(* senior
author)
The Singapore times (> end 2003):
1.
*G G
Dodson,
2.
*C J Brown, D Srinivasan, L H Jun,
D Coomber, C S Verma,
3.
A Dey, C S
Verma, D P Lane. Update on p53: modulation of p53
degradation as a therapeutic apporoach. Invited
review British J Cancer 98:4-8
(2008)
4.
S Gul,
M P. Thomas, S Hussain, C S Verma, E W Thomas, K Brocklehurst Investigation of interactions within the
active centre of papain using cationic reactivity
probes designed to bind to Asp158 and react with the thiolate
anion component of the (Cys25)–S–/(His159)–Im+H
ion-pair Biochemistry 47:2025-2035 (2008)
5.
S Liu, L Zhou, J Li, A. Suresh, C.S. Verma, Y H Foo, E.Yap, D. Tan and R.W. Beuerman
De Novo Linear Analogs of Human b-Defensin
3: Concept for Design of Antibacterial Peptides with Reduced Cytotoxicity to
Mammalian Cells. ChemBioChem (2008)
6.
*A Madhumular,
D J smith, C Verma. Stability of the core domain of
p53: insights from computer simulations BMC
Bioinformatics (2008) 9(Suppl 1):S17
7.
*Modulation of the p53-MDM2 interaction by phosphorylation of Thr18: a
computational study H J Lee, D Srinivasan, D Coomber, D P Lane, C S Verma Cell Cycle 6:2604-11
(2007)
8.
*Defensins: Antimicrobial peptides for therapeutic development C Verma, S Seebah, L Soo Mei,
Z Lei, L Shou Ping, L Jing,
R Beuerman Bitoechn
J 2:1353-9 (2007)
9.
*Substrate specificity of Cyclins determined by electrostatics H J Lee, G H
Chua, A Krishnan,
10.
*Wavelet analysis of protein dynamics K H Kiat, H
J Lee, B Veeravalli, C Verma Lecture Notes in
Bioinformatics (2007)
11.
*Enthalpic and entropic contributions in the transesterification of
sucrose: computational study of lipases and subtilisin
G. Fuentes, A. Ballesteros, C S Verma J Biomol Str Dyn
25:145-55 (2007)
12.
On the resolution of chiral substrates by a
retro-Claisenase enzyme. Biotransformations
of heteroannular bicylcic
b-diketones by 6-oxo camphor hydrolase.
C. L. Hill, C. H. Lee, D. J. Smith, C. S. Verma, G. Grogan Adv Synth Catal 349:1353-60
(2007)
13.
Desymmetrisations of 1-alkylbicyclo[3.3.0]octane-2,8-diones
by enzymatic retro-Claisen reaction yield
optically enriched 2,3-substituted cyclopentanones.
C. L. Hill, C.
14.
*Hydration of hydrophobic moieties: A simulation study of
interleukin-1beta.
15.
*Defensins Knowledgebase:
A manually curated database and information source
focused on the defensins family of antimicrobial peptides. S. Seebah, A. Suresh, R. Beuerman,
C. S. Verma. Nucleic Acids Res 35: D265 (2007)
16.
*Oligomerization in
defensins: a modelling study across mammals. A
Suresh, C Verma BMC Bioinformatics 7:S17 (2006)
17. *M.
Ortiz-Lombardia, C S Verma Proteins as data storage
devices: insights from computer models J Phys: Conf Ser 34 7-14 (2006)
18.
W. G. Lim, B. J. Tan, Y Zhu, S. Zhou, J. S. Armstrong, Q. T.
Li, Q. Dong, E. Chan, D. Smith, C. Verma, S-L Tan & W. Duan The very C-terminus of PRK1/PRK is essential for its
activation by RhoA and downstream
signalling. Cellular
Signalling 18:1473-1481 (2006)
19. Leonard PM, Brzozowski
AM, Lebedev A, Marshall CM, Smith, DJ, Verma, CS,
Walton, NJ and Grogan G The 1.8 Å 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 Cryst. D62,
1494-1501 (2006)
20. S.
S. Yeong, Y. Zhu, D. Smith, C. Verma, W. G. Lim, B. J. Tan, J. A. Armstrong, S.
Zhou, S-L Tan, N.S. Cheung & W. Duan The last ten amino acid residues
beyond the hydrophobic motif are critical for the catalytic competence and
function of protein kinase Ca. J.
Biol. Chem
281:30768-30781 (2006)
21. M
Witkowska-Zimny; M M Hryniewicz; P Neumann; A J. Wilkinson; A M. Brzozowski; C
S. Verma; J Zaim; G D. Bujacz Structural Basis of the Sulfate
Starvation Response in E. coli: Crystal Structure and Mutational Analysis of
the Cofactor-Binding Domain of the Cbl Transcriptional Regulator E Stec; J Mol Biol 364:309-322 (2006).
22. *S. Vijayakrishnan, R. Qaamra, C. S. Verma, R. Sen
& S. Mande Molecular Dynamics
Simulations of the M. tuberculosis
chaperonin-10: the role of metal ions J Biomol Str Dyn 23:365-375 (2006)
23. Y.
Zhu, D. Smith, C. Verma, W. G. Lim, B. J.
Tan, J. S. Armstrong, S. Zhou, E. Chan, S-L Tan, Y-Z Zhu, N. S. Cheung & W. Duan The very C-terminus of protein
kinase C is critical for the full catalytic competence but its hydrophobic motif
is dispensable for the interaction with 3-phosphoinositide-dependant kinase-1 Cellular Signalling 18:807-818 (2006)
24.
*G G Dodson &
C S Verma. Protein
flexibility: role in structure and mechanism revealed by molecular simulations Cell Mol Life Sci 63:207-219 (2006)
25.
C. S. Allardyce,
P. J. Dyson, C. S. Verma, J. Coffey & N. Johnson. Characterisation of the transferrin cisplatin-binding
site using mass spectrometry and molecular modelling. ChemBioChem
6 1788-1795 (2005)
26. *M. Akif, K. Suhre,
C. Verma, S.C. Mande Conformational flexibility of M. tuberculosis Thiredoxin reductase: crystal structure and normal mode
analysis Acta Cryst Sect D
D61:1603-1611 (2005)
27.
*V. Renugopalakrishnan, M
Ortiz-Lombardia, C Verma Electrostatics of cytochrome-c assemblies J
Mol Model.11 :265-270 (2005)
28.
V Renugopalakrishnan,
R Garduno-Juarez, G Narasimhan,
C S Verma, X Wei and P Li Rational design of
thermally stable proteins: relevance to bionanotechnology
(Review). Jl Nanosci Nanotech
5 1759-1767 (2005)
29. A. De Simone, G. G. Dodson, C. S. Verma, A. Zagari, F.
Fratarnali. Prion dry spots and water hot spots: key roles for
structural stability Proc Natl Acad Sci USA 102:7535-7540 (2005)
30.
K R Sakharkar, M K Sakharkar, C Verma, V T K Chow Comparative study of
overlapping genes in bacteria, with special reference to Rickettsia
prowazekii and Rickettsia conorii Int J Syst Evol
Microbiol. 55 1205-9 (2005)
31.
*C S Verma & S Fischer Protein stability & ligand
binding: new paradigms from in-silico
experiments, Biophys Chem 115
295-302 (2005)
32. A. Kumar, P.
C. Mishra, M. Durai, C. S. Verma and V. Renugopalakrishnan A Density Functional Study
of the Heme Moiety of Cytochrome c Int J Quant Chem 102 1002-1009 (2005)
33.
*G. L. Fuentes, A. R. Ballesteros & C. S. Verma Dynamic control of
specificity in enzymes: computational study of transesterification of sucrose
using lipases Protein Science 13 3092-3103 (2004)
34.
*R. B. Greaves,
G. G. Dodson, C. S. Verma. Altered ionisation of the B13-Glu in
insulin mutants: a computational analysis. Protein
35.
H. J. Dubbink, R. Hersmus, M. van Royen, C. S.
Verma, J. van Tol, A. C. J.
Ziel-van der Made, A. O. Brinkmann,
A. B. Houtsmuller, A. C.W. Pike, J. Trapman Distinct modes of recognition of FXXLF and LXXLL
motifs by the androgen receptor Molecular
Endocrinology 18 2132-2150 (2004).
36.
J. L. Whittingham, I. Jonassen, S. Havelund, S. M.
Roberts, E. J. Dodson, C. S. Verma and G. G. Dodson. Crystallographic analysis
and solution studies of N-lithocholyl insulin: a new
generation of prolonged-acting insulins. Biochemistry
43 5987-5995 (2004)
37.
M. Prabhakaran, S. H. Gursahani,
C. S. Verma, R. Garduno- Juarez, and V. Renugopalakrishnan. Cytochrome C: The effect of temperature
and pressure from molecular dynamics simulations J. Phys. Chem. Solids 65 1615-1622 (2004)
38.
L. F. Haire,
S. M. Whyte, N. Vashisht,
A. C. Gill, C. Verma, E. J. Dodson, G. G. Dodson and P. M. Bayley.
The crystal strucure of a truncated sheep prion
protein J. Mol. Biol 336 1175-1183 (2004).
Pre-Singapore era (< end 2003 – The
Chapters in Books:
·
K.Brocklehurst, A.B.Watts, M.Patel, C.Verma & E.W.Thomas Cysteine
Proteinases: in Comprehensive Biological Catalysis:
ed. M. Sinot, Academic Press, 1998.
·
R. Gill, C. Verma, J. Pitts, P. De-Meyts, A. Wollmer, S. Wood.
Structure and function of human IGF-1: In Recent research developments in protein
engineering, Vol 1, Research Signpost Publication,
1.
*N. P. Barton, C.
S. Verma & L. S. D. Caves. Inherent flexibility of calmodulin
domains: a normal mode analysis study: II J.
Phys. Chem. B 107 2170-2170 (2003)
2. S. Hussain, S. Pinitglang, T. S. F. Bailey, J. D. Reid, M. A. Noble, M. Resmini, E. W. Thomas, R. B. Greaves, C. S. Verma, K. Broklehurst.Variation in the pH-dependant pre-steady state and steady state kinetic characteristics of cysteine proteinase mechanism. Evidence for eletrostatically-modulation of ctaytic function by the neighbouring carboxylate Biochem J 372 735–746 (2003)
3.
*Primary and 3-d modelled structures
of two cyclotides from Viola odorata. Erika Svangårda,
U.Göransson, D.Smith,C.Verma,A.
Backlund, L. Bohlin, P. Claeson Phytochemistry
64 135-142 (2003)
4.
G. Grogan, J. L. Whittingham,
J. P. Turkenberg, C. S. Verma, M. Walsh. The 2.0A
resolution crystal structure of 6-oxo camphor hydrolase
reveals unexpected structural diversity n the crotonase
superfamily J.
Biol. Chem. 278 1744-1750 (2003)
5.
*N. P. Barton,
C. S. Verma,
6.
*G. Fuentes, M. A. Cruces, F. J. Plou, A. Ballesteros & C. S.
Verma Computational studies of transesterification of sugars using subtilisins: importance of entropic effects ChemBioChem 3 907-910 (2002)
7.
A. A. McCarthy, M. A. Walsh, M. Reinhold, C. S. Verma, D. P.
O’Connell, G. N. Yalloway, D. d’Arcy, T. M. Higgins,
G. Voordouw, & S. G. Mayhew. Crystallographic
investigation of the role of aspartate 95 in the
modulation of the redox potentials of Desulfovibrio vulgaris
flavodoxin Biochemistry
41 10950-10962 (2002)
8.
A. M. Brzozowski, F. De Beer, E. J.
Dodson, G. G. Dodson, G. N. Murschudov, C. S. Verma,
J. P. Turkenberg & Z. Dauter.
9.
S. Krzywda, A. M.
Brzozowski, C. Verma, K. Karata, T. Ogura & A. J. Wilkinson. The
crystal structure of the AAA domain of the ATP-dependant protease FtsH of Eschericia Coli at 1.5A
resolution. Structure 10 1073-1083 (2002)
10.
*J. C. Smith, F.
Merzel, C. S. Verma & S. Fischer. Protein hydration water:
structure and thermodynamics J. Mol. Liq 101
27-33 (2002)
11.
*R. Dvorsky, J. Sevcik,
V. Hornak, G.P.Tyrrell, L.S.D.Caves & C.S.Verma.
Molecular dynamics simulations of Rnase-Sa: a window
complementary to NMR/Xray J. Phys. Chem B 106 6038-6048 (2002)
12.
L.S.D.Caves
& C.S.Verma Congruent behaviour of complete and
reconstructed phase space trajectories from biomolecular dynamics simulation Proteins: Str Fn
Gen 47 25-30 47 25-30 (2002)
13.
*S. Fischer, J. Smith & C. S.
Verma Dissecting the vibrational entropy change on protein/ligand binding:
burial of a water molecule in bovine pancreatic trypsin inhibitor J Phys Chem B 105 8050-8055 (2001)
14.
J. Reid, S. Hussain,
S. Srredharan, T. Bailey, S. Pinitglang,
E. Thomas, C. Verma & K. Brocklehurst. Variation
in aspects of cysteine proteinase catalytic mechanism deduced by spectroscopic obseravtion of dithioester
intermediates, kinetic analysis and molecular dynamics simulations Biochem J 357 343-352 (2001)
15.
K. Karata, C. S.
Verma, A. J. Wilkinson & T. Ogura. Probing the
mechanism of ATP hydrolysis and substrate translocation in the AAA protease FtsH by mutagenesis and modeling Molecular Microbiology 39 890-903 (2001)
16.
17.
A. A. Antson,
D. J. Smith, D. I. Roper, S. Lewis, L. S. D. Caves, C. S. Verma, S. L. Buckley,
P. J. Lillford & R. E. Hubbard. The mechanism of
ice binding by type III antifreeze proteins J. Mol. Biol. 305, 875-889 (2001)
18.
*R. Dvorsky, J. Sevcik,
L.S.D. Caves & C. S. Verma.Temperature effects on
protein motions: a molecular dynamics study of Rnase-Sa
J Phys Chem B
104 10387-10397 (2000)
19.
A.M. Brzozowski, H. Savage, C. S.
Verma, J. P. Turkenburg, D. M. Lawson, A. Svendsen & S. Patkar.
Structural origins of the interfacial activation in Thermomyces (Humicola) lanuginosa lipase Biochemistry 39 15071-15082 (2000).
20.
L. Hewitt, V. Kasche,
K. Lummer, R. J. Lewis, G. N. Murshudov,
C. S. Verma, G. G. Dodson & K. Wilson. Structure of a slow processing
precursor penicillin acylase from Escherichia Coli revelas
the linker peptide blocking the active site cleft. J. Mol. Biol 302 887-898
(2000)
21.
M. A. Noble, S. Gul, C. S. Verma & K. Brocklehurst.
The ionization characteristics and chemical influences of D158 of papain and caricain determined by
structure-related kinetic and computational techniques: multiple electrostatic
modulators of active centre chemistry. Biochemical
Journal 351, 723-733 (2000).
22.
*S. Fischer &
C. S. Verma. Binding of buried water increases the flexibility of
proteins. Proc. Nat. Acad. Sci USA 96, 9613-9615 (1999).
23.
L. Tang, J. L. Whittingham,
C. S. Verma, L. S. D. Caves & G. G. Dodson. Structural consequences of the
B5 His->Tyr mutation in human insulin characterized by X-ray crystallography
and conformational analysis. Biochemistry
38, 12041-12051 (1999).
24.
R. Gill, C. Verma, B. Wallach, , B. Urso, J. Pitts, A. Wollmer, P. Demeyts & S.
Woods. Disulphide swapping in human insulin-like growth factor: implications
for receptor binding. Protein Engg 12, 297-303
(1999))
25.
C. G. Suresh, A. V. Pundle, H. SivaRaman, K. N. Rao, J. A. Brannigan, C. McVey,
C. S. Verma, Z. Dauter, E. J. Dodson,& G. G.
Dodson. Penicillin V Acylase crystal structure reveals new Ntn-hydrolase
family members. Nature Structural
Biology 6, 414-416 (1999)
26.
*S. Jääskeläinen,
C. S. Verma,
27.
D. G. Truhlar, W. L. Jorgensen, M.
T. Nguyen, J. B. Anderson, D. Chandler, S. HammesSchiffer,
P. G. Bolhuis, I. H. Hillier, C. Dellago,
J. N. L. Connor, M. V. Basilevsky, J. C. Tully, J. M.
Bowman, E. M. Goldfield, G. Katz, T. J. Martinez, W. Jakubetz,
H. W. Schranz, K. J. Schulten, M. Sprik,
G. C. Schatz, J. T. Hynes, I. H. Williams, P. R. Taylor, C. S. Verma, A. Lagana, K. Morokuma, C. Trindle, H. F. Schaefer, N. A. Burton & L. Blancafort. General discussion Faraday Disscn., 110, 477-520
(1999).
28.
J. H. Ullah,
T. R. Walsh, I. A. Taylor, D. C. Emery, C. S. Verma, S. J. Gamblin
& J. Spencer The
crystal structure of the L1 metallo-beta-lactamase
from Stenotrophomonas maltophilia
at 1.7A resolution J. Mol. Biol.
284, 125-136 (1998).
29.
*S. Jääskeläinen,
C. S. Verma, R. E. Hubbard, P. Linko & L. S. D.
Caves. Probing the conformational change in the activation of
lipase Protein Science, 7, 1359-1367
(1998).
30.
*S. Fischer, C.
S. Verma & R. E. Hubbard. Rotation of buried water inside a
protein: calculation of the rate and vibrational entropy of activation: J Phys Chem B, 102, 1797-1805 (1998).
31.
S. Pinitglang,
A. B. Watts, M. Patel, J. D. Reid, M. A. Noble, S. Gul,
A. Bokth, A. Naeem, H.
Patel, E. W. Thomas, S. K. Sreedharan, C. Verma &
K. Brocklehurst. A classical enzyme active centre
motif lacks catalytic competence until modulated electrostatically. Biochemistry, 36, 9968-9982 (1997).
32.
M. Resmini, R.
Vigna, C. Simms, N. J. Barber, E. P. Hagi-Pavli, A. B. Watts, C. Verma, G.
Gallacher & K. Brocklehurst. Characterisation of the hydrolytic
activity of a polyclonal catalytic antibody preparation by pH-dependence and
chemical modification studies. Evidence for the involvement of Tyr and Arg sidechains as hydrogen bond donors. Biochemical Journal, 326, 279-287
(1997).
33.
*C. S. Verma, L.
S. D. Caves, R. E. Hubbard & G. C. K. Roberts. Domain
motions in dihydrofolate reductase: a molecular dynamics study. J Mol Biol, 266,
776-796 (1997).
34.
J. Plou, D. Kowlessur, J. P. G. Malthouse, G. W. Mellor, M. J. Hartshorn,
S. Pinitglang, H. Patel, C. M. Thomas, E. W. Thomas,
C. Verma & K. Brocklehurst. Characterization of
the electrostatic perturbation of a catalytic site (Cys)-S-/(His)-Im(+)H ion-pair in one type
of serine proteinase architecture by kinetic and computational studies on
chemically mutated subtilisin variants. J
Mol Biol, 257, 1088-1111 (1996).
35.
R. Gill, B. Wallach,
C. Verma, B. Urso, E. Dewolf,
J. Grotzinger, J. MurrarRust,
J. Pitts, A. Wollmer, P. Demeyts
& S. Woods. Engineering the C-region of human Insulin-like Growth Factor-I
- implications for receptor binding. Protein
Engineering, 9, 1011-1019 (1996).
36.
K. Sreedharan,
C. Verma,
37.
*C. S. Verma, S.
Fischer, L. S. D. Caves, G. C. K. Roberts & R. E. Hubbard.
Calculation of the reaction pathway for the
aromatic ring flip in methotrexate
complexed to dihydrofolate reductase. J
Phys Chem, 100, 2510-2518 (1996).
38.
P. Thomas, C. Verma, S. M. Boyd &
K. Brocklehurst. The structural origins of the
unusual specificities observed in the isolation of chymopapain-M
and actinidin by covalent chromatography and the lack
of inhibition of chymopapain-M by cystatin.
Biochemical Journal, 306,
39-46 (1995).
39.
M. Lawson, A. M. Brozozowski,
S. Rety, C. Verma & G. G. Dodson. Probing the
nature of substrate binding in Humicola Lanuginosa lipase through X-ray crsytallographic and intuitive modelling. Protein Engineering, 7, 543-550
(1994).
40.
C. S. Verma, M.
Green & R. M. Wing. Kinetic recognition of the
5'-phosphate group in the attack of cisplatin type
systems on DNA. Journal of the Chemical
Society - Chemical Communications. 884-886 (1988).
41.
S. Gul,
S. Pinitglang, E. W. Thomas, C. Verma & K. Brocklehurst. Senistivities of
transition state geometries to P1-P2 binding in reactions
of papain and actinidin. Biochemical Society Transactions 26,
S171 (1998).
42.
A. Khan, I. F. Connerton,
N. J. Cummins, S. Hussain, M. A. Noble, M. A. J.
Taylor, E. W. Thomas, C. Verma & K. Brocklehurst.
The kinetically influential ionizations of caricain
D158N revealed by using 4,4’-dipyrimidyl disulfide as
a reactivity probe. Biochemical Society
Transactions 26, S172 (1998).
43.
K. Brocklehurst,
E. W. Thomas, C. Verma, M. Patel & S. K. Sreedharan.
Design and synthesis of substrate-derived N-acylaminoalkyl
2-pyridyl disulphides as probes of cysteine proteinase mechanism. Biochemical Society Transactions 25,
92S (1997).
44.
S. Gul, A.
Clarke, B. Field, M. P. Thomas, F. Willenbrock, S. Pinitglang, C. Verma, E. W. Thomas & K. Brocklehurst. Investigation of the electrostatic field of
the papain active centre by using monoprotonated
and diprotonated pyridyl (pY) disulphides as reactivity probes. Biochemical Society Transactions 25, 91S (1997).
45.
M. Noble, D.
Abramson, C. Verma & K. Brocklehurst. Evidence that
the carboxy groups of Asp158 in papain
and caricain have abnormally low pKa values and thus
do not contribute the key ionisations with pKa 4 that generate catalytic
competence. Biochemical Society
Transactions 25, 90S (1997).
46.
B. Reid, S. Pinitglang,
C. P. Thomas, C. Verma, E. W. Thomas & K. Brocklehurst.
Actinidin and chymopapain B
provide variation in the common electrostatic environment of Glu50 in papain and caricain. Biochemical Society Transactions, 25,
89S (1997).
47.
S. Pinitglang,
M. Patel, M. Noble, S. K. Sreedharan, C. Verma, E. W.
Thomas & K. Brocklehurst. Effects of the quality
of the P2-S2 hydrophobic contacts on the catalytic activities of papain, caricain and ficin and their generation by electrostatic switches. Biochemical Society Transactions, 25,
88S (1997).
48.
A
49.
S. Gul, P.
S. Dhillon, C. Verma, E. W. Thomas & K. Brocklehurst. Investigation of electrostatic interactions
and binding effects in papain-ligand interaction. Biochemical Society Transactions 24,
473S (1996).
50.
S. Pinitglang, M.
Noble, C. Verma, E. W. Thomas
& K. Brocklehurst. Studies on the enhancement of
the reactivity of the Cys25-S-/His159-Im+H ion-pair of papain by deprotonation across
pKa 4. Biochemical Society Transactions
24, 468S (1996).
51.
M. Green, S. S. Eapen,
D. J. Evans, K. Percival, C. Verma & R. M. Wing. Rates of reaction of Guanosine derivatives with cis-[pt(NH3)2(OH2)2]
& cis-[Pt(NH3)2(OH2)(OH)]. Recueil Des Travaux Chimiques des Pays-Bas
106, 194 (1987).
(* corr
author)