Side-chain conformations in 4-alpha-helical bundles.
The distribution of the chi(1), chi(2) dihedral angles in a dataset consisting of 12 unrelated 4-alpha-helical bundle proteins was determined and qualitatively compared with that observed in globular proteins. The analysis suggests that the 4-alpha-helical bundle motif could occasionally impose steric constraints on side chains: (i) the side-chain conformations are limited to only a subset of the conformations observed in globular proteins and for some amino acids they are sterically more constrained than those in helical regions of globular proteins; (ii) aspartic acid and asparagine occasionally adopt rotamers that have not been previously reported for globular or helical proteins; (iii) some rotamers of tyrosine and isoleucine are predominantly or exclusively associated with hydrophobic core positions (a, d); (iv) mutations in the hydrophobic core occur preferentially between residue types which among other physicochemical properties also share a predominant rotamer.
Fadouloglou
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VE
Department of Biology, University of Crete, P.O. Box 2208, GR-71409 Heraklion and Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology (IMBB), P.O. Box 1527, GR-71110 Heraklion, Crete, Greece.
Glykos
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NM
Kokkinidis
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M
D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D016208:Databases, Factual; D006801:Humans; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins