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9783540205661

Orotidine Monophosphate Decarboxylase

by ; ; ; ; ; ;
  • ISBN13:

    9783540205661

  • ISBN10:

    3540205667

  • Format: Hardcover
  • Copyright: 2004-09-01
  • Publisher: Springer Verlag
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List Price: $279.99

Summary

Illustrates how many different mechanistic tools are used in the problem of understanding the origins of catalysis by ODCase. Features abundant halftone illustrations. For researchers.

Table of Contents

What Have Theory and Crystallography Revealed About the Mechanism of Catalysis by Orotidine Monophosphate Decarboxylase?
1(22)
K. N. Houk
Dean J. Tantillo
Courtney Stanton
Yunfeng Hu
Introduction
2(2)
Mechanistic Investigations of ODCase
4(1)
Crystallographic Studies
5(8)
Initial Reports
5(4)
Recent Studies
9(1)
Ligand-Free ODCase
10(1)
Inhibitor Complexes
10(1)
ODCase Mutants
11(2)
Theoretical Studies of ODCase
13(8)
Oxygen Protonation
13(2)
Ground State Destabilization or Transition State Stabilization?
15(1)
C5 Protonation
16(1)
Loop Dynamics
17(1)
Large Quantum Mechanical Models
17(1)
Car-Parrinello Molecular Dynamics
17(2)
Iminium Ion Formation
19(2)
Conclusion
21(2)
References
21(2)
Crystallographic Studies of Native and Mutant Orotidine 5'-Phosphate Decarboxylases
23(20)
Ning Wu
Emil F. Pai
Overview of Structural Analyses of ODCases from Various Sources
24(1)
Structural Studies of Native M. thermoautotrophicum ODCase
25(6)
Description of the Overall Structure
25(3)
Interactions between Various Inhibitors and the Enzyme's Active Site
28(3)
Structural Studies of Mutants of M. thermoautotrophicum ODCase
31(7)
Base-Recognition Mutants
31(1)
Charge Network Mutants
32(4)
ΔR203A, a Phosphate-Binding-Loop Mutant
36(2)
Identification of an Alternate Binding Mode
38(2)
Mechanistic Discussions
40(1)
Future Directions
41(2)
References
41(2)
Insight into the Catalytic Mechanism of Orotidine 5'-Phosphate Decarboxylase from Crystallography and Mutagenesis
43(20)
Brian G. Miller
Introduction
44(2)
Proposed Mechanisms of Enzymatic Decarboxylation
46(3)
Structure of Yeast ODCase in the Presence and Absence of a Potential Transition State Analog
49(2)
Contribution of Enzyme-Phosphoryl Contacts to Catalysis by ODCase
51(3)
Contribution of Enzyme-Ribofuranosyl Contracts to Ground State and Transition State Affinity
54(1)
Importance of the Charged Network to Catalysis by ODCase
55(3)
Summary and Future Prospects
58(2)
Concluding Remarks
60(3)
References
61(2)
Survey of Enzymological Data on ODCase
63(16)
Jeffrey A. Smiley
Introduction
64(1)
The Uncatalyzed Decarboxylation of OMP Analogs
65(1)
Enhanced Affinity of Nucleotide Inhibitors with Anionic Nitrogenous Rings
66(1)
Isotope Effects in the ODCase Reaction
67(4)
Alternate Substrates for ODCase
71(2)
Reconciling Enzymological Data with Structural Data: Is ODCase a Two-faced Enzyme?
73(6)
References
77(2)
Developing Active Site Models of ODCase---from Large Quantum Models to a QM/MM Approach
79(34)
Marcus Lundberg
Margareta R. A. Blomberg
Per E. M. Siegbahn
Introduction
80(5)
Mechanisms Proposed for the Enzymatic Decarboxylation in ODCase
81(1)
Modeling Enzymatic Reactions Using Accurate QM Models
82(2)
Adding the Surrounding Protein to an Accurate QM Model
84(1)
Computational Details
85(2)
Concerted Protonation Mechanism
87(8)
QM Model with Lys93 as Proton Donator
87(1)
Effects of Hydrogen Bonds to O2 and O4
88(1)
Including the Network of Charged and Invariant Amino Acids
88(2)
Effects of Long-Range Electrostatics
90(1)
Analyzing the Influence of Protein Strain
90(2)
Developing a QM/MM Treatment of the Concerted Mechanism
92(3)
Base Protonation Mechanisms
95(8)
Calculating Protonation Costs Using QM Models
96(2)
Calculating Reaction Barriers Using Improved Models of the Charged Network
98(1)
Calculating Reaction Barriers Using Improved Models of the Environment around O2
99(3)
Calculating Protonation Costs for the Pyrimidine Ring Using QM/MM Models
102(1)
C--C Bond Cleavage Prior to Proton Donation
103(4)
Reactant and Intermediate with a Restricted QM Model
104(2)
Reactant and TS with a QM/MM Model
106(1)
Reproducing the QM/MM Results with a QM Model
106(1)
Insights/Discussion
107(6)
References
110(3)
Catalysis by Enzyme Conformational Change
113(24)
Jiali Gao
Kyoungrim Lee Byun
Ronald Kluger
Introduction
114(2)
Free Energy Decomposition
116(4)
Computational Approach
120(3)
Potential Energy Function
120(2)
Potential of Mean Force
122(1)
Free Energy Decomposition Analysis
123(1)
Results
123(4)
Potential of Mean Force
123(3)
Intrinsic Binding Free Energy and Enzyme Conformational Energy
126(1)
The Mechanism of the ODCase Reaction
127(7)
Conclusions
134(3)
References
134(3)
Author Index Volumes 201-238 137(12)
Subject Index 149

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