The Study of REMD Simulation of SEB-Binding Repetitive Peptide Sequences

Nesrin KILIÇ, Kadir DEMİR

Abstract


We investigated whether the conformational differences of modified peptides play a role for affinity or not.  For this purpose, we have performed the replica exchange molecular dynamic simulation (REMD) to obtain the conformational states and secondary structural propensities of repetitive peptide sequences changed the affinity of binding to staphylococcal enterotoxin B (SEB). The results obtained from REMD simulations have shown that the secondary structures of these repetitive peptide sequences were mainly random coil, bend and turn structures with a small amount of helix and β-bridge structures for all temperatures. Besides it was shown that, with repeating the sequence, while the percentage of random coil structures decreased, the ones of bend structures increased. These results are consistent with the ones which obtained from circular dicroism spectroscopy. In terms of principal component analysis (PCA), the free energy landscapes of peptide sequences were obtained and found several local minima. The secondary structures corresponding with these minima have mainly coil, turn and bend structures for both peptides. In addition to these dominant structures considerable amount of helix and β-bridge structures were also outstanding. Its observed that while the number of repetition of peptide sequence increases, the percentage of random coil structures are decreases and this transformation in the random coil structures emerges in the form of increases in the rates of bend, turn, helix and β-bridge structures with the chosen temperature and region. The results pointed that it was not monitored a directly relationship between the affinity and secondary structures propensities of repetitive peptides.  


Keywords


replica exchange molecular dynamics, secondary structure, peptide ligands, principal component analysis, free energy landscape, SEB-binding peptides

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DOI: http://dx.doi.org/10.7212%2Fzkufbd.v1i1.531

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