Structural Basis of Drug Resistance by Genetic Variants of HIV Type 1 Clade C Protease from India

Using computer modeling of three-dimensional structures and structural information available on the crystal structures of HIV-1 protease, we investigated the structural effects of mutations, in treatment-naive and treatment-exposed individuals from India and postulated mechanisms of resistance in clade C variants. A large number of models (14) have been generated by computational mutation of the available crystal structures of drug bound proteases. Localized energy minimization was carried out in and around the sites of mutation in order to optimize the geometry of interactions present. Most of the mutations result in structural differences at the flap that favors the semiopen state of the enzyme. Some of the mutations were also found to confer resistance by affecting the geometry of the active site. The E35D mutation affects the flap structure in clade B strains and E35N and E35K mutation, seen in our modeled strains, have a more profound effect. Common polymorphisms at positions 36 and 63 in clade C also affected flap structure. Apart from a few other residues Gln-58, Asn-83, Asn-88, and Gln-92 and their interactions are important for the transition from the closed to the open state. Development of protease inhibitors by structure-based design requires investigation of mechanisms operative for clade C to improve the efficacy of therapy.

Rayleigh-Benard convection during solidification of an eutectic solution cooled from the top

The interaction between laminar Rayleigh-Benard convection and directional solidification is studied for the case of an eutectic solution kept in a rectangular cavity cooled from the top. Experiments and numerical simulations are carried out using an NH4Cl-H2O solution as the model fluid. The flow is visualized using a sheet of laser light scattered by neutrally buoyant, hollow-glass spheres seeded in the fluid. The numerical modeling is performed using a pressure-based finite-volume method according to the SIMPLER algorithm. The present configuration enables us to visualize flow vortices in the presence of a continuously evolving solid/liquid interface. Clear visualization of the Rayleigh-Benard convective cells and their interaction with the solidification front are obtained. It is observed that the convective cells are characterized by zones of up-flow and down-flow, resulting in the development of a nonplanar interface. Because of the continuous advancement of the solid/liquid interface, the effective liquid height of the cavity keeps decreasing. Once the height of the fluid layer falls below a critical value, the convective cells become weaker and eventually die out, leading to the growth of a planar solidification front. Results of flow visualization and temperature measurement are compared with those from the numerical simulation, and a good agreement is found.