Paper Citing NAMD - Abstract
Jana, Sankar; Dalapati, Sasanka; Ghosh, Shalini; Guchhait, Nikhil
Study of microheterogeneous environment of protein Human Serum Albumin by an extrinsic fluorescent reporter: A spectroscopic study in combination with Molecular Docking and Molecular Dynamics Simulation
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, 112:48-58, JUL 2 2012
We report extrinsic fluorescent probe 5-(4-dimethylamino-phenyl)-penta-2,4-dienoic acid (DMAPPDA) as a molecular reporter for studying microheterogeneous environment of protein Human Serum Albumin (HSA) via spectral modification of the probe under physiological condition. Steady state emission, fluorescence anisotropy. Red Edge Excitation Shift (REES), far-UV Circular Dichroism (CD), Atomic Force Microscopy (AFM) imaging, time resolved spectral measurements, Molecular Docking and Molecular Dynamics (MD) Simulation techniques have been used to fulfill this achievement. Interaction of the probe with HSA is signaled by the blue shift of the fluorophore emission maxima with enhancement of fluorescence intensity. The increase in steady state anisotropy, REES and fluorescence lifetime values with increasing protein concentrations indicates interaction and movement of the probe from free aqueous media to the more restricted less polar hydrophobic interior of protein. Experimental results obtained from Benesi-Hildebrand plot support the formation of 1:1 HSA-DMAPPDA complex with high binding constant and negative free energy change. Thermal denaturation of the probe bound protein has also been tracked using the spectral response of DMAPPDA. Molecular Docking studies revealed binding of the probe with in the hydrophobic cavity of subdomain IIA of HSA. MD Simulation supports greater stability of HSA-DMAPPDA complex compared to free protein. (c) 2012 Elsevier B.V. All rights reserved.
