AUREMOL-QTA, a program package for NMR based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation:
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| Format: | Thesis Book |
| Language: | English |
| Published: |
2011
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| Subjects: | |
| Online Access: | Volltext https://nbn-resolving.org/urn:nbn:de:bvb:355-epub-231967 Inhaltsverzeichnis |
| Physical Description: | XVI, 223 S. Ill., graph. Darst. |
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Record in the Search Index
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| adam_text | IMAGE 1
TABLE OF CONTENTS
ABSTRACT ACKNOWLEDGEMENTS II
TABLE OF CONTENTS I
LIST OF TABLES I
LIST OF FIGURES
LIST OF ABBREVIATIONS XV
INTRODUCTION 1
1.1 PROTEINS
1.2 NUCLEAR MAGNETIC RESONANCE
1.3 NMR EXPERIMENTS
1.3.1 1D-NMR EXPERIMENT
1.3.2 2D-NMR EXPERIMENT
1.4 PROTEIN STRUCTURE DETERMINATION
1.4.1 PROTEIN STRUCTURE DETERMINATION FROM NMR DATA
1.4.1.1 AUREMOL
1.5 FAST FOURIER TRANSFORM (FFT)
1.6 WINDOW FUNCTIONS
1.7 LINE WIDTHS
IV
HTTP://D-NB.INFO/1032282193
IMAGE 2
2 MATERIALS AND METHODS 27
2.1 INTRODUCTION 27
2.2 MATERIALS 29
2.2.1 BACK-CALCULATED DATASET 29
2.2.1.1 HPR PROTEIN FROM STAPHYLOCOCCUS AUREUS (WILD TYPE) 29
2.2.1.2 HPR PROTEIN FROM STAPHYLOCOCCUS AUREUS (MUTANT HI5A) 31
2.2.1.3 HPR PROTEIN FROM STAPHYLOCOCCUS AUREUS (PARTIALLY DENATURED) 31
2.2.1.4 HPR PROTEIN FROM STAPHYLOCOCCUS AUREUS (FULLY DENATURED) 32
2.2.2 EXPERIMENTAL DATASET 32
2.2.2.1 HPR PROTEIN FROM STAPHYLOCOCCUS AUREUS (WILD AND MUTANT H15A) 32
2.2.2.2 HUMAN PRION PROTEIN (/IUPRP C ): LIGAND BINDING WITH XENON 33
2.2.2.3 HUMAN PRION PROTEIN (/IUPRP C ): HIGH PRESSURE NMR 34
2.3 METHODS 35
2.3.1 SOFTWARE 35
-3 RESULTS 36
3.1 GENERAL CONSIDERATIONS 36
3.2 PROJECT OVERVIEW 38
3.3 THE DEVELOPED INTERFACES 42
3.3.1 THE AUREMOL-FFT INTERFACE 42
3.3.2 THE AUREMOL-LW (LINE WIDTH) INTERFACE 46
3.4 IMPLEMENTATION OF THE AUREMOL-QTA MODULE 47
3.4.1 THE PRE-PROCESSING LEVEL 47
3.4.1.1 STANDARDIZATION OF THE EXTERNAL PARAMETERS 48
3.4.1.2 THE GLOBAL SHIFT OF THE SPECTRUM 49
3.4.1.3 MULTIPLE SPECTRUM REFERENCING 53
3.4.2 LOW-LEVEL ANALYSIS: A BOTTOM-UP APPROACH 54
3.4.2.1 COLLECTION OF PEAK FEATURES 55
3.4.2.2 SEARCH OF MULTIPLET PEAKS ! 56
V
IMAGE 3
3.4.2.2.1 MULTIPLET SEARCH ANALYSIS: THE MASK 58
3.4.2.2.2 MULTIPLET SEARCH ANALYSIS: THE DYNAMIC DATA
SMOOTHING 59
3.4.2.2.3 MULTIPLET SEARCH ANALYSIS: LOCAL ADAPTION OF PEAK
MAXIMA 61
3.4.2.3 ANALYSIS OF THE FEATURES FOR ASSOCIATING PEAKS 64
3.4.2.3.1 THE LIST OF NEIGHBORS (NLST) AND THE
NEIGHBORHOOD DISTANCE 64
3.4.2.3.2 THE ANALYSIS OF PEAK LOCAL SHIFT 67
3.4.2.3.2.1 THE LOCAL SHIFT ALGORITHM: THE FIRST
PEAK ASSOCIATIONS AND THE VOLUME
SCALING FACTOR 69
3.4.2.3.2.2 THE LOCAL SHIFT ALGORITHM: THE SECOND
PEAK ASSOCIATIONS 73
3.4.2.4 LINE WIDTH COMPARISON 80
3.4.2.5 THE HYBRID TIME-FREQUENCY DOMAIN ANALYSIS 83
3.4.3 MID-LEVEL ANALYSIS: FROM A SCORE-LIKE TO A PROBABILITY-LIKE SYSTEM
90
3.4.3.1 PEAK PROBABILITIES 90
3.4.3.2 ASSESSMENT OF INDIVIDUAL FEATURE OF PEAKS 92
3.4.3.3 ASSESSMENT OF COMPLETE SPECTRA 98
3.4.3.4 SPECTRAL MATCHING RATIOS 98
3.4.3.5 KOLMOGOROV-SMIRNOV ANALYSIS 102
3.4.4 HIGH-LEVEL ANALYSIS: INVESTIGATING STRUCTURAL CHANGES 105
3.4.4.1 INTERPRETATION OF PEAKS 105
3.4.4.2 GLOBAL SYMMETRY ANALYSIS AND REFINEMENT OF PEAKS 108
3.4.4.2.1 SIGNAL PATTERNS RECOGNITION OF RESIDUES IN
NOESY AND TOCSY SPECTRA 112
3.4.4.2.2 APPLICATION OF THE SIGNAL PATTERN RECOGNITION
(NOESY CASE) 114
3.4.4.3 STRUCTURAL ANALYSIS 117
VI
IMAGE 4
TEST CASE: HPR PROTEIN FROM STAPHYLOCOCCUS AUREUS 120
4.1 INTRODUCTION 120
4.2 AUREMOL-QTA MAIN INTERFACE 122
4.3 HPR PROTEIN FROM STAPHYLOCOCCUS AUREUS 124
4.3.1 THE WILD AND THE MUTANT H15A HPR PROTEIN 124
4.3.1.1 THE QUALITY CONTROL OF THE WILD AND MUTANT H15A MEASURED
SPECTRA OF THE HPR PROTEIN FROM STAPHYLOCOCCUS AUREUS 126
4.3.1.2 QUALITY CONTROL DETAILED RESULTS 128
4.3.1.3 ANALYSIS OF THE PEAK FEATURES THROUGH THE BAYESIAN PROBABILITIES
131
4.3.1.4 PEAKS THAT HAVE NOT BEEN ASSOCIATED BETWEEN THE SPECTRA
(NEW, MISSING AND AMBIGUOUS SIGNALS) 134
4.3.1.5 GENERAL RESULTS OF THE QUALITY CONTROL 139
4.3.2 THE QUALITY CONTROL OF THE MEASURED WILD, THE MEASURED
MUTANT (H15A) AND THE SIMULATED SPECTRUM (WILD TYPE)
OF THE H PR PROTEIN FROM STAPHYLOCOCCUS AUREUS 142
4.3.2.1 THE QUALITY CONTROL OF THE WILD-MUTANT-SIMULATED SPECTRA OF HPR
143
4.3.3 RECOGNITION OF PARTIAL DENATURATION OF A PROTEIN 147
4.3.3.1 THE QUALITY CONTROL OF THE FOLDED AND THE PARTIALLY DENATURED
SPECTRA
OF THE WILD HPR PROTEIN FROM STAPHYLOCOCCUS AUREUS 148
4.3.4 THE COMPLETELY DENATURED H PR PROTEIN FROM STAPHYLOCOCCUS AUREUS
151
4.3.4.1 THE QUALITY CONTROL OF THE NATIVE AND THE FULLY DENATURED
SPECTRA OF THE WILD HPR PROTEIN FROM STAPHYLOCOCCUS AUREUS 152
TEST CASE: HUMAN PRION PROTEIN 155
5.1 INTRODUCTION 155
5.2 PRION PROTEIN [HUPRP 0 ) 156
5.2.1 GENERAL CONSIDERATIONS 156
5.2.2 QUALITY CONTROL OF THE XENON-BINDING DATASET 159
5.2.2.1 QUALITY CONTROL DETAILED RESULTS 162
5.2.2.2 BAYESIAN FEATURE ANALYSIS 165
VII
IMAGE 5
5.2.2.2.1 PEAKS THAT HAVE NOT BEEN ASSOCIATED AMONG
THE SPECTRA (MISSING SIGNALS) 174
5.2.2.3 STRUCTURAL ANALYSIS BY MEANS OF HISTOGRAMS 175
5.2.2.4 GENERAL RESULTS OF THE QUALITY CONTROL 180
5.2.3 QUALITY CONTROL OF THE HIGH PRESSURE AND TEMPERATURE DATASETS 182
5.2.3.1 QUALITY CONTROL DETAILED RESULTS 183
5.2.3.2 BAYESIAN FEATURE ANALYSIS 185
5.2.3.2.1 PEAKS THAT HAVE NOT BEEN ASSOCIATED AMONG
THE SPECTRA (MISSING SIGNALS) 188
5.2.3.3 STRUCTURAL ANALYSIS BY MEANS OF HISTOGRAMS 190
5.2.3.4 QUALITY CONTROL GENERAL RESULTS 191
6 CONCLUSIONS AND DISCUSSIONS 193
6.1 GENERAL CONSIDERATIONS 193
6.2 STATE OF THE ART AND FUTURE DEVELOPMENTS OF THE PRE-PROCESSING STAGE
194
6.3 STATE OF THE ART AND FUTURE DEVELOPMENTS OF THE LOW-LEVEL ANALYSIS
195
6.4 STATE OF THE ART AND FUTURE DEVELOPMENTS OF THE MID-LEVEL ANALYSIS
197
6.5 STATE OF THE ART AND FUTURE DEVELOPMENTS OF THE HIGH-LEVEL ANALYSIS
198
7 APPENDICES 202
7.1 THE LEVENBERG-MARQUARDT ALGORITHM 202
7.2 THE WELCH S T-TEST 203
7.3 APPENDIX C 204
7.4 APPENDIX D 208
7.5 APPENDIX E 210
BIBLIOGRAPHY 213
VIII
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| any_adam_object | 1 |
| author | Malloni, Wilhelm Massimiliano |
| author_facet | Malloni, Wilhelm Massimiliano |
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| author_sort | Malloni, Wilhelm Massimiliano |
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| bvnumber | BV040682169 |
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| collection | ebook |
| ctrlnum | (OCoLC)826598596 (DE-599)BVBBV040682169 |
| discipline | Biologie |
| format | Thesis Book |
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| language | English |
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| spelling | Malloni, Wilhelm Massimiliano Verfasser aut AUREMOL-QTA, a program package for NMR based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation vorgelegt von Wilhelm Massimiliano Malloni 2011 XVI, 223 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Regensburg, Univ., Diss., 2011 Konformationsanalyse (DE-588)4164967-9 gnd rswk-swf Computerunterstütztes Verfahren (DE-588)4139030-1 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf Mehrdimensionale NMR-Spektroskopie (DE-588)4346802-0 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Proteine (DE-588)4076388-2 s Konformationsanalyse (DE-588)4164967-9 s Mehrdimensionale NMR-Spektroskopie (DE-588)4346802-0 s Computerunterstütztes Verfahren (DE-588)4139030-1 s b DE-604 Erscheint auch als Online-Ausgabe urn:nbn:de:bvb:355-epub-231967 http://epub.uni-regensburg.de/23196/ Verlag kostenfrei Volltext https://nbn-resolving.org/urn:nbn:de:bvb:355-epub-231967 Resolving-System DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025508536&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Malloni, Wilhelm Massimiliano AUREMOL-QTA, a program package for NMR based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation Konformationsanalyse (DE-588)4164967-9 gnd Computerunterstütztes Verfahren (DE-588)4139030-1 gnd Proteine (DE-588)4076388-2 gnd Mehrdimensionale NMR-Spektroskopie (DE-588)4346802-0 gnd |
| subject_GND | (DE-588)4164967-9 (DE-588)4139030-1 (DE-588)4076388-2 (DE-588)4346802-0 (DE-588)4113937-9 |
| title | AUREMOL-QTA, a program package for NMR based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation |
| title_auth | AUREMOL-QTA, a program package for NMR based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation |
| title_exact_search | AUREMOL-QTA, a program package for NMR based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation |
| title_full | AUREMOL-QTA, a program package for NMR based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation vorgelegt von Wilhelm Massimiliano Malloni |
| title_fullStr | AUREMOL-QTA, a program package for NMR based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation vorgelegt von Wilhelm Massimiliano Malloni |
| title_full_unstemmed | AUREMOL-QTA, a program package for NMR based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation vorgelegt von Wilhelm Massimiliano Malloni |
| title_short | AUREMOL-QTA, a program package for NMR based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation |
| title_sort | auremol qta a program package for nmr based automated recognition and characterization of local and global conformational changes in proteins induced by ligand binding as external perturbation |
| topic | Konformationsanalyse (DE-588)4164967-9 gnd Computerunterstütztes Verfahren (DE-588)4139030-1 gnd Proteine (DE-588)4076388-2 gnd Mehrdimensionale NMR-Spektroskopie (DE-588)4346802-0 gnd |
| topic_facet | Konformationsanalyse Computerunterstütztes Verfahren Proteine Mehrdimensionale NMR-Spektroskopie Hochschulschrift |
| url | http://epub.uni-regensburg.de/23196/ https://nbn-resolving.org/urn:nbn:de:bvb:355-epub-231967 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025508536&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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