2Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; fax: (495) 939-2374; E-mail: firstname.lastname@example.org
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Received March 5, 2011; Revision received April 29, 2011
Conformational and dynamic properties of proteins and peptides play an important role in their functioning. However, mechanisms that underlie this influence have not been fully elucidated. In the present work we computationally constructed analogs of heptapeptide AFP14-20 (LDSYQCT) – one of the biologically active sites of human α-fetoprotein (AFP) – to study their conformational and dynamic properties using molecular dynamics simulation. Analogs were obtained by point substitutions of amino acid residues taking into account differences in their physicochemical properties and also on the basis of analysis of amino acid substitutions in the AFP14-20-like motifs revealed in different physiologically active proteins. It is shown that changes in conformational mobility of amino acid residues of analogs are due to disruption or arising of intramolecular interactions that, in turn, determine existence of steric restrictions during rotation around covalent bonds of the peptide backbone. Substitution of an amino acid by another one with significant difference in physicochemical properties may not lead to remarkable changes in conformational and dynamic properties of the peptide if intramolecular interactions remain unchanged.
KEY WORDS: α-fetoprotein, AFP, analogs of heptapeptide AFP14-20, molecular dynamics, intramolecular interactions