Computational Protein Design

Armando Jerome de Jesus, Hang Yin, de Jesus, Armando Jerome, Yin, Hang

Ilan Samish

Computer simulations have become an indispensable tool in studying molecular biological systems. The unmatched spatial and temporal resolution that it offers enables for microscopic-level views into the dynamics and mechanics of biological systems. Recent advances in hardware resources have also opened up to computer simulations the investigation of longer timescale biological processes and larger systems. The study of membrane proteins or peptides especially benefits from simulations due to difficulties related to crystallization of such proteins in a membrane environment. In this chapter, we outline the method of molecular dynamics and how it is applied to simulations that involve a peptide and lipid bilayers. In particular, the simulation of a membrane-curvature sensing peptide is examined, and ways of employing computational simulations to design such peptides are discussed.