Mattaparthi Venkata Satish Kumar

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Ever since lysozyme was discovered by Fleming in 1922, this protein has emerged as a model for investigations on protein structure and function. Over the years, several high-resolution structures have yielded a wealth of structural data on this protein. Extensive studies on folding of lysozyme have shown how different regions of this protein dynamically(More)
Understanding the dendrimer-drug interaction is of great importance to design and optimize the dendrimer-based drug delivery system. Using atomistic molecular dynamics (MD) simulations, we have analyzed the release pattern of four ligands (two soluble drugs, namely, salicylic acid (Sal), L-alanine (Ala), and two insoluble drugs, namely, phenylbutazone (Pbz)(More)
Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three(More)
The dynamics of HIV-1 protease (HIV-pr), a drug target for HIV infection, has been studied extensively by both computational and experimental methods. The flap dynamics of HIV-pr is considered to be more important for better ligand binding and enzymatic actions. Moreover, it has been demonstrated that the drug-induced mutations can change the flap dynamics(More)
Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated (corresponding to neutral pH) poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single stranded DNAs (ssDNAs). The four ssDNA strands that are attached via alkythiolate(More)
The loops which connect or flank helices/sheets in protein structures are known to be functionally important. However, ironically they also belong to the part of protein whose structure is least accurately predicted. Here, a new method to isolate and analyze loop regions in protein structure is proposed using the spatial coordinates of the solved(More)
We report DNA assisted self-assembly of polyamidoamine (PAMAM) dendrimers using all atom Molecular Dynamics (MD) simulations and present a molecular level picture of a DNA-linked PAMAM dendrimer nanocluster, which was first experimentally reported by Choi et al. (Nano Lett., 2004, 4, 391-397). We have used single stranded DNA (ssDNA) to direct the(More)
The conformational dynamics of HIV-1 protease (HIV-pr) is known to be essential for ligand binding and determination of cavity size, which changes with several common physiological parameters like temperature, pressure, pH conditions and of course the protein backbone mutations. In this work, the effect of pressure on the conformation and dynamics of HIV-pr(More)
Scheduling of machines and transportation devices like Automated Guided Vehicles (AGVs) in a Flexible Manufacturing System(FMS) is a typical N-P hard problem. Even though several algorithms were employed to solve this combinatorial optimization problem, most of the work concentrated on solving the problems of machines and material handling independently. In(More)
Uracil phosphoribosyltransferase (UPRT) enzyme has immense potential in prodrug-mediated cancer therapy. Molecular docking and enzyme inhibition studies are important for understanding drug–protein interaction in modern drug design. Herein, we experimentally determined the enzyme inhibition constant (K i) of 5-fluorouracil (5FU)—a competitive inhibitor of(More)