title: Computational Design of Membrane Curvature-Sensing Peptides.
abstract: 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.
authors.affiliation: Department of Chemistry and Biochemistry and The BioFrontiers Institute, University of Colorado, UCB 596, Boulder, CO, 80309, USA.
authors.forename: Armando Jerome
authors.initials: AJ
authors.lastname: de Jesus
authors.affiliation: Department of Chemistry and Biochemistry and The BioFrontiers Institute, University of Colorado, UCB 596, Boulder, CO, 80309, USA. hubert.yin@colorado.edu.
authors.forename: Hang
authors.initials: H
authors.lastname: Yin
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008051:Lipid Bilayers / Q000737:chemistry; D008563:Membrane Lipids / Q000737:chemistry / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D015202:Protein Engineering / Q000379:methods*
chemical_list: D008051:Lipid Bilayers; D008563:Membrane Lipids; D008565:Membrane Proteins; D010455:Peptides
keywords: CHARMM; Curvature-sensing peptides; Membrane curvature; Molecular dynamics; Protein–lipid interactions