Abstract
Conformations of biomolecules are the basis for their property studies and the predictions of peptide structures are of high interest in life science but very difficult in practice. The potential energy surfaces of five tetrapeptides, GGGG, GVGG, GTGG, GGYG and GSDG, are thoroughly explored here by considering all combinations of their internal single bond rotamers. The structural features of all the important tetrapeptide conformers are analyzed in detail and are characterized with five hydrogen bond configurations. Close connections between the conformations of tetrapeptides and their constituting dipeptides are found. A method for finding all important tetrapeptide conformers by splicing the parent dipeptide conformations is deduced. The splicing method is validated to be both efficient and reliable for all the tetrapeptides examined. Application of the splicing method to pentaglycine provides results far better than the literature. It also yields conformations with characteristic secondary structures such as strands, helices, and turns which are highly populated in proteins. Further development of the splicing method is a promising way to find a reliable and efficient amino acid sequence based protein structure prediction method.
Published Version
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