title: In silico identification and computational analysis of the nucleotide binding site in the C-terminal domain of Hsp90.
abstract: Hsp90 contains two distinct Nucleotide Binding Sites (NBS), in its N-terminal domain (NTD) and C-terminal domain (CTD), respectively. The NTD site belongs to the GHKL super-family of ATPases and has been the subject of extensive characterization. However, a structure of the nucleotide-bound form of CTD is still unavailable. In this study molecular modeling was employed to incorporate experimental data using partial constructs of the CTD, from work published by many research groups, onto existing structural models of its apo- form. Our attempts to locate potential nucleotide ligand-binding sites or cavities yielded one major candidate-a structurally unconventional site-exhibiting the requisite shape and volume for accommodation of tri-phosphate nucleotides. Its structure was refined by molecular dynamics (MD)-based techniques. We reproducibly docked the Mg2+complexed form of ATP, GTP, CTP, TTP and UTP to this putative NBS. These docking simulations and calculated ligand-binding scores are in general agreement with published data about experimentally measured binding to the CTD. The overall pattern of interactions between residues lining the site and docked nucleotides is conserved and broadly similar to that of other nucleotide-binding sites. Our docking simulations suggest that nucleotide binding stabilizes the only structurally labile region, thereby providing a rationale for the increased resistance to thermal denaturation and proteolysis. The docked nucleotides do not intrude onto the surface of residues involved in dimerization or chaperoning. Our molecular modeling permitted recognition of larger structural changes in the nucleotide-bound CTD dimer, including stabilization of helix-2 in both chains and intra- and inter- chain interactions between three residues (I613, Q617, R620).
authors: Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
authors: Samir S
authors: SS
authors: Roy
authors: Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada. Electronic address: mkapoor37@yahoo.com.
authors: Manju
authors: M
authors: Kapoor
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D017124:Conserved Sequence; D003374:Coumarins / Q000737:chemistry; D018841:HSP90 Heat-Shock Proteins / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D009711:Nucleotides / Q000378:metabolism*; D000072417:Protein Domains; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D059748:Proteolysis
chemical_list: D003374:Coumarins; D018841:HSP90 Heat-Shock Proteins; D008024:Ligands; D009711:Nucleotides; C030123:coumarin
keywords: C-terminal domain; Homology modeling; Hsp90; Molecular docking; Nucleotide binding site