Pravindra Kumar - Department of Biosciences and Bioengineering,Indian Institute of Technology Roorkee
Pravindra Kumar
Pravindra Kumar Head of department 91-1332-285072
Areas of Interest
  • Infectious disease and therapeutics, Plasticizers biodegradation, Crystallography and Bioinformatics, Use of structural biology to develop novel biocatalysts and therapeutics
Professional Background
2018-01-01OngoingProfessorIIT Roorkee
2012-01-016 years Associate ProfessorIIT Roorkee
2005-01-017 years Assistant ProfessorIIT Roorkee
2001-01-014 years Post-Doctoral Research AssociatePurdue University (U.S.A.)
1996-01-013 years Senior DemonstratorAll India Institute of Medical Sciences
Multiple Posts
2017-01-013 years Associate Dean (Corporate Interaction)I.I.T. Roorkee
2013-01-013 years Chief Advisor SportsSports Council, I.I.T. ROORKEE
2010-01-013 years Deputy Chief Advisor Students ClubI.I.T. Roorkee
2006-01-012 years WardenI.I.T. Roorkee
Honors and Awards
ASM- Professorship, 2017American Society of Microbiology and INDO-US forum2017
National Bioscience AwardDBT, Department of Science and Technology, Govt. of India2015
Indo-US grant by IUSSTFIUSSTF2014
BOYSCAST FellowshipDepartment of Science and Technology, Govt. of India2008
Gold Medal for Best Ph.D. Award ( SV Talekar Award) All India Institute of Medical Sciences (A.I.I.M.S.)2001
Awarded the CSIR Senior Research fellowship All India Institute of Medical Sciences1999
Educational Details
Ph.D.Biophysics (Structural Biology)All India Institute of Medical Sciences- New Delhi2001
M.Sc.Physics (Electronics)C.C.S. University, Meerut1995
Sponsored Research Projects
TopicFunding AgencyStart DatePeriod
Studies on Phthalate dioxygenaseNational bioscience award, DBT2017-013 years 5 months
Structural characterization of FabIICMR2016-013 years
Str. studies on MurA enzymeDRDO2017-012 years
Structural studies on 11S globulinDBT2015-014 years 7 months
Microbial degradation of toxic aromatic compounds using structural biology approachDRDO2012-014 years
Structural studies of chorismate synthaseCSIR2013-014 years
Structure-based development of anti-bacterial enzyme inhibitors against enzyme involved in lipooligoICMR2012-014 years
Structural studies of biphenyl dehydrogenase from Comamonas testosteroni strain B-356CSIR2011-014 years
Structural analysis of DAHP synthase from Arabidopsis thalianaDST2013-014 years
Structural Characterization Of DAHP Synthase For Designing Rational Inhibitors As Antibact. DrugMHRD2011-014 years
Structural Studies of Aromatic-ring-Hydroxylating Dioxygenasees and their complexes with toxic PolyaDST2006-014 years
  • Indian Biophysical Society, Member
  • American Chemical Society, Member
  • Electron Microscope Society of India, Member
  • Environment Mutagen Society of India, Member
  • American Society of Microbiology, MEMBER
  • Bureau of Indian Standards, Bureau Member
Teaching Engagements
TitleCourse CodeClass NameSemester
Structural BiologyBT-204B.Tech. (Biotechnology) Spring
Molecular BiophysicsBTN-521M.Sc. BiotechnologySpring
Structural BiologyBT-632M.Sc.Spring
Macromolecular CrystallographyIBT02B.TechSpring
BioinformaticsBT 217B.TechAutumn
BioinformaticsBT 614M.Sc.Spring
Macromolecular CrystallographyIBT02B.TechAutumn
BiochemistryBT106Btech Biotechnology2Spring
Research Scholar Groups
Scholar NameInterest
Ms. Preeti DhakaDiscovery of therapeutic agents for COVID19 using drug repurposing approach
Ms. VishakhaStructural studies of oxidoreductases
Mr. Amith KumarDiscovery of therapeutic agents for COVID19
Ms. Vishakha Singh TomarStructural studies of FmtA gene as a methicillin resistance factor
Ms. Monica SharmaDiscovery of new therapeutics for bacterial and viral infections using AI and ML
Mr. JaikrishnaStructural characterization of enzymes in biodegradation of plasticizers (Phthalates)
Ms. Poonam DhanakarProtein engineering of DyP peroxidases for decolorizing dyes
Ms. NeetuStructural studies of bacterial enzymes and exploring new therapeutics
PHDs Supervised
TopicScholar NameStatus of PHDRegistration Date
Structural studies of FmtA in Staphylococcus aureusVikram DalalA2016-07
Structural and biochemical characterization of protein drug targets from human pathogensDr. Madhusudhanarao KatikiA2012-01
Structural and functional studies of plant proteinsDr. Pooja KesariA2013-01
Structural Sudies Of Shikimate And Fatty Acid Biosynthesis Pathway’s EnzymesDr. Vijay KumarA2012-01
Xenobiotic Compounds Degradation And Their Effects On Important EnzymesDr. Neha SinghA2012-01
Biophysical, Biochemical and Structural Characterization of Drug Targets from BacteriaDr. Anchal SharmaA2012-01
Studies on peroxiredoxin anti-oxidant system from Candidatus liberibacter asiaticusDr. Anamika SinghA2009-01
Structural studies of enzymes involved in bioremediationDr. Sonali DhindwalA2009-01
Structural studies of drug targets fromdrug resistant pathogenic bacteriaDr. Shivendra PratapA2008-01
Structural studies on MurA and type II chorismate mutaseDr. Aditya DevA2008-01
Structural studies on 11S globulin and 2S albumin from Wrightia tinctoriaDr. Pramod KumarA2009-01
Structure-function studies of Miraculin-like ProteinsDr. P SelvakumarA2007-01
Structural studies of trypsin inhibitor and its complex with trypsin and Factor XaDr. Dipak N. PatilA2007-01
Structural characterization of chitinase.Dr. Manali DattaA2006-01
Structural studies on some mettaloproteins: Biphenyl dioxygenase and Dahp synthaseDr. Sushmita BhattacharyaA2006-01
Purification and structural characterization of an 11S globulin from Wrightia tinctoria at Delhi-2015 2nd Plant Proteomics Workshop, Department of Botany, University of Delhil2015-01
INDO-FRENCH seminar on the topic “Application of Structural Biology in Translational Research & Structure- Guided- Drug- Design at ACTREC-Navi Mumbai, November 19-20, 2015 on "Active-Site Plasticity is Essential to Carbapenem Hydrolysis by OXA-58 Class D ACTREC Navi Mumbai2015-01
Indo-US International Conference/workshop on "Recent Advances in Structural Biology and Drug Discovery,9-11 October 2014, IIT Roorkee“Ligand bound structures of 3-deoxy- D-manno-octulosonate 8-phosphate phosphatase fromMoraxella catarrhalis reveals waterIndo-US at IIT Roorkee2014-01
Structural studies of enzymes involved in biphenyl degrading pathway, at JNU-201342nd National Seminar on Crystallography, JNU Delhi2013-01
National Conference on Recent Trends in Protein Structural Biology will be held during December 16-18, 2013 at Jamia Millia Islamia on " structural studies of enzymes involved in the biodegradation oftoxic aromatic compounds"Jamia Millia Islamia, Delhi2013-01
Structural Proteomics of therapeutic proteins in plants at Delhi 20131st Plant Proteomics workshop, Department of Botany, University of Delhi2013-01
Invited for a lecture for "Current Trends in Structural Biology (CTSB)- 2012", held during 2nd April 2012, Department of Biophysics, AIIMS;"Biochemical studies and ligand-bound structures of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 revAll India Institute of Medical Sciences Delhi2012-01
in Proteomics-2012 held in Las Vegas, USA during July 02-04, 2012 on "Structural analysis of chorismate synthase from Plasmodium falciparum: a novel target for antimalaria drug discovery"Proteomics-2012 held in Las Vegas, USA 2012-01
Indo-US symposium on "Modern Trends in Macromolecular Structires" Feb 21-24th 2011 held IIT BombayIIT Bombay2011-01
"Lactoferrin or Transferrin? Crystal Structure of Lactoferrin" Purdue University (U.S.A.)2002-01
"Structure solution of a 40 kDa protein from goat secretions". at discussion meeting on Macromolecular crystallography Feb 6-7, 1998. at MBU, IISc. Banglore.IISC Bangalore1998-01
Participation in short term courses
Couse NameSponsored ByDate
‘Hands-on-Training on Modern Techniques in Biotechnology (Nano/structural biotechnology)’USBD2013-01
Workshop for National Science Talent Scholarship in RoorkeeNCERT2012-01
Courses or Conferences Organised
Conference NameSponsored ByDate
Indo-US conference on "Structural Biology and Drug Discovery"IUSSTF, DRDO, DST, ICMR, INSA2014-01
Macromolecular CrystallographyI.I.T. Roorkee2010-01
National International Collaboration
Drug resistanceDr. Dasantila Kotra, York University, Toronto, Canada
Protein engineeringProf. Michel Sylvestre:Centre INRS–Institut Armand-Frappier
Plant hemoglobinProf. Suman Kundu:Delhi University (South Campus)
Globulins from Wrightia tinctoria and other plant proteinsDr. Girish Mishra:Delhi University (North Campus)
Protein from momordica charantiaNBRI Lucknow
Biodegradation of toxic aromatic compoundsProf. J.T. Bolin: Purdue University (U.S.A.)
Particulars of course - 1. Macromolecular Crystallography: Institute elective 2. Bioinformatics: M.Sc. & B.Tech. (Biotechnology) 3. Structural Biology: B.Tech. (Biotechnology) 4. Structure based drug design: B.Tech. (Biotechnology) 5. protein crystallography: B.Tech. (Biotechnology)
Books Authored
Biodegradation And Bioremediation of the series  Env. Sci. & Engg.

Environmental Pollution:  Monitoring, Modeling and Control


Refereed Journal Papers

Publication list (*Corresponding author).



1.     Dhankhar P, Dalal V, Mahto JK, Gurjar BR, Tomar S, Sharma AK, Kumar P*. (2020) Characterization of dye-decolorizing peroxidase from Bacillus subtilis. Archives of Biochemistry and Biophysics. 2020 Oct 30;693:108590. doi: 10.1016/ Epub 2020 Sep 21. PMID: 32971035.


2.     Neetu N, Sharma M, Mahto JK, Kumar P*. (2020). Biophysical and In-Silico Studies of Phytochemicals Targeting Chorismate Synthase from Drug-Resistant Moraxella Catarrhalis. The Protein Journal. 2020 Oct 10:1-2. doi: 10.1007/s10930-020-09923-y. Epub 2020 Oct 10. PMID: 33037984.



3.     Dhankhar P, Dalal V, Singh V, Tomar S, Kumar P*. (2020). Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2. Journal of Biomolecular Structure and Dynamics. 2020 Nov 23:1-6. doi: 10.1080/07391102.2020.1852968. PMID: 33251943.


4.     Dhankhar P, Dalal V, Kotra DG, Kumar P*. (2020). In-silico approach to identify novel potent inhibitors against GraR of S. aureus. Front Biosci 2020 Mar 1;25:1337-1360. PMID: 32114436.



5.     Kumar P, Dalal V, Sharma N, Kokane S, Ghosh DK, Kumar P, Sharma AK*. (2020). Characterization of the heavy metal binding properties of periplasmic metal uptake protein CLas-ZnuA2. Metallomics. 2020 Feb 26;12(2):280-289. doi: 10.1039/c9mt00200f. PMID: 31853532.


6.     Kesari P, Pratap S, Dhankhar P, Dalal V, Mishra M, Singh PK, Chauhan H, Kumar P*. (2020). Structural characterization and in-silico analysis of Momordica charantia 7S globulin for stability and ACE inhibition. Sci Rep. 2020 Jan 24;10(1):1160. doi: 10.1038/s41598-020-58138-9. PMID: 31980708; PMCID: PMC6981215.



7.     Kumar P, Dalal V, Kokane A, Singh S, Lonare S, Kaur H, Ghosh DK, Kumar P, Sharma AK*. (2020). Mutation studies and structure-based identification of potential inhibitor molecules against periplasmic amino acid binding protein of Candidatus Liberibacter asiaticus (CLasTcyA). Int J Biol Macromol. 2020 Mar 15;147:1228-1238. doi: 10.1016/j.ijbiomac.2019.09.250. Epub 2019 Nov 15. PMID: 31739071.


8.     Neetu N, Katiki M, Dev A, Gaur S, Tomar S, Kumar P*. (2020). Structural and biochemical analyses reveal that chlorogenic acid inhibits the shikimate pathway. Journal of Bacteriology. 2020 Aug 25;202(18). doi: 10.1128/JB.00248-20. Epub 2020 Aug 25. PMID: 32661075.



9.     Singh N, Dalal V, Kumar P*. (2020). Molecular docking and simulation analysis for elucidation of toxic effects of dicyclohexyl phthalate (DCHP) in glucocorticoid receptor-mediated adipogenesis. Molecular Simulation. 2020 Jan 2;46(1):9-21. doi: 10.1089/107555302317371479.


10.  Kumari N, Dalal V, Kumar P, Rath SN*. (2020). Antagonistic interaction between TTA-A2 and paclitaxel for anti-cancer effects by complex formation with T-type calcium channel. Journal of Biomolecular Structure and Dynamics. 23:1-2. doi: 10.1080/07391102.2020.1839558. PMID: 33103598.



  1. Dalal V, Kumar P, Rakhaminov G, Qamar A, Fan X, Hunter H, Tomar S, Golemi-Kotra D, Kumar P*. (2019). Repurposing an ancient protein core structure: structural studies on FmtA, a novel esterase of staphylococcus aureus. J Mol Biol.;431(17):3107- 3123. doi: 10.1016/j.jmb.2019.06.019. Epub 2019 Jun 28. PMID: 31260692.

2.     Kaur R, Mudgal R, Jose J, Kumar P, Tomar S*. (2019). Glycan-dependent chikungunya viral infection divulged by antiviral activity of NAG specific chi-like lectin. Virology. 2019 Jan 2;526:91-98. doi: 10.1016/j.virol.2018.10.009. Epub 2018 Oct 25. PMID: 30388630


3.     Saini G, Dalal V, Savita BK, Sharma N, Kumar P, Sharma AK*. (2019). Molecular docking and dynamic approach to virtual screen inhibitors against Esbp of Candidatus Liberibacter asiaticus. J Mol Graph Model. 2019 Nov; 92:329-340. doi:10.1016/j.jmgm.2019.08.012. Epub 2019 Aug 16. PMID: 31446203.



4.     Singh N, Dalal V, Kumar V, Sharma M, Kumar P*. (2019). Characterization of phthalate reductase from Ralstonia eutropha CH34 and in silico study of phthalate dioxygenase and phthalate reductase interaction. J Mol Graph Model. 2019 Nov; 92:329-340. doi: 10.1016/j.jmgm.2019. 08.012. Epub 2019 Aug 16. PMID: 31446203.


5.     Kumar P, Kesari P, Kokane S, Ghosh DK, Kumar P, Sharma AK*. (2019). Crystal structures of a putative periplasmic cystine‐binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding. FEBS J. 286(17):3450-3472. doi: 10.1111/febs.14921. Epub 2019 May 24. PMID: 31063259.



6.     Kumar P, Dalal V, Kokane A, Singh S, Lonare S, Kaur H, Ghosh DK, Kumar P, Sharma AK*. (2019). Mutation studies and structure-based identification of potential inhibitor molecules against periplasmic amino acid binding protein of Candidatus Liberibacter asiaticus (CLasTcyA). Int J Biol Macromol. 147:1228-1238. doi: 10.1016/j.ijbiomac.2019.09.250. Epub 2019 Nov 15. PMID: 31739071.




1.     Kumar V, Sharma A, Pratap S, Kumar, P* (2018). Biochemical and biophysical characterization of 1,4-Naphthoquinone as a dual inhibitor of two key enzymes of type II fatty acid biosynthesis from Moraxella catarrhalis. Biochim Biophys Acta.  Protein and Proteomics 1866(11):1131-1142..


2.     Narwal M, Singh H, Pratap S, Malik A, Kuhn RJ, Kumar, P, Tomar S. (2018). Crystal structure of chikungunya virus nsP2 cysteine protease reveals a putative flexible loop blocking its active site. Int J Biol Macromol. 116:451-462. PubMed PMID: 29730006.


3.     Sharma A, Kumar V, Pratap S, Kumar, P*. (2018). The inhibitory and binding studies of methyl-sulfone hydroxamate based inhibitors against LpxC from drug resistant Moraxella catarrhalis using biophysical, biochemical and in silico approaches. Int J Biol Macromol.  PubMed PMID: 30017978.


4.     Kumar V, Sharma A, Pratap S, Kumar, P*. (2018). Biophysical and in silico interaction studies of aporphine alkaloids with Malonyl-CoA: ACP transacylase (FabD) from drug resistant Moraxella catarrhalis. Biochimie. (2018); 149:18-33. PubMed PMID: 29604333.



5.     Kumar V, Sharma A, Pratap S, Kumar, P*.(2018). Characterization of isoflavonoids as inhibitors of β-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Moraxella catarrhalis: Kinetics, spectroscopic, thermodynamics and in silico studies. Biochim Biophys Acta. 1862(3):726-744. PubMed PMID: 29092780.



6.     Sharma R, Kesari P, Kumar, P, Tomar S*.(2018). Structure-function insights into chikungunya virus capsid protein: Small molecules targeting capsid hydrophobic pocket. Virology (2018); 515:223-234.


7.     Singh N, Dalal V, Kumar, P*.(2018).  Structure based mimicking of Phthalic acid esters (PAEs) and inhibition of hACMSD, an important enzyme of the tryptophan kynurenine metabolism pathway. Int J Biol Macromol. (2018); 108:214-224.


8.     Kumar V, Sharma A, Pratap S, Kumar, P*. (2018). Characterization of isoflavonoids as inhibitors of β-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Moraxella catarrhalis: Kinetics, spectroscopic, thermodynamics and in silico studies.     Biochim Biophys Acta. (General Subjects) (2018); 1862(3):726-744.


9.     Sharma A, Kumar V, Chatrath A, Dev A, Prasad R, Sharma AK, Tomar S, Kumar, P* (2018). In vitro metal catalyzed oxidative stress in DAH7PS: Methionine modification leads to structure destabilization and induce amorphous aggregation. Int J Biol Macromol. (2018);106:1089-1106.




  1. Aggarwal M, Kaur R, Saha A, Mudgal R, Yadav R, Dash PK, Parida M, Kumar, P, Tomar S*. (2017). Evaluation of antiviral activity of piperazine against Chikungunya virus targeting hydrophobic pocket of alphavirus capsid protein. Antiviral Res. (2017);146:102-111.


  1. Pratap S, Dev A, Kumar V, Yadav R, Narwal M, Tomar S, Kumar, P*. (2017). Structure of Chorismate Mutase-like Domain of DAHPS from Bacillus subtilis Complexed with Novel Inhibitor Reveals Conformational Plasticity of Active Site. Nature Publishing group Sci Rep. (2017); 25;7(1):6364.


  1. Kumar, P, Kesari P, Dhindwal S, Choudhary AK, Katiki M, Neetu, Verma A, Ambatipudi K, Tomar S, Sharma AK, Mishra G, Kumar, P*. (2017). A novel function for globulin in sequestering plant hormone: Crystal structure of Wrightia tinctoria 11S globulin in complex with auxin. Nature Publishing group Sci Rep. (Nature Publishing Journal) (2017); 7(1):4705.



  1. Singh N, Dalal V, Mahto JK, Kumar, P*. (2017). Biodegradation of phthalic acid esters (PAEs) and in silico structural characterization of mono-2-ethylhexyl phthalate (MEHP) hydrolase on the basis of close structural homolog. J Hazard Mater. (2017); 15;338:11-22.


  1. Kesari P, Neetu, Sharma A, Katiki M, Kumar, P, Gurjar BR, Tomar S, Sharma AK, Kumar, P*. (2017). Structural, Functional and Evolutionary Aspects of Seed Globulins. Protein Pept Lett. (2017); 24(3):267-277.


  1. Sharma A, Kumar, P, Kesari P, Chaudhary N, Katiki M, Mishra M, Singh PK, Gurjar, BR, Sharma AK, Tomar S, Kumar, P*.(2017).            Purification and Characterization of 2S albumin from seeds of Wrightia tinctoria exhibiting Antibacterial and DNase Activity.   Protein Pept Lett. (2017); 24(4):368-378.


  1. Pratap S, Kesari, P, Yadav R, Dev A, Narwal M & Kumar, P*. (2017). Acyl chain preference and inhibitor identification of Moraxella catarrhalis LpxA: Insight through crystal structure and computational studies. Int J Biol Macromol. (2017); 96:759-765.




  1. Dhindwal S, Gomez-Gil L, Neau DB, Pham TT, Sylvestre M, Eltis LD, Bolin JT, Kumar, P*. (2016). The structural basis of the enhanced pollutant-degrading capabilities of an engineered biphenyl dioxygenase. J Bacteriol. (2016); 198(10) 1499-512.



  1. Dhindwal S, Kesari P, Singh H, Kumar, P, Tomar S*. (2016). Conformer and pharmacophore  based identification of peptidomimetic inhibitors of chikungunya virus nsP2 protease.    J Biomol Struct Dyn. (2017); 35(16):3522-3539.


  1. Sharma R, Fatma B, Saha A, Bajpai S, Sistla S, Dash PK, Parida M, Kumar, P,Tomar S*. (2016). Inhibition of chikungunya virus by picolinate that targets viral capsid  protein. Virology. (2016); 498:265-276. PubMed PMID: 27614702.


  1. Batra M, Sharma R, Malik A, Dhindwal S, Kumar, P, Tomar S*. (2016).            Crystal structure of pentapeptide-independent chemotaxis receptor methyltransferase (CheR) reveals  idiosyncratic structural determinants for receptor recognition J Struct Biol. (2016); 196(3):364-374
  2. Tomar JS, Narwal M, Kumar, P, Peddinti RK*. (2016). Characterization of substrate binding and enzymatic removal of a 3-methyladenine lesion from genomic DNA with TAG of MDR A. baumannii. Mol Biosyst. (2016); 12(11):3259-3265. PubMed PMID: 27714027.


  1. Mukhi N, Dhindwal S, Uppal S, Kapoor A, Arya R, Kumar, P, Kaur J, Kundu S*. (2016). Structural and Functional Significance of the N- and C-Terminal Appendages in Arabidopsis Truncated Hemoglobin. Biochemistry.(2016); 55(12):1724-40.




  1. Pratap S, Katiki M, Gill P, Kumar, P*, Golemi-Kotra D. (2015). Active-Site Plasticity is Essential to Carbapenem Hydrolysis by OXA-58 Class D β-Lactamase of Acinetobacter baumannii. Antimicrob Agents Chemother. (2015); 60(1):75-86.


  1. Dhindwal S, Priyadarshini P, Patil DN, Tapas S, Kumar, P, Tomar S, Kumar, P*. (2015). Ligand-bound structures of 3-deoxy-D-manno octulosonate 8-phosphate phosphatase from Moraxella catarrhalis reveal a water channel connecting the active site for the second step of catalysis. Acta Crystallogr D Biol Crystallogr. (2015); 71(Pt 2):239-55.



3.     Sharma N, SelvaKumar, P, Bhose S, Ghosh DK, Kumar, P, Sharma AK. (2015). Crystal  structure of a periplasmic solute binding protein in metal-free, intermediate and metal-bound states from Candidatus Liberibacter asiaticus. J Struct Biol. (2015); 189(3):184-94


  1. Aggarwal M, Sharma R, Kumar, P, Parida M, Tomar S. (2015). Kinetic characterization of trans-proteolytic activity of Chikungunya virus capsid protease and development of a FRET-based HTS assay. Nature Publishing group Sci Rep. (2015); 5:14753.


  1. Kesari P, Patil DN, Kumar, P, Tomar S, Sharma AK, Kumar, P*. (2015). Structural and functional evolution of chitinase- like-proteins from plants.  Proteomics. 15(10):1693-705.



  1. SelvaKumar, P, Sharma N, Tomar PP, Kumar, P, Sharma AK            (2014). Structural insights into the aggregation behavior of Murraya koenigii miraculin-like protein below pH 7.5. Proteins (2014); 82(5):830-40.



  1. Aggarwal M, Dhindwal S, Kumar, P, Kuhn RJ, Tomar S. (2015). trans-Protease activity and structural insights into the active form of the alphavirus capsid protease. J Virol. (2014); 88(21):12242-53.


1.   Colbert CL†, Agar NY†, Kumar, P†, Chakko MN, Sinha SC, Powlowski JB, Eltis LD, Bolin JT. (2013) Structural characterization of Pandoraea pnomenusa B-356 biphenyl dioxygenase reveals features of potent polychlorinated biphenyl-degrading enzymes PLoS One. (2013); 8(1):e52550 (†Contributed equally).


1.     Patil DN, Datta M, Dev A, Dhindwal S, Singh N, Dasauni P, Kundu S, Sharma AK, Tomar S, Kumar, P*.       Structural Investigation of a Novel N-Acetyl Glucosamine Binding Chi-Lectin Which Reveals Evolutionary Relationship with Class III Chitinases. PLoS One. (2013);  23;8(5):e63779.


2.   Mukhi N, Dhindwal S, Uppal S, Kumar, P, Kaur J, Kundu S.     X-Ray crystallographic structural characteristics of Arabidopsis hemoglobin I and their functional implications. Biochim Biophys Acta. (2013); 1834(9):1944-56.


3.   Preeti, Tapas S, Kumar, P, Madhubala R, Tomar S.       Structural insight into DFMO resistant ornithine decarboxylase from Entamoeba histolytica: an inkling to adaptive evolution. PLoS One.(2013); 8(1):e53397.



4.   Aggarwal M, Tapas S, Preeti, Siwach A, Kumar, P, Kuhn RJ, Tomar S. Crystal structure of aura virus capsid protease and its complex with dioxane: new insights into capsid-glycoprotein molecular contacts. PLoS One.(2013); 7(12):e51288.



  1. Patil, D.N., Chaudhry, A., Sharma, A.K., Tomar, S., Kumar, P*. Structural basis for dual inhibitory role of tamarind Kunitz inhibitor (TKI) against factor Xa and trypsin. FEBS J  (2012); 279(24):4547-64.


  1. Kumar, P, Mohammadi M, Dhindwal S., Bolin JT &Sylvestre M. Structural insights into the metabolism of 2-chlorodibenzofuran by an evolved biphenyl dioxygenase   BBRC (2012);  421(4):757-62.


  1. Kumar, P., Patil, D.N., Chaudhary, A., Tomar, S.,Yernool, D., Singh, N., Dasauni, P.,  Kundu, S., & Kumar, P*., Purification and biophysical characterization of 11S globulin from Wrightia tinctoria exhibiting hemagglutinating activity. Protein & peptide letters (2012); 20(5):499-509.


  1. Preeti, Tapas S, Kumar, P, Madhubala R, Tomar S.       Biochemical, Mutational and In Silico Structural Evidence for Functional Dimeric Form of the Ornithine Decarboxylase from Entamoeba histolytica. PLoSNegl Trop Dis. (2012); 6(2):e1559.


  1. Narayanan A, Paul LN, Tomar S, Patil DN, Kumar, P, Yernool DA.            Structure-function studies of DNA binding domain of response regulator KdpE reveals equal affinity interactions at DNA half-sites. PLoS One.(2012); 7(1):e30102.



  1. Dhindwal S, Patil DN, Mohammadi M, Sylvestre M, Tomar S, Kumar, P*. Biochemical studies and ligand-bound structures of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 reveal a basis for broad specificity of the enzyme. J Biol Chem. (2011); Oct 21;286(42):37011-22.


  1. Mohammadi, M.†, Viger, J.F.,†, Kumar, P.,†, Barriault, D., Bolin, J.T., &Sylvestre, M.. (2011); Fine tuning  Rieske -type oxygenases reactive atoms to expand their substrate range. J. Biol. Chem. (2011); 286(31):27612-35. (†Contributed equally).



  1. Kumar, P., Mohammadi, M., Viger, J.F., Barriault, D., Gomez-Gil, L., Eltis, LD., Bolin J.T. &Sylvestre M.       (2011) Structural Insight into the Expanded PCB-Degrading Abilities of a Biphenyl Dioxygenase Obtained by Directed Evolution. J Mol Biol. (2011); 405(2):531-47.


  1. Aggarwal, M., Dhindwal, S., Pratap, S.,  Kuhn, R.J.,  Kumar, P.,& Tomar, S. (2011) Crystallization, high- resolution data collection and preliminary crystallographic analysis of Aura virus capsid protease and its complex with dioxane.          Acta Cryst. F (2011); 67, 1394-1398.


  1. Bhattacharya, S., & Kumar, P.  (2011) An insilico approach to structural elucidation of 3-deoxy-d arabino-heptulosonate 7-phosphate synthase from Arabidopsis thaliana: Hints for herbicide design. Phytochemistry. (2011); 73(1):7-14.


  1. Tapas, S., Kumar, A., Dhindwal, S., Preeti, Kumar, P*. (2011); Structural analysis of chorismate synthase from Plasmodium falciparum: A novel target for antimalaria drug discovery.     Int J Biol Macromol. (2011); 49(4), 767-77.


  1. Kumar, P*., Gómez-Gil, L., Mohammadi, M., Sylvestre, M., Eltis, L.D. & Bolin, J.T. Anaerobic crystallization and initial X-ray diffraction data of biphenyl 2,3-dioxygenase from Burkholderiaxenovorans LB400: addition of agarose improved the quality of the crystals.  Acta Crystallogr Sect F (2011); 67, 59-62.



  1. Sakshi, Patil, D.N., Tomar, S., Sylvestre, M., & Kumar, P*.       (2010) Expression, purification, crystallization and preliminary crystallographic studies of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from Pandoraea pnomenusa B-356. Acta Crystallogr Sect F (2010); 66:1517-20.


  1. Gahloth, D., Selvakumar, P., Shee, C., Kumar, P*., Sharma., A.K. (2010) Cloning, sequence analysis and crystal structure determination of a miraculin-like protein from Murraya koenigii.  Arch Biochem Biophys. (2010); 1;494(1):15-22.



  1. Tomar, S., Patil, D.N., Datta, M., Tapas, S., Preeti, Chaudhary, A., Sharma, A.K., Tomar, S., Kumar, P*.(2009)  Crystallization and preliminary X-ray diffraction analysis of the complex of Kunitz-type tamarind trypsin inhibitor and porcine pancreatic trypsin. Acta Crystallogr Sect F (2009); 1;65(Pt 11):1179-81.


  1. Patil, D.N., Datta, M., Chaudhary, A., Tomar, S., Sharma, A.K. & Kumar, P*.      (2009) Isolation, purification, crystallization and preliminary crystallographic studies of chitinase from tamarind (Tamarindus indica) seeds. Acta Crystallogr Sect F (2009); 65(Pt 4):343-5.


  1. Patil, D.N., Preeti, Chaudhry, A., Sharma, A.K., Tomar, S., Kumar, P*.            (2009) Purification, crystallization and preliminary crystallographic studies of a Kunitz-type proteinase inhibitor from tamarind (Tamarindus indica) seeds. Acta Crystallogr Sect F (2009); 65(Pt 7):736-8.



  1. Chaudhary, N.S., Shee, C., Islam, A., Ahmad, F., Yernool, D., Kumar, P. & Sharma, A.K*.      (2009)  Purification and characterization of a trypsin inhibitor from Putranjivaroxburghii seeds. Phytochemistry. (2008); 69(11):2120-6.


  1. Shee, C., Singh, T.P., Kumar, P. & Sharma, A.K. (2007)Crystallization and preliminary X-ray diffraction studies of Murrayakoenigii trypsin inhibitor.           Acta Crystallogr Sect F (2007); 63(Pt 4):318-9.


Post Doctoral Work


  1. Horsman, G.P., Bhowmik, S., Seah, S.Y., Kumar, P., Bolin, J.T. &Eltis, L.D.     (2007) The tautomeric half-reaction of BphD, a C-C bond hydrolase. Kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad.          J Biol Chem. (2007); 282(27):19894-904.


  1. Gomez-Gil L., Kumar, P., Barriault, D., Bolin, J.T., Sylvestre, M. &Eltis, L.D. Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme.            J Bacteriol. (2007); 189(15):5705-1


  1.  PhD work




  1. Dey, S., Vijayaraghavan, R., Goel, V.K., Kumar, S.,  Kumar, P. & Singh, T.P.        Design of a model peptide with a, b-dehydro-residues: Synthesis of Boc-Ile- DAla-OCH3 and its crystal structures obtained from two different solvents. J. Mol.  Struct. (2004); 737 27-3.




  1. Vijayaraghavan, R., Makker, J., Kumar, P.,Dey, S., Singh, T. P.            Crystal structure of Boc-Trp (CHO) - ΔPhe-Ile-ΔPhe-Leu-OCH3, C48H59N6O10. ZeitschriftfuerKristallographie - New Crystal Structures (2003);    218(1), 52-54.


  1. Makker, J., Dey, S., Kumar, P., Singh, T. P.      Crystal structure of Boc-ILe-ΔPhe-Ile-OCH3, C27H43N3O7.            ZeitschriftfuerKristallographie - New Crystal Structures (2003);  218, 179-180.


  1. Vijayaraghavan R., Makker, J., Kumar, P., Dey S., Singh T.P.            Design of peptides with a, b -dehydro-residues: syntheses, crystal structures and molecular conformations of two ΔPhe-Trp containing   peptides. Journal of Molecular Structure, (2003); 654(1-3),  103-110.


  1. Makker, J., Dey, S., Mukherjee, S., Vijayaraghavan, R., Kumar, P., Singh, T. P.       Design of peptides with  a, b  -dehydro-residues: synthesis, crystal structure and molecular conformation of a tetrapeptide Z-ΔVal-Val-ΔPhe-Ile-Ome. Journal of Molecular Structure,(2003); 654(1-3), 119-124.


  1. Vijayaraghavan R., Kumar, P., Dey S., Singh T.P.         Design of peptides with branched beta-carbon dehydro- residues: syntheses, crystal structures and molecular conformations of two peptides, (I) N-Carbobenzoxy-DeltaVal-Ala-Leu-OCH3 and (II) N-Carbobenzoxy-DeltaIle-Ala-Leu-OCH3. J. Pept. Res. (2003); 62(2):63-9.


  1. Mohanty A.K., Singh G., Paramasivam M., Saravanan K., Jabeen T., Sharma S., Yadav S., Kaur P., Kumar, P., Srinivasan A, Singh  T.P Crystal structure of a novel regulatory 40-kDa mammary gland protein (MGP-40) secreted during involution. J. Biol. Chem.(2003); 278(16):14451-60.



  1. Makker, J., Dey, S., Mukherjee, S., Kumar, P., Singh, T. P.            Crystal structure of Boc-Leu-ΔPhe-ΔPhe-Ile-OCH3,  C36H48N4O7. Zeitschriftfuer Kristallographie-New Crystal Structures (2002); 217(3), 372-374.


  1. Makkar, J., Dey, S., Kumar, P., Singh, T.P.       Crystal structure of Boc-Leu-ΔPhe-Ile-ΔPhe-Ile-OCH3,C42H59N5O8. Zeitschriftfuer Kristallographie - New Crystal Structures (2002); 217(3), 369-371.


  1. Kumar, P., Yadav, S. & Singh, T.P.      Crystallization and structure determination of goat lactoferrin at 4.0 Å  resolution: A new form of packing in lactoferrins with a high solvent in crystals. Ind. J. Biochem. Biophys. (2002); 39(1):16-21.


  1. Makkar, J., Dey, S., Kumar, P., Singh, T.P.       Design of peptides with alpha, beta-dehydro residues: pseudo-tripeptideN-benzyloxycarbonyl-DeltaLeu-L-Ala-L-Leu-OCH3.         Acta Crystallogr C58 (2002); 212-4.


  1. Kumar, P., Khan, J.A., Yadav, S. & Singh, T.P. Crystal structure of equine apolactoferrin at 303 K providing further evidence of closed conformations of N and C lobes. Acta Crystallogr  D58 (2002); 225-32.





  1. Singh, J.D., Milton, M.D., Bhalla, G. Khandelwal, B. L., Kumar, P., Singh, T. P., Butcher, R. J. Design, synthesis and structural aspects of acyclic N3E2 (E = Se or Te) type donors and its complexes with Group 12 metals. Phosphorus, Sulfur and Silicon and the Related  Elements. (2001); (171-172)  477-484.


  1. Milton, M.D., Singh, J. D., Khandelwal, B. L.; Kumar, P., Singh, T. P., Butcher, R. J.    Design, synthesis and  structural aspects of terdentate (N,O,Se/Te) donors and their competitive coordination behavior towards Pt(II). Phosphorus,Sulfur and Silicon and the Related Elements, (2001); (171-172)  485-492.


  1. Tomar, S., Yadav, S., Chandra, V., Kumar, P., Singh, T.P. Purification, crystallization and preliminary X-ray diffraction studies of disintegrin (schistatin) from saw-scaled viper (Echiscarinatus). Acta Crystallogr  D57(2001);1669-70.


  1. Vijayaraghavan, R., Kumar, P., Dey, S., Singh, T.P.      Design of peptides with alpha, beta-dehydro residues: a dipeptide with a branched beta-carbon dehydro residue at the (i+1) position, methyl N - (benzyloxycarbonyl) - alpha, beta - didehydrovalyl - L – tryptophanate. Acta Crystallogr C57 (2001); 1220-1.


  1. Khan, J.A., Kumar, P., Sharma, S., Mohanty, A.K., Jabeen, T., Paramasivam, M., Yadav, S., Srinivasan, A. & Singh, T.P. Mechanism of iron-uptake and iron-release in lactoferrins.    Proc. Ind. Nat. Sc. Acad. B67 (2001);1-17.


  1. Kumar, P., Yadav, S., Srinivasan, A., Bhatia, K.L. & Singh, T.P. A novel 40 kDa protein from goat mammary secretions: purification, crystallization and preliminary X-ray diffraction studies. Acta Crystallagr. D5765; 1332-3.


  1. Sharma, S., Kumar, P., Betzel, C., Singh, T.P.   Structure and function of proteins involved in milk allergies. J Chromatogr B Biomed Sci Appl. (2001); 756(1-2), 183-7.


  1. Khan, J.A., Kumar, P., Paramsivam, M., Yadav, R.S., Sahni, M.S., Sharma, S., Srinivasan, A. & Singh, T.P. Structure of camel apolactoferrin at 2.6Å resolution and structural basis of its dual role as a transferrin-cum-lactoferrin. J. Mol. Biol.  (2001); 309(3), 751-61.


  1. Khan J.A., Kumar, P., Srinivasan, A., Singh, T.P. Protein intermediate trapped by the simultaneous crystallization process. Crystal structure of an iron-saturated intermediate in the Fe3+ binding pathway of camel lactoferrin at 2.7 Å  resolution. J.Biol. Chem.  (2001); 276(39), 36817-23.


  1. Betzel, C., Gourinath, S., Kumar, P., Kaur, P., Perbandt, M., Eschenburg, S. & Singh, T.P. Structure of a serine protease proteinase K from Tritirachium album   Limber at 0.98Å resolution. Biochemistry. (2001); 40(10), 3080-8.




  1. Bhatia, S., Kumar, P., Kaur, P., & Singh, T.P. Design of peptides with a ,b - dehydro-residues: synthesis, and crystal and molecular structure of a 310-helical tetrapeptideBoc-L-Val-D Phe-D Phe-L-Ile-OCH3. J. Pept. Res. (1999); 54, 249-256.



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