria
(498)
38.3 Avogadro´s Number Is a Very Big Number
(501)
38.4 Diffusion, Crowding, and Enzyme Efficiency
(505)
38.5 Consecutive Reactions and Metabolite Channeling
(511)
38.6 Summing Up
(518)
References
(519)
39: Future of Enzymology: An Appraisal
(521)
39.1 Transition-State Analysis and Computational Enzymology
(522)
39.2 Single-Molecule Enzymology
(523)
39.3 Structure-Function Dissection of Enzyme Catalysis
(524)
39.4 Designing Novel Catalysts
(531)
39.5 Enzymes Made to Order
(539)
39.6 Summing Up
(547)
References
(547)
General
(547)
Transition State Analysis and Computational Enzymology
(547)
Single Molecule Enzymology
(548)
Structure-Function Dissection of Enzyme Catalysis
(548)
Designing Novel Catalysts
(549)
Enzymes Made to Order
(550)
40: Closure - Whither Enzymology
(552)
References
(556)
Bibliography
(557)
Books
(557)
General and Historical
(557)
Enzyme Kinetics
(557)
Enzyme Chemical Mechanisms
(558)
Practical Enzymology
(558)
Enzymology Texts
(559)
Enzyme Regulation and Applications
(559)
Series
(560)
Volumes Covering Advances in Enzymology
(560)
Biochemistry Textbooks
(560)
For Background Material on Protein Structure, Metabolism and Gene Regulation
(560)
