Model-building codes for membrane proteins.

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We have developed a novel approach to modeling the transmembrane spanning helical bundles of integral membrane proteins using only a sparse set of distance constraints, such as those derived from MS3-D, dipolar-EPR and FRET experiments. Algorithms have been written for searching the conformational space of membrane protein folds matching the set of distance constraints, which provides initial structures for local conformational searches. Local conformation search is achieved by optimizing these candidates against a custom penalty function that incorporates both measures derived from statistical analysis of solved membrane protein structures and distance constraints obtained from experiments. This results in refined helical ... continued below

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75 p.

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Shirley, David Noyes; Hunt, Thomas W.; Brown, W. Michael; Schoeniger, Joseph S. (Sandia National Laboratories, Livermore, CA); Slepoy, Alexander; Sale, Kenneth L. (Sandia National Laboratories, Livermore, CA) et al. January 1, 2005.

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Description

We have developed a novel approach to modeling the transmembrane spanning helical bundles of integral membrane proteins using only a sparse set of distance constraints, such as those derived from MS3-D, dipolar-EPR and FRET experiments. Algorithms have been written for searching the conformational space of membrane protein folds matching the set of distance constraints, which provides initial structures for local conformational searches. Local conformation search is achieved by optimizing these candidates against a custom penalty function that incorporates both measures derived from statistical analysis of solved membrane protein structures and distance constraints obtained from experiments. This results in refined helical bundles to which the interhelical loops and amino acid side-chains are added. Using a set of only 27 distance constraints extracted from the literature, our methods successfully recover the structure of dark-adapted rhodopsin to within 3.2 {angstrom} of the crystal structure.

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75 p.

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  • Report No.: SAND2004-6383
  • Grant Number: AC04-94AL85000
  • DOI: 10.2172/920776 | External Link
  • Office of Scientific & Technical Information Report Number: 920776
  • Archival Resource Key: ark:/67531/metadc899813

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  • January 1, 2005

Added to The UNT Digital Library

  • Sept. 27, 2016, 1:39 a.m.

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  • Dec. 7, 2016, 5:42 p.m.

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Shirley, David Noyes; Hunt, Thomas W.; Brown, W. Michael; Schoeniger, Joseph S. (Sandia National Laboratories, Livermore, CA); Slepoy, Alexander; Sale, Kenneth L. (Sandia National Laboratories, Livermore, CA) et al. Model-building codes for membrane proteins., report, January 1, 2005; United States. (digital.library.unt.edu/ark:/67531/metadc899813/: accessed October 21, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.