title: Molecular dynamics simulations on the conformational transitions from the GA98 (GA88) to GB98 (GB88) proteins.
abstract: We performed conventional and targeted molecular dynamics simulations to address the dynamic transition mechanisms of the conformational transitions from the GA98 protein with only 1 mutation of Leu45Tyr to GB98 and from the GA88 protein with 7 mutations of Gly24Ala, Ile25Thr, Ile30Phe, Ile33Tyr, Leu45Tyr, Ile49Thr, and Leu50Lys to GB88. The results show that the conformational transition mechanism from the mutated 3α GA98 (GA88) state to the α+4β GB98 (GB88) state via several intermediate conformations involves the bending of loops at the N and C termini firstly, the unfolding of αA and αC, then the traversing of αB, and the formation of the 4β layer with the conversion of the hydrophobic core. The bending of loops at the N and C termini and the formation of the crucial transition conformation with the full unfolded structure are key factors in their transition processes. The communication of the interaction network, the bending directions of loops, and the traversing site of αB in the transition of GA98 to GB98 are markedly different from those in GA88 to GB88 because of the different mutated residues. The analysis of the correlations and the calculated mass center distances between some segments further supported their conformational transition mechanisms. These results could help people to better understand the Paracelsus challenge. Copyright © 2016 John Wiley & Sons, Ltd.
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Chunnian
authors.initials: C
authors.lastname: Song
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Wang
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Tuo
authors.initials: T
authors.lastname: Xue
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Guangju
authors.initials: G
authors.lastname: Chen
mesh_terms: D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*
chemical_list: D011506:Proteins
keywords: GA98 (GA88); GB98 (GB88); molecular dynamics simulations; protein G of group C and G Streptococci; transition mechanism