A molecular dynamics study of the pentacyclo-undecane (PCU) cage polypeptides of the type Ac-3Ala-Cage-3Ala-NHMe |
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| Authors: | K Bisetty H G Kruger J J Perez |
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| Institution: | 1. Department of Chemistry , Durban University of Technology , Steve Biko campus, P.O. Box 1334, Durban, 4000, South Africa bisettyk@dut.ac.za;3. School of Chemistry , University of Kwa-Zulu Natal , Durban, 4041, South Africa;4. Department d'Enginyeria Química , UPC. ETS d'Enginyers Industrials , Av. Diagonal, 647, 08028, Barcelona, Spain |
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| Abstract: | An extensive exploration of the conformational space of the seven-residue peptide sequences, Ac-Ala-Ala-Ala-Cage-Ala-Ala-Ala-NHMe and the model peptide Ac-Ala-Ala-Ala-Ala-Ala-Ala-Ala-NHMe, was carried out using single trajectories of molecular dynamics (MD) in the solution phase using the periodic boundary conditions. Our MD studies revealed that the majority of the motifs of the PCU cage peptide exist as type I–III β-turns along with their mirror conformations, viz. type I′–III′ β-turns. This peptide sequence adopted a U-shaped backbone, with alpha-helical characteristics. The results reported here provide further evidence that the PCU cage amino acid exhibits C7eq, C7aq, αR and αL conformations in aqueous solution. |
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| Keywords: | Unnatural amino acids Pentacyclo-undecane cage dipeptide Conformational analysis AMBER Reverse-turn characteristics β-Turns |
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