Dynamic effects on peptide structure: molecular dynamics simulations of a peptide employing ensemble of peptides

Abstract

Interactions between molecular surfaces are fundamental to all natural processes. Based on these interactions, living systems such as animals, plants, and microorganisms maintain complex regulatory and metabolic interaction networks that in concert form the processes of life. The development of molecular modeling tools for understanding molecular interactions has been used extensively. However, elucidation of the mechanism of molecular interaction between nanosystems like proteins is quite complex. Feedback from the current results plays a role in increasing the complexity of such interactions. Such feedback loops demonstrate the need for creating novel computational model for complex phenomena like protein-protein interactions. Experimental measurements of protein interactions involve averaging over an ensemble of molecules. However, theoretical and computational models typically predict conformations of a peptide or protein on the basis of a single, isolated molecule in a box of solvent. In the present study, we have developed a simulation system consisting of ensemble of peptides (as shown below, a two peptide system). The dynamic effects on peptide structure in this simulation system are compared with the isolated single peptide simulation. The results clearly suggest that it is more appropriate to consider peptides in an ensemble during MD simulations. While the single peptide simulations consider the intramolecular interactions, it completely ignores the vital intermolecular interactions between two peptides molecules.