A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure.

Autor: Saša Malkov, Miodrag Živković, Miloš Beljanski, Michael Hall, Snežana Zarić
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Zdroj: Journal of Molecular Modeling; Aug2008, Vol. 14 Issue 8, p769-775, 7p
Abstrakt: Abstract  The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: α-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their Cβ and Cγ atoms that predicts their preference for a particular secondary structure. All α-helix preferrers have neither polar heteroatoms on Cβ and Cγ atoms, nor branching or aromatic group on the Cβ atom. All strand preferrers have aromatic groups or branching groups on the Cβ atom. All turn and bend preferrers have a polar heteroatom on the Cβ or Cγ atoms or do not have a Cβ atom at all. These new rules could be helpful in making predictions about non-natural amino acids. [ABSTRACT FROM AUTHOR]
Databáze: Complementary Index
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