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Driving forces for transmembrane alpha-helix oligomerization.

ABSTRACT: We present what we believe to be a novel statistical contact potential based on solved structures of transmembrane (TM) alpha-helical bundles, and we use this contact potential to investigate the amino acid likelihood of stabilizing helix-helix interfaces. To increase statistical significance, we have reduced the full contact energy matrix to a four-flavor alphabet of amino acids, automatically determined by our methodology, in which we find that polarity is a more dominant factor of group identity than is size, with charged or polar groups most often occupying the same face, whereas polar/apolar residue pairs tend to occupy opposite faces. We found that the most polar residues strongly influence interhelical contact formation, although they occur rarely in TM helical bundles. Two-body contact energies in the reduced letter code are capable of determining native structure from a large decoy set for a majority of test TM proteins, at the same time illustrating that certain higher-order sequence correlations are necessary for more accurate structure predictions.

SUBMITTER: Sodt AJ

PROVIDER: S-EPMC2895374 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

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Driving forces for transmembrane alpha-helix oligomerization.

Sodt Alex J AJ Head-Gordon Teresa T

Biophysical journal 20100701 1

We present what we believe to be a novel statistical contact potential based on solved structures of transmembrane (TM) alpha-helical bundles, and we use this contact potential to investigate the amino acid likelihood of stabilizing helix-helix interfaces. To increase statistical significance, we have reduced the full contact energy matrix to a four-flavor alphabet of amino acids, automatically determined by our methodology, in which we find that polarity is a more dominant factor of group ident ...[more]

PMID: 20655851

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