Analysis of Helix-Helix Interactions of Bacteriorhodopsin by Replica-Exchange Simulations
نویسندگان
چکیده
منابع مشابه
Prediction of transmembrane helix configurations by replica-exchange simulations
We propose a method for predicting helical membrane protein structures by computer simulations. Our method consists of two parts. In the first part, amino-acid sequences of the transmembrane helix regions are obtained from one of existing WWW servers. In the second part, we perform a replica-exchange simulation of these transmembrane helices with some constraints and identify the predicted stru...
متن کاملRole of helix-helix interactions in assembly of the bacteriorhodopsin lattice.
The purple membrane of Halobacterium salinarium is a two-dimensional lattice of lipids and the integral membrane protein bacteriorhodopsin (BR). To determine whether helix-helix interactions within the membrane core stabilize this complex, we substituted amino acid residues at the helix-helix interface between BR monomers and examined the assembly of the protein into the lattice. Lattice assemb...
متن کاملReplica exchange Monte-Carlo simulations of helix bundle membrane proteins: rotational parameters of helices
We propose a united-residue model of membrane proteins to investigate the structures of helix bundle membrane proteins (HBMPs) using coarse-grained (CG) replica exchange Monte-Carlo (REMC) simulations. To demonstrate the method, it is used to identify the ground state of HBMPs in a CG model, including bacteriorhodopsin (BR), halorhodopsin (HR), and their subdomains. The rotational parameters of...
متن کاملHelix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins
MOTIVATION In many proteins, helix-helix interactions can be critical to establishing protein conformation (folding) and dynamics, as well as determining associations between protein units. However, the determination of a set of rules that guide helix-helix interaction has been elusive. In order to gain further insight into the helix-helix interface, we have developed a comprehensive package of...
متن کاملIon-mediated nucleic acid helix-helix interactions.
Salt ions are essential for the folding of nucleic acids. We use the tightly bound ion (TBI) model, which can account for the correlations and fluctuations for the ions bound to the nucleic acids, to investigate the electrostatic free-energy landscape for two parallel nucleic acid helices in the solution of added salt. The theory is based on realistic atomic structures of the helices. In monova...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2009
ISSN: 0006-3495
DOI: 10.1529/biophysj.108.129015