Structural and dynamical properties of a full-length HIV-1 integrase: molecular dynamics simulations.
The structural and dynamical properties of the complete full-length structure of HIV-1 integrase were investigated using Molecular Dynamics approach. Simulations were carried out for the three systems, core domain only (CORE), full-length structure without (FULL) and with a Mg2+ (FULL+ION) in its active site, aimed to investigate the difference in the molecular properties of the full-length models due to their different construction procedures as well as the effects of the two ends, C- and N-terminal, on those properties in the core domain. The full-length structure was prepared from the two experimental structures of two-domain fragment. The following properties were observed to differ significantly from the previous reports: (i) relative topology formed by an angle between the three domains; (ii) the cavity size defined by the catalytic triad, Asp64, Asp116, and Glu152; (iii) distances and solvation of the Mg2+; and (iv) conformation of the catalytic residues. In addition, the presence of the two terminal domains decreases the mobility of the central core domain significantly.
Wijitkosoom
Atchara
A
Department of Chemistry, Faculty of Science, Chulalongkorn University, Patumwan, Bangkok 10330 Thailand.
Tonmunphean
Somsak
S
Truong
Thanh N
TN
Hannongbua
Supot
S
D001665:Binding Sites; D020134:Catalytic Domain; D003198:Computer Simulation; D019427:HIV Integrase / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation
D010446:Peptide Fragments; D019427:HIV Integrase