Conservation of amino acids in multiple alignments: aspartic acid has unexpected conservation

FEBS Letters
A FiserG J Barton

Abstract

Analysis of the relationship between surface accessibility and amino acid conservation in multiple sequence alignments of homologous proteins confirms expected trends for hydrophobic amino acids, but reveals an unexpected difference between the conservation of Asp, Glu and Gln. Even when not in an active site, Asp is more highly conserved than Glu. There is a clear preference for conserved and buried Asp to be present in coil, but there is no tendency for Asp to conserve phi/psi in the ++ region of the Ramachandran map. Glu does not show any preference to be conserved in a particular secondary structure. Analysis of recently derived substitution matrices (e.g. BLOSUM) confirms that Glu tends to substitute more frequently with other amino acids than does Asp. Analysis of relative accessibility versus relative conservation for individual amino acid positions in alignments shows a negative correlation for all amino acid types. With the exception of Arg, Lys, Gly, Glu, Asp and Tyr, a relative conservation of > 2 suggests the amino acid will have a relative accessibility of < 50%. Observation of conserved Cys, Gly or Asp in a reliable multiple alignment suggests a position important for the structure of the protein. Furthermore, the...Continue Reading

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Citations

Feb 19, 2000·Biopolymers·H O Villar, R T Koehler
Jan 28, 2003·Journal of Molecular Biology·Ruslan Sadreyev, Nick Grishin
Jun 26, 2003·Nucleic Acids Research·Zsuzsanna DosztányiIstván Simon
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