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Systematic molecular dynamics searching in a lipid bilayer: Application to the glycophorin A and oncogenic ErbB-2 transmembrane domains
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Beevers, Andrew J. and Kukol, Andreas. (2006) Systematic molecular dynamics searching in a lipid bilayer: Application to the glycophorin A and oncogenic ErbB-2 transmembrane domains. JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 25 (2). pp. 226-233. ISSN 1093-3263
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Official URL: http://dx.doi.org/10.1016/j.jmgm.2005.12.008
Abstract
Molecular dynamics (MD) simulations of proteins in a lipid bilayer environment are usually undertaken with one or a few starting structures. Here we report a search protocol for systematically exploring the possible interactions in helical bundle transmembrane proteins, a frequently occurring structural motif. The search protocol correctly identifies the experimentally known structure of the dimeric human glycophorin A transmembrane domain as the lowest energy structure among five different models without any prior assumptions, whilst an identical in vacuo search fails to identify the correct structure. The lowest energy structure from the search in a lipid bilayer has a root mean square deviation of 1.1 angstrom to the experimental structure. We have applied the same search protocol to the unknown transmembrane structure of the oncogenic mutant ErbB-2 protein, a member of the family of epidermal growth factor receptors. Resulting structures show the role of glutamic acid hydrogen bonding and close helical packing. Water molecules may also play a key role in stabilisation of the transmembrane helix association. (c) 2006 Elsevier Inc. All rights reserved.
| Item Type: | Journal Article |
|---|---|
| Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software Q Science > QD Chemistry Q Science > QH Natural history > QH301 Biology |
| Journal or Publication Title: | JOURNAL OF MOLECULAR GRAPHICS & MODELLING |
| Publisher: | ELSEVIER SCIENCE INC |
| ISSN: | 1093-3263 |
| Date: | October 2006 |
| Volume: | 25 |
| Number: | 2 |
| Number of Pages: | 8 |
| Page Range: | pp. 226-233 |
| Identification Number: | 10.1016/j.jmgm.2005.12.008 |
| Publication Status: | Published |
| URI: | http://wrap.warwick.ac.uk/id/eprint/32854 |
Data sourced from Thomson Reuters' Web of Knowledge
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