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Journal of Computer-Aided Molecular Design

, Volume 15, Issue 6, pp 533–552 | Cite as

A sequence and structural study of transmembrane helices

  • Robert P. Bywater
  • David Thomas
  • Gerrit Vriend
Article

Abstract

A comparison is made between the distribution of residue preferences, three dimensional nearest neighbour contacts, preferred rotamers, helix-helix crossover angles and peptide bond angles in three sets of proteins: a non-redundant set of accurately determined globular protein structures, a set of four-helix bundle structures and a set of membrane protein structures. Residue preferences for the latter two sets may reflect overall helix stabilising propensities but may also highlight differences arising out of the contrasting nature of the solvent environments in these two cases. The results bear out the expectation that there may be differences between residue type preferences in membrane proteins and in water soluble globular proteins. For example, the β-branched residue types valine and isoleucine are considerably more frequently encountered in membrane helices. Likewise, glycine and proline, residue types normally associated with `helix-breaking' propensity are found to be relatively more common in membrane helices. Three dimensional nearest neighbour contacts along the helix, preferred rotamers, and peptide bond angles are very similar in the three sets of proteins as far as can be ascertained within the limits of the relatively low resolution of the membrane proteins dataset. Crossing angles for helices in the membrane protein set resemble the four helix bundle set more than the general non-redundant set, but in contrast to both sets they have smaller crossing angles consistent with the dual requirements for the helices to form a compact structure while having to span the membrane. In addition to the pairwise packing of helices we investigate their global packing and consider the question of helix supercoiling in helix bundle proteins.

helix-helix crossing angle membrane proteins peptide bond angles residue preferences rotamers supercoiling 

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Copyright information

© Kluwer Academic Publishers 2001

Authors and Affiliations

  • Robert P. Bywater
    • 1
  • David Thomas
    • 2
  • Gerrit Vriend
    • 2
  1. 1.Biostructure GroupNovo Nordisk A/SMÅLØV, Denmark
  2. 2.Biocomputing GroupEMBLHeidelbergGermany

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