title: Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: insights from molecular dynamics simulation and free energy analysis.
abstract: Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes  3LWH  and  3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA. The simulation results indicate that Cren7 stabilizes DNA duplex in a certain temperature range in the binary complex compared with the unbound DNA molecules. At the same time, DNA molecules were found to undergo B-like to A-like form transitions with increased temperature. The results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on the structure of DNA molecules. Our work can give important information to understand the interactions of proteins with nucleic acids and other ligands.
authors.affiliation: State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China.
authors.forename: Lin
authors.initials: L
authors.lastname: Chen
authors.forename: Ji-Long
authors.initials: JL
authors.lastname: Zhang
authors.forename: Li-Ying
authors.initials: LY
authors.lastname: Yu
authors.forename: Qing-Chuan
authors.initials: QC
authors.lastname: Zheng
authors.forename: Wen-Ting
authors.initials: WT
authors.lastname: Chu
authors.forename: Qiao
authors.initials: Q
authors.lastname: Xue
authors.forename: Hong-Xing
authors.initials: HX
authors.lastname: Zhang
authors.forename: Chia-Chung
authors.initials: CC
authors.lastname: Sun
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D055550:Protein Stability; D016944:Sulfolobus / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics
chemical_list: D019843:Archaeal Proteins; D004268:DNA-Binding Proteins; D004247:DNA