Folding of bundles of α-helices in solution, membranes, and adsorbed overlayers

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2001-03, Vol.42 (4), p.481-494
• Main Authors: Zhdanov, V.P., Kasemo, B.
• Format: Article
• Language: English
• Subjects: Algorithms; and refolding times; chain rigidity; Chemical Phenomena; Chemistry, Physical; conformational changes; Cytochrome b Group - chemistry; denaturation; Escherichia coli Proteins; folding; folding temperature; folding, denaturation, and refolding times; Membrane Proteins - chemistry; Models, Molecular; Molecular Structure; monomer-membrane and monomer-surface interactions; monomer-monomer; monomer–monomer, monomer–membrane and monomer–surface interactions; Monte Carlo lattice model; Monte Carlo Method; Poissonian and non-Poissonian kinetics; Protein Folding; Protein Structure, Secondary; Solutions
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/1097-0134(20010301)42:4<481::AID-PROT70>3.0.CO;2-N

We propose a coarse‐grained lattice model for Monte Carlo simulations of folding of proteins consisting of several α‐helices. A chain representing a protein is considered to contain A and B monomers forming relatively stiff A subchains, mimicking helices, and flexible B links between these subchains, respectively. Using this model, we simulate (1) folding of four‐helix proteins in solution; (2) folding of membrane proteins containing one, two, or four helices; and (3) refolding of four‐helix proteins adsorbed at the liquid–solid interface. For these cases, we show typical scenarios of protein folding and refolding and study the dependence of the folding time on the chain length. Combining the latter results with those already available in the literature, we discuss the relative rates of folding of proteins belonging to different classes. Proteins 2001;42:481–494. © 2001 Wiley‐Liss, Inc.