DeutschesFachbuch.de : Structural Approaches to Sequence Evolution Molecules, Networks, Populations

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Contents
Part I Molecules: Proteins and RNA
1 Modeling Conformational Flexibility and Evolution of Structure: RNA as an ...
P.Schuster and P.F. Stadler 3
1.1 Definition and Computation of RNA Structures 3
1.1.1 RNA Secondary Structures 4
1.1.2 Compatibility of Sequences and Structures 8
1.1.3 Sequence Space, Shape Space, and Conformation Space 11
1.1.4 Computation of RNA Secondary Structures 14
1.1.5 Mapping Sequences into Structures 15
1.1.6 Suboptimal Structures and Partition Functions 18
1.2 Design of RNA Structures 19
1.2.1 Inverse Folding 19
1.2.2 Multiconformational RNAs 20
1.2.3 Riboswitches 22
1.3 Processes in Conformation, Sequence, and Shape Space 23
1.3.1 Kinetic Folding 23
1.3.2 Evolutionary Optimization 25
1.3.3 Evolution of Noncoding RNAs 30
References 32
2 Gene 3 D and Understanding Proteome Evolution
J.G.Ranea, C. Yeats, R. Marsden, and C. Orengo 37
2.1 Protein Family Clustering 42
2.1.1 SYSTERS 42
2.1.2 Proto-Net 42
2.1.3 ADDA 42
2.1.4 ProDom 43
2.2 The PFscape Method 43
2.3 The NewFams 44
2.4 Describing the Proteome 45
2.5 Superfamily Evolution and Genome Complexity 46
2.6 Superfamily Evolution and Functional Relationships 48
2.7 Limits to Genome Complexity in Prokaryotes 50
2.8 The Bacterial Factory 52
2.9 Conclusions 53
References 54
3 The Evolution of the Globins: We Thought We Understood It
A.M.Lesk 57
3.1 Introduction 58
3.2 Coordinates and Calculations 59
3.3 Results 59
3.3.1 Description of Secondary and Tertiary Structure of Full-Length (~ 150-...
3.3.2 Description of Secondary and Tertiary Structure of Truncated Globins 60
3.3.3 Alignment 60
3.4 Helix Contacts 62
3.4.1 Geometry of Inter-Helix Contacts 62
3.4.2 Pairs of Helices Making Contacts 63
3.4.3 Structures of Helix Interfaces in Truncated Globins, Compared to Those...
3.4.4 The B/G Interface 65
3.4.5 The A/H Interface 66
3.4.6 The B/E Interface 67
3.5 Patterns of Residue-Residue Contacts at Helix Interfaces 68
3.5.1 The G/H Interface 69
3.6 Haem Contacts 72
3.7 The Tunnel 72
3.8 Conclusions 72
References 73
4 The Structurally Constrained Neutral Model of Protein Evolution
U.Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo 75
4.1 Aspects of Population Genetics 76
4.1.1 Population Size and Mutation Rate 76
4.1.2 Natural Selection 77
4.1.3 Mutant Spectrum 78
4.1.4 Neutral Substitutions 80
4.1.5 Beyond the Small M μ Regime: Neutral Networks 81
4.2 Structural Aspects of Molecular Evolution 83
4.2.1 Neutral Theory and Protein Folding Thermodynamics 83
4.2.2 Structural Conservation and Functional Changes in Protein Evolution 84
4.2.3 Models of Molecular Evolution with Structural Conservation 85
4.3 The SCN Model of Evolution 87
4.3.1 Representation of Protein Structures 88
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Index
AACNUC, 207-231
adaptation, 299, 301, 304, 327, 334, 345
adaptive landscape, 299
ADDA, 42
adjacency matrix, 6, 19, 326
amino acid, 220-231
- composition, 157
antigenic drift, 346
antiviral drugs, 346
archea, 39
AT content, 153-158
Bbacteriocyte, 149-150
Baumannia cicadellinicola, 149-162
Bayesian inference, 170, 185
beta distribution, 186, 187
binding cooperativity, 279, 280
binomial distribution, 184
blind-ant regime, 76, 77, 82
Blochmannia floridanus, 149-162
breakpoint distances, 160
Buchnera aphidicola, 149-162
Ccapside, 341
Carsonella ruddii, 149-162
CATH, 37, 41
- domains, 41
cellular computation, 130
chaperones, 158
chemokines, 197
chromosomal rearrangements, 153-162
CLUSTAL format, 214
codon, 221-231
- usage, 231
- usage bias, 153, 156
combinatorics, 4, 20
commensalism, 149
compatibility, 8, 10, 12, 20, 21
compensatory substitutions, 293
conjugate prior distribution, 186
consensus sequence, 310, 344
cooption, 295, 296
correspondence analysis, 225
CRAN, 207-231
DDALI, 65
data storage medium, 129
databases, 207-231
defective genomes, 353
delta method, 172-175
designability, 104
detailed balance, 78, 107, 273
disintegration rate, 159
distance-based method, 178, 179, 181, 184
divergence
- expression, 235, 240, 241, 243, 246, 247
- sequence, 236, 246, 247
DNA, 207-231
- loss, 158-159
- methylation, 185
- uptake, 159
dot chart, 222
dynamic programming, 264
Eelectrophoresis, 288
EMBL, 207-231
endocytobiosis, 149
endosymbiosis, 149
environments
- simple vs diverse, 292
epistasis, 299, 314-316, 325
equilibrium frequencies, 172, 174
equilog, 116
error threshold, 299, 307-310, 312-320, 323, 324, 327, 334-336, 350, 351, 353
evolution
- convergent, 113-124
- divergent, 113-124
evolutionary trajectory, 91, 93, 328, 330-332
- correlations, 91, 93- fluctuations, 91, 93 expression
- conservation, 250
- divergence, 235, 240, 241, 243, 246, 247
- natural selection, 248
- neutral changes, 247, 248
- probe-to-gene mapping, 241, 242
- level, 243
- clustering, 245, 246
- pattern, 235
- polymorphism, 249
- profile, 244
extinction, 348, 352
FFASTA format, 213-231
Fast-ME, 178, 184
Fibonacci numbers, 22
Fisher's model, 294
Fitch-Margoliash, 178, 184 fitness, 236, 238, 239, 246, 247, 300, 301, 303, 306, 308,...
- landscape, 299-301, 303, 304, 306-308, 310, 311, 313-317, 319, 321-328, 332-336, 34...
- Malthusian, 300, 303, 316, 317, 321, 323, 324, 332-334
- step-wise increase, 327, 328, 335
- Wrightian, 301, 303, 306, 308, 314-317, 321, 322, 324 fixation, 76
- probability, 77, 291
FM criterion, 178-180, 185
foot and mouth disease virus, 352-359
frequency distribution of the fitness effects, 293 functional
- annotation, 113-122
- conservation, 84 functional flexibility score, 118
Ggamma-distributed rates, 180
GC content, 153-158
GenBank, 207-231
gene
- duplication, 31, 32, 191, 193
- inactivation, 155-163
- interaction, 254, 280
- loss, 158
- networks, 280
- ontology, 118
- regulation, 253, 254, 259, 260, 263-271, 273-280
- Bayesian model, 263-265, 277
- binding cooperativity, 279, 280
- evolution, 266-271, 273-276
- evolutionary equilibria, 270, 271, 274, 276
- evolvability, 260
- neutral evolution, 273
- programmability, 260
- score-fitness relation, 274
- selection, 275
Gene 3 D, 37, 41
genealogy, 27
genetic
- background effects, 296
- code, 211, 231
- distance, 170-172, 174, 176, 178, 180
- diversity, 343
- drift, 299, 328, 335, 343
- load, 287
- regulatory network, 286
- bottom-up evolution, 295
genome
- changes, 162
- complexity, 294
- evolution, 135, 136- formatting, 131- rearrangement rates, 160- reduction, 158-163
- segment reassort ment, 343, 344
- stasis, 160
genotype-phenotype map, 301, 322
globins, 57
- secondary and tertiary structure, 59
Hhaem group, 59
haemoglobin, 57
Hamming distance, 302, 344
homolog, 32
- identification, 236
horizontal gene transfer, 159, 160
human immunodeficiency virus, 343-359
hypermutation, 342, 353
Iidentification
- ortholog, 236
immune enhancement, 350
- cross-immunity, 348, 349
- strain-trascending immunity, 349
indel bias, 159
influenza, 344-359
informative site, 181, 182
insertion sequence, 163
interaction systems, 287
interactivity parameters, 98
intersection theorem, 21, 22
inversion distances, 160
Ising model, 304, 306, 307, 309, 314
JJC 69 model, 171, 174, 183
KK 80 model, 173, 174
Llattice structure graph, 119
likelihood, 169, 170, 177, 178, 181-189
long-branch
- attraction, 180, 182
- repulsion, 180
LS criterion, 180
lupin leghaemoglobin, 68
MMarkov chain, 171, 176, 186
MASE format, 214
master sequence, 310, 312-316, 318-320, 323, 332, 333, 344
matching, 6, 8, 15, 19, 21
ME criterion, 179, 180
metazoa, 58
methylation, 185
mobile genetic elements, 131, 136
modular structures, 285, 287
molecular
- clock, 75, 287, 288
- phylogenetics, 169, 170, 176, 187
monomorphic site, 181
MSF format, 214
Muller's ratchet, 156, 336, 355, 358
multidomain, 38, 39
multigene families, 191
multiple hits, 170
multivariate analyses, 225-231
mutagenesis, 351
- lethal, 352
mutant spectrum, 78, 344
- advantageous mutations, 78
- nearly neutral mutations, 78, 79
- neutral mutations, 78-80
- strongly deleterious mutations, 78
mutation, 76, 343
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