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  Biography Details
 
Dr. Chandra Verma
Head of Division
 
Areas of Research Interest
 
  • Structural/Functional dynamics of biological molecules
  • Peptide/anti-microbial design
  • Virtual screening
 
Biography
 
Chandra Verma joined the Bioinformatics Institute (BII) A*STAR, Singapore, in November 2003. He heads the division of Biomolecular Modelling and Design and leads a group that applies physics based models to understand the links between protein sequence, structure and biological function. His group works closely with experimental laboratories where the hypotheses generated are tested. In addition, the group is also involved in designing peptides and small molecules (through virtual screening) both for interrogating biology as well as for therapeutic purposes. Prior to joining Singapore, he worked as a research fellow/reader at the Structural Biology Laboratory in York, UK where he liaised with several experimental laboratories, building mechanistic models underpinning a range of biochemical and biological functions (see for example http://www.ysbl.york.ac.uk/~chandra/AAA). He obtained his undergraduate degree at the Indian Institute of Technology, India and his D. Phil at the University of York where he remained, first as a postdoctoral fellow followed by a tenured position.
 
Selected Publications
(for full list please see http://web.bii.a-star.edu.sg/~chandra/allpubs)
 
  1. Brown CJ, Srinivasan D, Jun LH, Coomber D, Verma CS, Lane DP.
    The electrostatic surface of MDM2 modulates the specificity of its interaction with phosphorylated and unphosphorylated p53 peptides.
    Cell Cycle. 2007 Dec 26;7(5) [Epub ahead of print]
    PMID: 18256546 [PubMed - as supplied by publisher]


  2. Dodson GG, Lane DP, Verma CS.
    Molecular simulations of protein dynamics: new windows on mechanisms in biology.
    EMBO Rep. 2008 Feb;9(2):144-50.
    PMID: 18246106 [PubMed - in process]


  3. Gul S, Hussain S, Thomas MP, Resmini M, Verma CS, Thomas EW, Brocklehurst K.
    Generation of Nucleophilic Character in the Cys25/His159 Ion Pair of Papain Involves Trp177 but Not Asp158.
    Biochemistry. 2008 Feb 19;47(7):2025-2035. Epub 2008 Jan 29.
    PMID: 18225918 [PubMed - as supplied by publisher]


  4. Dey A, Verma CS, Lane DP.
    Updates on p53: modulation of p53 degradation as a therapeutic approach.
    Br J Cancer. 2008 Jan 15;98(1):4-8. Epub 2008 Jan 8.
    PMID: 18182973 [PubMed - in process]


  5. Lee HJ, Srinivasan D, Coomber D, Lane DP, Verma CS.
    Modulation of the p53-MDM2 interaction by phosphorylation of Thr18: a computational study.
    Cell Cycle. 2007 Aug;6(21):2604-11. Epub 2007 Aug 20.
    PMID: 17957142 [PubMed - indexed for MEDLINE]


  6. Lee HJ, Chua GH, Krishnan A, Lane DP, Verma CS.
    Substrate specificity of cyclins determined by electrostatics.
    Cell Cycle. 2007 Jul;6(18):2219-26. Epub 2007 Jul 6.
    PMID: 17890901 [PubMed - indexed for MEDLINE]


  7. Verma C, Seebah S, Low SM, Zhou L, Liu SP, Li J, Beuerman RW.
    Defensins: antimicrobial peptides for therapeutic development.
    Biotechnol J. 2007 Nov;2(11):1353-9. Review.
    PMID: 17886240 [PubMed - indexed for MEDLINE].


  8. Fuentes G, Ballesteros A, Verma CS.
    Enthalpic and entropic contributions in the transesterification of sucrose: computational study of lipases and subtilisin.
    J Biomol Struct Dyn. 2007 Oct;25(2):145-55.
    PMID: 17718593 [PubMed - indexed for MEDLINE]


  9. Somani S, Chng CP, Verma CS.
    Hydration of a hydrophobic cavity and its functional role: a simulation study of human interleukin-1beta.
    Proteins. 2007 Jun 1;67(4):868-85.
    PMID: 17380484 [PubMed - indexed for MEDLINE]


  10. Suresh A, Verma C.
    Modelling study of dimerization in mammalian defensins.
    BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S17.
    PMID: 17254301 [PubMed - indexed for MEDLINE]


  11. Seebah S, Suresh A, Zhuo S, Choong YH, Chua H, Chuon D, Beuerman R, Verma C.
    Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D265-8. Epub 2006 Nov 7.
    PMID: 17090586 [PubMed - indexed for MEDLINE]


  12. Leonard PM, Brzozowski AM, Lebedev A, Marshall CM, Smith DJ, Verma CS, Walton NJ, Grogan G.
    The 1.8 A resolution structure of hydroxycinnamoyl-coenzyme A hydratase-lyase (HCHL) from Pseudomonas fluorescens, an enzyme that catalyses the transformation of feruloyl-coenzyme A to vanillin.
    Acta Crystallogr D Biol Crystallogr. 2006 Dec;62(Pt 12):1494-501. Epub 2006 Nov 23.
    PMID: 17139085 [PubMed - indexed for MEDLINE]


  13. Stec E, Witkowska-Zimny M, Hryniewicz MM, Neumann P, Wilkinson AJ, Brzozowski AM, Verma CS, Zaim J, Wysocki S, Bujacz GD.
    Structural basis of the sulphate starvation response in E. coli: crystal structure and mutational analysis of the cofactor-binding domain of the Cbl transcriptional regulator.
    J Mol Biol. 2006 Dec 1;364(3):309-22. Epub 2006 Jun 30.
    PMID: 17010379 [PubMed - indexed for MEDLINE]


  14. Yeong SS, Zhu Y, Smith D, Verma C, Lim WG, Tan BJ, Li QT, Cheung NS, Cai M, Zhu YZ, Zhou SF, Tan SL, Duan W.
    The last 10 amino acid residues beyond the hydrophobic motif are critical for the catalytic competence and function of protein kinase Calpha.
    J Biol Chem. 2006 Oct 13;281(41):30768-81. Epub 2006 Aug 8.
    PMID: 16895917 [PubMed - indexed for MEDLINE]


  15. Lim WG, Tan BJ, Zhu Y, Zhou S, Armstrong JS, Li QT, Dong Q, Chan E, Smith D, Verma C, Tan SL, Duan W.
    The very C-terminus of PRK1/PKN is essential for its activation by RhoA and downstream signaling.
    Cell Signal. 2006 Sep;18(9):1473-81. Epub 2006 Jan 19.
    PMID: 16427251 [PubMed - indexed for MEDLINE]


  16. Dodson G, Verma CS.
    Protein flexibility: its role in structure and mechanism revealed by molecular simulations.
    Cell Mol Life Sci. 2006 Jan;63(2):207-19. Review.
    PMID: 16389462 [PubMed - indexed for MEDLINE]


  17. Verma CS, Fischer S.
    MProtein stability and ligand binding: new paradigms from in-silico experiments.
    Biophys Chem. 2005 Apr 1;115(2-3):295-302. Epub 2005 Jan 5.


  18. De Simone A, Dodson GG, Verma CS, Zagari A, Fraternali F.
    Prion and water: tight and dynamical hydration sites have a key role in structural stability.
    Proc Natl Acad Sci U S A. 2005 May 24;102(21):7535-40. Epub 2005 May 13.
    PMID: 15894615 [PubMed - indexed for MEDLINE]


  19. Dubbink HJ, Hersmus R, Verma CS, van der Korput HA, Berrevoets CA, van Tol J, Ziel-van der Made AC, Brinkmann AO, Pike AC, Trapman J.
    Distinct recognition modes of FXXLF and LXXLL motifs by the androgen receptor.
    Mol Endocrinol. 2004 Sep;18(9):2132-50. Epub 2004 Jun 3.
    PMID: 15178743 [PubMed - indexed for MEDLINE]


  20. Whittingham JL, Jonassen I, Havelund S, Roberts SM, Dodson EJ, Verma CS, Wilkinson AJ, Dodson GG.
    Crystallographic and solution studies of N-lithocholyl insulin: a new generation of prolonged-acting human insulins.
    Biochemistry. 2004 May 25;43(20):5987-95.
    PMID: 15147182 [PubMed - indexed for MEDLINE]


  21. Haire LF, Whyte SM, Vasisht N, Gill AC, Verma C, Dodson EJ, Dodson GG, Bayley PM.
    The crystal structure of the globular domain of sheep prion protein.
    J Mol Biol. 2004 Mar 5;336(5):1175-83.
    PMID: 15037077 [PubMed - indexed for MEDLINE]


  22. Svangard E, Goransson U, Smith D, Verma C, Backlund A, Bohlin L, Claeson P.
    Primary and 3-D modelled structures of two cyclotides from Viola odorata.
    Phytochemistry. 2003 Sep;64(1):135-42.
    PMID: 12946412 [PubMed - indexed for MEDLINE]


  23. Whittingham JL, Turkenburg JP, Verma CS, Walsh MA, Grogan G.
    The 2-A crystal structure of 6-oxo camphor hydrolase. New structural diversity in the crotonase superfamily.
    J Biol Chem. 2003 Jan 17;278(3):1744-50. Epub 2002 Nov 5.
    PMID: 12421807 [PubMed - indexed for MEDLINE]


  24. Brzozowski AM, Dodson EJ, Dodson GG, Murshudov GN, Verma C, Turkenburg JP, de Bree FM, Dauter Z.
    Structural origins of the functional divergence of human insulin-like growth factor-I and insulin.
    Biochemistry. 2002 Jul 30;41(30):9389-97.
    PMID: 12135360 [PubMed - indexed for MEDLINE]


  25. Caves LS, Verma CS.
    Congruent qualitative behavior of complete and reconstructed phase space trajectories from biomolecular dynamics simulation.
    Proteins. 2002 Apr 1;47(1):25-30.
    PMID: 11870862 [PubMed - indexed for MEDLINE]


  26. Ducros VM, Lewis RJ, Verma CS, Dodson EJ, Leonard G, Turkenburg JP, Murshudov GN, Wilkinson AJ, Brannigan JA.
    Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis.
    J Mol Biol. 2001 Mar 2;306(4):759-71.
    PMID: 11243786 [PubMed - indexed for MEDLINE]


  27. Antson AA, Smith DJ, Roper DI, Lewis S, Caves LS, Verma CS, Buckley SL, Lillford PJ, Hubbard RE.
    Understanding the mechanism of ice binding by type III antifreeze proteins.
    J Mol Biol. 2001 Jan 26;305(4):875-89.
    PMID: 11162099 [PubMed - indexed for MEDLINE]


  28. Brzozowski AM, Savage H, Verma CS, Turkenburg JP, Lawson DM, Svendsen A, Patkar S.
    Structural origins of the interfacial activation in Thermomyces (Humicola) lanuginosa lipase.
    Biochemistry. 2000 Dec 12;39(49):15071-82.
    PMID: 11106485 [PubMed - indexed for MEDLINE]


  29. Hewitt L, Kasche V, Lummer K, Lewis RJ, Murshudov GN, Verma CS, Dodson GG, Wilson KS.
    Structure of a slow processing precursor penicillin acylase from Escherichia coli reveals the linker peptide blocking the active-site cleft.
    J Mol Biol. 2000 Sep 29;302(4):887-98.
    PMID: 10993730 [PubMed - indexed for MEDLINE]


  30. Tang L, Whittingham JL, Verma CS, Caves LS, Dodson GG.
    Structural consequences of the B5 histidine --> tyrosine mutation in human insulin characterized by X-ray crystallography and conformational analysis.
    Biochemistry. 1999 Sep 14;38(37):12041-51.
    PMID: 10508408 [PubMed - indexed for MEDLINE]


  31. Fischer S, Verma CS.
    Binding of buried structural water increases the flexibility of proteins.
    Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9613-5.
    PMID: 10449741 [PubMed - indexed for MEDLINE]
 

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