Protein Crystallography, NFFMC, Solid State Physics Division, Trombay, B.A.R.C., Mumbai-400085. INDIA Alt. e-mail: amitdas@barc.gov.in Tel:91-22-25594688/4061-64 Fax:91-22-25505151
amitd453@gmail.com
I am working in the field of Macromolecular Crystallography.I am interested in the investigating the structure-function relationship of macromolecules, understanding the mechanism of enzymatic action, structure-based drug design and kinetic crystallography. I am also interested in developmental work for newer experimental setup-design at the synchrotron beamlines to enhance our understanding of the dynamics of macromolecules in action.
Abstract: The human seminal plasma protein PSP94 is a small protein of 94 residues that contains ten cysteines. Since its discovery about 25 years ago, several potential biological functions have been reported for this protein. Many PSP94 homologues have also been identified since then from various species, but no crystal structure has been determined to date. PSP94 has been purified from human seminal plasma and crystallized. These crystals diffracted to 2.3 Ã… resolution and belonged to space group P41212, with unit-cell parameters a = 107.9, b = 107.9, c = 92.1 Ã…. There are four molecules in the asymmetric unit. Structure solution by the heavy-atom method is currently in progress.
Abstract: We report here the 2.5A structure of HIV-1 protease tethered-dimer ritonavir complex. The inhibitor bound in the active site has different conformations in the two orientations. There is only one hydrogen bond between the inhibitor and the enzyme. The conserved flap-water is not found in the present complex.
Abstract: HIV-1 protease is an effective target for designing drugs against AIDS, and structural information about the true transition state and the correct mechanism can provide important inputs. We present here the three-dimensional structure of a bi-product complex between HIV-1 protease and the two cleavage product peptides AETF and YVDGAA. The structure, refined against synchrotron data to 1.65 A resolution, shows the occurrence of the cleavage reaction in the crystal, with the product peptides still held in the enzyme active site. The separation between the scissile carbon and nitrogen atoms is 2.67 A, which is shorter than a normal van der Waal separation, but it is much longer than a peptide bond length. The substrate is thus in a stage just past the G'Z intermediate described in Northrop's mechanism [Northrop DB (2001) Acc Chem Res 34:790-797]. Because the products are generated in situ, the structure, by extrapolation, can give insight into the mechanism of the cleavage reaction. Both oxygens of the generated carboxyl group form hydrogen bonds with atoms at the catalytic center: one to the OD2 atom of a catalytic aspartate and the other to the scissile nitrogen atom. The latter hydrogen bond may have mediated protonation of scissile nitrogen, triggering peptide bond cleavage. The inner oxygen atoms of the catalytic aspartates in the complex are 2.30 A apart, indicating a low-barrier hydrogen bond between them at this stage of the reaction, an observation not included in Northrop's proposal. This structure forms a template for designing mechanism-based inhibitors.
Abstract: The native form of serum albumin is the most important soluble protein in the body plasma. In order to investigate the structural changes of Bovine serum albumin (BSA) during its unfolding in the presence of urea, a small-angle neutron scattering (SANS) study was performed. The scattering curves of dilute solutions of BSA with different concentrations of urea in D2O at pH 7.2 ± 0.2 were measured at room temperature. The scattering profile was fitted to a prolate ellipsoidal shape (a, b, b) of the protein witha = 52.2 Å andb = 24.2 Å. The change in the dimensions of the protein as it unfolds was found to be anisotropic. The radius of gyration of the compact form of the protein in solution decreased as the urea concentration was increased.
