Structure-function relationships in membrane protein families:
Gespeichert in:
| 1. Verfasser: | |
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2012
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| Schlagworte: | |
| Online-Zugang: | kostenfrei https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20120626-1096028-1-5 Inhaltsverzeichnis |
| Beschreibung: | Zsfassung in dt. Sprache |
| Beschreibung: | XV, 162 S. graph. Darst. |
Internformat
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Datensatz im Suchindex
| _version_ | 1804149354161766400 |
|---|---|
| adam_text | IMAGE 1
CONTENTS
ABSTRACT III
ZUSAMMENFASSUNG V
ACKNOWLEDGMENTS VII
CONTENTS XI
LIST OF FIGURES XIV
LIST OF TABLES XV
1 INTRODUCTION 1
1.1 MEMBRANE PROTEINS 1
1.1.1 BASIC PRINCIPLES 2
1.1.2 MEMBRANE STRUCTURE SPACE 3
1.1.3 MEMBRANE PROTEIN TOPOLOGY 8
1.1.4 GENOME-WIDE ANALYSIS 11
1.2 CLASSIFICATION OF PROTEINS 13
1.2.1 SEQUENCE-BASED CLASSIFICATION 13
1.2.2 STRUCTURE-BASED CLASSIFICATION 15
1.2.3 FUNCTION-BASED CLASSIFICATION 18
1.3 FROM SEQUENCE TO STRUCTURE TO FUNCTION 19
1.3.1 SEQUENCE-STRUCTURE RELATIONSHIPS 19
1.3.2 STRUCTURE-FUNCTION RELATIONSHIPS 20
1.4 MOTIVATION AND OUTLINE 21
2 CLASSIFICATION O F MEMBRANE PROTEINS BASED ON 3D STRUCTURE 2 3
2.1 INTRODUCTION 24
2.1.1 COMPARISON OF SCOP AND CATH 24
2.1.2 CONTINUITY OF FOLD SPACE 25
IX
HTTP://D-NB.INFO/1029093997
IMAGE 2
CONTENTS
2.2 MATERIALS AND METHODS 26
2.2.1 DATASETS 26
2.2.2 COMPARING DOMAIN ASSIGNMENTS 27
2.2.3 COMPARING FOLD ASSIGNMENTS 28
2.3 RESULTS AND DISCUSSION 29
2.3.1 MEMBRANE PROTEIN FOLDS IN SCOP AND CATH 29
2.3.2 COMPARISON OF DOMAIN ASSIGNMENTS 30
2.3.3 COMPARISON OF FOLD ASSIGNMENTS - FOLD AGREEMENTS 33
2.3.4 COMPARISON OF FOLD ASSIGNMENTS - FOLD DISAGREEMENTS 35
2.4 SUMMARY 44
2.5 CLARIFICATION OF CONTRIBUTION 44
3 CLASSIFICATION O F MEMBRANE PROTEINS BASED ON I D AND 2D STRUCTURE 4 5
3.1 INTRODUCTION 46
3.1.1 HIDDEN MARKOV MODELS 46
3.1.2 IMPORTANCE OF INTER HELICAL LOOP REGIONS 47
3.2 MATERIALS AND METHODS 49
3.2.1 DATASET 49
3.2.2 ANALYSIS OF DOMAIN CONTENT 49
3.2.3 INITIAL CLUSTERING 50
3.2.4 DETERMINATION OF TMH CORE REGIONS 50
3.2.5 DERIVATION OF SC-CLUSTERS 51
3.2.6 DERIVATION OF FH- AND MD-CLUSTERS 58
3.2.7 COMPARING SC-CLUSTERS WITH OTHER DATABASES 58
3.2.8 COMPARING FH-CLUSTERS WITH ENZYME 60
3.2.9 MAPPING TO EXTERNAL DATABASES 60
3.2.10 AVAILABILITY 61
3.3 RESULTS AND DISCUSSION 61
3.3.1 MODIFICATIONS AND IMPROVEMENTS IN CAMPS 2.0 61
3.3.2 EMPIRICAL RULES VERSUS META-MODELS 64
3.3.3 DOMAIN CONTENT OF MEMBRANE PROTEINS 66
3.3.4 STRUCTURAL CLASSIFICATION USING META-MODELS 69
3.3.5 COMPARISON OF SC-CLUSTERS WITH PFAM 73
3.3.6 COMPARISON OF SC-CLUSTERS WITH TCDB 78
3.3.7 COMPARISON OF SC-CLUSTERS WITH SCOP AND CATH 83
X
IMAGE 3
CONTENTS
3.3.8 LAYERED ORGANIZATION OF THE CAMPS DATABASE 89
3.3.9 QUALITY OF THE CAMPS CLUSTERING 90
3.3.10 CAMPS WEBSITE 91
3.4 SUMMARY 93
3.5 CLARIFICATION OF CONTRIBUTION 94
4 CLASSIFICATION O F MEMBRANE PROTEINS BASED ON HELIX-HELIX INTERACTIONS
95 4.1 INTRODUCTION 96
4.1.1 IMPORTANCE OF HELIX-HELIX INTERACTIONS 96
4.1.2 PREDICTION OF HELIX-HELIX INTERACTIONS 97
4.2 MATERIALS AND METHODS 97
4.2.1 DATASET 97
4.2.2 PREDICTION OF CONSENSUS HELIX ARCHITECTURES 98
4.2.3 LARGE-SCALE CLASSIFICATION OF CONSENSUS HELIX ARCHITECTURES 100
4.2.4 GO ENRICHMENT ANALYSIS 101
4.3 RESULTS AND DISCUSSION 101
4.3.1 GENERATION OF CONSENSUS HELIX ARCHITECTURES 101
4.3.2 VALIDATION OF MCL CLUSTERS 104
4.3.3 EXPLORING THE MEMBRANE PROTEIN STRUCTURE SPACE 109
4.4 SUMMARY 116
4.5 CLARIFICATION OF CONTRIBUTION 116
5 CONCLUSIONS AND OUTLOOK 117
5.1 COMPARATIVE ANALYSIS OF MEMBRANE PROTEINS IN SCOP AND CATH . . . .
117
5.2 FOLD DEFINITIONS FOR SOLUBLE AND MEMBRANE PROTEINS 118
5.3 CLASSIFICATION BASED ON ID AND 2D STRUCTURE 119
5.4 STRUCTURAL COVERAGE OF MEMBRANE PROTEIN SPACE 119
5.5 PROGRESSIVE DEVELOPMENT OF CAMPS DATABASE 120
5.6 MEMBRANE PROTEIN STRUCTURE SPACE 121
5.7 OUTLOOK 121
6 BIBLIOGRAPHY 123
7 APPENDIX 151
LIST OF PUBLICATIONS 162
X I
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| spelling | Neumann, Sindy Verfasser (DE-588)1029093822 aut Structure-function relationships in membrane protein families Sindy Neumann 2012 XV, 162 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Zsfassung in dt. Sprache München, Techn. Univ., Diss., 2012 Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 gnd rswk-swf Strukturaufklärung (DE-588)4183788-5 gnd rswk-swf Klassifikation (DE-588)4030958-7 gnd rswk-swf Membranproteine (DE-588)4130026-9 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Membranproteine (DE-588)4130026-9 s Strukturaufklärung (DE-588)4183788-5 s Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 s Klassifikation (DE-588)4030958-7 s b DE-604 Erscheint auch als Online-Ausgabe urn:nbn:de:bvb:91-diss-20120626-1096028-1-5 http://mediatum.ub.tum.de/node?id=1096028 Verlag kostenfrei Volltext https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20120626-1096028-1-5 Resolving-System DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025179529&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Neumann, Sindy Structure-function relationships in membrane protein families Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 gnd Strukturaufklärung (DE-588)4183788-5 gnd Klassifikation (DE-588)4030958-7 gnd Membranproteine (DE-588)4130026-9 gnd |
| subject_GND | (DE-588)4183784-8 (DE-588)4183788-5 (DE-588)4030958-7 (DE-588)4130026-9 (DE-588)4113937-9 |
| title | Structure-function relationships in membrane protein families |
| title_auth | Structure-function relationships in membrane protein families |
| title_exact_search | Structure-function relationships in membrane protein families |
| title_full | Structure-function relationships in membrane protein families Sindy Neumann |
| title_fullStr | Structure-function relationships in membrane protein families Sindy Neumann |
| title_full_unstemmed | Structure-function relationships in membrane protein families Sindy Neumann |
| title_short | Structure-function relationships in membrane protein families |
| title_sort | structure function relationships in membrane protein families |
| topic | Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 gnd Strukturaufklärung (DE-588)4183788-5 gnd Klassifikation (DE-588)4030958-7 gnd Membranproteine (DE-588)4130026-9 gnd |
| topic_facet | Struktur-Aktivitäts-Beziehung Strukturaufklärung Klassifikation Membranproteine Hochschulschrift |
| url | http://mediatum.ub.tum.de/node?id=1096028 https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20120626-1096028-1-5 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025179529&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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