Abdul Rajjak Shaikh
Summary
Molecular modelling and molecular dynamics studies for polymer membrane-biomolecular interactions, enzyme catalyzed reaction, computer-aided drug designing, biomimetic membranes etc. I also used density functional theory method to understand reaction mechanism.
Specially Appointed Assistant Professor
SHAIKH ABDUL RAJJAK SHAIKH RAMAJU 
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Specially Appointed Assistant Professor
SHAIKH ABDUL RAJJAK SHAIKH RAMAJU
SHAIKH ABDUL RAJJAK SHAIKH RAMAJU
LINKS
Experience
Assistant Professor
Kobe University
Molecular dynamics studies for polymer membrane and foulant interaction to understand membrane fouling phenomenon in water treatment using membranes.
Computational studies for absorption of CO2 in Ionic liquids.
Computational studies for absorption of CO2 in Ionic liquids.
Postdoctoral Fellow
King Abdullah University of Science and Technology
Computational studies for incorporation of unnatural amino acids in green fluorescent protein.
DFT studies for organometallic reactions.
Enzyme Catalysis
DFT studies for organometallic reactions.
Enzyme Catalysis
Research Fellow
National University of Singapore
Computational studies for effect of additive on aggregation of therapeutic protein.
Research fellow
Kyoto University
Quantum mechanical molecular mechanical (QMMM) studies for ATP hydrolysis catalyzed by F1-ATPase.
Senior Chemist
Dr. Reddy's Laboratories
Molecular modelling and drug designing: Docking, QSAR, Pharmacophore generation, Virtual Screening, De novo drug design, Structure absed drug design, ligand based drug designing, combinatorial library
Publications
Preparation and characterization of antifouling poly(vinyl chloride-co-poly(ethylene glycol)methyl ether methacrylate) membranes
Journal of Membrane Science
Two series of antifouling microfiltration membranes (MF) with different pure water permeabilities were fabricated using poly(vinyl chloride-co-poly(ethylene glycol)methyl ether methacrylate) (poly(VC-co-PEGMA)) copolymers with different PEGMA segment percentage via nonsolvent-induced phase separation (NIPS) method. For each series of the prepared membranes, the initial pure water permeability was...more
Interaction of arginine, lysine, and guanidine with surface residues of lysozyme: implication to protein stability
Journal of Biomolecular Structure and Dynamics
March 2, 2015
Additives are widely used to suppress aggregation of therapeutic proteins. However, the molecular mechanisms of effect of additives to stabilize proteins are still unclear. To understand this, we herein perform molecular dynamics simulations of lysozyme in the presence of three commonly used additives: arginine, lysine, and guanidine. These additives have different effects on stability of proteins...more
Effects of Water Concentration on the Free Volume of Amino Acid Ionic Liquids Investigated by Molecular Dynamics Simulations
The Journal of Physical Chemistry B
December 15, 2014
Amino acid ionic liquids (AAILs) are gaining attention because of their potential in CO2 capture technology. Molecular dynamics simulations of AAILs tetramethylammonium glycinate ([N1111][Gly]), tetrabutylammonium glycinate ([N4444][Gly]), and 1,1,1-trimethylhydrazinium glycinate ([aN111][Gly]) and their corresponding mixtures with water were performed to investigate the effect of water...more
A Saccharomyces cerevisiae Assay System to Investigate Ligand/AdipoR1 Interactions That Lead to Cellular Signaling
PLOS ONE
June 7, 2013
Adiponectin is a mammalian hormone that exerts anti-diabetic, anti-cancer and cardioprotective effects through interaction with its major ubiquitously expressed plasma membrane localized receptors, AdipoR1 and AdipoR2. Here, we report a Saccharomyces cerevisiae based method for investigating agonist-AdipoR interactions that is amenable for high-throughput scale-up and can be used to study both...more
Molecular mechanism of ATP hydrolysis in F1-ATPase revealed by molecular simulations and single-molecule observations
Journal of the American Chemical Society
May 11, 2012
Enzymatic hydrolysis of nucleotide triphosphate (NTP) plays a pivotal role in protein functions. In spite of its biological significance, however, the chemistry of the hydrolysis catalysis remains obscure because of the complex nature of the reaction. Here we report a study of the molecular mechanism of hydrolysis of adenosine triphosphate (ATP) in F1-ATPase, an ATP-driven rotary motor protein....more
Dynamic and structural changes in the minimally restructuring EcoRI bound to a minimally mutated DNA chain
Journal of Biomolecular Structure and Dynamics
February 1, 2012
The dynamics of a protein plays an important role in protein functionality. Here, we examine the differences in the dynamics of a minimally restructuring protein, EcoRI, when it is bound to its cognate DNA and to a noncognate sequence which differs by just a single basepair. Molecular dynamics simulations of the complexes and essential dynamics analyses reveal that the overall dynamics of the...more
Arginine–aromatic interactions and their effects on arginine‐induced solubilization of aromatic solutes and suppression of protein aggregation
Biotechnology progress
January 1, 2012
We examine the interaction of aromatic residues of proteins with arginine, an additive commonly used to suppress protein aggregation, using experiments and molecular dynamics simulations. An aromatic-rich peptide, FFYTP (a segment of insulin), and lysozyme and insulin are used as model systems. Mass spectrometry shows that arginine increases the solubility of FFYTP by binding to the peptide, with...more
Effects of arginine on heat‐induced aggregation of concentrated protein solutions
Biotechnology progress
March 1, 2011
Arginine is one of the commonly used additives to enhance refolding yield of
proteins, to suppress aggregation of proteins, and to increase solubility of proteins, and yet
the molecular interactions that contribute to the role of arginine are unclear. Here, we
present experiments, using bovine serum albumin (BSA), lysozyme (LYZ), and β-
lactoglobulin (BLG) as model proteins, to show that...more
proteins, to suppress aggregation of proteins, and to increase solubility of proteins, and yet
the molecular interactions that contribute to the role of arginine are unclear. Here, we
present experiments, using bovine serum albumin (BSA), lysozyme (LYZ), and β-
lactoglobulin (BLG) as model proteins, to show that...more
Education
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