Folding dynamics of RNA secondary structures: a structure based approach
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| 1. Verfasser: | |
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2014
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | 85 S. Ill., graph. Darst. |
Internformat
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Datensatz im Suchindex
| _version_ | 1804153209504137216 |
|---|---|
| adam_text | CONTENTS
1. INTRODUCTION 9
1.1. RNA IN CELLS 9
1.2. RNA FOLDING SIMULATIONS 11
1.3. STRUCTURE BASED MODELS 12
1.4. CONTENT OF THIS WORK 13
2. MODEL AND SIMULATION METHOD 15
2.1. THE STRUCTURE BASED RNA MODEL 15
2.2. SIMULATION METHOD 17
2.3. SIMULATION OF GROWING RNA 18
2.4. FREE ENERGY CALCULATION 18
2.5. LIMITATIONS OF THE APPROACH 21
3. FREE FOLDING OF RNA 23
3.1. THE AGCEUE HAIRPIN . . 23
3.2. SHORT HAIRPINS: A
N
G
M
U
N
25
3.3. FREE FOLDING OF A TRNA 29
3.4. FOLDING AGAINST AN EXTERNAL FORCE 31
3.4.1. INCLUDING AN EXTERNAL PULLING FORCE 31
3.4.2. FOLDING OF THE P5AB HAIRPIN 31
3.5. COMPARING SIMULATED WITH EXPERIMENTAL FOLDING TIMES 36
3.6. SUMMARY 39
4. COTRANSCRIPTIONAL FOLDING 41
4.1. INTRODUCTION TO RIBOSWITCHES 41
4.2. FOLDING THE APTAMER REGION OF THE ADENINE RIBOSWITCH 42
4.3. FOLDING OF THE COMPLETE ADENINE RIBOSWITCH 46
5
HTTP://D-NB.INFO/1069775819
4.4. FOLDING THE APTAMER REGION OF THE SAM-I RIBOSWITCH 48
4.5. FOLDING THE COMPLETE SAM-I RIBOSWITCH 50
4.6. COMPARISON TO MD STUDIES OF APTAMER FOLDING 54
4.7. SUMMARY 57
5. TRYPTOPHAN ATTENUATOR 59
6. SUMMARY AND DISCUSSION 65
A. APPENDIX 69
A.L. SIMULATIONS INCLUDING NON-NATIVE CONTACTS 69
A. 1.1. COMPUTATIONAL SPEEDUP 69
A. 1.2. EFFECTS ON THE FOLDING DYNAMICS 70
A.2. SIMPLE ENERGY PARAMETERIZATION 73
A.3. THREE STATE MODEL CALCULATIONS 75
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| any_adam_object | 1 |
| author | Faber, Michael |
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| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.88330285 |
| dewey-search | 572.88330285 |
| dewey-sort | 3572.88330285 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Thesis Book |
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| spelling | Faber, Michael Verfasser (DE-588)106889427X aut Folding dynamics of RNA secondary structures a structure based approach von Michael Faber 2014 85 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Potsdam, Univ., Diss., 2014 (DE-588)4113937-9 Hochschulschrift gnd-content DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027915763&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Faber, Michael Folding dynamics of RNA secondary structures a structure based approach |
| subject_GND | (DE-588)4113937-9 |
| title | Folding dynamics of RNA secondary structures a structure based approach |
| title_auth | Folding dynamics of RNA secondary structures a structure based approach |
| title_exact_search | Folding dynamics of RNA secondary structures a structure based approach |
| title_full | Folding dynamics of RNA secondary structures a structure based approach von Michael Faber |
| title_fullStr | Folding dynamics of RNA secondary structures a structure based approach von Michael Faber |
| title_full_unstemmed | Folding dynamics of RNA secondary structures a structure based approach von Michael Faber |
| title_short | Folding dynamics of RNA secondary structures |
| title_sort | folding dynamics of rna secondary structures a structure based approach |
| title_sub | a structure based approach |
| topic_facet | Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027915763&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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