Publications by Tom L. Blundell 1998 - 2003

C. M. Lobley, F. Schmitzberger, M. L. Kilkenny, H. Whitney, H. H. Ottenhof, E. Chakauya, M. E. Webb, L. M. Birch, K. L. Tuck, C. Abell, A. G. Smith, and T. L. Blundell.
Structural insights into the evolution of the pantothenate- biosynthesis pathway .
Biochem. Soc. Trans., 31(3):563-571, Jun 2003.
Medline link.
T. L. Blundell.
Life is Enhanced by Crystal Gazing, Artistic Insights, and Musical Stimuli .
Chem Biol, 10(4):299-300, Apr 2003.
Medline link.
P. C. Evans, T. S. Smith, M. J. Lai, M. G. Williams, D. F. Burke, K. Heyninck, M. M. Kreike, R. Beyaert, T. L. Blundell, and P. J. Kilshaw.
A novel type of deubiquitinating enzyme .
J. Biol. Chem., 10(4):299-300, Apr 2003.
Medline link.
N. J. Harmer, D. Chirgadze, K. Hyun Kim, L. Pellegrini, and T. L. Blundell.
The structural biology of growth factor receptor activation .
Biophys Chem, 100(1-3):545-553, Jan 2003.
Medline link.
M. A. DePristo, P. I. de Bakker, S. C. Lovell, and T. L. Blundell.
Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles .
Proteins: Struct. Funct. Genet., 51(1):41-55, Apr 2003.
Medline link.
P. I. de Bakker, M. A. DePristo, D. F. Burke, and T. L. Blundell.
Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model .
Proteins: Struct. Funct. Genet., 51(1):21-40, Apr 2003.
Medline link.
L. Pellegrini, D. S. Yu, T. Lo, S. Anand, M. Lee, T. L. Blundell, and A. R. Venkitaraman.
Insights into DNA recombination from the structure of a RAD51-BRCA2 complex .
Nature, 420(6913):287-293, Nov 2002.
Medline link.
B. Gonzalez, M. A. Pajares, H. P. Too, F. Garrido, T. L. Blundell, and J. Sanz-Aparicio.
Crystallization and preliminary X-ray study of recombinant betaine-homocysteine S-methyltransferase from rat liver .
Acta Crystallogr. D, 58(Pt 9):1507-1510, Sep 2002.
Medline link.
S. Patel, M. Martinez-Ripoll, T. L. Blundell, and A. Albert.
Structural enzymology of Li(+)-sensitive/Mg(2+)-dependent phosphatases .
J. Mol. Biol., 320(5):1087-1094, Jul 2002.
Medline link.
T. L. Blundell, H. Jhoti, and C. Abell.
High-throughput crystallography for lead discovery in drug design .
Nat Rev Drug Discov, 1(1):45-54, Jan 2002.
Medline link.
K. Watanabe, D. Y. Chirgadze, D. Lietha, H. de Jonge, T. L. Blundell, and E. Gherardi.
A new crystal form of the NK1 splice variant of HGF/SF demonstrates extensive hinge movement and suggests that the NK1 dimer originates by domain swapping .
J. Mol. Biol., 319(2):283-288, May 2002.
Medline link.
A. Pomes, M. D. Chapman, L. D. Vailes, T. L. Blundell, and V. Dhanaraj.
Cockroach allergen Bla g 2: structure, function, and implications for allergic sensitization .
Am J Respir Crit Care Med, 165(3):391-397, Feb 2002.
Medline link.
S. Patel, L. Yenush, P. L. Rodriguez, R. Serrano, and T. L. Blundell.
Crystal structure of an enzyme displaying both inositol- polyphosphate-1-phosphatase and 3'-phosphoadenosine-5'- phosphate phosphatase activities: a novel target of lithium therapy .
J. Mol. Biol., 315(4):677-685, Jan 2002.
Medline link, PDB:1JP4.
D. Matak-Vinkovic, M. Vinkovic, S. A. Saldanha, J. L. Ashurst, F. von Delft, T. Inoue, R. N. Miguel, A. G. Smith, T. L. Blundell, and C. Abell.
Crystal structure of Escherichia coli ketopantoate reductase at 1.7 Å resolution and insight into the enzyme mechanism .
Biochemistry, 40(48):14493-14500, Dec 2001.
Medline link, PDB:1KS9, PDF file (local only).
B. L. Sibanda, S. E. Critchlow, J. Begun, X. Y. Pei, S. P. Jackson, T. L. Blundell, and L. Pellegrini.
Crystal structure of an Xrcc4-DNA ligase IV complex .
Nat. Struct. Biol., 8(12):1015-1019, Dec 2001.
Medline link, PDB:1IK9, PDF file (local only).
D. Lietha, D. Y. Chirgadze, B. Mulloy, T. L. Blundell, and E. Gherardi.
Crystal structures of nk1-heparin complexes reveal the basis for nk1 activity and enable engineering of potent agonists of the met receptor.
EMBO J., 20(20):5543-5555, 2001.
Article on-line, PDB:1GMO, PDB:1GMN, PDF file (local only).
P. I. de Bakker, A. Bateman, D. F. Burke, R. N. Miguel, K. Mizuguchi, J. Shi, H. Shirai, and T. L. Blundell.
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families .
Bioinformatics, 17(8):748-749, Aug 2001.
Medline link Article on-line.
H. Shirai, T. L. Blundell, and K. Mizuguchi.
A novel superfamily of enzymes that catalyze the modification of guanidino groups .
Trends Biochem. Sci., 26(8):465-468, Aug 2001.
Medline link.
M. G. Williams, H. Shirai, J. Shi, H. G. Nagendra, J. Mueller, K. Mizuguchi, R. N. Miguel, S. C. SC, C. A. Innis, C. M. Deane, L. Chen, N. Campillo, D. F. Burke, T. L. Blundell, and P. I. de Bakker.
Sequence-structure homology recognition by iterative alignment refinement and comparative modeling .
Proteins: Struct. Funct. Genet., 45 Suppl 5:92-97, 2001.
Medline link.
H. G. Nagendra, A. E. Harrington, N. J. Harmer, L. Pellegrini, T. L. Blundell, and D. F. Burke.
Sequence analyses and comparative modeling of fly and worm fibroblast growth factor receptors indicate that the determinants for FGF and heparin binding are retained in evolution .
FEBS Lett., 501(1):51-58, Jul 2001.
Medline link, Article on-line, PDF file (local only).
J. Shi, T. L. Blundell, and K. Mizuguchi.
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure- dependent gap penalties .
J. Mol. Biol., 310(1):243-257, Jun 2001.
Medline link, Article on-line, PDF file (local only).
C. M. Deane, Q. Kaas, and T. L. Blundell.
SCORE: predicting the core of protein models .
Bioinformatics, 17(6):541-550, Jun 2001.
Medline link, Article on-line, PDF file (local only).
F. von Delft, A. Lewendon, V. Dhanaraj, T. L. Blundell, C. Abell, and A. G. Smith.
The Crystal Structure of E. coli Pantothenate Synthetase Confirms It as a Member of the Cytidylyltransferase Superfamily .
Structure, 9(5):439-450, May 2001.
Medline link, PDF file (local only).
J. Mendes, H. A. Nagarajaram, C. M. Soares, T. L. Blundell, and M. A. Carrondo.
Incorporating knowledge-based biases into an energy-based side-chain modeling method: Application to comparative modeling of protein structure .
Biopolymers, 59(2):72-86, Aug 2001.
Medline link.
C. M. Deane and T. L. Blundell.
CODA: A combined algorithm for predicting the structurally variable regions of protein models .
Protein Sci., 10(3):599-612, Mar 2001.
Medline link Article on-line.
C. A. Innis, J. Shi, and T. L. Blundell.
Evolutionary trace analysis of TGF-beta and related growth factors: implications for site-directed mutagenesis .
Prot. Engng, 13(12):839-847, Dec 2000.
Medline link Article on-line, PDF file (local only).
T. L. Blundell, D. F. Burke, D. Chirgadze, V. Dhanaraj, M. Hyvonen, C. A. Innis, E. Parisini, L. Pellegrini, M. Sayed, and B. L. Sibanda.
Protein-protein interactions in receptor activation and intracellular signalling .
Biol. Chem., 381(9-10):955-959, SepOct 2000.
Medline link.
L. Pellegrini, D. F. Burke, F. von Delft, B. Mulloy, and T. L. Blundell.
Crystal structure of fibroblast growth factor receptor ectodomain bound to ligand and heparin .
Nature, 407(6807):1029-1034, Oct 2000.
Medline link, PDF file (local only), PDB:1e0o.
D. F. Burke, C. M. Deane, and T. L. Blundell.
Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure .
Bioinformatics, 16(6):513-519, Jun 2000.
Medline link Article on-line, PDF file (local only).
M. O. Badasso, J. A. Read, V. Dhanaraj, J. B. Cooper, S. P. Wood, T. L. Blundell, T. Dreyer, and J. Winther.
Purification, co-crystallization and preliminary X-ray analysis of the natural aspartic proteinase inhibitor IA3 complexed with saccharopepsin from saccharomyces cerevisiae .
Acta Crystallogr. D, 56 (Pt 7)(6):915-917, Jul 2000.
Medline link, PDF file (local only).
C. Marino-Buslje, M. Martin-Martinez, K. Mizuguchi, K. Siddle, and T. L. Blundell.
The insulin receptor: from protein sequence to structure .
Biochem. Soc. Trans., 27(4):715-726, Aug 1999.
Medline link.
C. M. Deane and T. L. Blundell.
A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins .
Proteins: Struct. Funct. Genet., 40(1):135-144, Jul 2000.
Medline link, PDF file (local only).
A. Albert, L. Yenush, M. R. Gil-Mascarell, P. L. Rodriguez, S. Patel, M. Martinez-Ripoll, T. L. Blundell, and R. Serrano.
X-ray structure of yeast Hal2p, a major target of lithium and sodium toxicity, and identification of framework interactions determining cation sensitivity .
J. Mol. Biol., 295(4):927-938, Jan 2000.
Medline link, PDB:1QGX, PDF file (local only).
H. A. Nagarajaram, B. V. Reddy, and T. L. Blundell.
Analysis and prediction of inter-strand packing distances between -sheets of globular proteins .
Prot. Engng, 12(12):1055-1062, Dec 1999.
Medline link Article on-line, PDF file (local only).
C. M. Deane, F. H. Allen, R. Taylor, and T. L. Blundell.
Carbonyl-carbonyl interactions stabilize the partially allowed Ramachandran conformations of asparagine and aspartic acid .
Prot. Engng, 12(12):1025-1028, Dec 1999.
Medline link Article on-line, PDF file (local only).
K. Mizuguchi, V. Dhanaraj, T. L. Blundell, and A. G. Murzin.
N-ethylmaleimide-sensitive fusion protein (NSF) and CDC48 confirmed as members of the double-psi -barrel aspartate decarboxylase/formate dehydrogenase family .
Structure, 7(9):R215-R216, Sep 1999.
Medline link, PDF file (local only).
D. F. Burke, C. M. Deane, H. A. Nagarajaram, N. Campillo, M. Martin-Martinez, J. Mendes, F. Molina, J. Perry, B. V. Reddy, C. M. Soares, R. E. Steward, M. Williams, M. A. Carrondo, T. L. Blundell, and K. Mizuguchi.
An iterative structure-assisted approach to sequence alignment and comparative modeling .
Proteins: Struct. Funct. Genet., Suppl 3(9):55-60, 1999.
Medline link, PDF file (local only).
A. G. Pavlovsky, M. G. Williams, Q. Z. Ye, D. F. Ortwine, C. F. Purchase, 2nd, A. D. White, V. Dhanaraj, B. D. Roth, L. L. Johnson, D. Hupe, C. Humblet, and T. L. Blundell.
X-ray structure of human stromelysin catalytic domain complexed with nonpeptide inhibitors: implications for inhibitor selectivity .
Protein Sci., 8(7):1455-1462, Jul 1999.
Medline link, PDB:1B8Y.
V. Dhanaraj, M. G. Williams, Q.-Z. Ye, F. Molina, L.L.Johnson, D. F. Ortwine, A. Pavlovsky, J. R. Rubin, R. W. Skeean, A. D. White, C. Humblet, D. J. Hupe, and T. L. Blundell.
X-ray structure of gelatinase a catalytic domain complexed with a hydroxamate inhibitor.
Croatica Chemica Acta, 72:575-, 1999.
A. R. Walker, P. A. Davison, A. C. Bolognesi-Winfield, C. M. James, N. Srinivasan, T. L. Blundell, J. J. Esch, M. D. Marks, and J. C. Gray.
The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein .
Plant Cell, 11(7):1337-1350, Jul 1999.
Medline link Article on-line.
R. M. Castillo, K. Mizuguchi, V. Dhanaraj, A. Albert, T. L. Blundell, and A. G. Murzin.
A six-stranded double-psi barrel is shared by several protein superfamilies .
Structure, 7(2):227-236, Feb 1999.
Medline link, PDF file (local only).
C. A. Arias, M. Martin-Martinez, T. L. Blundell, M. Arthur, P. Courvalin, and P. E. Reynolds.
Characterization and modelling of VanT: a novel, membrane- bound, serine racemase from vancomycin-resistant Enterococcus gallinarum BM4174 .
Mol Microbiol, 31(6):1653-1664, Mar 1999.
Medline link.
N. Srinivasan, M. Antonelli, G. Jacob, I. Korn, F. Romero, A. Jedlicki, V. Dhanaraj, M. F. Sayed, T. L. Blundell, C. C. Allende, and J. E. Allende.
Structural interpretation of site-directed mutagenesis and specificity of the catalytic subunit of protein kinase CK2 using comparative modelling .
Prot. Engng, 12(2):119-127, Feb 1999.
Medline link, PDF file (local only).
I. Korn, S. Gutkind, N. Srinivasan, T. L. Blundell, C. C. Allende, and J. E. Allende.
Interactions of protein kinase CK2 subunits .
Mol Cell Biochem, 191(1-2):75-83, Jan 1999.
Medline link.
B. V. Reddy, H. A. Nagarajaram, and T. L. Blundell.
Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins .
Protein Sci., 8(3):573-586, Mar 1999.
Medline link.
S. A. Islam, D. Carvin, M. J. Sternberg, and T. L. Blundell.
HAD, a data bank of heavy-atom binding sites in protein crystals: a resource for use in multiple isomorphous replacement and anomalous scattering .
Acta Crystallogr. D, 54(1 ( Pt 6)):1199-1206, Nov 1998.
Medline link Article on-line.
R. Sowdhamini, D. F. Burke, C. Deane, J. F. Huang, K. Mizuguchi, H. A. Nagarajaram, J. P. Overington, N. Srinivasan, R. E. Steward, and T. L. Blundell.
Protein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies .
Acta Crystallogr. D, 54(1 ( Pt 6)):1168-1177, Nov 1998.
Medline link Article on-line.
D. Y. Chirgadze, J. P. Hepple, H. Zhou, R. A. Byrd, T. L. Blundell, and E. Gherardi.
Crystal structure of the NK1 fragment of HGF/SF suggests a novel mode for growth factor dimerization and receptor binding .
Nat. Struct. Biol., 6(1):72-79, Jan 1999.
Medline link, PDB:1NK1, PDF file (local only).
C. Marino-Buslje, K. Mizuguchi, K. Siddle, and T. L. Blundell.
A third fibronectin type III domain in the extracellular region of the insulin receptor family .
FEBS Lett., 441(2):331-336, Dec 1998.
Medline link, PDF file (local only).
M. R. Groves, V. Dhanaraj, M. Badasso, P. Nugent, J. E. Pitts, D. J. Hoover, and T. L. Blundell.
A 2.3 Å resolution structure of chymosin complexed with a reduced bond inhibitor shows that the active site - hairpin flap is rearranged when compared with the native crystal structure .
Prot. Engng, 11(10):833-840, Oct 1998.
Medline link, PDF file (local only).
M. A. Rodionov and T. L. Blundell.
Sequence and structure conservation in a protein core .
Proteins: Struct. Funct. Genet., 33(3):358-366, Nov 1998.
Medline link, PDF file (local only).
K. Mizuguchi, C. M. Deane, T. L. Blundell, and J. P. Overington.
HOMSTRAD: a database of protein structure alignments for homologous families .
Protein Sci., 7(11):2469-2471, Nov 1998.
Medline link, Article on-line.
L. Pellegrini, P. Commander, B. Mulloy, M. Martin-Martinez, T. L. Blundell, and D. F. Burke.
The role of heparin in the complex formation between fibroblast growth factor 2 and its high affinity receptor: comparative modelling and biochemical studies .
Biochem. Soc. Trans., 26(3):545-549, Aug 1998.
Medline link.
R. Sowdhamini, D. F. Burke, J. F. Huang, K. Mizuguchi, H. A. Nagarajaram, N. Srinivasan, R. E. Steward, and T. L. Blundell.
CAMPASS: a database of structurally aligned protein superfamilies .
Structure, 6(9):1087-1094, Sep 1998.
Medline link Article on-line, PDF file (local only).
D. H. Brotherton, V. Dhanaraj, S. Wick, L. Brizuela, P. J. Domaille, E. Volyanik, X. Xu, E. Parisini, B. O. Smith, S. J. Archer, M. Serrano, S. L. Brenner, T. L. Blundell, and E. D. Laue.
Crystal structure of the complex of the cyclin D-dependent kinase Cdk6 bound to the cell-cycle inhibitor p19INK4d [published erratum appears in Nature 1998 Nov 26;396(6709):390] .
Nature, 395(6699):244-250, Sep 1998.
Medline link, PDB:1BLX, PDB:1CIZ, PDF file (local only).
A. Loew, Y. K. Ho, T. Blundell, and B. Bax.
Phosducin induces a structural change in transducin .
Structure, 6(8):1007-1019, Aug 1998.
Medline link, Article on-line, PDB:1A0R, PDF file (local only).
K. Mizuguchi, C. M. Deane, T. L. Blundell, M. S. Johnson, and J. P. Overington.
JOY: protein sequence-structure representation and analysis .
Bioinformatics, 14(7):617-623, 1998.
Medline link Article on-line, PDF file (local only).
K. Mizuguchi, J. S. Parker, T. L. Blundell, and N. J. Gay.
Getting knotted: a model for the structure and activation of Spätzle .
Trends Biochem. Sci., 23(7):239-242, Jul 1998.
Medline link Article on-line.
D. Y. Chirgadze, J. Hepple, R. A. Byrd, R. Sowdhamini, T. L. Blundell, and E. Gherardi.
Insights into the structure of hepatocyte growth factor/scatter factor (HGF/SF) and implications for receptor activation .
FEBS Lett., 430(1-2):126-129, Jun 1998.
Medline link, PDF file (local only).
T. L. Blundell.
Leaving the structured world of Oxford .
Nat. Struct. Biol., 5(7):533, Jul 1998.
Medline link.
C. F. Snook, G. A. Woolley, G. Oliva, V. Pattabhi, S. F. Wood, T. L. Blundell, and B. A. Wallace.
The structure and function of antiamoebin I, a proline-rich membrane-active polypeptide .
Structure, 6(6):783-792, Jun 1998.
Medline link, PDB:1JOH Article on-line.
M. Cordeiro, T. Lowther, B. M. Dunn, K. Guruprasad, T. Blundell, M. S. Pais, and P. E. Brodelius.
Substrate specificity and molecular modelling of aspartic proteinases (cyprosins) from flowers of Cynara cardunculus subsp. flavescens cv. cardoon .
Adv Exp Med Biol, 436(6):473-479, 1998.
Medline link.
A. Domingos, Z. T. Xue, K. Guruprasad, A. Clemente, T. Blundell, M. S. Pais, and P. E. Brodelius.
An aspartic proteinase from flowers of Centaurea calcitrapa. Purification, characterization, molecular cloning, and modelling of its three-dimensional structure .
Adv Exp Med Biol, 436(6):465-472, 1998.
Medline link.
A. Albert, T. L. Blundell, V. Dhanaraj, L. E. Donate, M. Groves, K. Guruprasad, P. G. Nugent, P. Orprayoon, J. E. Pitts, S. Rufino, N. Srinivasan, M. Williams, and J. Wilsher.
Protein engineering aspartic proteinases. Site-directed mutagenesis, biochemical characterisation, and X-ray analysis of chymosins with substituted single amino acid substitutions and loop replacements .
Adv Exp Med Biol, 436(6):169-177, 1998.
Medline link.
T. L. Blundell, K. Guruprasad, A. Albert, M. Williams, B. L. Sibanda, and V. Dhanaraj.
The aspartic proteinases. An historical overview .
Adv Exp Med Biol, 436(6):1-13, 1998.
Medline link.
A. Albert, V. Dhanaraj, U. Genschel, G. Khan, M. K. Ramjee, R. Pulido, B. L. Sibanda, F. von Delft, M. Witty, T. L. Blundell, A. G. Smith, and C. Abell.
Crystal structure of aspartate decarboxylase at 2.2 Å resolution provides evidence for an ester in protein self- processing .
Nat. Struct. Biol., 5(4):289-293, Apr 1998.
Medline link, PDB:1AW8.
D. Burke, D. Wilkes, T. L. Blundell, and S. Malcolm.
Fibroblast growth factor receptors: lessons from the genes .
Trends Biochem. Sci., 23(2):59-62, Feb 1998.
Medline link Article on-line.
V. Olsen, K. Guruprasad, N. X. Cawley, H. C. Chen, T. L. Blundell, and Y. P. Loh.
Cleavage efficiency of the novel aspartic protease yapsin 1 (Yap3p) enhanced for substrates with arginine residues flanking the P1 site: correlation with electronegative active-site pockets predicted by molecular modeling .
Biochemistry, 37(9):2768-2777, Mar 1998.
Medline link Article on-line, PDB:1YPS, PDF file (local only).
E. Gherardi, G. Hartmann, J. Hepple, D. Chirgadze, N. Srinivasan, and T. Blundell.
Domain structure of hepatocyte growth factor/scatter factor (HGF/SF) .
Ciba Found Symp, 212(9):84-93 93, 1997.
Medline link.
M. G. Williams, J. Wilsher, P. Nugent, A. Mills, V. Dhanaraj, M. Fabry, J. Sedlacek, J. M. Uusitalo, M. E. Penttila, J. E. Pitts, and T. L. Blundell.
Mutagenesis, biochemical characterization and X-ray structural analysis of point mutants of bovine chymosin .
Prot. Engng, 10(9):991-997, Sep 1997.
Medline link, PDF file (local only).
B. Bax, T. L. Blundell, J. Murray-Rust, and N. Q. McDonald.
Structure of mouse 7S NGF: a complex of nerve growth factor with four binding proteins .
Structure, 5(10):1275-1285, Oct 1997.
Medline link Article on-line, PDB:1SGF, PDF file (local only).
T. Blundell.
Value-added Frontiers programme [letter; comment] .
Nature, 386(6627):755, Apr 1997.
Medline link.
C. F. Aguilar, N. B. Cronin, M. Badasso, T. Dreyer, M. P. Newman, J. B. Cooper, D. J. Hoover, S. P. Wood, M. S. Johnson, and T. L. Blundell.
The three-dimensional structure at 2.4 Å resolution of glycosylated proteinase A from the lysosome-like vacuole of Saccharomyces cerevisiae .
J. Mol. Biol., 267(4):899-915, Apr 1997.
Medline link, PDB:2JXR.
S. D. Rufino, L. E. Donate, L. H. Canard, and T. L. Blundell.
Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling .
J. Mol. Biol., 267(2):352-367, Mar 1997.
Medline link, PDF file (local only).
C. M. Topham, N. Srinivasan, and T. L. Blundell.
Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables .
Prot. Engng, 10(1):7-21, Jan 1997.
Medline link.