Modelling of GPCRS: a practical handbook
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Dordrecht [u.a.]
Springer
2013
|
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | IX, 218 S. Ill., graph. Darst. |
| ISBN: | 9789400745957 |
Internformat
MARC
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| 008 | 121023s2013 ad|| |||| 00||| eng d | ||
| 010 | |a 2012938366 | ||
| 020 | |a 9789400745957 |c (alk. paper) |9 978-94-007-4595-7 | ||
| 035 | |a (OCoLC)812568680 | ||
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| 041 | 0 | |a eng | |
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| 100 | 1 | |a Strasser, Andrea |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Modelling of GPCRS |b a practical handbook |c Andrea Strasser ; Hans-Joachim Wittmann |
| 264 | 1 | |a Dordrecht [u.a.] |b Springer |c 2013 | |
| 300 | |a IX, 218 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 700 | 1 | |a Wittmann, Hans-Joachim |e Verfasser |4 aut | |
| 856 | 4 | 2 | |m HBZ Datenaustausch |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025345338&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-025345338 | ||
Datensatz im Suchindex
| _version_ | 1804149565161472000 |
|---|---|
| adam_text | Titel: Modelling of GPCRS
Autor: Straßer, Andrea
Jahr: 2013
Contents
1 Introduction................................................... 1
2 G Protein Coupled Receptors.................................... 5
2.1 Structure of GPCRs......................................... 5
2.2 Different GPCR Families.................................... 5
2.3 Activation of GPCRs and Their Interaction with G Proteins........ 7
2.4 Important Internet Sources with Regard to GPCRs............... 10
3 Sequence Alignment and Homology Modelling.................... 13
3.1 Selection of a Template...................................... 13
3.2 Crystal Structures of GPCRs................................. 14
3.3 Amino Acid Sequences and Sequence Alignment................ 18
3.3.1 Amino Acid Sequences - Where to Get From?............ 18
3.3.2 Ballesteros Nomenclature............................. 20
3.3.3 Amino Acid Sequences - Templates..................... 20
3.3.4 Sequence Alignment.................................. 22
3.4 Homology Modelling....................................... 23
3.4.1 Modelling of the Transmembrane Domains............... 23
3.4.2 Modelling of Loops.................................. 23
3.4.3 Modelling of Internal Water............................ 25
3.4.4 Modelling of the C-Terminal Part of the Ga Subunit or the
Whole Ga Subunit................................... 25
3.4.5 Refinement of the Receptor Model...................... 26
4 Construction of Ligands........................................ 29
5 Lipids ........................................................ 37
5.1 Structure of Lipids.......................................... 37
5.2 Structure of the Phospholipid Bilayer.......................... 39
5.3 Lipid Bilayer Models Used in Molecular Modelling.............. 40
5.4 Internet Sources for Lipid Bilayer Models...................... 40
5.5 Embedding a GPCR into a Lipid Bilayer....................... 42
viii Contents
6 Minimization and Molecular Dynamics........................... 59
6.1 Generating a Complete Model of the Interesting GPCR.......... 60
6.2 Embedding the GPCR in a Lipid Bilayer...................... 60
6.3 Solvation of the Lipid-GPCR-Complex, Achiving
Electroneutrality of the Simulation Box and Minimization....... 60
6.4 Molecular Dynamic Simulation of your System................ 62
7 Calculation of Gibbs Energy of Solvation......................... 75
7.1 Theory - Link Between Microscopic and Macroscopic World .... 75
7.1.1 Statistical Mechanical Basics......................... 75
7.1.2 From Potential Energy to the Chemical Potential......... 77
7.1.3 The Concept of the Coupling Parameter Within MD
Simulations........................................ 79
7.2 Examples - Conceptual and Practical Considerations............ 80
7.2.1 Example 1 : Ethanol in Water - Conceptual
Considerations..................................... 80
7.2.2 Example 2: Ligand-Receptor-Complex and
Affinity - Conceptual Considerations .................. 83
7.2.3 Example 1: Ethanol in Water - Practical Considerations ... 85
7.2.4 Example 2: Gibbs Energy of Binding .................. 99
8 Special Topics in GPCR Research................................ 105
8.1 Interaction Between a GPCR and the Goc-subunit............... 105
8.2 Process of Ligand Binding from the Extracellular Side
into the Binding Pocket of a GPCR.......................... 112
9 Force Fields................................................... 121
9.1 The Force Field Energy.................................... 121
9.1.1 The Stretching Energy............................... 121
9.1.2 The Bending Energy ................................ 122
9.1.3 The Torsional Energy................................ 123
9.1.4 The van der Waals Energy............................ 124
9.1.5 The Electrostatic Energy............................. 124
9.2 The All-atom-concept and Site-concept....................... 124
9.3 The Force Field Parameters................................. 125
10 Thermodynamics of Ligand-Receptor Interaction.................. 131
10.1 Motivation............................................... 131
10.2 Ligand-Receptor Model.................................... 131
10.3 Thermodynamic Basics .................................... 132
10.4 Evaluating AH0 and AS°................................... 136
10.5 Special Topics............................................ 138
Contents ix
11 Important UNIX/LINUX Commands............................. 139
11.1 Some Basic Aspects of the Operating System UNIX/LINUX..... 139
11.2 The Use of Shell Operators and Meta-Characters in Tcsh
Environments............................................. 139
11.3 Shell Substitutions ........................................ 140
11.3.1 File Name Substitution............................. 141
11.3.2 Variable Substitution............................... 141
11.3.3 Command Substitution............................. 143
11.3.4 Protection Mechanism for Meta-Characters
of the TC-Shell.................................... 143
11.4 Discussion of Selected LINUX Commands.................... 144
11.5 Loops Statements of the Tcsh Shell .......................... 152
11.6 Working with Shell Scripts.................................. 153
11.7 A More Extensive Example................................. 155
Appendix......................................................... 161
References........................................................ 209
Index ............................................................ 217
|
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| id | DE-604.BV040498515 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T00:25:03Z |
| institution | BVB |
| isbn | 9789400745957 |
| language | English |
| lccn | 2012938366 |
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| physical | IX, 218 S. Ill., graph. Darst. |
| publishDate | 2013 |
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| spelling | Strasser, Andrea Verfasser aut Modelling of GPCRS a practical handbook Andrea Strasser ; Hans-Joachim Wittmann Dordrecht [u.a.] Springer 2013 IX, 218 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Wittmann, Hans-Joachim Verfasser aut HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025345338&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Strasser, Andrea Wittmann, Hans-Joachim Modelling of GPCRS a practical handbook |
| title | Modelling of GPCRS a practical handbook |
| title_auth | Modelling of GPCRS a practical handbook |
| title_exact_search | Modelling of GPCRS a practical handbook |
| title_full | Modelling of GPCRS a practical handbook Andrea Strasser ; Hans-Joachim Wittmann |
| title_fullStr | Modelling of GPCRS a practical handbook Andrea Strasser ; Hans-Joachim Wittmann |
| title_full_unstemmed | Modelling of GPCRS a practical handbook Andrea Strasser ; Hans-Joachim Wittmann |
| title_short | Modelling of GPCRS |
| title_sort | modelling of gpcrs a practical handbook |
| title_sub | a practical handbook |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025345338&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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