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J Phys Chem B. 2012 Jun 7;116(22):6288-301. doi: 10.1021/jp3013305. Epub 2012 May 22.

Initiation of the reaction of deamidation in triosephosphate isomerase: investigations by means of molecular dynamics simulations.

Author information

1
Department of Chemistry, Boğaziçi University, 34342 Bebek, Istanbul, Turkey.

Abstract

Deamidation of asparagine is the spontaneous degradation of this residue into aspartic acid. The kinetics of this slow reaction is mainly dependent on the nature of the adjacent amino acid that follows asparagine in a peptide or protein primary sequence. In the homodimer triosephosphate isomerase (TPI), there are two main deamidation sites per subunit: Asn15-Gly16 and Asn71-Gly72 for which deamidation dynamics are known to be interrelated. In this study, we investigate the initiation of the deamidation reaction in TPI by means of molecular dynamics. Simulations based on classical AMBER force field are performed in a 60 to 90 ns time scale for six distinct samples. Conformational changes, desolvation effects, and hydrogen bond networks are analyzed to interpret the experimental findings and previous quantum mechanical (QM) results. Results that are based on desolvation analysis clarify the assignments in the literature about the different behaviors of two deamidating sites in TPI. Conformational analysis supports findings suggested by QM studies: the most favorable reaction mechanism is the one that yields to succinimide intermediate via one or two step routes. The mechanism leading to the succinimide intermediate most likely involves the formation of a tetrahedral intermediate that is formed either directly from asparagine or via a side chain tautomer intermediate. In all cases, surrounding water molecules are present to assist the reaction.

PMID:
22574817
DOI:
10.1021/jp3013305
[Indexed for MEDLINE]

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