Lipid-protein interactions at the membrane interface: = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche
Saved in:
| Main Author: | |
|---|---|
| Format: | Thesis Book |
| Language: | English |
| Published: |
Erlangen ; Nürnberg
[2017]
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | xlviii, 135 Seiten Illustrationen, Diagramme |
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| 245 | 1 | 0 | |a Lipid-protein interactions at the membrane interface |b = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche |c vorgelegt von Angelica Sandoval-Perez aus Bogota-Colombia |
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| 264 | 1 | |a Erlangen ; Nürnberg |c [2017] | |
| 300 | |a xlviii, 135 Seiten |b Illustrationen, Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
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| 338 | |b nc |2 rdacarrier | ||
| 502 | |b Dissertation |c Friedrich-Alexander-Universität Erlangen-Nürnberg |d 2017 | ||
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Record in the Search Index
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|---|---|
| adam_text | C ONTENTS
DECLARATION O F AUTHORSHIP III
ABSTRACT V
ZUSAMMENFASSUNG VII
ACKNOWLEDGEMENTS IX
CONTENTS XI
LIST OF FIGURES XV
LIST O F TABLES XIX
ABBREVIATIONS XXI
INTRODUCTION XXV
1 M ETHODS 1
1.1 MD
SIMULATIONS.......................................................................................
1
1.2 THE POTENTIAL OF MEAN F O RCE
.................................................................
6
1.2.1 PULLING AND UMBRELLA S AM P LIN G
............................................... 8
2 THE MOLECULAR SWITCHING MECHANISM AT THE CONSERVED D (E )R Y
M OTIF IN CLASS-A G PC R S 11
2.1 A B STRA C
T....................................................................................................
13
2.2
INTRODUCTION.............................................................................................
14
2.3 M ETH O D
S........................................................................................................16
2.3.1 PEPTIDE SEQUENCES USED IN MD
CALCULATIONS..................................16
2.3.2 DETAILS OF MD SIM
ULATIONS........................................................ 17
2.3.3 DETERMINATION OF GLU27 PKA ON HELICAL PEPTIDES AND UNSTRUC-
TURED
PEPTIDES..............................................................................
18
2.3.4 INFRARED SPECTROSCOPY OF LIPID-RECONSTITUTED MODEL PEPTIDES
AND OPSIN M U T A N T S
.........................................................................
19
2.4 R ESU
LTS...........................................................................................................
20
2.4.1 COUPLING OF GLU27 PROTONATION TO TRANSMEMBRANE HELICITY . . 20
2.4.2 DYNAMICS OF GLU27 SIDE CHAIN CONFORMATION
................................
22
2.4.3 PROTONATION-DEPENDENT TRANSMEMBRANE POSITIONING OF THE
HELICAL BACKBONE
............................................................................23
2.4.4 COUPLING OF GLU27 SIDE CHAIN PKA TO DIELECTRIC ENVIRONMENT . 23
2.4.5 GLU27 PROTONATION EXERTS LONG-RANGE DIELECTRIC EFFECTS WITHIN
THE BILAY ER
........................................................................................
26
2.4.6 SIDE CHAIN-DEPENDENT DYNAMICS OF THE SUB-HEADGROUP H-
BOND N E TW O RK
..................................................................................
27
2.5 D
ISCUSSION.....................................................................................................29
2.6 ACKNOWLEDGEMENT
........................................................................................
33
3 CRITICAL COMPARISON OF BIOMEMBRANE FORCE FIELDS: PROTEIN-LIPID
INTERACTIONS AT THE M EMBRANE INTERFACE 35
3.1 A B S TRA C T................- .
...........................................
.....................................
37
3.2
INTRODUCTION..................................................................................................37
3.3 MATERIALS AND M ETH O D S
..............................................
39
3.3.1 TRANSMEMBRANE PROTEIN SIM ULATIONS
.............................................
40
3.3.2 TRANSMEMBRANE PEPTIDE SIMULATIONS
.............................................
42
3.3.3 INSERTION DEPTH OF OLIGOPEPTIDES AT THE MEMBRANE INTERFACE . 42
3.3.4 ENERGY PROFILES OF INDIVIDUAL AMINO ACIDS
.....................................
44
3.3.5 ENERGY PROFILES OF DIPEPTIDES
.........................................................
46
3.3.6 FREE
ENERGIES OF ABSORPTION OF OLIGOPEPTIDES
..................................47
3.4 R
ESULTS...........................................................................................................
47
3.4.1 CONSERVATION OF SECONDARY STRU CTU
RE.............................................47
3.4.2 TRANSMEMBRANE PEPTIDE
POSITIONING...............................................48
3.4.3 ABSORPTION OF WIMLEY-WHITE PEPTIDES TO THE MEMBRANE IN
TERFACE.................................................................................................
50
3.4.4 PROFILES OF UNCAPPED AMINO ACIDS
...................................................
51
3.4.5 VALIDATION OF LINEAR MEMBRANE ABSORPTION FREE ENERGY FOR
P E P TID E S
............................................................................................53
3.4.6 INSERTION ENERGY OF WIMLEY-WHITE PEPTIDES. .
.
.........................
54
3.5 DISCUSSION AND GONCLUSIONS
......................................................................56
3.6 ACKNOWLEDGMENTS
........................................................................................
58
4 INTERFACIAL M EMBRANE BINDING REGULATES TOXICITY O F ANTIMICROBIAL
PEPTIDES 61
SUMMARY AND CONCLUSIONS 69
APPENDICES 71
A SUPPLEMENTARY INFORMATION: THE MOLECULAR SWITCHING MECHANISM
AT THE CONSERVED D (E )R Y M OTIF IN CLASS-A G PC R S 71
B SUPPLEMENT ARY INFORMATION: CRITICAL COMPARISON O F BIOM EM
BRANE FORCE FIELDS: PROTEIN-LIPID INTERACTIONS AT THE MEMBRANE
INTERFACE 73
C SUPLEMENTARY INFORMATION: INTERFACIAL MEMBRANE BINDING REGU-
LATES TOXICITY OF ANTIMICROBIAL PEPTIDES 101
BIBLIOGRAPHY
121
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| indexdate | 2024-07-10T07:55:36Z |
| institution | BVB |
| language | English |
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| physical | xlviii, 135 Seiten Illustrationen, Diagramme |
| publishDate | 2017 |
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| spelling | Sandoval-Perez, Angelica Verfasser aut Lipid-protein interactions at the membrane interface = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche vorgelegt von Angelica Sandoval-Perez aus Bogota-Colombia Lipid-Protein Wechselwirkungen an der Membrangrenzfläche Erlangen ; Nürnberg [2017] xlviii, 135 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Dissertation Friedrich-Alexander-Universität Erlangen-Nürnberg 2017 Proteine (DE-588)4076388-2 gnd rswk-swf Wechselwirkung (DE-588)4064937-4 gnd rswk-swf Biomembran (DE-588)4006884-5 gnd rswk-swf Molekulardynamik (DE-588)4170370-4 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Biomembran (DE-588)4006884-5 s Molekulardynamik (DE-588)4170370-4 s Wechselwirkung (DE-588)4064937-4 s Proteine (DE-588)4076388-2 s DE-604 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029947586&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Sandoval-Perez, Angelica Lipid-protein interactions at the membrane interface = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche Proteine (DE-588)4076388-2 gnd Wechselwirkung (DE-588)4064937-4 gnd Biomembran (DE-588)4006884-5 gnd Molekulardynamik (DE-588)4170370-4 gnd |
| subject_GND | (DE-588)4076388-2 (DE-588)4064937-4 (DE-588)4006884-5 (DE-588)4170370-4 (DE-588)4113937-9 |
| title | Lipid-protein interactions at the membrane interface = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche |
| title_alt | Lipid-Protein Wechselwirkungen an der Membrangrenzfläche |
| title_auth | Lipid-protein interactions at the membrane interface = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche |
| title_exact_search | Lipid-protein interactions at the membrane interface = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche |
| title_full | Lipid-protein interactions at the membrane interface = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche vorgelegt von Angelica Sandoval-Perez aus Bogota-Colombia |
| title_fullStr | Lipid-protein interactions at the membrane interface = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche vorgelegt von Angelica Sandoval-Perez aus Bogota-Colombia |
| title_full_unstemmed | Lipid-protein interactions at the membrane interface = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche vorgelegt von Angelica Sandoval-Perez aus Bogota-Colombia |
| title_short | Lipid-protein interactions at the membrane interface |
| title_sort | lipid protein interactions at the membrane interface lipid protein wechselwirkungen an der membrangrenzflache |
| title_sub | = Lipid-Protein Wechselwirkungen an der Membrangrenzfläche |
| topic | Proteine (DE-588)4076388-2 gnd Wechselwirkung (DE-588)4064937-4 gnd Biomembran (DE-588)4006884-5 gnd Molekulardynamik (DE-588)4170370-4 gnd |
| topic_facet | Proteine Wechselwirkung Biomembran Molekulardynamik Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029947586&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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