title: Right- and left-handed three-helix proteins. II. Similarity and differences in mechanical unfolding of proteins.
abstract: Here, we study mechanical properties of eight 3-helix proteins (four right-handed and four left-handed ones), which are similar in size under stretching at a constant speed and at a constant force on the atomic level using molecular dynamics simulations. The analysis of 256 trajectories from molecular dynamics simulations with explicit water showed that the right-handed three-helix domains are more mechanically resistant than the left-handed domains. Such results are observed at different extension velocities studied (192 trajectories obtained at the following conditions: v = 0.1, 0.05, and 0.01 Å ps(-1) , T = 300 K) and under constant stretching force (64 trajectories, F = 800 pN, T = 300 K). We can explain this by the fact, at least in part, that the right-handed domains have a larger number of contacts per residue and the radius of cross section than the left-handed domains.
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Glyakina
authors.forename: Ilya V
authors.initials: IV
authors.lastname: Likhachev
authors.forename: Nikolay K
authors.initials: NK
authors.lastname: Balabaev
authors.forename: Oxana V
authors.initials: OV
authors.lastname: Galzitskaya
mesh_terms: D030562:Databases, Protein; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D011506:Proteins
keywords: explicit model of water; handedness; intermediate state; mechanical unfolding pathway; molecular dynamics; number of contacts