Construction of an implicit membrane environment for the lattice Monte Carlo simulation of transmembrane protein.
Due to the complexity of biological membrane, computer simulation of transmembrane protein's folding is challenging. In this paper, an implicit biological membrane environment has been constructed in lattice space, in which the lipid chains and water molecules were represented by the unoccupied lattice sites. The biological membrane was characterized with three features: stronger hydrogen bonding interaction, membrane lateral pressure, and lipophobicity index for the amino acid residues. In addition to the hydrocarbon core spanning region and the water solution, the lipid interface has also been represented in this implicit membrane environment, which was proved to be effective for the transmembrane protein's folding. The associated Monte Carlo simulations have been performed for SARS-CoV E protein and M2 protein segment (residues 18-60) of influenza A virus. It was found that the coil-helix transition of the transmembrane segment occurred earlier than the coil-globule transition of the two terminal domains. The folding process and final orientation of the amphipathic helical block in water solution are obviously influenced by its corresponding hydrophobicity/lipophobicity. Therefore, this implicit membrane environment, though in lattice space, can make an elaborate balance between different driving forces for the membrane protein's folding, thus offering a potential means for the simulation of transmembrane protein oligomers in feasible time.
Chen
Yantao
Y
Shenzhen Key Laboratory of Functional Polymer, College of Chemistry and Chemical Engineering, Shenzhen University, Shenzhen 518060, China. ytchen@szu.edu.cn
Wang
Mingliang
M
Zhang
Qianling
Q
Liu
Jianhong
J
D003198:Computer Simulation; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008563:Membrane Lipids / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry*; D008567:Membranes, Artificial; D008958:Models, Molecular; D009010:Monte Carlo Method; D017510:Protein Folding; D013816:Thermodynamics; D014759:Viral Envelope Proteins / Q000737:chemistry; D014763:Viral Matrix Proteins / Q000737:chemistry; D000086082:Viroporin Proteins
C501689:E protein, SARS coronavirus; C488937:M2 protein, Influenza A virus; D008563:Membrane Lipids; D008565:Membrane Proteins; D008567:Membranes, Artificial; D014759:Viral Envelope Proteins; D014763:Viral Matrix Proteins; D000086082:Viroporin Proteins