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E-grāmata: Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems

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Normal Mode Analysis: Theory and Applications to Biological and Chemical SystemsPalielināt
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Rapid developments in experimental techniques continue to push back the limits in the resolution, size, and complexity of the chemical and biological systems that can be investigated. This challenges the theoretical community to develop innovative methods for better interpreting experimental results. Normal Mode Analysis (NMA) is one such technique. Capable of providing unique insights into the structural and dynamical properties of complex systems, it is now finding a wide range of applications in chemical and biological problems.

From the fundamental physical ideas to cutting-edge applications and beyond, this book presents a broad overview of normal mode analysis and its value in state-of-the-art research. The first section introduces NMA, examines NMA algorithm development at different resolutions, and explores the application of those techniques in the study of biological systems. Later chapters cover method developments based on or inspired by NMA but going beyond the harmonic approximation inherent in standard NMA techniques.

Normal mode analysis complements traditional approaches with computational efficiency and applicability to large systems that are beyond the reach of older methods. This book offers a unique opportunity to learn from the experiences of an international, interdisciplinary panel of top researchers and explore the latest developments and applications of NMA to biophysical and chemical problems.
Normal Mode Theory and Harmonic Potential Approximations
1(16)
Konrad Hinsen
Introduction
1(1)
Potential Wells
2(3)
Normal Modes
5(6)
Vibrational Modes
7(2)
Langevin and Brownian Modes
9(2)
Interpretation and Analysis of Normal Modes
11(4)
Conclusion
15(2)
References
16(1)
All-Atom Normal Mode Calculations of Large Molecular Systems Using Iterative Methods
17(24)
Liliane Mouawad
David Perahia
Introduction
17(2)
Normal Mode Theory
19(2)
Iterative Methods
21(2)
Methods Based on the Rayleigh Quotient
21(1)
Perturbation Method
22(1)
Mixed Basis Method
23(1)
The DIMB Method
23(4)
Initial Guess Vectors
24(1)
Iterative Procedure for Obtaining the NMs
24(1)
Convergence Criteria
24(3)
Applications of DIMB
27(6)
Neocarzinostatin
27(1)
Comparison between DIMB and the SM
28(1)
Utilization of DIMB with a Different Partition
29(1)
Coupling Between Backbone Collective Motions and Side-Chains
30(2)
Hemoglobin
32(1)
Concluding Remarks
33(8)
Appendix A Detailed Description of the DIMB Method
34(1)
Initial Guess Vectors
34(2)
Iterative Procedure for Obtaining the NMs
36(1)
References
36(5)
The Gaussian Network Model: Theory and Applications
41(24)
A.J. Rader
Chakra Chennubhotla
Lee-Wei Yang
Ivet Bahar
Introduction
41(3)
Conformational Dynamics: A Bridge Between Structure and Function
43(1)
Functional Motions of Proteins Are Cooperative Fluctuations Near the Native State
43(1)
The Gaussian Network Model
44(5)
A Minimalist Model for Fluctuation Dynamics
44(1)
GNM Assumes Fluctuations Are Isotropic and Gaussian
44(2)
Statistical Mechanics Foundations of the GNM
46(2)
Influence of Local Packing Density
48(1)
Method and Applications
49(10)
Equilibrium Fluctuations
49(1)
GNM Mode Decomposition: Physical Meaning of Slow and Fast Modes
50(3)
What Is ANM? How Does GNM Differ from ANM?
53(2)
Applicability to Supramolecular Structures
55(3)
iGNM: A Database of GNM Results
58(1)
Future Prospects
59(6)
References
61(4)
Normal Mode Analysis of Macromolecules: From Enzyme Active Sites to Molecular Machines
65(26)
Guohui Li
Adam Van Wynsberghe
Omar N.A. Demerdash
Qiang Cui
Introduction
65(1)
Basic Theories and Implementations
66(5)
NMA with Hybrid QM/MM Potentials
67(2)
Coarse-Grained NMA with Physical Potentials
69(2)
Illustrative Applications
71(12)
Active Site of Mb--CO
71(4)
Flexibility of Molecular Machines --- Comparison between BNM and ANM
75(1)
The Hammerhead Ribozyme
75(4)
The 30S and 50S Ribosomes
79(4)
Conclusions and Future Perspectives
83(8)
Acknowledgments
84(1)
References
84(7)
Functional Information from Slow Mode Shapes
91(20)
Yves-Henri Sanejouand
Introduction
91(2)
Conformational Change of AdK Arising from NMA
93(10)
Standard Normal Mode Calculation
93(1)
Comparison with the Conformational Change
94(1)
Effective Number of Modes Required for the Description
95(1)
RTB Approximation
96(2)
Tirion's Approach
98(3)
Description of the Conformational Change with Approximate Modes
101(2)
Conformational Change of DHFR and NMA
103(2)
Applications
105(1)
Conclusion
106(5)
References
106(5)
Unveiling Molecular Mechanisms of Biological Functions in Large Macromolecular Assemblies Using Elastic Network Normal Mode Analysis
111(26)
Florence Tama
Charles L. Brooks III
Introduction
112(1)
Theory and Method
113(6)
Normal Mode Theory
113(1)
Multi-Scale Energy Functions Using Elastic Networks
114(1)
Rotation-Translation Block Method
115(2)
Multi-Scale NMA Using Elastic Network Hamiltonians and the RTB Method
117(1)
Mapping the Pathway of Conformational Change Using NMA
117(1)
Linear Interpolation between Endpoints Using Normal Mode Directions
117(1)
Nonlinear/Iterative Approach
118(1)
Applications
119(14)
Unveiling Molecular Mechanisms of Conformational Changes of Large Macromolecular Assemblies
120(1)
The Mechanism and Pathway of pH Induced Swelling in Cowpea Chlorotic Mottle Virus
120(3)
Dynamic Reorganization of the Functionally Active 70S Ribosome
123(3)
Myosin II ATPase Inhibition
126(2)
Exploration of Global Distortions and Interpretation of Low-Resolution Structural Information
128(1)
Global Distortions of Biological Molecules from Low-Resolution Structural Information
128(1)
Flexible Fitting of Atomic Structures into Low-Resolution Electron Density Maps
129(4)
Conclusions
133(4)
Acknowledgments
133(1)
References
134(3)
Applications of Normal Mode Analysis in Structural Refinement of Supramolecular Complexes
137(18)
Jianpeng Ma
Introduction
137(1)
Methods of NMA
138(2)
Basic Theory of NMA
138(1)
Elastic NMA
139(1)
Structural Refinement in Cryo-EM Measurement
140(6)
NMA Based on Low-Resolution Density Maps
140(4)
QEDM-Assisted Cryo-EM Structural Refinement
144(2)
Structural Refinement in Fiber Diffraction
146(9)
NMA at Length Scales of Several Microns
146(2)
Fiber Diffraction Refinement Based on Long-Range Normal Modes
148(2)
Acknowledgments
150(1)
References
151(4)
Normal Mode Analysis in Studying Protein Motions with X-Ray Crystallography
155(16)
George N. Phillips, Jr.
Introduction
155(4)
Comparison of Theory and Diffraction Experiment
159(2)
Effect of Displacements on the Bragg Peaks
161(3)
Normal Mode Predictions of X-Ray Diffuse Scattering
163(1)
Complete Refinement Strategies
164(7)
Acknowledgments
165(1)
References
165(6)
Optimizing the Parameters of the Gaussian Network Model for ATP-Binding Proteins
171(16)
Taner Z. Sen
Robert L. Jernigan
Introduction
171(1)
Methods
172(4)
Proteins
172(1)
Gaussian Network Model
173(2)
Spring Constants
175(1)
Correlation Coefficient
176(1)
Results
176(9)
Conformational Changes
176(1)
Pair Distribution Functions
177(1)
Correlations
178(1)
Correlation Coefficients at Different Cutoff Distances and Spring Constants
178(2)
Cases of Highest Correlations
180(1)
Mean-Square Fluctuation Predictions for the Cases That Show Highest Correlations
181(1)
Comparison of Fluctuations for Different Spring Constants
181(4)
Comparison of Fluctuations at Different Cutoff Distances
185(1)
Conclusion
185(2)
References
185(2)
Effects of Sequence, Cyclization, and Superhelical Stress on the Internal Motions of DNA
187(26)
Atsushi Matsumoto
Wilma K. Olson
Introduction
188(1)
Methodological Overview
189(4)
Molecular Representation
189(1)
DNA Force Field
190(1)
Kinetic Energy
191(1)
Normal Modes
192(1)
Imposed Superhelical Stress
192(1)
Dominant Modes
193(2)
Comparative Spectra
193(1)
Linear DNA
193(1)
Circular DNA
194(1)
Role of Intrinsic Structure
195(5)
Intrinsic Bending and Single-Molecule Stretching
195(2)
Intrinsic Curvature and DNA Ring Puckering
197(1)
Intrinsic Curvature and Enzyme Cutting Patterns
198(2)
Role of Sequence-Dependent Deformability
200(2)
Dimer Deformability and Large-Scale Anisotropy of Linear DNA
200(1)
Dimer Deformability and Rotational Positioning of Circular DNA
201(1)
Role of Conformational Coupling
202(4)
Roll-Slide Interdependence and Supercoiling of Circular DNA
202(2)
Twist-Rise Coupling and Overstretching of Linear DNA
204(2)
Summary
206(7)
Acknowledgments
207(1)
References
207(6)
Symmetry in Normal Mode Analysis of Icosahedral Viruses
213(20)
Herman W.T. van Vlijmen
Introduction
213(2)
Methods
215(4)
Theory
215(3)
Calculation Details
218(1)
Results
219(9)
(Dialanine)60
219(1)
Poliovirus
220(7)
Rhinovirus and CCMV
227(1)
Discussion
228(5)
Acknowledgments
230(1)
References
230(3)
Extension of the Normal Mode Concept: Principal Component Analysis, Jumping-Among-Minima Model, and Their Applications to Experimental Data Analysis
233(20)
Akio Kitao
Introduction
233(1)
Collective-Mode Description of Protein Dynamics
234(1)
Principal Component Analysis
235(3)
Langevin Mode
238(1)
Conservation and Convergence of Collective Variables
239(2)
Anharmonicity of Energy Landscape and JAM Model
241(2)
Application of JAM Concept
243(3)
Application of the Normal Mode Concept to the Dynamics Crystallographic Refinement
246(1)
Neutron Scattering
247(2)
Concluding Remarks
249(4)
References
249(4)
Imaginary-Frequency, Unstable Instantaneous Normal Modes, the Potential Energy Landscape, and Diffusion in Liquids
253(28)
T. Keyes
Introduction
254(2)
Unstable Modes and Diffusion
256(14)
Statistical Mechanics on the PEL
257(1)
The Partition Function and the Im --- ω Density of States
257(3)
The Composite Landscape
260(1)
The Functional Form of the Density of States
261(1)
The Escape Rate and D
262(4)
The Random Energy Model
266(1)
The Fraction of Unstable Frequencies, Dynamics, and Tc
267(2)
The Configurational Entropy Sc
269(1)
Diffusive and Nondiffusive Unstable Modes
270(5)
Potential Energy Profile Based Methods
271(1)
Landscape Based Methods
272(1)
Escape Modes
272(1)
Saddle Order
273(1)
Partial Minimization
273(2)
Summary and Conclusions
275(6)
Acknowledgments
276(1)
References
276(5)
Driven Molecular Dynamics for Normal Modes of Biomolecules without the Hessian, and Beyond
281(20)
Martina Kaledin
Alexey L. Kaledin
Alex Brown
Joel M. Bowman
Introduction
281(2)
Driven Molecular Dynamics
283(2)
Theory
283(2)
Computational Implementation
285(1)
Applications
285(11)
The Harmonic Limit: Trp-Cage
285(1)
The Driving Parameter λ
286(1)
Spectral Density and Resolution
286(2)
Atomic Fluctuations
288(2)
Correlation of Atomic Motion
290(1)
Entropy
291(1)
Beyond the Harmonic Limit: Dialanine
292(1)
Anharmonic Driving of Interatomic Distances
293(1)
Electric Dipole-Driven Dynamics
294(2)
Summary and Conclusions
296(5)
Acknowledgments
298(1)
References
298(3)
Probing Vibrational Energy Relaxation in Proteins Using Normal Modes
301(24)
Hiroshi Fujisaki
Lintao Bu
John E. Straub
Introduction
301(1)
Cytochrome c
302(1)
QCF Approach
303(6)
Fermi's Golden Rule
304(1)
Quantum Correction Factor
305(1)
NM Calculations for Cyt c
306(1)
Application to VER of the CD Bond in Cyt c
307(1)
Fluctuation of the CD Bond Frequency
308(1)
Reduced Model Approach
309(6)
Reduced Model for a Protein
310(1)
Maradudin-Fein Formula
311(1)
Third-Order Coupling Elements
312(1)
Width Parameter
313(2)
Temperature Dependence
315(1)
Discussion
315(3)
Comparison with Experiment
315(1)
Validity of Fermi's Golden Rule
316(1)
Higher-Order Coupling Terms
317(1)
Summary
318(7)
Acknowledgments
320(1)
References
320(5)
Anharmonic Decay of Vibrational States in Proteins
325(24)
Xin Yu
David M. Leitner
Introduction
325(3)
Computation of Vibrational Lifetimes
328(2)
Vibrational Energy Transfer in Proteins
330(9)
Cytochrome c
330(5)
Photoactive Yellow Protein
335(4)
Concluding Remarks
339(10)
Acknowledgments
341(1)
Appendix: Force Field for Chromophore
342(1)
References
343(6)
Collective Coordinate Approaches to Extended Conformational Sampling
349(18)
Michael Nilges
Roger Abseher
Introduction
349(1)
Extended Sampling Methods
350(9)
Principal Component Analysis
350(2)
Constraint Method
352(2)
Conformational Flooding
354(1)
Principal Component Restraints
354(5)
Applications
359(4)
Characterization of the Free Energy Surface Around the Native Structure
359(1)
Rapid Conformational Sampling
359(2)
Large Conformational Motions: Allosteric Transitions, Unfolding, Folding
361(2)
Conclusions
363(4)
Acknowledgments
363(1)
References
363(4)
Using Collective Coordinates to Guide Conformational Sampling in Atomic Simulations
367(22)
Haiyan Liu
Zhiyong Zhang
Jianbin He
Yunyu Shi
Introduction
368(2)
Biomolecular Simulations and Enhanced Conformation Sampling
368(1)
A Qualitative Picture of the Conformational Energy Landscape
368(1)
Objectives and Basic Strategies for Enhanced Conformation Sampling
369(1)
Using Collective Coordinates for Enhanced Conformation Sampling
370(2)
Collective Coordinate Descriptions of Protein Dynamics
370(1)
Enhanced Sampling Methods Employing Collective Coordinates
371(1)
The Amplified Collective Motion Method
372(6)
The Weak Coupling Method for Constant Temperature MD Simulations
372(1)
The ACM Scheme
373(2)
Using ANM to Guide Atomic Simulations in the ACM Scheme
375(1)
The Amplified Collective Motion-Assisted Minimum Escaping (ACM-AME) Scheme
376(2)
Examples
378(6)
Interdomain Motions of Bacteriophage T4 Lysozyme
378(2)
Folding of an S-Peptide Analog
380(3)
ACM-AME Sampling of Peptide Conformations
383(1)
Summary
384(5)
Acknowledgments
385(1)
References
385(4)
Index 389


Qiang Cui, Ivet Bahar
Biežāk uzdotie jautājumi par e-grāmatām Biežāk uzdotie jautājumi par e-grāmatām
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