Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments: Bayesian inference of macromolecule structures
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| Main Author: | |
|---|---|
| Format: | Thesis Book |
| Language: | English |
| Published: |
München
Verl. Dr. Hut
2011
|
| Edition: | 1. Aufl. |
| Series: | Physik
|
| Subjects: | |
| Online Access: | Volltext https://nbn-resolving.org/urn:nbn:de:bvb:19-135739 Inhaltsverzeichnis |
| Physical Description: | VII, 189 S. graph. Darst. 240 mm x 170 mm, 423 g |
| ISBN: | 9783868539820 3868539824 |
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| 245 | 1 | 0 | |a Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments |b Bayesian inference of macromolecule structures |c Adam Marek Muschielok |
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Record in the Search Index
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| adam_text | IMAGE 1
CONTENTS
ABSTRACT III
1 INTRODUCTION 1
2 BASICS 3
2.1 FLUORESCENCE 3
2.1.1 PHYSICAL MODEL OF FLUORESCENCE 3
2.1.2 TIME-DEPENDENT FLUORESCENCE DECAY 3
2.1.3 FLUORESCENCE POLARIZATION 4
2.1.4 FLUORESCENCE ANISOTROPY 5
2.2 FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET) 6
2.2.1 PHYSICAL MODEL OF FRET 6
2.2.2 DEFINITION OF FRET EFFICIENCY 7
2.2.3 DEFINITION OF FRET ANISOTROPY 9
2.2.4 MEASUREMENT OF FRET EFFICIENCY 9
2.3 FRET IN LABELED MACROMOLECULES 10
2.3.1 FLUORESCENCE ANISOTROPY OF A MACROMOLECULE-BOUND FLUOROPHORE . .
10 2.3.2 INFLUENCE OF SEGMENTAL MOTION ON THE FRET EFFICIENCY AND
ANISOTROPY 11 2.4 PROBABILISTIC DATA ANALYSIS 14
2.4.1 PROBABILITY CALCULUS 14
2.4.2 BAYESIAN PARAMETER ESTIMATION 15
2.4.3 ASSIGNMENT OF PRIORS 18
2.4.4 CHARACTERIZATION OF CONTINUOUS PROBABILITY DISTRIBUTIONS 20 2.4.5
BAYESIAN MODEL SELECTION 22
2.4.6 APPLICATION TO REAL PROBLEMS 24
2.5 SAMPLING FROM PROBABILITY DENSITIES 25
2.5.1 MARKOV CHAIN MONTE CARLO 26
2.5.2 NESTED SAMPLING 28
3 DEVELOPMENT OF THE NANO-POSITIONING SYSTEM 35
3.1 THE POSITION - FOERSTER DISTANCE MODEL 37
3.1.1 MODEL ASSUMPTIONS AND PARAMETRIZATION 37
3.1.2 LIKELIHOOD 38
3.1.3 PRIOR 38
3.1.4 POSTERIOR 40
3.1.5 EVIDENCE 43
3.2 THE POSITION - ORIENTATION MODEL 43
3.2.1 MODEL ASSUMPTIONS AND PARAMETRIZATION 43
3.2.2 LIKELIHOOD 45
3.2.3 PRIOR 46
3.2.4 POSTERIOR AND EVIDENCE 47
3.3 THE POSITION - ORIENTATION MODEL WITH DOCKING 47
3.3.1 MODEL ASSUMPTIONS, PARAMETRIZATION AND LIKELIHOOD 47
BIBLIOGRAFISCHE INFORMATIONEN HTTP://D-NB.INFO/1014217547
DIGITALISIERT DURCH
IMAGE 2
CONTENTS
3.3.2 PRIOR 48
3.3.3 POSTERIOR AND EVIDENCE 49
4 THE EUKARYOTIC RNA POLYMERASE II 51
4.1 STRUCTURE AND FUNCTION 51
4.2 QUESTIONS ADDRESSED 53
5 MATERIALS AND METHODS 55
5.1 EXPERIMENTAL METHODS, DATA ACQUISITION AND DATA PRE-PROCESSING 55
5.1.1 MACROMOLECULAR COMPLEXES 55
5.1.2 ISOTROPIE FOERSTER DISTANCE MEASUREMENTS 57
5.1.3 FRET EFFICIENCY MEASUREMENTS 57
5.1.4 FLUORESCENCE ANISOTROPY MEASUREMENTS 58
5.1.5 FRET ANISOTROPY DATA 58
5.2 NPS SOFTWARE 59
5.2.1 POSITION - FOERSTER DISTANCE MODEL 59
5.2.2 POSITION - ORIENTATION MODEL WITH OPTIONAL DOCKING 62
5.3 SIMULATION AND VISUALIZATION 62
5.3.1 CALCULATION OF ACCESSIBLE VOLUMES 62
5.3.2 MONTE CARLO SIMULATION OF FOERSTER DISTANCES 65
5.3.3 MEASURING STATISTICAL DEPENDENCE 66
5.3.4 ARTIFICIAL DATA FOR TEST CALCULATIONS 66
5.3.5 PROBABILITY DENSITY VISUALIZATION 67
5.3.6 NPS MEASUREMENT CONSISTENCY CHECK 68
5.3.7 CHARACTERIZATION OF FLUOROPHORE POSITIONS AND ORIENTATIONS 69 5.4
COMPUTATION OF THE ANTENNA POSITION ESTIMATE IN THE POSITION - FOERSTER
DIS- TANCE MODEL 70
5.5 A SAMPLING ENGINE FOR BAYESIAN DATA ANALYSIS 72
5.5.1 REQUIREMENTS 72
5.5.2 WORKING WITH SMALL NUMBERS 73
5.5.3 IMPLEMENTATION OF PRIOR INFORMATION 73
5.5.4 MARKOV CHAIN MONTE CARLO 74
5.5.5 AUTOMATIC ADJUSTMENT OF MONTE CARLO PARAMETER SETTINGS 81 5.5.6
PARALLELIZATION 84
5.5.7 SETTINGS USED FOR NPS ANALYSIS 84
5.5.8 IMPLEMENTATION 86
6 RESULTS AND DISCUSSION 89
6.1 SIMULATION I - FOERSTER DISTANCES 89
6.1.1 EFFECTS OF FLUORESCENCE ANISOTROPY ON THE FOERSTER DISTANCE
DISTRIBUTION 89 6.1.2 DISCUSSION 89
6.1.3 FOERSTER DISTANCE CORRELATIONS 92
6.1.4 DISCUSSION 94
6.2 APPLICATION I - RNA IN THE POL II ELONGATION COMPLEX 96
6.2.1 NPS INFERENCE OF THE 3VRNA END POSITION 96
6.2.2 DISCUSSION 98
6.2.3 NPS INFERENCE OF THE 5 RNA END POSITION 99
6.2.4 DISCUSSION 101
6.3 SIMULATION II - IMPROVEMENT OF LOCALIZATION ACCURACY 104
6.3.1 EFFECTS OF ANISOTROPY AND ORIENTATION ON THE LOCALIZATION
UNCERTAINTY 105 6.3.2 DISCUSSION 106
IMAGE 3
CONTENTS
6.3.3 POSITION - ORIENTATION NPS MODEL TEST CALCULATIONS 108
6.3.4 DISCUSSION 118
6.4 APPLICATION II - NONTEMPLATE DNA IN THE ELONGATION COMPLEX 121 6.4.1
NPS INFERENCE 121
6.4.2 DISCUSSION 127
6.5 SIMULATION III - FRET-ASSISTED DOCKING 129
6.5.1 FRET-ASSISTED DOCKING OF TWO MACROMOLECULES 130
6.5.2 DISCUSSION 132
6.6 APPLICATION III - POSITION AND ORIENTATION OF TBP IN THE ITC 133
6.6.1 NPS INFERENCE 133
6.6.2 DISCUSSION 135
6.7 GENERAL DISCUSSION 138
6.7.1 NPS AND OTHER FRET ANALYSIS METHODS 138
6.7.2 WELL-DEFINED FRET STATES AS TOOLS FOR STRUCTURAL BIOLOGY 142 6.7.3
INTERPRETATION OF NPS RESULTS 143
6.7.4 OPTIMAL FRET NETWORK DESIGN 146
6.7.5 DATA PRE-PROCESSING AND MODEL SELECTION 152
7 SUMMARY AND OUTLOOK 157
LIST OF ABBREVIATIONS AND VARIABLES 165
APPENDIX I: COUPLING OF DATA PRE-PROCESSING TO NPS 167
APPENDIX II: DATA 169
BIBLIOGRAPHY 177
|
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| physical | VII, 189 S. graph. Darst. 240 mm x 170 mm, 423 g |
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| spelling | Muschielok, Adam Marek Verfasser (DE-588)1016513771 aut Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments Bayesian inference of macromolecule structures Adam Marek Muschielok 1. Aufl. München Verl. Dr. Hut 2011 VII, 189 S. graph. Darst. 240 mm x 170 mm, 423 g txt rdacontent n rdamedia nc rdacarrier Physik Zugl.: München, Univ., Diss., 2010 Biochemische Analyse (DE-588)4255721-5 gnd rswk-swf Fluoreszenz-Resonanz-Energie-Transfer (DE-588)4773018-3 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Fluoreszenz-Resonanz-Energie-Transfer (DE-588)4773018-3 s Biochemische Analyse (DE-588)4255721-5 s DE-604 Erscheint auch als Online-Ausgabe urn:nbn:de:bvb:19-135739 http://edoc.ub.uni-muenchen.de/13573/ Verlag kostenfrei Volltext https://nbn-resolving.org/urn:nbn:de:bvb:19-135739 Resolving-System DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024510490&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Muschielok, Adam Marek Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments Bayesian inference of macromolecule structures Biochemische Analyse (DE-588)4255721-5 gnd Fluoreszenz-Resonanz-Energie-Transfer (DE-588)4773018-3 gnd |
| subject_GND | (DE-588)4255721-5 (DE-588)4773018-3 (DE-588)4113937-9 |
| title | Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments Bayesian inference of macromolecule structures |
| title_auth | Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments Bayesian inference of macromolecule structures |
| title_exact_search | Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments Bayesian inference of macromolecule structures |
| title_full | Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments Bayesian inference of macromolecule structures Adam Marek Muschielok |
| title_fullStr | Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments Bayesian inference of macromolecule structures Adam Marek Muschielok |
| title_full_unstemmed | Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments Bayesian inference of macromolecule structures Adam Marek Muschielok |
| title_short | Development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments |
| title_sort | development and application of a quantitative analysis method for fluorescence resonance energy transfer localization experiments bayesian inference of macromolecule structures |
| title_sub | Bayesian inference of macromolecule structures |
| topic | Biochemische Analyse (DE-588)4255721-5 gnd Fluoreszenz-Resonanz-Energie-Transfer (DE-588)4773018-3 gnd |
| topic_facet | Biochemische Analyse Fluoreszenz-Resonanz-Energie-Transfer Hochschulschrift |
| url | http://edoc.ub.uni-muenchen.de/13573/ https://nbn-resolving.org/urn:nbn:de:bvb:19-135739 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024510490&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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