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2001 | 48 | 1 | 53-64
Article title

Novel approach to computer modeling of seven-helical transmembrane proteins: Current progress in the test case of bacteriorhodopsin.

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EN
Abstracts
EN
G-protein coupled receptors (GPCRs) are thought to be proteins with 7-membered transmembrane helical bundles (7TM proteins). Recently, the X-ray structures have been solved for two such proteins, namely for bacteriorhodopsin (BR) and rhodopsin (Rh), the latter being a GPCR. Despite similarities, the structures are different enough to suggest that 3D models for different GPCRs cannot be obtained directly employing 3D structures of BR or Rh as a unique template. The approach to computer modeling of 7TM proteins developed in this work was capable of reproducing the experimental X-ray structure of BR with great accuracy. A combination of helical packing and low-energy conformers for loops most close to the X-ray structure possesses the r.m.s.d. value of 3.13 Å. Such a level of accuracy for the 3D-structure prediction for a 216-residue protein has not been achieved, so far, by any available ab initio procedure of protein folding. The approach may produce also other energetically consistent combinations of helical bundles and loop conformers, creating a variety of possible templates for 3D structures of 7TM proteins, including GPCRs. These templates may provide experimentalists with various plausible options for 3D structure of a given GPCR; in our view, only experiments will determine the final choice of the most reasonable 3D template.
Publisher

Year
Volume
48
Issue
1
Pages
53-64
Physical description
Dates
published
2001
received
2000-12-20
accepted
2001-01-31
Contributors
  • Department of Biochemistry and Molecular Biophysics, Washington University, Campus Box 8036, St. Louis, MO 63110, U.S.A.
  • Department of Biochemistry and Molecular Biophysics, Washington University, Campus Box 8036, St. Louis, MO 63110, U.S.A.
author
  • Latvian Institute of Organic Synthesis, Riga, LV-1006, Latvia
  • Department of Biochemistry and Molecular Biophysics, Washington University, Campus Box 8036, St. Louis, MO 63110, U.S.A.
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Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv48i1p53kz
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