Protein Bioinformatics: From Sequence to Function

Cover......Page 1
Half-title......Page 2
Praise from the Field......Page 3
Inside Cover......Page 4
ISBN-13: 9788131222973......Page 5
Dedication......Page 6
Foreword......Page 7
Preface......Page 9
Acknowledgments......Page 11
1.1.1 Amino acids......Page 12
1.1.2 Formation of peptide bonds......Page 14
1.2.1 Primary structure......Page 15
1.2.2 Secondary structure......Page 16
1.3.1 Fibrous proteins......Page 18
1.3.2 Classification of globular proteins......Page 19
1.4.1 Protein Information Resource......Page 20
1.4.2 SWISS-PROT and TrEMBL......Page 23
1.4.4 Other protein sequence databases......Page 25
1.5.1 Protein Data Bank......Page 27
1.5.2 Database for nonredundant PDB structures......Page 30
1.5.3 PDB-related databases......Page 32
1.5.4 Databases for structural classification of proteins......Page 33
1.6 Literature databases......Page 34
1.7 Exercises......Page 35
References......Page 37
2.1 Sequence alignment......Page 39
2.2.1 Basic Local Alignment Search Tool (BLAST)......Page 40
2.2.2 FASTA......Page 43
2.2.3 ClustalW......Page 44
2.2.4 PSI-BLAST......Page 46
2.2.7 Hidden Markov Models......Page 47
2.3.3 Total and average amino acid property......Page 49
2.3.5 Motifs......Page 51
2.3.6 Conservation score......Page 55
2.3.7 Nonredundant protein sequences......Page 56
2.4.1 alpha-helices......Page 58
2.4.2 beta-strands......Page 59
2.4.3 Hydrophobic moment for measuring amphipathicity......Page 61
2.5 Amino acid properties for sequence analysis......Page 62
2.6 Exercises......Page 66
References......Page 68
3.1 Assignment of secondary structures......Page 73
3.2 Computation of solvent accessibility......Page 74
3.2.2 Naccess......Page 76
3.2.4 DSSP......Page 77
3.3 Representation of solvent accessibility......Page 78
3.3.1 ASAView......Page 79
3.4.1 Residue–residue contacts in protein structures......Page 81
3.4.2 Variation of sequence separation for defining residue–residue contacts......Page 82
3.5 Amino acid clusters in protein structures......Page 83
3.6.1 Development of effective potentials......Page 84
3.6.4 Inter-residue contact potentials......Page 85
3.6.5 Potentials based on distance criteria......Page 87
3.7 Cation-pi interactions in protein structures......Page 88
3.9.1 Hydrophobic free energy......Page 90
3.9.3 Hydrogen bonding free energy......Page 93
3.9.5 Force fields for computing free energy terms......Page 94
3.10.1 Medium- and long-range contacts......Page 95
3.10.3 Surrounding hydrophobicity......Page 96
3.10.4 Accessible surface area and transfer free energy......Page 97
3.10.6 Flexibility......Page 98
3.11 Parameters for proteins......Page 99
3.11.3 Stabilization center......Page 100
3.11.4 Atom depth......Page 101
3.11.6 Structure-sequence relationship in disordered proteins......Page 102
3.12.1 DALI......Page 104
3.12.2 Combinatorial extension......Page 105
3.12.4 MATRAS......Page 106
3.13 Exercises......Page 107
References......Page 108
4.1 Φ-value analysis......Page 116
4.1.1 Experimental studies......Page 118
4.2 Folding nuclei and Φ-values......Page 124
4.3 Relationship between amino acid properties and Φ-values......Page 127
4.3.3 Exposed mutations......Page 128
4.4.1 Hydrophobic clusters......Page 129
4.4.3 Hydrophobic clusters and long-range contacts......Page 130
4.5 Kinetic database for proteins......Page 132
4.6 Prediction of protein folding rates......Page 133
4.6.1 Protein tertiary structure......Page 134
4.6.2 Amino acid properties and secondary structure......Page 137
4.6.4 Chain length......Page 138
4.6.5 Other parameters......Page 139
4.6.6 Amino acid sequence......Page 140
4.7 Relationship between Φ-values and folding rates......Page 144
4.8 Exercises......Page 146
References......Page 147
5.1 Protein structural class......Page 151
5.2 Secondary structure content......Page 154
5.3 Secondary structural regions......Page 155
5.3.1 Measures of accuracy......Page 156
5.3.2 Statistical analysis......Page 157
5.3.3 Sequence alignment......Page 161
5.3.4 Hydrophobicity profiles......Page 162
5.3.5 Neural network and alignment profiles......Page 163
5.3.6 Support vector machines......Page 166
5.4.1 Hydrophobicity profile method......Page 167
5.4.2 Positive-inside rule......Page 168
5.4.4 Statistical method......Page 169
5.4.6 Physicochemical parameters......Page 170
5.4.7 Dynamic programming......Page 171
5.4.8 Neural networks and multiple sequence alignments......Page 172
5.4.10 Joint method for transmembrane helix prediction......Page 173
5.5 Discrimination of transmembrane strand proteins......Page 174
5.5.1 Structure-based sequence alignment......Page 175
5.5.4 Statistical methods......Page 176
5.5.5 Nearest neighbor algorithm......Page 177
5.6 Identification of membrane-spanning beta-strand segments......Page 178
5.6.3 Hydrophobicity profiles......Page 180
5.6.6 Neural networks......Page 181
5.6.8 Radial basis function networks and PSSM profiles for predicting the numberof beta-strands and membrane-spanning segments......Page 182
5.7 Discrimination of disordered proteins and domains......Page 184
5.8 Solvent accessibility......Page 187
5.8.3 Machine learning......Page 188
5.8.7 NETASA......Page 189
5.8.8 Real Value ASA Prediction......Page 190
5.8.9 Neural network......Page 191
5.8.11 Support vector machines for real-value prediction......Page 192
5.9 Inter-residue contact prediction......Page 193
5.10 Protein tertiary structure prediction......Page 195
5.10.1 Comparative modeling......Page 196
5.10.2 Fold recognition......Page 197
5.10.3 New fold methods......Page 199
5.10.4 Ab initio protein structure prediction......Page 200
5.10.5 Modeling on the Web......Page 201
5.11 Exercises......Page 203
References......Page 205
6.1.1 Differential scanning calorimetry......Page 216
6.1.2 Calculation of thermodynamic functions......Page 217
6.2 Thermodynamic database for proteins and mutants......Page 218
6.2.2 Contents of ProTherm......Page 219
6.2.3 Search option and access to ProTherm......Page 222
6.2.4 Display and sorting options in ProTherm......Page 223
6.2.5 Tutorials and the usage of ProTherm......Page 224
6.3 Relative contribution of noncovalent interactionsto protein stability......Page 225
6.3.4 Prediction of protein stability......Page 226
6.4 Stability of thermophilic proteins......Page 227
6.4.1 Prokaryotic growth temperature database......Page 228
6.4.3 Sequence analysis......Page 229
6.4.4 Amino acid properties and protein stability......Page 230
6.4.5 Dipeptide composition and protein stability......Page 231
6.4.7 Electrostatic interactions......Page 232
6.4.10 Hydrophobic interactions......Page 233
6.4.12 Identifying the stabilizing residues in protein structures......Page 234
6.5.1 Amino acid properties......Page 237
6.5.2 Effective potentials......Page 240
6.5.3 Energy functions......Page 241
6.5.4 Machine learning techniques......Page 242
6.5.5 Average assignment method......Page 245
6.5.6 Human readable rules for understanding protein mutant stability......Page 246
6.6 Exercises......Page 247
References......Page 248
7.1.1 Databases for protein–protein interactions......Page 253
7.1.2 Structural analysis of protein–protein interactions......Page 260
7.1.4 Hydrogen bonds and salt bridges across protein–protein interfaces......Page 262
7.1.5 Prediction of binding sites in protein–protein complexes......Page 264
7.1.6 Energy-based approach for understanding the recognitionmechanism in protein–protein complexes......Page 266
7.1.7 Prediction of protein–protein interaction pairs......Page 269
7.2 Protein–DNA interactions......Page 272
7.2.1 Structural analysis on protein–DNA interactions......Page 273
7.2.2 DNA stiffness and protein–DNA binding specificity......Page 274
7.2.3 Inter- and intramolecular interactions in protein–DNA recognition......Page 275
7.2.4 Discrimination of DNA-binding proteins/domains and predictionof DNA-binding sites......Page 278
7.2.5 Databases for protein–DNA interactions......Page 281
7.3 Protein–RNA interactions......Page 284
7.3.1 Structural analysis of protein–RNA complexes......Page 286
7.3.2 Prediction of RNA-binding sites......Page 287
7.4.1 Prediction of ligand-binding sites......Page 288
7.4.2 Protein–ligand docking......Page 290
7.4.3 Estimation of protein–ligand binding free energy......Page 291
7.4.4 Validating ligand and active site residues in protein structures......Page 292
7.4.5 Protein-ligand database......Page 294
7.5 Quantitative structure activity relationshipin protein–ligand interactions......Page 295
7.6 Exercises......Page 298
References......Page 299
Appendix A......Page 309
Index......Page 318
Color Plates......Page 326