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Abstract
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Recent dramatic advances in methodologies for the synthesis,modification, and analysis of peptides have
increased the ease with which novel sequences can be prepared. native protein sequence, thereby allowing one to
evaluate how one or more side chains contribute to the physical and biological properties of a protein. Furthermore,
as our understanding of the determinants of peptide and protein structure expands, it should be increasingly possible
to design peptides and proteins with predetermined structures and properties. Nevertheless, by carefully considering
the structures of natural proteins and by judiciously applying computational and graphical techniques in conjunction
with physical models, it appears possible to achieve this goal. Understanding the dynamics and mechanism of
protein folding continues to be one of the central problems in molecular biology. Peptides have many of the features
and complexities of proteins. In general , the competition between configurational entropy, hydrogen bond formation,
solvation, hydrophobic coreformation and ionpair formation determines the folding rate and stability of proteins.
This competition plays an essential role throughout the folding process and determines the thermodynamic
equilibrium between folded and unfolded states. Modeling this competition is a standing challenge in peptide
folding simulations.There are different empirical techniques for identifying the structural and dynamic aspects of the
proteins. In addition to the empirical methods, molecular dynamics (MD) simulation is a powerful tool for
completing and interpreting experimental results.
Here, in order to study the effect of hydrophobicity of residues on the interaction of a cyclopetid with water, we
simulated three hexa-cyclo peptids composed from Glycine and Serine amino acids. The considered peptides are
fromed from glycine, glycine-serine and serine residues. The tree dimentioanl structures of the considered peptides
were prepared by the help of p
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