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Interaction of Adjacent Amino Acids
Author(s) -
Schlag E. W.,
Sheu ShehYi,
Selzle H. L.,
Yang DahYen
Publication year - 2006
Publication title -
journal of the chinese chemical society
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.329
H-Index - 45
eISSN - 2192-6549
pISSN - 0009-4536
DOI - 10.1002/jccs.200600031
Subject(s) - ramachandran plot , chemistry , dihedral angle , amino acid , torsion (gastropod) , crystallography , amino acid residue , diagonal , protein structure , geometry , peptide sequence , mathematics , molecule , biochemistry , medicine , hydrogen bond , surgery , organic chemistry , gene
Abstract Ramachandran plots display the dihedral angles of a single protein residue. We propose a crossed torsion angle plot called SSY‐plot between two neighboring amino acids and demonstrate that a special coherence motion can exist between some very special amino acid pairs leading to spontaneous unusual structures. A 6mer was extracted from a BBA polypeptide chain which in this plot shows two diagonal domains for the Ser‐Arg pair after some induction time. Other amino acid pairs in general do not show this kind of split domain. This shows that a special pair is required for stabilizing two distinct native structures in protein folding. We suggest that the existence of these two domains corresponds to a bifurcation between two different protein structures and that the special pair is the key to producing these two structures. These two different structures are produced spontaneously without an external agent.