Protein-protein and domain-domain interactions:
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Singapore
Springer
[2018]
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xix, 207 Seiten Illustrationen, Diagramme |
| ISBN: | 9789811073465 9789811339424 |
Internformat
MARC
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| 020 | |a 9789811073465 |c Hardcover |9 978-981-10-7346-5 | ||
| 020 | |a 9789811339424 |c Softcover |9 978-981-13-3942-4 | ||
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| 100 | 1 | |a Kangueane, Pandjassarame |e Verfasser |0 (DE-588)1155849892 |4 aut | |
| 245 | 1 | 0 | |a Protein-protein and domain-domain interactions |c Pandjassarame Kangueane, Christina Nilofer |
| 264 | 1 | |a Singapore |b Springer |c [2018] | |
| 300 | |a xix, 207 Seiten |b Illustrationen, Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 0 | 7 | |a Wechselwirkung |0 (DE-588)4064937-4 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Protein-Protein-Wechselwirkung |0 (DE-588)4745193-2 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Domäne |g Biochemie |0 (DE-588)4582302-9 |2 gnd |9 rswk-swf |
| 653 | |a Protein-protein interactions | ||
| 653 | |a domain-domain interactions | ||
| 653 | |a gene fusion | ||
| 653 | |a Protein complexes | ||
| 653 | |a Drug discovery | ||
| 653 | |a Vaccine development | ||
| 689 | 0 | 0 | |a Protein-Protein-Wechselwirkung |0 (DE-588)4745193-2 |D s |
| 689 | 0 | |5 DE-604 | |
| 689 | 1 | 0 | |a Domäne |g Biochemie |0 (DE-588)4582302-9 |D s |
| 689 | 1 | 1 | |a Wechselwirkung |0 (DE-588)4064937-4 |D s |
| 689 | 1 | |5 DE-604 | |
| 700 | 1 | |a Nilofer, Christina |e Verfasser |0 (DE-588)1155850165 |4 aut | |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe |z 978-981-10-7347-2 |
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-030301782 | ||
Datensatz im Suchindex
| _version_ | 1804178468132356096 |
|---|---|
| adam_text | Contents
1 Introduction 1
1 1 Proteins 1
1 2 Covalent Bond and Bond Length 1
1 3 Disulfide Bond 1
1 4 Protein Structure Representation 1
1 5 Structural Motifs 3
1 6 Protein Surface and Core 4
1 7 Central Dogma of Molecular Biology 8
1 8 Types of Proteins 8
1 9 Multi-domain Protein 8
1 10 Accessible Surface Area (ASA) 8
1 11 Protein-Protein Interface 10
1 12 Interface Area 11
1 13 Van Der Waals (vdW) Interactions 11
1 14 Hydrogen Bonds 11
1 15 Salt Bridges 12
Exercises 13
References 14
2 Protein-Protein Binding 15
2 1 Molecular Functions of Protein Complexes 15
2 2 Homodimer Protein Complex 20
2 3 Heterodimer Protein Complex 20
2 4 Interface Hydrogen Bonds 20
2 5 Interface Salt Bridges 20
2 6 Interface Peptide Segment 20
2 7 Principles of Protein-Protein Binding 23
Exercises 32
References 32
3 Low-Resolution Protein Complexes 35
3 1 Protein Complexes 35
3 2 Protein Hetero Complexes 35
321 AB Dimer Protein Complex 37
322 A2B Trimer Protein Complex 37
xi
xii Contents
323 ABC Trimer Protein Complex 37
324 ABCD Tetramer Protein Complex 37
325 A2B2 Tetramer Protein Complex 42
326 A3B3 Hexamer Protein Complex 42
327 A2B2C2 Hexamer Protein Complex 45
3 3 Protein Homo Complexes 48
331 A2 Homodimer Protein Complex 49
332 A3 Homo Trimer Protein Complex 49
333 A4 Homo Tetramer Protein Complex 49
334 A5 Homo Pentamer Protein Complex 51
335 A6 Homo Hexamer Protein Complex 51
336 A8 Homo Octamer Protein Complex 53
337 A12 Homo Dodecamer Protein Complex 53
Exercises 53
References 54
4 Heterodimer Protein Complexes 55
4 1 Heterodimer Protein Complex 55
4 2 Interface Size 55
4 3 Interface Area and Interface Size 55
4 4 Inter-residue Analysis of Complexes 57
4 5 Nonpolar and Polar Interfaces 57
4 6 Protein Complexes and Molecular Function 57
4 7 Nonpolar and Polar Interfaces with Known Molecular Function 59
4 8 Interface Size, Energy, and Function 59
4 9 vdW, Interface Size, and Function 62
4 10 Hydrogen Bonds, Interface Size, and Function 62
4 11 Electrostatics, Interface Size, and Function 65
4 12 Conclusion 67
Exercises 68
References 68
5 Homo Multimer Protein Complexes 69
5 1 Creation of Homo Multimer Protein Complex Dataset 69
5 2 Distribution of Homo Multimer Protein Complexes 69
5 3 Homo Trimer Protein Complexes 69
5 4 Homo Tetramer Protein Complexes 70
5 5 Homo Pentamer Protein Complexes 70
5 6 Homo Hexamer Protein Complexes 76
5 7 Homo Octamer Protein Complexes 76
5 8 Homo Dodecamer Protein Complexes 77
Exercises 77
References 78
Contents
xiii
6 Hetero Multimer Protein Complexes 79
6 1 Creation of Hetero Multimer Protein Complex Dataset 79
6 2 Distribution of Hetero Multimer Protein Complexes 79
6 3 ABC Hetero Trimer Protein Complex 79
6 4 A2B Hetero Trimer Protein Complex 82
6 5 ABCD Hetero Tetramer Protein Complex 82
6 6 A2B2 Hetero Tetramer Protein Complex 82
6 7 A3B3 Hetero Hexamer Protein Complex 84
6 8 A2B2C2 Hetero Hexamer Protein Complex 84
Exercises 86
References 86
7 Hot Spots at the Protein-Protein Interface 87
7 1 Interface Hot Spots 87
7 2 Alanine-Scanning Energetics Database (ASEdb) 87
7 3 Interatomic Interface Interaction 87
7 4 Favorable and Unfavorable Contacts 88
7 5 Databases for Interface Hot Spots 91
7 6 Interface Hot Spot Prediction 91
Exercises 91
References 92
8 Principles of Protein-Protein Interaction 93
8 1 Protein Size, Shape, and Complementation 93
8 2 Protein-Protein Interfaces 93
8 3 Interface, Surface, and Core in Complexes 93
8 4 Protein-Protein Interface Features 96
8 5 Interface Size 96
8 6 Interface Hydrophobic Effects 96
8 7 Hydrophobic Interface 100
8 8 Hydrophilic Interface 100
8 9 Interface Residues in Homo and Hetero dimer 101
8 10 Interface Side Chain-Side Chain Interaction 101
8 11 Interface Hot Spots 102
8 12 Interface Hydrogen Bonds and Salt Bridges 102
8 13 Interface Binding Energy 102
8 14 Interface Van Der Waals (vdW) 103
8 15 Interface Hydrogen Bonds 104
8 16 Interface Electrostatics 105
8 17 Gene Fusion and Fusion Protein 105
8 18 Conclusion 109
Exercises 110
References Ill
xiv Contents
9 Databases for Protein-Protein Interaction 113
9 1 PPI Databases 113
9 2 General PPI Database 113
921 DIP 113
922 MINT 113
923 IntAct 114
924 ChiTaRS 3 1 114
925 xComb 114
926 ANCHOR 115
927 ADAN 115
928 2P2Idbv2 115
929 Interpare 117
9 2 10 Death Domain DB 117
9 2 11 PDZbase 117
9 2 12 InterDom 117
9 2 13 PARPs 117
9 2 14 PCRPi-DB (Presaging Critical Residues
in Protein Interfaces Database) 118
9 3 PPI Repositories for Model Organisms 118
931 MIPS 118
932 SpirPro 118
933 HAPPI (Human Annotated and Predicted
Protein Interaction) 118
934 AraPPISite 118
935 PPIM (Protein-Protein Interaction Database for Maize) 118
936 FPPI {Fusarium graminearum Protein-Protein
Interaction) 118
937 SPIDer {Saccharomyces Protein-Protein
Interaction Database) 119
938 PCPPI {Penicillium-Crop Protein-Protein
Interactions) 119
939 HPID (Human Protein Interaction Database) 119
9 3 10 I2D (Interologous Interaction Database) 119
9 3 11 HPRD (Human Protein Reference Database) 119
9 3 12 OPHID (Online Predicted Human Interaction
Database) 119
9 3 13 PIPs (Human Protein-Protein Interaction Prediction) 119
9 3 14 HitPredict 119
9 4 PPI Network Databases 120
941 BIND (Biomolecular Interaction Network Database) 120
942 TRIP Database 2 0 (Transient Receptor Potential
Channel-Interacting Protein) 120
943 STRING 7 120
944 IntNetDB (Integrated Network Database) 120
945 PRIMOS (Protein Interaction and Molecule Search) 120
946 IsoBase 120
Contents
xv
947 ComPPI (Compartment-Specific Database
for Protein-Protein Interaction) 121
9 5 Structural Data for PPI 121
951 SNAPPI-DB (Structures, iNterfaces and Alignments
for Protein-Protein Interactions-Database) 121
952 SCOPPI (Structural Classification of Protein-Protein
Interfaces) 121
953 3did (3D Interacting Domains) 121
954 PIBASE 121
955 ProtCom (PROTein COMplexes) 122
956 JET2 Viewer 122
9 6 PPI in Pathways 122
961 KEGG (Kyoto Encyclopedia of Genes and Genomes 122
Exercises 122
References 123
10 Homodimer Protein Folding and Binding 125
10 1 Homodimer Folding Mechanisms 125
10 2 Homodimer Structures 126
10 2 1 2S Homodimer Protein Complexes 126
10 2 2 3SMI Homodimer Protein Complexes 126
10 2 3 3SDI Homodimer Protein Complexes 126
10 3 Interface Area to Monomer Size Among 2S and 3S Structures 126
10 4 Ratio of Interface to Monomer Protein Size 128
10 5 Large, Medium, and Small Interfaces 128
Exercises 128
References 132
11 Protein Subunit-Subunit to Domain-Domain Interactions 133
11 1 Fusion Protein or Rosetta Stone 133
11 2 HisH-HisF Interface 133
11 3 DNA Gyrase A and B Interface 134
11 4 Acetate CoA Transferase a and ß Interface 134
11 5 DNA pol III a and e Interface 137
11 6 Glutamyl Phosphate Reductase-Glutamate Kinase Interface 141
11 7 His2-His 10 Interface 141
11 8 Conclusion 141
Exercises 141
References 142
12 Domain-Domain Interactions 143
12 1 Chimeric Protein with Dimer-Dimer Interface 143
12 2 Domain-Domain Interaction (DDI) Databases 143
12 3 Domain-Domain Interactions and Networks 143
12 4 Domain-Domain Interaction Analysis 144
12 5 Prediction of Domain-Domain Interaction 144
Exercises 145
References 145
XVI
Contents
13 Protein-Protein Interaction Tools 147
13 1 PPI Tools for Protein 147
13 2 PPI Prediction Tools 147
13 2 1 BindML+ 147
13 2 2 PIC (Protein Interactions Calculator) 147
13 23M APPIS (Multiple Alignment of Protein-Protein
Interfaces) 149
13 2 4 HotPOINT (Hot Spot Prediction Server for Protein
Interfaces) 149
13 2 5 PSOPIA (Prediction Server of Protein-Protein
Interactions) 151
13 2 6 APID (Agile Protein Interaction DataAnalyzer) 151
13 2 7 PROTORP (Protein-Protein Interaction
Analysis Server) 151
13 2 8 iFrag 151
13 2 9 Interactome3D 153
13 2 10 PRED_PPI (Predicting Protein-Protein Interaction) 153
13 2 11 PCRPi-W (Presaging Critical Residues
in Protein Interfaces-Web Server) 153
13 2 12 PPCheck 153
13 3 Tool for Predicting PPI Binding Sites 153
13 3 1 Meta-PPISP 153
13 3 2 BindML 153
13 3 3 Sppider (Solvent Accessibility-Based Protein-Protein
Interface Identification and Recognition) 154
13 3 4 InterProSurf 154
13 4 Tools for PPI Analysis in Model Organism 154
13 4 1 TRI_tool (Transcriptional Regulation Interactions) 154
13 4 2 HIVsemi 154
13 4 3 ChiPPI (Chimeric Protein-Protein Interaction) 154
13 4 4 HIPPIE (Human Integrated Protein-Protein
Interaction Reference) 154
13 4 5 InteroPORC (Interaction and Clusters
of Orthologous Proteins) 155
13 5 Tools for Structure-Based PPI Prediction 155
13 5 1 PrISE (Prediction of Protein-Protein Interface
Residues Using Structural Elements) 155
13 5 2 InterPreTS (Interaction Prediction Through Tertiary
Structure) 155
13 5 3 iLoops 155
13 5 4 Struct2Net 155
13 5 5 PRISM 2 0 (Protein Interactions by Structural
Matching 2 0) 155
13 5 6 SAPIN (Structural Analysis of Protein Interaction
Networks) 156
Contents xvii
13 6 Tools for Predicting PPI Networks 156
13 6 1 PPI Spider 156
13 6 2 Path2PPI 156
13 6 3 POINeT 156
13 6 4 MyProteinNet 156
13 6 5 RedNemo (Repeated Diffusion with Neighborhood
Modifications) 156
13 7 Other PPI-Related Tools 157
13 7 1 FunFold2 157
13 7 2 Ligplot+ 157
13 7 3 Ligplot 157
13 7 4 Pepsite 157
13 7 5 PPIMpred (Prediction of Protein-Protein Interaction
Modulators) 157
13 8 Conclusion 157
Exercises 158
References 158
14 Protein-Protein Docking: Methods and Tools 161
14 1 Protein-Protein Docking 161
14 2 CAPRI 161
14 3 CAPRI Validated Models and Tools 161
14 3 1 ClusPro 162
14 3 2 PatchDock and SymmDock 162
14 3 3 GRAMM-X 162
14 3 4 PIPER 162
14 3 5 RosettaDock 164
14 3 6 FoXSDock 164
14 3 7 SwarmDock 164
14 3 8 pyDockWEB 164
14 3 9 HADDOCK 164
14 3 10 HDOCK 164
14 4 CAPRI Non-validated Models and Tools 164
14 4 1 CombDock (Combinatorial Docking) 166
14 4 2 FireDock (Fast Interaction Refinement) 166
14 4 3 FibreDock (Flexible Induced-Fit Backbone
Refinement) 166
14 4 4 HexServer 166
14 4 5 F2Dock (Fast Fourier Docking) 166
14 4 6 MEGADOCK 166
14 4 7 ZDOCK 166
14 4 8 FRODOCK (Fast Rotational Docking) 167
14 4 9 PRODIGY (Protein Binding Energy Prediction) 167
Exercises 167
References 167
xviii
Contents
15 HLA-Peptide Interaction to Short Peptide Vaccine Design 169
15 1 Short Peptide Vaccine Design 169
15 2 HLA Polymorphism 169
15 3 Functional HLA Informatics 170
15 4 HLA-Peptide Interaction 173
15 5 HLA-Peptide Binding Prediction 175
15 6 HLA Super-Types 176
Exercises 176
References 178
16 Protein-Protein Interfaces and Diseases 179
16 1 Cholera Toxin (CT) Structural Complex 179
16 2 CTB Interfaces in Cholera Toxin 179
16 3 Interface Representation in Cholera Toxin 179
16 4 Mutations in Cholera Toxin Structures 182
16 5 Interface Mutations in Cholera Toxin 183
16 6 HIV-1/GP160 (GP120/GP40) Trimer ENV Spike Complex 183
Exercises 187
References 187
17 Patented Protein Structural Complexes in Discovery Platform 189
17 1 Patented Protein Complexes 189
17 2 Selection of Patented Protein Complex Structures 189
17 3 Breast Cancer-Associated BCAT Complexes 189
17 4 Kidney Disease-Associated KCAT Complexes 191
17 5 Inducible Nitric Oxide Synthase (iNOS) 191
17 6 Human Galactose-1-Phosphate Uridyly 1-Transferase 192
Exercises 197
Reference 197
18 Proteome-Scale Analysis of Protein Complexes 199
18 1 Protein Complexes in Proteomes 199
Exercises 200
References 200
19 Conclusions and Challenges 203
Useful Formula
|
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| id | DE-604.BV044908175 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T08:04:27Z |
| institution | BVB |
| isbn | 9789811073465 9789811339424 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-030301782 |
| oclc_num | 1035444091 |
| open_access_boolean | |
| owner | DE-29T DE-19 DE-BY-UBM DE-11 |
| owner_facet | DE-29T DE-19 DE-BY-UBM DE-11 |
| physical | xix, 207 Seiten Illustrationen, Diagramme |
| publishDate | 2018 |
| publishDateSearch | 2018 |
| publishDateSort | 2018 |
| publisher | Springer |
| record_format | marc |
| spelling | Kangueane, Pandjassarame Verfasser (DE-588)1155849892 aut Protein-protein and domain-domain interactions Pandjassarame Kangueane, Christina Nilofer Singapore Springer [2018] xix, 207 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Wechselwirkung (DE-588)4064937-4 gnd rswk-swf Protein-Protein-Wechselwirkung (DE-588)4745193-2 gnd rswk-swf Domäne Biochemie (DE-588)4582302-9 gnd rswk-swf Protein-protein interactions domain-domain interactions gene fusion Protein complexes Drug discovery Vaccine development Protein-Protein-Wechselwirkung (DE-588)4745193-2 s DE-604 Domäne Biochemie (DE-588)4582302-9 s Wechselwirkung (DE-588)4064937-4 s Nilofer, Christina Verfasser (DE-588)1155850165 aut Erscheint auch als Online-Ausgabe 978-981-10-7347-2 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030301782&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Kangueane, Pandjassarame Nilofer, Christina Protein-protein and domain-domain interactions Wechselwirkung (DE-588)4064937-4 gnd Protein-Protein-Wechselwirkung (DE-588)4745193-2 gnd Domäne Biochemie (DE-588)4582302-9 gnd |
| subject_GND | (DE-588)4064937-4 (DE-588)4745193-2 (DE-588)4582302-9 |
| title | Protein-protein and domain-domain interactions |
| title_auth | Protein-protein and domain-domain interactions |
| title_exact_search | Protein-protein and domain-domain interactions |
| title_full | Protein-protein and domain-domain interactions Pandjassarame Kangueane, Christina Nilofer |
| title_fullStr | Protein-protein and domain-domain interactions Pandjassarame Kangueane, Christina Nilofer |
| title_full_unstemmed | Protein-protein and domain-domain interactions Pandjassarame Kangueane, Christina Nilofer |
| title_short | Protein-protein and domain-domain interactions |
| title_sort | protein protein and domain domain interactions |
| topic | Wechselwirkung (DE-588)4064937-4 gnd Protein-Protein-Wechselwirkung (DE-588)4745193-2 gnd Domäne Biochemie (DE-588)4582302-9 gnd |
| topic_facet | Wechselwirkung Protein-Protein-Wechselwirkung Domäne Biochemie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030301782&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT kangueanepandjassarame proteinproteinanddomaindomaininteractions AT niloferchristina proteinproteinanddomaindomaininteractions |