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Tables of Contents for Computational Molecular Biology
Chapter/Section Title
Page #
Page Count
Hybrid potentials for large molecular systems
1
34
P. Amara
M.J. Field
Introduction
1
4
Hybrid Potentials
5
6
Challenges
11
11
Treatment of covalent interactions at the QM/MM interface
12
6
Including MM polarization
18
2
Extending the QM region
20
2
Applications
22
6
Lactate and malate dehydrogenases
24
1
Acetylcholinesterase
25
1
Chorismate mutase
25
1
Carbonic anhydrase
25
1
Ni-Fe hydrogenase
26
1
Tyrosine phosphatase
26
1
HIV protease
27
1
Aspartylglucosaminidase and triosephosphate isomerase
28
1
Other systems
28
1
Conclusions
28
7
Proton transfer in models biomolecules, S. Scheiner
35
50
Introduction
35
2
Intrinsic proton transfer properties
37
3
Hydrogen bond length
40
8
Hydrogen bond flexibility
41
4
Asymmetric hydrogen bonds
45
3
Hydrogen bond angles
48
6
Intramolecular H-bonds
48
3
Intermolecular H-bonds
51
3
Reversals in relative pKa
54
3
Environmental effects
57
8
External ions
57
4
Surrounding dipoles
61
1
Polarizable dielectric medium
62
3
Very strong hydrogen bonds
65
20
Computational approaches to the studies of the interactions of nucleic acid bases
85
34
J. Sponer
P. Hobza
J. Leszczynski
Introduction
85
3
Historical overview of ab initio studies on nucleic acid base pairs
88
3
Methods
91
5
Levels of ab initio treatment of base pairs
91
1
Choice of basis set
92
1
Evaluation of interaction energies
93
2
Basis set superposition error
95
1
Geometry optimization
95
1
Results
96
17
Structures of H-bonded DNA base pairs
96
3
Energies of H-bonded DNA base pairs
99
3
Base stacking interactions
102
6
Interactions of amino groups of bases
108
1
Interactions of bases and base pairs with metal cations
109
4
Concluding remarks
113
6
Nucleic acid bases in solution
119
48
M. Orozco
E. Cubero
X. Barril
C. Colominas
F.J. Luque
The solvent
119
7
Computational approaches to solvation
126
13
Pure classical methods
128
8
Mixed methods
136
3
The effect of solvent on nucleic acid bases
139
20
The solvation of nucleic acid bases
139
2
The effect of solvent on the molecular geometry
141
4
Molecular topology
145
5
Reactive properties
150
5
Intermolecular interactions in nucleic acid bases
155
4
Conclusion
159
8
Current trends in modeling interactions of DNA fragments with polar solvents
167
44
L. Gorb
J. Leszczynski
Introduction
167
2
Continuum models of solvation
169
8
The family of PCM models
169
1
The family of SCRF models
170
2
The dispersion forces
172
2
The cavitation forces
174
1
SMx family of solvation models
175
2
Supermolecular approximation
177
1
The hydration of the prototypic molecules
177
6
The hydration of heterocycles---parent compounds of DNA bases
183
5
Hydration of the DNA bases
188
12
Structural parameters of the monohydrated DNA bases
188
5
Structural parameters of the polyhydrated DNA bases
193
1
Relative stability
194
3
Intramolecular proton transfer
197
3
Hydration of DNA base pairs
200
4
Conclusion
204
7
Radiation-induced DNA damage and repair: An approach from ab initio MO method
211
34
M. Aida
M. Kaneko
M. Dupuis
Introduction
211
3
Structures of pyrimidine dimers
214
2
Characteristics of thymine dimer
216
4
Methods
216
1
Ionization potential of T<>T
216
2
Structural characteristics of T<>T and T<>(•+)
218
2
Fragmentation mechanism of T<>T(•+)
220
11
Methods
220
1
Structure of thymine dimer radical cation at CAS(3e+4o)
221
1
Fragmentation pathway
222
4
Initial thymine dimer radical cation
226
1
Structural change and spin distribution change along the fragmentation path
227
1
Comparison with the case of (C2H4)2 •+ complex
228
1
Comparison with experiments
229
1
T<>T(•+) dissociation in DNA
229
2
Other pyrimidine dimers
231
10
Methods
231
1
Structural and electronical characteristics of pyrimidine dimers
231
10
Conclusion
241
4
Application of molecular orbital theory to elucidation of radical processes induced by radiation damage to DNA
245
34
A.-O. Colson
M.D. Sevilla
Background
245
2
Role of theory
247
1
Individual DNA bases
247
4
DNA base ionization potentials
248
2
DNA base electron affinities
250
1
Base pairs
251
2
Hydrogen bonding
251
1
Proton transfer processes in neutral and ion radical base pairs
252
1
Base pair ionization potentials
253
1
Base pair electron affinities
253
1
Base pair stacking
253
2
Effect of waters of hydration
255
3
Solvation effects on ionization potentials
255
3
Solvation effects on electron affinities
258
1
Sugar-phosphate backbone
258
3
Phosphate radicals in DNA
258
1
Deoxyribose radicals in DNA
259
1
Ionization potentials of base, deoxyribose and phosphate portions of DNA
260
1
DNA base H• and •OH adduct radicals
261
9
Electron affinities of neural adduct radicals
262
3
Ionization potentials of neural adduct radicals
265
1
Redox potentials of neural adduct radicals
265
1
Energetics of radical reactions initiated by radiolytic damage to DNA
266
2
Structural features of base adduct radicals
268
2
Radioprotection
270
9
Methyl mercaptan and cysteamine
270
9
Exploring the structural repertoire of Guanine-rich DNA sequences: Computer modelling studies
279
46
M. Bansal
M. Ravikiran
S. Chowdhury
Introduction
279
2
Guanine rich triple helical structures
281
17
Model building of d(C)12 •d(G)12 triple helices
284
1
Protocol for molecular dynamics of (C)12 •d(G)12 *d(G)12 triple helices
285
1
Structural parameters for (C)12 •d(G)12 *d(G)12 triple helices
286
3
Analysis of structural variability in (C)12 *d(G)12 *d(G)12 triplexes
289
9
Parallel and folded back quadruplex structures
298
19
Protocol for molecular dynamics of d(G)7 quadruplex structures
301
1
Structural analysis of d(G)7 parallel quadruplex structures
302
15
Conclusions
317
8
Third strand can be in either orientation in (C)12 *d(G)12*d(G)12 triplex
317
1
Intercalated ions make the G-quadruplex structure rigid and stable
318
7
The calculation of relative binding thermodynamics of molecular associations in aqueous environments
325
44
G.J. Tawa
I.A. Topol
S.K. Burt
Introduction
326
6
Theory
332
6
Fundamental statistical mechanical derivation of the relative binding free energy
332
3
Special considerations regarding ligands binding to HIV-1 protease
335
3
Computational protocol
338
6
The relative binding free energies of peptidic inhibitors to HIV-1 protease and its 184V mutant
344
7
Protonation states of the ASP 25, 125 dyad
344
1
The thermodynamics of binding
345
6
Concluding remarks
351
18
Theoretical tools for analysis and modelling electrostatic effects in biomolecules
369
28
W.A. Sokalski
P. Kedzierski
J. Grembecka
P. Dziekonski
K. Strasburger
Introduction
369
1
Methods
370
11
Hybrid variation-perturbation decomposition of SCF interaction energy
370
4
Electrostatic interactions
374
5
Differential transition state/product stabilization approach
379
2
Applications
381
10
Nonempirical analysis of pKa shifts in mutated subtilisines
381
1
Physical nature of the solvent induced proton transfer
382
1
Analysis of reactant interactions in ribonuclease A active site
383
1
Electrostatic nature of catalytic activity in aminoacyl t-RNA synthetases
384
3
Electrostatic nature of inhibitor binding in leucine aminopeptidase
387
4
Conclusions
391
6
Application of reduced models to protein structure prediction
397
44
J. Skolnick
A. Kolinski
A.R. Ortiz
Introduction
397
7
Energy functions and search protocols
398
1
Protein representation
398
2
Use of simplified models to obtain general insights into protein folding
400
1
Threading approaches to tertiary structure prediction
401
1
Exact restraint models of proteins
402
1
Restraint free ab initio protein folding
402
1
Evolutionary-based approaches to protein structure prediction
403
1
Exact restraint models
404
11
Secondary and tertiary restraints in assembly of protein structures
404
2
Models with exact secondary structure but no tertiary restraints
406
3
Models with exact but loose secondary structure and tertiary restraints
409
5
How can these approaches be integrated with experiment
414
1
Tertiary structure predictions by ab initio model building
415
11
Predictions by restraint free folding
415
3
Prediction by restraint driven folding: Evolutionary based approaches
418
8
Limitations and outlook
426
1
What is the requisite resolution of predicted structures?
426
1
Techniques for low to high resolution modelling
427
2
Role of structure prediction in the genomics revolution
429
1
Outlook
430
11
Modelling DNA-protein interactions
441
44
K. Zakrzewska
R. Lavery
The first steps
441
1
Analysing protein-DNA recognition
442
20
Geometry
445
3
Electrostatics
448
4
Thermodynamics
452
10
Molecular mechanics and dynamics simulations
462
13
Transcription factors
463
1
Hormone receptors
464
4
Minor groove binding proteins
468
4
Larger scale modelling
472
3
Protein-DNA docking
475
3
The next steps
478
7
Interactions of small molecules and peptides with membranes
485
52
A. Pohorille
M.A. Wilson
C. Chipot
M.H. New
K. Schwieghofer
Introduction
485
3
Approach
488
6
Transport of small solutes and ions across membrane interfaces
494
13
Small, neutral solutes in membranes
495
7
Unassisted transport of ions across membranes
502
5
Interactions of peptides and membranes
507
15
Peptides at aqueous interfaces
507
6
Peptides in membranes
513
4
Simulations of transmembrane channels
517
5
Hydration forces
522
4
Conclusions and future directions
526
11
Modeling of antifreeze proteins
537
32
J.D. Madura
A. Wierzbicki
Introduction
537
2
Modeling AFPS on ice
539
13
Winter Flounder on the (201)
539
1
Shorthorn Sculpin on the (2-1 0)
540
8
Sea Raven on the (111)
548
2
Ocean Eel Pout on the (100)
550
2
Simulations of AFPS with explicit water
552
4
Shorthorn Sculpin in a rectangular box
552
2
Sea Raven in truncated Octahedron
554
1
Ocean Eel Pout in a periodic box
555
1
Simulations of AFPS in a continuum
556
7
Shorthorn Sculpin
557
3
Ocean Eel Pout
560
3
Simulations of the Winter Flounder at the ice/water interface
563
2
Summary
565
4
The role of computational techniques in retrometabolic drug design strategies
569
50
N. Bodor
P. Buchwald
M.-J. Huang
Introduction
569
1
Principles of retrometabolic drug design
570
2
Predicting properties
572
10
Molecular size
573
2
Octanol-water partition coefficient
575
6
Water solubility
581
1
Soft drugs
582
10
Soft anticholinergics
584
4
Soft β-blockers
588
4
Computer-aided design
592
10
Structure generation
593
1
Ranking
594
2
Illustration of computer-aided soft drug design
596
6
Chemical delivery systems
602
11
Brain-targeting chemical delivery systems
602
3
Predicting partition properties
605
1
Cyclodextrin complexes
606
7
Conclusions
613
6
Computational aspects of neural membrane biophysics
619
20
R. Wallace
Introduction
619
2
Algorithmic complexity and the principles of molecular computing
621
5
Linear superposition permits massive parallelism
623
1
Transduction and amplification require macroscopic-microscopic informational state-space mapping
624
1
Memory is constrained by quantum recurrence
625
1
Membrane studies in cell biology
626
2
Hydrophobic mismatch: a candidate mechanism for neuromolecular computing
628
1
Hydrophobic mismatch and molecular computation
629
1
Genetic regulation of neuromolecular computing
630
1
Potential experiments in neuromolecular computation
631
2
Conclusion
633
6
Index
639