Protein simulations in confined environments

Murat Cetinkaya; Jorge Sofo; Melik C. Demirel

doi:10.1117/12.558733

2 August 2004 Protein simulations in confined environments

Murat Cetinkaya, Jorge Sofo, Melik C. Demirel

Proceedings Volume 5509, Nanomodeling; (2004) https://doi.org/10.1117/12.558733
Event: Optical Science and Technology, the SPIE 49th Annual Meeting, 2004, Denver, Colorado, United States

Abstract

Materials surfaces mimic cell like architecture and proteins can be encapsulated by these material surfaces (e.g. a porous glass or gold). Depending on the number and types of surface interactions, this confine environment could destroy the protein or help it maintain its bioactivity. We developed computer models and simulation tools for the understanding of surface-protein interaction at the atomistic levels. At the molecular level, molecular dynamics simulations are very powerful, but the high computational cost of molecular simulations is a drawback. A viable alternative method to study protein-surface interactions is the coarse-grained molecular simulations of simplified models, such as elastic network model. At the atomic interaction level, we used ab initio simulations to calculate the potential between surface and protein atoms.

Citation Download Citation

Murat Cetinkaya, Jorge Sofo, and Melik C. Demirel "Protein simulations in confined environments", Proc. SPIE 5509, Nanomodeling, (2 August 2004); https://doi.org/10.1117/12.558733

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