title: Replica exchange molecular dynamics simulations of an α/β-type small acid soluble protein (SASP).
abstract: Small acid soluble proteins (SASPs) of α/β-type play a major role in the resistance of spore DNAs to external assaults. It has been found that α/β-type SASP exhibits intrinsic disorder on isolation, but it acquires a defined native state upon binding to DNA. This disorder to order transition is not yet understood. Other questions related to the role of the thermodynamics and structure of the individual protein in the complex formation remain elusive. Characterization of the unbound state of α/β-type SASP in experiments could be a challenging problem because of the heterogeneous nature of the ensemble. Here, computer simulations can help gain more insights into the unbound state of α/β-type SASP. In the present work, by using replica exchange molecular dynamics (REMD), we simulated an α/β-type SASP on isolation with an implicit solvent. We found that α/β-type SASP undergoes a continuous phase transition with a small free energy barrier, a common feature of intrinsically disordered proteins (IDPs). Additionally, we detected the presence of residual α-helical structures at local level and a high degree of plasticity in the chain which can contribute to the fast disorder to order transition by reducing the fly-casting mechanism.
authors.affiliation: Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, IN 46202, USA. Electronic address: pojedama@iupui.edu.
authors.forename: P
authors.initials: P
authors.lastname: Ojeda-May
authors.forename: Jingzhi
authors.initials: J
authors.lastname: Pu
mesh_terms: D001412:Bacillus subtilis / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins
keywords: Intrinsic disordered protein; MD simulations; Molecular simulation; Proteins