Abdul Rajjak Shaikh, Assistant Professor at Kobe University

Abdul Rajjak Shaikh

Assistant Professor at Kobe University

Kobe University

Department of Chemical Science and Engineering

Kobe, Japan

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.

Research gate : Abdul Rajjak Shaikh

Specially Appointed Assistant Professor
SHAIKH ABDUL RAJJAK SHAIKH RAMAJU 

Membranes are widely used in water purification. Main aim of our research is to understand membrane fouling phenomenon using computational methods. Molecular dynamics studies are used to investigate polymeric membrane and biomolecular interactions which result in membrane fouling and on the development of new and improved membranes for contaminant removal and water desalination.

LINKS

https://jp.linkedin.com/in/abdul-rajjak-shaikh-a2954715

https://www.researchgate.net/profile/Abdul_Rajjak_Shaikh

Experience

Assistant Professor

Kobe University

March 2013 – Present (2 years 9 months)Kobe, Hyogo, Japan

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.

Postdoctoral Fellow

King Abdullah University of Science and Technology

January 2011 – February 2013 (2 years 2 months)Thuwal, Saudi Arabia

Computational studies for incorporation of unnatural amino acids in green fluorescent protein.
DFT studies for organometallic reactions.
Enzyme Catalysis

Research Fellow

National University of Singapore

June 2008 – July 2010 (2 years 2 months)Singapore

Computational studies for effect of additive on aggregation of therapeutic protein.

Research fellow

Kyoto University

November 2007 – May 2008 (7 months)

Quantum mechanical molecular mechanical (QMMM) studies for ATP hydrolysis catalyzed by F1-ATPase.

Senior Chemist

Dr. Reddy's Laboratories

August 2001 – August 2004 (3 years 1 month)

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

Complete list of Publications can be found on Google Scholar website http://scholar.google.co.jp/citations?user=LAFWpPcAAAAJ&hl=en(Link)

Preparation and characterization of antifouling poly(vinyl chloride-co-poly(ethylene glycol)methyl ether methacrylate) membranes(Link)

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(Link)

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(Link)

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(Link)

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(Link)

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(Link)

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(Link)

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(Link)

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

Education

Tohoku University

PhD, Computational Chemistry

2004 – 2007

I did PhD in Tohoku University

Computational Studies for Structural and Functional Analysis of Cytochrome P450 Enzyme

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Ahmednagar College, University of Pune

M.Sc., Drug chemistry

1999 – 2001

Master of Science

Jamkhed Mahavidyalaya Jamkhed, University of Pune

B.Sc., Chemistry

1996 – 1999

Bachelor of Science

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