Showing papers by "Parvez Alam published in 2015"

Elucidating the interaction of limonene with bovine serum albumin: a multi-technique approach

Abstract: The interaction of Bovine Serum Albumin (BSA) with limonene has been studied by UV-visible spectroscopy, fluorescence spectroscopy and molecular docking, and its effects on protein conformation, topology and stability were determined by Circular Dichroism (CD), Dynamic Light Scattering (DLS) and Differential Scanning Calorimetry (DSC). A gradual decrease in Stern–Volmer quenching constants with the increase in temperature showed the static mode of fluorescence quenching. The obtained binding constant (Kb) was ∼104 M−1. The temperature dependent Kb, Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) changes were calculated, which revealed that the reaction is spontaneous and exothermic. The UV-visible spectra showed a change in the peaks within the aromatic region indicating hydrophobic interactions with Trp, Tyr and Phe in the protein. Moreover, limonene induced an increase in α-helical contents probably on the cost of random coils or/and β-sheets of BSA, as observed from the far-UV CD spectra. The topology of BSA in the presence of limonene was slightly altered, as obtained from DLS results. The stability was also enhanced as revealed through thermal denaturation study by DSC and CD. Molecular docking study depicted that limonene fits into the hydrophobic pocket close to Sudlow site I in domain IIA of BSA. The present study will be helpful in understanding the binding mechanism of limonene and associated stability and conformational changes.

The surfactant-induced conformational and activity alterations in Rhizopus niveus lipase.

Abstract: In this study, we have reported the effect of nonionic, anionic, cationic, and zwitterionic detergents on the enzymatic activity and structural stability of Rhizopus niveus lipase Secondary structural changes were monitored by Far-UV CD which shows that surfactant induces helicity in the Rhizopus niveus lipase protein which was maximum in case of CTAB followed by SDS, CHAPS, and Brij-35 Similarly, tertiary structural changes were monitored by tryptophan fluorescence We also carried out enzyme kinetics assays which showed that activity was enhanced by 15- and 11-fold in the presence of CHAPS and Brij-35, respectively Furthermore, there was a decline in activity by 20 and 30 % in case of SDS and CTAB, respectively These studies may be helpful in understanding detergent–lipase interaction in greater detail as lipases are used in many industrial processes

Unraveling Comparative Anti-Amyloidogenic Behavior of Pyrazinamide and D-Cycloserine: A Mechanistic Biophysical Insight.

Abstract: Amyloid fibril formation by proteins leads to variety of degenerative disorders called amyloidosis. While these disorders are topic of extensive research, effective treatments are still unavailable. Thus in present study, two anti-tuberculosis drugs, i.e., pyrazinamide (PYZ) and D-cycloserine (DCS), also known for treatment for Alzheimer’s dementia, were checked for the anti-aggregation and anti-amyloidogenic ability on Aβ-42 peptide and hen egg white lysozyme. Results demonstrated that both drugs inhibit the heat induced aggregation; however, PYZ was more potent and decelerated the nucleation phase as observed from various spectroscopic and microscopic techniques. Furthermore, pre-formed amyloid fibrils incubated with these drugs also increased the PC12/SH-SY5Y cell viability as compare to the amyloid fibrils alone; however, the increase was more pronounced for PYZ as confirmed by MTT assay. Additionally, molecular docking study suggested that the greater inhibitory potential of PYZ as compare to DCS may be due to strong binding affinity and more occupancy of hydrophobic patches of HEWL, which is known to form the core of the protein fibrils.

Interaction mode of polycarbazole-titanium dioxide nanocomposite with DNA: Molecular docking simulation and in-vitro antimicrobial study.

Abstract: A polycarbazole-titanium dioxide (PCz/TiO2-8) nanocomposite was synthesized for the first time by in-situ oxidative polymerization with APS as an oxidizing agent in the presence of TiO2 nanoparticles which was characterized by SEM, TEM, FT-IR, DTA and TGA techniques. The SEM and TEM results showed that PCz has polymerized on the surface of the TiO2. The results confirmed the incorporation of TiO2 in PCz indicating the formation of nanocomposite due to strong interaction between TiO2 and PCz matrix affecting the properties as compared to pristine PCz. The PCz/TiO2-8 nanocomposite was tested for antimicrobial activity and found to exhibit activity against gram negative and gram positive strains at micromolar concentrations. The four types of 3D molecular field descriptors or field points as extrema of electrostatic, steric, and hydrophobic fields were explained. These field points were used to define the properties necessary for a molecule to bind in a characteristic way into a specified active site. A molecular docking simulation was used to predict the modes of interactions of the drugs (PCz and PCz/TiO2-8) with DNA. The molecular docking conclusion indicated that the modes of interactions between two (PCz and PCz/TiO2-8) and DNA helix can be regarded as minor groove binder. The K value (3.55 × 10(4) M(-1) and 2.13 × 10(5) M(-1)) obtained from fluorescence data are indicative of binding of PCz and PCz/TiO2-8 with DNA helix.