Download publications (last five years) - Structural and Molecular Biology

PUBLICATIONS (LAST FIVE YEARS)
Lachenmann, M. J., Ladbury, J. E., Dong, J., Huang, K., Carey, P., & Weiss, M. A. (2004)
Why zinc fingers prefer zinc: Ligand-field symmetry and the hidden thermodynamics of
metal-ion selectivity Biochemistry – in press
Lachenmann, M. J., Ladbury, J. E., Qian, X., Huang, K., Singh, R., & Weiss, M. A. (2004)
The hidden thermodynamics of a zinc finger probed by non-standard repair of a protein
crevice. Protein Science – in press.
Bergqvist, S., Williams, M. A., O’Brien, R., & Ladbury, J. E. (2004) Heat capacity effects of
water molecules and ions at a protein-DNA interface. Journal of Molecular Biology 336,
829-842.
Kowanetz, K., Szymkiewicz, I., Haglund, K., Kowanetz, M., Husnjak, K., Taylor, J. D.,
Soubeyran, P., Engstrom, U., Ladbury, J. E. & Dikic, I. (2003) Identification of a novel
proline-arginine motif involved in CIN85-dependent clustering of Cbl and downregulation of
EGF receptors. Journal of Biological Chemistry 278, 39735-39746.
Esposito, D., Petrovic, A., Harris, R., Ono, S., Eccleston, J. F., Mbabaali, A., Haq, I.,
Higgins, C. F., Hinton, J. C. D., Driscoll, P. C., & Ladbury, J. E. (2002) H-NS
oligomerization domain structure reveals the mechanism for high order self-association of
the intact protein. Journal of Molecular Biology 324, 841-850.
Salek, R. M., Williams, M. A., Prodromou, C., Pearl, L. H., & Ladbury, J. E. (2002)
Backbone resonance assignments of the 25 kD N-terminal ATP-ase domain from the
Hsp90 chaperone. Journal of Biomolecular NMR 23, 327-328.
Flatman, R., McLauchlan, W. R., Juge, N., Furniss, C. S., Berrin, J. G., Hughes, R. K.,
Manzanares, P., Ladbury, J. E., O'Brien, R., & Williamson, G. (2002) Interactions defining
the specificity between fungal xylanases and the wheat proteinaceous inhibitor, XIP-I.
Biochemical Journal 365, 773-781.
Low, L. Y., Hernandez, H., Robinson, C., O’Brien, R., Grossmann, J. G., Ladbury, J. E. &
Luisi, B. (2002) Metal-dependent folding and stability of nuclear hormone receptor DNAbinding domains. Journal of Molecular Biology 319, 87-106.
Bergqvist, S., Williams, M. A., O’Brien, R., & Ladbury, J. E. (2002) Reversal of halophilicity
in a protein-DNA interaction by limited mutation strategy. Structure with Folding and
Design 10, 629-63.
Lachenman, M., Ladbury, J. E., Narayana, N., Qian. X., & Weiss, M. A. (2002) The hidden
thermodynamics of a zinc finger. Journal of Molecular Biology 312, 969-989.
Haq, I., O’Brien, R., Lagunavicius, A., Siksnys, V., & Ladbury, J. E. (2001) Specific DNA
recognition by the type II restriction endonucleoase MunI: The effect of pH. Biochemistry
40,14960-14967.
Henriques, D. A., & Ladbury, J. E. (2001) Inhibitors to the Src SH2 domain: A lesson in
thermodynamic structural correlation in drug design. Archives in Biochemistry and
Biophysics 390, 158-168.
Lee, L., Stollar, E., Chang, J. –F., Grossman, J. G., O’Brien, R., Ladbury, J., Carpenter, B.,
Roberts, S., & Luisi, B. (2001) Expression of the Oct-1 transcription factor and
characterization of its interactions with the Bob1 coactivator. Biochemistry 40, 6580-6588.
Arold, S. T., Ulmer, T. S., Mulhern, T. D., Werner, J. M., Ladbury, J. E., Campbell, I. D.,
Noble, M. E. M. (2001) The role of the Src homology 3 – Src homology 2 interface in the
regulation of the Src kinases. Journal of Biological Chemistry 276, 17199-17205.
Joseph, C., Stier, G., O’Brien, R., Politou, A. S., Atkinson, R. A., Bianco, A., Ladbury, J. E.,
Martin, S. R., & Pastore, A. (2001) A structural characterization of theinteraction between
titin Z repeats and the -actinin C-terminal domain. Biochemistry 40, 4957-4965.
Renzoni, D., Esposito, D., Pfuhl, M., Hinton, J. C. D., Higgins, C. F., Driscoll, P. C., &
Ladbury, J. E. (2001) Structural characterization of the N-terminal oligomerization domain
of the bacterial chromatin-structuring protein, H-NS. Journal of Molecular Biology 306,
1127-1137.
Bergqvist, S., O’Brien, R., & Ladbury, J. E. (2001) Site-specific cation binding mediates the
TATA binding protein-DNA interaction from a hyperthermophilic archaeon. Biochemistry
40, 2419-2425.
Payne, J. W., Grail, B. M., Gupta, S., Ladbury, J. E., Marshall, N. J., O, Brien, R., & Payne,
G. M. (2000) Structural basis for recognition of dipeptides by peptide transporters.
Archives of Biochemistry and Biophysics 384, 9-23.
Henriques, D. A., Ladbury, J. E., & Jackson, R. M. (2000) Comparison of binding energies
of SrcSH2-phosphotyrosyl peptides with Structure-based prediction using surface area
based empirical parameterization. Protein Science 9, 1975-1985.
Pacini, S., Valensin, S., Telford, J. L., Ladbury, J. E., & Baldari, C. T. (2000) Temporally
regulated assembly of a dynamic signalling complex associated with the activated TCR.
European Journal of Immunology 30, 2620-2631.
Prodromou, C., Panaretou, B., Chohan, S., Siligardi, G., O’Brien, R., Ladbury, J. E., Roe,
S. M., Piper, P. W., & Pearl, L. H. (2000) The ATPase cycle of Hsp90 drives a molecular
‘clamp’ via transient dimerisation of the N-terminal domains. EMBO Journal 19, 43834392.
Kahmann, J. D., O’Brien, R., Werner, J. M., Heinegård, D., Ladbury, J. E., Campbell, I. D.,
& Day, A., J. (2000) Localization and Characterization of the Hyaluronan Binding-site on
the Link Module from Human TSG-6. Structure 8, 763-774.
Lundbäck, T., Chang, J. –F., Phillips, K., Luisi, B., Ladbury, J. E. (2000) Characterisation
of sequence-specific DNA-binding by the transcription factor Oct-1. Biochemistry 39, 75707579.
Smyth, C. P., Lundbäck, T., Renzoni, D. Siligardi, G., Beavil, R., Layton, M., Sidebotham,
J. M., Hinton, J. C. D., Driscoll, P. C., Higgins, C. F., & Ladbury, J. E. (2000)
Oligomerisation of the chromatin-structuring protein, H-NS. Molecular Microbiology 36,
962-972.
O’Brien, R., Rugman, P., Renzoni, D., Layton, M., Handa, R., Hilyard, K., Waterfield, M.
D., Driscoll, P. C., & Ladbury, J. E. (2000). Alternative modes of binding of proteins with
tandem SH2 domains. Protein Science 9, 570-579
Rostom, A. A., Tame, J. R. H., Ladbury, J. E., & Robinson, C. V. (2000) Specificity and
interactions of the protein OppA: Partitioning solvent binding effects using mass
spectrometry. Journal of Molecular Biology 296, 269-279.
Chung, E. W., Henriques, D. A., Renzoni, D., Morton, C. J., Mulhern, T. D., Pitkeathly, M.
C., Ladbury, J., E., & Robinson, C. V. (1999) Probing the nature of interactions in SH2
binding interfaces – Evidence from electrospray ionization mass spectrometry. Protein
Science 8, 1962-1970.
Sleigh, S. H., Seavers, P. R., Wilkinson, A. J., Ladbury, J. E., & Tame, J. R. H. (1999)
Crystallographic and calorimetric analysis of peptides binding to OppA protein. Journal of
Molecular Biology 291, 393-415.
Chang, J. –F., Phillips, K., Lundbäck, T., Gstaiger, M., Ladbury, J. E., & Luisi, B. (1999)
Oct-1 POU and octomer DNA co-operate to recognise the BOB-1 transcription co-activator
via induced folding. Journal of Molecular Biology 288, 941-952
Willcox, B. E., Gao, G. F., Wyer, J. R., Ladbury, J. E., Bell, J. I., Jakobsen, B. K., & van der
Merwe, P. A. (1999) TCR binding to peptide-MHC stabilises a flexible recognition
interface. Immunity 10, 357 – 365.
Baraldi, E., Carugo, K. D., Hyvönen, M., Lo Surdo, P., Riley,A. M., Potter, B. V. L., O’Brien,
R., Ladbury, J. E. & Saraste, M. (1999) Structure of the PH domain from Bruton’s tyrosine
kinase in complex with inositol 1,3,4,5-tetrakisphosphate. Structure 7, 449-460.
Prodromou, C., Siligardi, G., O’Brien, R., Woolfson, D. N., Regan, L., Panaretou, B.,
Ladbury, J. E., Piper, P. W. & Pearl, L. H. (1999) Regulation of Hsp90 ATPase activity by
tetratricopeptide repeat (TPR)-domain cochaperones. EMBO Journal 18, 754-762.
Roe, S. M., Prodromou, C., O’Brien, R., Ladbury, J. E., Piper, P. W., & Pearl, L. H. (1999)
The structural basis for the inhibition of the Hsp90 molecular chaperone by the anti-tumour
antibiotics radicicol and geldanamycin. Journal of Medicinal Chemistry 42, 260-265.
ARTICLES AND REVIEWS (LAST FIVE YEARS)
Ladbury, J. E. & Williams, M. A. (2004) The extended interface: measuring non-local
effects in biomolecular interactions. Current Opinions in Structural Biology. 14, 562-569.
Cliff, M. J., Gutierrez, A., & Ladbury, J. E. (2004) A survey of the year 2003 literature on
applications of isothermal titration calorimetry. Journal of Molecular Recognition 17, 513523.
Cliff, M. J. & Ladbury, J. E. (2003) A survey of recent literature of applications of
isothermal titration calorimetry. Journal of Molecular Recognition 16, 383-391.
O’Rourke, L., & Ladbury, J. E. (2003) Specificity is complex and time consuming: Mutual
exclusivity in tyrosine kinase-mediated signalling. Accounts of Chemical Research 36,
410-416.
Bergqvist, S., Williams, M. A., O’Brien, R., & Ladbury, J. E. (2003) Halophilic adaptation of
protein-DNA interactions. Biochemical Society Transactions 31, 677-680.
Ladbury, J. E. (2001) Isothermal titration calorimetry: Application to structure-based drug
design. Thermochimica Acta 380, 209-215.
Ladbury, J. E. (2001) Calorimetry takes the heat off drug discovery. European
Biopharmaceutical Review (winter 2001) 70-72.
Haq, I., & Ladbury, J. E. (2000) Drug-DNA recognition: Energetics and implications for
design. Journal of Molecular Recognition 13, 188-197.
Ladbury, J. E., & Arold, S. (2000) Searching for specificity in SH domains. Chemistry &
Biology 7, R3-R8.
EDITED BOOKS
Ladbury, J. E., & Doyle, M. L.. (2004)Biocalorimetry II: Applications of Calorimetry in the
Study of Biological Systems. John Wiley & Sons Ltd. Chichester, Sussex, UK.
Ladbury, J. E., & Chowdhry, B. Z. (1998) Biocalorimetry: Applications of Calorimetry in the
Study of Biological Systems. John Wiley & Sons Ltd. Chichester, Sussex, UK.
Ladbury, J. E., & Connelly, P. R. (1997) Structure-Based Drug Design: Thermodynamics,
Modelling and Strategy. R. G. Landes, Austin, TX, USA.
BOOK CHAPTERS
Thomson, J. A., & Ladbury, J. E. (2004) Isothermal titration calorimetry: A tutorial. In
“Biocalorimetry II: Applications of Calorimetry in the Biological Sciences” Editors J. E.
Ladbury & M. L. Doyle. John Wiley & Sons Ltd. Chichester, Sussex, UK - in press.
Ladbury (2004) Protein-protein recognition in phosphotyrosine-mediated intracellular
signaling. In “Proteomics and Protein-Protein Interactions: Biology, Chemistry,
Bioinformatics and Drug Design”. Editor G. Waksman.- in press
Williams, M. A., & Ladbury J. E. (2003) Hydrogen bonds in protein-ligand interactions. In
“Protein-Ligand Interactions: From Molecular Recognition to Drug Design”. Editors H. –J
Böhm & G. Schneider. Methods and Principles in Medicinal Chemistry Series. Wiley-VCH.
Weinheim, Germany. ISBN 3-527-30521-1. pp. 137-161
O’Brien, R., Haq, I., & Ladbury, J. E. (2001) Direct measurement of thermodynamic
quantities. In “Thermodynamics of the Drug-Receptor Interaction”. Editor R. B. Raffa. John
Wiley & Sons Ltd. Chichester, UK. ISBN 0-471-72042-9. pp. 537-552.
Haq, I., O’Brien, R., & Ladbury, J. E. (2001) General thermodynamic definitions and
equations. In “Thermodynamics of the Drug-Receptor Interaction”. Editor R. B. Raffa. John
Wiley & Sons Ltd. Chichester, UK. ISBN 0-471-72042-9. pp. 61-82.
O’Brien, R., Chowdhry, B. Z. & Ladbury, J. E. (2001) Isothermal titration calorimetry. In “A
Practical Approach to Protein-Ligand Interactions”. Editor S. E. Harding & B. Z. Chowdhry.
IRL Press at Oxford University Press, Oxford, UK. ISBN 0-19-963749-0/6. pp. 263-286.
Panayotou, G. & Ladbury, J. E. (2000) Analysis of SH2 domain-phosphopeptide
interactions by isothermal titration calorimetry and surface plasmon resonance. In
“Methods for Molecular Biology: Protein kinase protocols”. Vol. 124. Editor A. Reith.
Humana Press Inc., Totowa, NJ. USA. ISBN 0-89603-700-2. pp. 295-311.
Schultz, D. A., Ladbury, J. E., Smith, G. P. & Fox, R. O. (1998) Interactions of
ribonuclease S with ligands from random peptide libraries. In “Biocalorimetry: Applications
of Calorimetry to the Biological Sciences”. Editors J. E. Ladbury & B. Z. Chowdhry. John
Wiley & Sons Ltd. Chichester, Sussex, UK. ISBN 0-471-97781-0. pp. 123-138.
Tame, J. R. H., O’Brien, R. & Ladbury, J. E. (1998) Isothermal titration calorimetry of
biomolecules. In “Biocalorimetry: Applications of Calorimetry to the Biological Sciences”.
Editors J. E. Ladbury & B. Z. Chowdhry. John Wiley & Sons Ltd. Chichester, Sussex, UK.
ISBN )-471-97781-0. pp. 27-38.
Renzoni, D. A., Zvelebil, M. J. J. M., Lundbäck, T., & Ladbury, J. E. (1997)
Exploring uncharted waters: Water molecules in drug design strategies. In “Structurebased drug design: Strategy, thermodynamics and modeling”. Editors J. E. Ladbury, & P.
R. Connelly. R. G. Landes Co. Austin TX. USA/Springer-Verlag, Berlin. ISBN 3-54063250-6. pp. 161-180.