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Biological and Chemical Sciences

Dr Sushil Mishra

BSc, MSc, Ph.D

Contact Details

Marie-Curie Fellow
Glycoscience Group
Biomedical Science Building
NUI Galway, Newcastle
Ireland
T: 091-49-2094
E: sushil.mishra_at_nuigalway.ie
 
researcher
 

Biography

Dr. Sushil Mishra is a Marie-Curie Fellow in Advance Glycoscience Research Cluster at NUI Galway. Sushil’s research focuses on understanding the structure and dynamics of glycans and their interaction with other biomolecules (lectins and antibodies). After finishing his M.Sc in Bioinformatics from the University of Allahabad, India, Sushil joined Ph.D. program in Biomolecular Chemistry at Masaryk University, Czech Republic and completed his Ph.D. in 2013. During his doctoral study, Sushil explored lectin-glycan interactions by using molecular modeling techniques. During the same time, Sushil had research stays in the laboratories of Prof. Johan Aqvist, Uppsala, Sweden, and Prof. Martin Zacharias, TUM, Munich, Germany. Following his Ph.D., Sushil worked as a postdoctoral researcher in Central European Institute of Technology (CEITEC), Czech Republic, where he was developing a workflow for reliable and accurate binding free energy predictions of monosaccharides binding to lectins. During his postdoc, he was visiting researcher at Dr. Julein Michel’s Group, Edinburgh, UK, and Prof Bojan Zagrovis’s Group, MFPL Labs, Vienna for a few months.

Later in January 2016, Sushil joined the Systems Glycobiology Research Group, RIKEN, Japan as a Japan Society for the Promotion of Science (JSPS) fellow and then later Tokyo Biochemical Research Foundation (TBRF) fellow. In July 2018, Sushil moved to NUI Galway as Marie Skłodowska-Curie  Fellow (Individual Fellowship), and now he is working on the structure-guided design of antibody fragments to recognize carbohydrate epitopes acting as an allergen or hallmark of malignancy in cells.

Research Interests

I have training in computational biochemistry and research interests are to develop and apply computational approaches for designing glycomimetics (binds to glycan-binding proteins), and recognition molecules (antibodies, lectins) which bind to glycans.   

My technical expertise includes: 
    • Computational modelling of protein-carbohydrate interactions in biomolecules
    • Protein structure prediction: Homology modelling and ab initio methods
    • Docking, In silico virtual screening, homology modeling, and classical MD simulations
    • Constrain Dynamics, Umbrella Sampling, and Adaptive Biasing Force simulations
    • Biasing-potential or /temperature Replica Exchange MD (RexMD) simulations
    • Free energy calculations of protein-ligand complexes (LIE, MM-PB/SA, MM-GB/SA, PMF)
    • Alchemical free energy calculations on protein-glycan complexes. 

              Peer Reviewed Journals

                Year Publication
              (2018) 'Identification of a Golgi GPI-N-acetylgalactosamine transferase with tandem transmembrane regions in the catalytic domain'
              Hirata, T;Mishra, SK;Nakamura, S;Saito, K;Motooka, D;Takada, Y;Kanzawa, N;Murakami, Y;Maeda, Y;Fujita, M;Yamaguchi, Y;Kinoshita, T (2018) 'Identification of a Golgi GPI-N-acetylgalactosamine transferase with tandem transmembrane regions in the catalytic domain'. Nature Communications, 9 [DOI] [Details]
              (2017) 'Distinct roles for each N-glycan branch interacting with mannose-binding type Jacalin-related lectins Orysata and Calsepa'
              Nagae, M;Mishra, SK;Hanashima, S;Tateno, H;Yamaguchi, Y (2017) 'Distinct roles for each N-glycan branch interacting with mannose-binding type Jacalin-related lectins Orysata and Calsepa'. Glycobiology, 27 :1120-1133 [DOI] [Details]
              (2018) 'Synthesis and properties of pi-conjugated donor-acceptor macrocycles derived from phenanthrylene building blocks'
              Phulwale, BV;Mishra, SK;Mazal, C (2018) 'Synthesis and properties of pi-conjugated donor-acceptor macrocycles derived from phenanthrylene building blocks'. Tetrahedron, 74 :3616-3623 [DOI] [Details]
              (2018) 'Implication of C-type lectin receptor langerin and keratan sulfate disaccharide in emphysema'
              Kizuka, Y;Mishra, S;Yamaguchi, Y;Taniguchi, N (2018) 'Implication of C-type lectin receptor langerin and keratan sulfate disaccharide in emphysema'. Cellular Immunology, 333 :80-84 [DOI] [Details]
              (2018) 'Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions'
              Mishra, SK;Koca, J (2018) 'Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions'. Journal Of Physical Chemistry B, 122 :8113-8121 [DOI] [Details]
              (2017) 'Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL'
              Houser, J;Kozmon, S;Mishra, D;Mishra, SK;Romano, PR;Wimmerova, M;Koca, J (2017) 'Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL'. Plos One, 12 [DOI] [Details]
              (2017) '3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy'
              Nagae, M;Mishra, SK;Neyazaki, M;Oi, R;Ikeda, A;Matsugaki, N;Akashi, S;Manya, H;Mizuno, M;Yagi, H;Kato, K;Senda, T;Endo, T;Nogi, T;Yamaguchi, Y (2017) '3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy'. Genes To Cells, 22 :348-359 [DOI] [Details]
              (2017) 'Novel missense mutation in DLL4 in a Japanese sporadic case of Adams-Oliver syndrome'
              Nagasaka, M;Taniguchi-Ikeda, M;Inagaki, H;Ouchi, Y;Kurokawa, D;Yamana, K;Harada, R;Nozu, K;Sakai, Y;Mishra, SK;Yamaguchi, Y;Morioka, I;Toda, T;Kurahashi, H;Iijima, K (2017) 'Novel missense mutation in DLL4 in a Japanese sporadic case of Adams-Oliver syndrome'. Human Genetics, 62 :851-855 [DOI] [Details]
              (2016) 'Phenanthrylene-butadiynylene and Phenanthrylene-thienylene Macrocycles: Synthesis, Structure, and Properties'
              Phulwale, BV;Mishra, SK;Necas, M;Mazal, C (2016) 'Phenanthrylene-butadiynylene and Phenanthrylene-thienylene Macrocycles: Synthesis, Structure, and Properties'. Journal Of Organic Chemistry, 81 :6244-6252 [DOI] [Details]
              (2015) 'Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes'
              Mishra, SK;Calabro, G;Loeffler, HH;Michel, J;Koca, J (2015) 'Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes'. Journal Of Chemical Theory And Computation, 11 :3333-3345 [DOI] [Details]
              (2014) 'Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation'
              Mishra, SK;Kara, M;Zacharias, M;Koca, J (2014) 'Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation'. Glycobiology, 24 :70-84 [DOI] [Details]
              (2012) 'In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding'
              Mishra, SK;Adam, J;Wimmerova, M;Koca, J (2012) 'In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding'. Journal Of Chemical Information And Modeling, 52 :1250-1261 [DOI] [Details]
              (2012) 'Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods'
              Wimmerova, M;Kozmon, S;Necasova, I;Mishra, SK;Komarek, J;Koca, J (2012) 'Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods'. Plos One, 7 [DOI] [Details]
              (2012) 'Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models'
              Mishra, SK;Sund, J;Aqvist, J;Koca, J (2012) 'Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models'. Journal Of Computational Chemistry, 33 :2340-2350 [DOI] [Details]

              Reviews

                Year Publication
              (2018) Tau Filaments and the Development of Positron emission Tomography Tracers.
              Goedert, M;Yamaguchi, Y;Mishra, SK;Higuchi, M;Sahara, N (2018) Tau Filaments and the Development of Positron emission Tomography Tracers. LAUSANNE: Reviews [DOI] [Details]

              Honours and Awards

                Year Title Awarding Body
              2013 NVIDIA hardware donation award GPU Grant Program. NVIDIA Carp.
              2012 Best publication activity award Faculty of science, Masaryk University, Czech Republic

              Employment

                Employer Position From / To
              RIKEN, Japan Researcher 25-JAN-16 / 31-MAR-18
              UP Council of Sugarcane Research Junior Research Fellow 01-MAY-08 / 30-APR-09
              National Center for Biomolecular Research, Masaryk University Graduate Student 25-MAY-09 / 20-MAR-13
              Central European Institute of Technology Postdoc 21-MAR-13 / 25-JAN-16

              Education

                Year Institution Qualification Subject
              2007 University of Allahabad M.Sc. Bioinformatics
              2013 Masaryk University PhD Biomolecular Chemistry
              2005 University of Allahabad B.Sc. Applied Science