Papers

 

Publications (170118))


My total number of publications according to ISI is ~158 (Spring 2015; with this advanced search {(au= jones ta and cu=sweden) or (au=jones ta and ci=martinsried)} but it misses 3 papers (#6,  #15, #28) with ~300 citations since they were published as Jones A.). According to my CV (including book chapters etc. ) the total is 163 and one patent. I have an h-index of  >= 64 (i.e. 64 of my publications have been cited at least 64 times or more), and over 32,000 citations in total (Spring 2015). According to Noorden  et al.  (Nature 2014, 514, X-Y) #55 is among the 100 most highly cited papers of all time, for a while at least.


1. R.  Huber, D.  Kukla, W.  Steigemann, J.  Deisenhofer, A. Jones (1974)

Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin

inhibitor.  Refinement  of the  crystal structure analysis.

Bayer-Symposium V "Proteinase Inhibitors"  497-512.


2. P.M. Colman, O. Epp, H. Fehlhammer, W. Bode, M. Schiffer, E.E. Lattman, T.A. Jones, W. Palm (1974)

X-ray studies on antibody fragments.

FEBS Letters (1974), 194-199.


3. O.H.W. Martini, R. Temkin, A. Jones, K. Rile, H.J. Gould (1975)

Quantitation of eukaryotic ribosomal proteins separated by two-dimensional

polyacrylamide gel electrophoresis.

FEBS Letters 56, 205-211.


4. S. Neidle & T.A. Jones (1975)

Crystal structure of proflavine, a DNA binding agent.

Nature 253, 284-285.


5. A. Jones & S. Neidle (1975)

The crystal and molecular structure of proflavine hemisulphate hydrate.

Acta Cryst. B31, 1324-1333.


6. P. Schwager, K. Bartels & A. Jones (1975)

Refinement of setting angles in screenless film methods.

J.  Appl.  Cryst. 8, 275-280.


7. H. Lotter, A. Jonesc & M. Sturm (1977)

Rontgenstrukturanalyse von Mezerin aus Daphne mezereum L.

Z. Naturforsch. 32c, 678-682.


8. H. Wagner, R. Brunig, H. Lotter &  A. Jones (1977)

Die Struktur von Cassinin, einem neuen Sesquiterpenalkaloid aus Cassine Meta-belica, Loes.

Tetrahedron Letters 125-128.


9. A. Jones, K. Bartels, P. Schwager (1977)

Refinement of crystal orientation parameters.

in: The Rotation Method in Crystallography. Edited by U.W. Arndt & A.J.Wonacott, North-Holland Publishing Company, Amsterdam/.


10. M. Matsushim, M. Marquardt, T.A. Jones, P.M. Colman, K. Bartels, R. Huber & W. Palm (1978)

Crystal structure of the human FAB fragment Kol and its comparison with the intact Kol molecule

J. Mol. Biol. 121, 441-459.


11. E. Weber, W. Steigemann, T.A. Jones & R. Huber (1978)

The structure of oxy-erythrocruorin at 1.4 Å resolution.

J. Mol. Biol. 120, 327-336.


12. J. Deisenhofer, T.A. Jones,  R. Huber,  J. Sjodahl &  J. Sjöquist (1978)

Crystallization, crystal structure analysis and atomic model of the complex formed by a human Fc fragment and fragment B of the protein A from Staphylococcus aureus.

Hoppe - Seylers's Z. Physiol. Chem. 359, 975-985.


13. T.A. Jones (1978)

A  graphics  model  building  and  refinement  system for macromolecules.

J. Appl. Cryst. 11, 268-272.


14. G. Wiegand, D. Kukla, H. Scholze, T.A. Jones & R. Huber (1979)

Crystal structure analysis of the tetragonal form and preliminary molecular model of pig heart citrate synthase.

Eur. J. Biochem. 93, 41-50.


15. R. Ladenstein, O. Epp, K. Bartels, A. Jones, R. Huber & A. Wendel

Structure analysis and molecular model of the selenoenzyme glutathione per-oxidase at 2.8 Å resolution.

J. Mol. Biol. 134, 199-218.


16. M. Spencer, S. Neidle & T.A. Jones (1979)

Crystallisation of tRNA Leu/CUG from Escherichia Coli after purification with hydroxyapatite.

Biochem. and Biophys. Research Communications 86, 66-70.


17. H. Eklund, J-P Samama, L. Wallen, C-I Brändén, Å. Åkeson & T.A. Jones (1981)

Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9  Å resolution.

J. Mol. Biol. 146, 561-587.


18. T.A. Jones (1982)

FRODO:  a graphics fitting program for macromolecules.

Computational Crystallography (Ed D. Sayre) 303-317.


19. L. Liljas, T. Unge, T.A. Jones, K. Fridborg, S. Lövgren, U. Skoglund & B. Strandberg (1982)

The structure of satellite tobacco necrosis virus at 3.0 Å resolution.

J. Mol. Biol. 159, 93-108.


20. M.G. Rossmann, C. Abad-Zapatero, M.R.N. Murthy, L. Liljas, T.A. Jones & B. Strandberg. (1983)

Structural  comparisons  of  some  small  spherical plant viruses.

J. Mol. Biol165, 711-736.


21. B.V. Plapp, H. Eklund, T.A. Jones & C-I Brändén.  (1983)

Three-dimensional structure of isonicotinimidylated liver alcohol dehydrogenase.

J.  Biol.  Chem. 258, 5537- 5547.


22. T.A. Jones & L. Liljas. (1984)

Crystallographic refinement of macromolecules having non-crystallographic symmetry.

Acta Cryst A40, 50-57.


23. T.A. Jones & L. Liljas (1984)

Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 Å resolution.

J. Mol. Biol. 177, 735-767.


24.M.E. Newcomer, T.A. Jones, J. Åqvist, J. Sundelin, U. Eriksson, L. Rask & P.A Peterson. (1984)

The three-dimensional structure of retinol-binding protein.

EMBO Journal 3, 1451-1454.


25. K.K. Kannan, M. Ramanadham & T.A. Jones (1984)

Structure, refinement and function of carbonic anhydrase isozymes: refinement

of human carbonic anhydrase I.

Annls.  New York Academy of Sciences 429, 49-60.


26. H. Eklund, J-P Samama & T.A. Jones (1984)

Crystallographic investigations of nicotinamide adenine dinucleotide binding to horse liver alcohol dehydrogenase.

Biochemistry 23, 5982-5996.


27. T.A. Jones (1985)

Interactive computer graphics:  FRODO.

Methods in Enzymology, Enzyme Structure: Diffraction Methods for Biological Macromolecules.   115, 157-171.


28.J. Sundelin, B.C. Laurent, H. Anundi, L. Trägårdh, D. Larhammar, L. Björck, U. Eriksson, B.Åkerström, A. Jones, M. Newcomer, P.A. Peterson &L. Rask (1985)

Amino acid sequence homologies between rabbit, rat and human serum retinol-binding proteins.

J. Biol. Chem. 260, 6472-6480.


29. B. Laurent, M. Nilsson, C. Bavik, T. A. Jones, J. Sundelin & P. Peterson (1985)

Characterization of the rat retinol-binding protein gene and its comparison to the three-dimensional structure of the protein.

J. Biol. Chem. 260, 11476-11480.


30. T.A. Jones & J. Pflugrath (1985)

An introduction to electron density map fitting using FRODO.

Crystallographic Computing 3: Data  Collection, Structure Determination, Proteins and Databases 286-294, Oxford University Press.


31. H. Eklund, T.A. Jones & G. Schneider (1986)

Active site in alcohol dehydrogenase.

Zinc Enzymes. Editors: Bertini, I., Luchinut, C., Maret, W. and Zeppezaur,  M. Birkhauser Boston, Inc.


32. E.A. Eriksson, T.A. Jones & A. Liljas (1986)

Crystallogrpahic studies of human carbonic anhydrase II (HCA II).

Zinc Enzymes. Editors: Bertini, I., Luchinut, C., Maret, W. and Zeppezaur, M. Birkhauser Boston, Inc.


33. T.A.  Jones (1987)

Electron density fitting with computer graphics:  a review and a glimpse.

Crystallography in Molecular Biology Ed. D. Moras, J. Drenth, B. Strandberg, D. Suck and K. Wilson, Plenum Press, New York.


34. T.A. Jones & S. Thirup (1986)

Using known substructures  in  protein  model  building and crystallography.

EMBO Journal 5, 819-822.


35. P. Sandblom, J. Åqvist, T.A. Jones, M.E. Newcomer, W.F. van Gunsteren & O. Tapia (1986)

Structural changes in retinol binding protein induced by retinol removal. A molecular dynamics study.

Biochem. and Biophys. Res. Comm. 139, 564-570.


36. J. Åqvist, P. Sandblom, T.A. Jones, M.E. Newcomer, W.F. van Gunsteren & O. Tapia. (1986)

Molecular dynamics simulations of the holo- and apo-forms of retinol binding protein.  Structural and dynamical changes induced by retinol removal.

J. Mol. Biol. 192, 593-604.


37. M. Papiz, L. Sawyer, E. Elipoulos, A. North, J Findlay, R. Sivaprasadarao, T.A. Jones, M.E. Newcomer & P.J. Kraulis. (1986)

The structure of B-lactoglobulin and its similarity to plasma retinol binding protein.

Nature 324, 383-385.


38. P. Kraulis & T. A. Jones (1987)

Solving solution structural problems by combining 2-D NMR data with known substructues from a protein data base.

Structure, Dynamics and Function of Biomolecules, Ed.: A. Ehrenberg, R. Rigler, A. Gräslund, L. Nilsson. Springer-Verlag, New York.


39. T. Bergfors, J. Sedzik, T. Unge, K. Fridborg, T.A. Jones & J. Weise (1987)

Crystallization of P2 myelin protein.

J. Mol.Biol. 198, 357-358.


40. P.J. Kraulis & T.A. Jones (1987)

Determination of three-dimensional protein structures from NMR data using fragments of known structures.

Proteins: Structure, Function and Genetics 2, 188-201.


41. B. Nilsson, T. Moks, B. Jansson, L. Abrahamsen, A. Elmblad, E. Holmgren,     C.

Henrickson, T.A. Jones & M. Uhlen (1987)

A synthetic IgG-binding domain based on staphylococcal protein A.

Protein Engineering 1, 107-113.


42. T.A. Jones, T. Bergfors, J. Sedzik & T. Unge (1988)

The three-dimensional structure of P2 myelin protein.

EMBO J. 7, 1597-1604.


43. E. Eriksson, T.A. Jones & A. Liljas (1988)

Refined structure of human carbonic anhydrase II at 2 Å resolution.

Proteins: Structure, Function, Genetics 4, 274-282.


44. E. Eriksson, P.M. Kylsten. T.A. Jones & A. Liljas (1988)

Inhibitor binding sites in human carbonic anhydrase II: A pentacoordinated binding of the SCN ion to the zinc at high pH.

Proteins: Structure, Function, Genetics 4, 283-293.


45. T.A. Holak, Å. Engström, P.J. Kraulis, G. Lindberg, H. Bennich, T.A. Jones, A.M. Gronenborn & G.M. Clore (1988).

The solution conformation of the antibacterial peptide cercropin A: A nuclear magnetic resonance and dynamical simulated annealing study.

Biochemistry 27, 7620-7629.


46. T.A. Jones, T. Bergfors, J. Sedzik & T. Unge (1988)

The three-dimensional structure of P2 myelin protein.

Zeitschrift für  Kristallographie 185, 120.


47. S.W. Cowan, T. Bergfors, T.A. Jones, G. Tibbelin, B. Olin, P.G. Board & B. Mannervik (1989)

Crystallization of GST2, a human class alpha glutathione transferase.

J. Mol. Biol.  208, 369-370.


48. P.J. Kraulis, G.M. Clore, M. Nilges, T.A. Jones, G. Pettersson, J. Knowles & A.M. Gronenborn (1989)

Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing.

Biochemistry 28, 7241-7257.


49.T.Bergfors, J. Rouvinen, P. Lehtovaara, X. Caldentey, P. Tomme, M.     Claeyssens, G. Pettersson, T. Teeri, J. Knowles & T.A. Jones (1989)

Crystallization of the core protein of cellobiohydrolase II from Trichoderma reesei.

J. Mol. Biol. 209, 167-169.


50. C.-I. Brändén & T.A. Jones (1990)

Between objectivity and subjectivity.

Nature  343, 687-689


51. S.W. Cowan, M.E. Newcomer and T.A. Jones (1990)

Crystallographic refinement of human serum retinol binding protein at 2 Å resolution.

Proteins: Structure, Function and Genetics  8, 44-61


52 J. Rouvinen, T. Bergfors, T. Teeri, J.K.C. Knowles & T.A. Jones (1990)

The three dimensional structure of Cellobiohydrolase II from Trichoderma reesei..

Science  249, 380-386.


53 T.A. Jones, S.W. Cowan, M.E. Newcomer & T. Bergfors (1990)

Crystallographic studies on two families of retinoid binding proteins

Frontiers in drug research, Alfred Benzon Symposium, 28, 267-276. Eds.: B. Jensen, F.S. Jörgensen, H. Kofod, Munksgaard, Copenhagen..


54. T.A. Jones, M. Bergdoll & M. Kjeldgaard (1990)

O: A macromolecular modeling environment.

In: Crystallographic and Modeling Methods in Molecular Design. Eds.: C. Bugg & S. Ealick. Springer-Verlag Press  189-195.


55. T.A. Jones, J-Y. Zou, S.W. Cowan & M. Kjeldgaard (1991)

Improved methods for the building of protein models in electron density maps and the location of errors in these models.

Acta Cryst. A47  110-119.


56. A.Müller-Fahrnow, U.Egner, T.A.Jones, H.Rüdel, F.Spener & W.Saenger  (1991)

Three-dimensional structure of fatty-acid-binding protein from bovine heart.

Eur. J. Biochem. 199, 271-276.


57. J.Zhang, Z-P.Liu, T.A.Jones. L.M.Gierasch & J.F.Sambrook (1992)

Mutating the charges residues in the binding pocket  of cellular retinoic acid-binding protein simultaneously reduces its binding affinity to retinoic acid and increases its thermostability.

Proteins: Structure, Function and Genetics 13, 87-99.


58. T.Reinikainen, L.Ruohonen, T.Nevanen, L.Laaksonen, P.Kraulis, T.A.Jones, J.K.C.Knowles & T.T.Teeri (1992)

Investigation of the function of mutated cellulose binding domains of Trichoderma Reesei  cellobiohydrolase I.

Proteins: Structure, Function and Genetics14, 475-483.


59. T.A. Jones (1992)

a, yaap, asap, @#*? A set of averaging programs.

In Molecular Replacement (Dodson, E.J. ed.) pp. SERC Daresbury Laboratory.


60. T.T. Teeri, T. Reinikainen, L. Ruohonen, T.A. Jones & J.K.C. Knowles (1992)

Domain function in Trichoderma reesei cellobiohydrolases.

J. Biotechnology 24, 169-176.


61. S.W. Cowan, M.E. Newcomer & T.A. Jones. (1993)

Crystallographic studies on a family of cellular lipophilic transport proteins. Refinement of P2 myelin protein and the structure determination and refinement of cellular retinol-binding protein in complex with all-trans-retinol.

J. Mol. Biol.  230, 1225-1246.


62. I. Sinning, G.J. Kleywegt, S.W. Cowan, P. Reinemer, H.W. Dirr, R. Huber, G.L. Gilliland, R.N. Armstrong, X. Ji, P.G. Board, B. Olin & B. Mannervik & T.A. Jones.(1993)

Structure determination and refinement of human alpha class glutathione transferase A1-1.

J. Mol. Biol 232, 192-212.


63. J. Newman, C.-I. Brändén & T.A. Jones. (1993)

Structure determination and refinement of Ribulose 1,5 biophosphate/oxygenase from Synechococcus   PCC6301.

Acta Cryst DD 49, 548-560.


64. I. Sinning, G.J. Kleywegt, B. Mannervik, P.G. Board & T.A. Jones. (1993)

The active site in class alpha glutathione transferases.

Structure and Function of Glutathione Transferases (Tew et al., eds.) CRC Press, 75-85


65. B. Mannervik, K. Berhane, R. Björnestedt, P.G. Board, T.A. Jones, R.H. Kolm, B. Olin, I. Sinning, G.E. Sroga, G. Stenberg, S. Tardioli & M. Widersten (1993)

Structural and functional characterization of the binding sites for glutathione (G-site) and the hydrophobic electrophilic substrate (H-site) in glutathione transferases.

Structure and Function of Glutathione Transferases (Tew et al., eds.) CRC Press, 29-38.


66. C.Divne, I.Sinning, J.Ståhlberg, G.Pettersson, M.Bailey, M.Siika-aho, E.Margolles-Clark, T.Teeri & T.A.Jones (1993)

Crystallization and preliminary x-ray studies on the Core protein of Cellobiohydrolase I and Endoglucanase I from Trichoderma reesei.

J.Mol.Biol. 234, 905-907.


67. J.Uppenberg, S.Patkar, T.Bergfors & T.A.Jones. (1994)

Crystallization and preliminary x-ray studies of lipase B from Candida antarctica

J.Mol.Biol. 235, 790-792.


68. G.J. Kleywegt & T.A.Jones. (1994)

Detection, delineation, measurement and display of cavities in macromolecular structures.

Acta Cryst. D 50, 178-185.


69. T.Bergfors, G.J.Kleywegt & T.A.Jones. (1994

Crystallization and preliminary x-ray analysis of recombinant bovine cellular retinoic acid binding protein.

Acta Cryst. D50, 370-374.


70. L. Banaszak, N. Winter, Z. Xu, D.A. Bernlohr, S. Cowan & T.A. Jones. (1994)

Lipid-binding proteins: a family of fatty acid & retinoid transport protein.

Advances in Protein Chemistry 45, 89-151.


71. J.Uppenberg, M.T.Hansen, S.Patkar & T.A.Jones. (1994)

The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica.

Structure  2:4, 293-308.


72. C.Divne, J.Ståhlberg, T.Reinikainen, L.Ruohonen, G.Pettersson, J.K.C. Knowles, T.T.Teeri & T.A.Jones. (1994)

The three-dimensional crystal structure of the catalytic core of cellobiohydrolase I from Trichoderma reesei . Science  265, 524-528.


73. J.Kleywegt, T.Bergfors, H.Senn, P.Le Motte, B.Gsell, K.Shudo & T.A.Jones.(1994) Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid. Structure  2:12, 1241-1258.


74. G J Kleywegt & T A Jones (1994)

Halloween ... Masks and Bones. “From First Map to Final Model” (S. Bailey, R. Hubbard & D. Waller, Eds.), pp. 59-66,SERC Daresbury Laboratory, Daresbury, U.K..


75. A.D.Cameron, I.Sinning, G.L'Hermite, B.Olin, P.G.Board, B.Mannervik, T.A.Jones (1995)

Structural analysis of human alpha-class glutathione transferase A1-1 in the apo-form and in complexes with ethacrynic acid and its glutathione conjugate.

Structure 3, 717-727.


76. J.Uppenberg, N.Öhrner, M.Norin, K.Hult, G.J.Kleywegt, S.Patkar, V.Waagen, T.Anthonsen, T.A.Jones (1995)

Crystallographic and Molecular-Modeling Studies of Lipase B from Candida antarctica  Reveal a Stereospecificity Pocket for Secondary Alcohols.

Biochemistry 34, 16838-16851


77. G J Kleywegt & T A Jones (1995)

Braille for Pugilists,

in “Making the Most of your Model”, (W N Hunter, J M Thornton, & S Bailey, Eds.), pp. 11-24, SERC Daresbury Laboratory, Daresbury, U.K..


78. G J Kleywegt & T A Jones (1995)

Where freedom is given, liberties are taken.

Structure 3, 535-540.


79. A E Sauer-Eriksson, G J Kleywegt, M Uhlén & T A Jones (1995)

Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG.

Structure 3, 265-278.


80. R. Björnstedt, G. Stenberg, M. Widersten, P.G. Board, I. Sinning, T.A. Jones & B. Mannervik (1995)

Functional significance of Arginine 15 in the active site of human class alpha glutathione trasferase A1-1,

J. Mol. Biol. 247, 765-773


81. G J Kleywegt, H Hoier & T A Jones (1996)

A re-evaluation of the crystal structure of chloromuconate cycloisomerase,

Acta Cryst. D, 858-863.


82. G J Kleywegt & T A Jones (1996)

xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection datasets.

Acta Cryst. D52, 826-828.


83. G J Kleywegt & T A Jones (1996)

Efficient rebuilding of protein structures.

Acta Cryst. D52,829-832.


84. J.-Y. Zou & T.A. Jones (1996)

Towards the automatic interpretation of macromolecular electron-density maps: qualitative and quantitative matching of protein sequence to map.

Acta Cryst. D52, 833-841


85. A. Koivula, T. Reinikainen, L. Ruohonen, A. Valkeajarvi, M. Claeyssens, O. Teleman, G.J. Kleywegt, M. Szardenings, J. Rouvinen, T.A, Jones & T.Teeri (1996)

The active site of Trichoderma reesei cellobiohydrolase II: the role of tyrosine-169,

Protein Engineering 9, 691-699.


86. J. Ståhlberg, C. Divne, A. Koiula, K. Piens, M. Claeyssens, T.T. Teeri & T.A.Jones (1996)

Activity studies and crystal structures of catalytically deficient mutants of cellobiohydrolase 1 from Trichoderma reesei

J. Mol. Biol. 264, 337-349


87. G J Kleywegt & T A Jones (1996)

Phi/Psi-chology: Ramachandran revisited

Structure 4, 1395-1400.


88. G J Kleywegt & T A Jones (1997)

Template convolution to enhance or detect structural features in macromolecular electron-density maps

Acta Cryst. D53, 179-185


89. A.D. Cameron, B. Olin, M. Ridderström, B. Mannervik & T.A. Jones (1997)

Crystal structure of human glyoxalase 1 - evidence for gene duplication and 3D swapping

EMBO J. 16, 3386-3395.


90.M. Ridderström, A.D. Cameron, T.A. Jones & B. Mannervik (1997)

Mutagenesis of residue 157 in the active site of human glyoxalase 1.

Biochem. J. 328, in press.


91. T.A.Jones. & M.Kjeldgard (1997)

Electron-Density Map Interpretation.

Methods in Enzymology 277, 173-208.


92. G J Kleywegt & T A Jones (1997)

Detecting folding motifs and similarities in protein structures.

Methods in Enzymology 277, 525-545.


93. G J Kleywegt & T A Jones (1997)

Model-building and refinement practice.

Methods in Enzymology 277, 208-230.


94. G.J. Kleywegt, J-Y. Zou, C. Divne, GJ. Davies, I. Sinning, J. Ståhlberg, T. Reinikainen, M. Srisodsuk, TT. Teeri & TA. Jones (1997)

The crystal structure of the catalytic core domain of endoglucanase 1 from Trichoderma reesei at 3.6Å resolution, and a comparison with related enzymes.

J. Mol. Biol. 272, 383-397.


95. JA. Sigrell, AD. Cameron, TA. Jones & SL. Mowbray (1997)

Purification, characterization and crystallization of Escherichia coli ribokinase.

Protein Sciences 6, 1-3


96. C. Divne, J. Ståhlberg, A. Koiula, K. Piens, M. Claeyssens, T.T. Teeri & T.A.Jones (1998)

High-resolution crystal structures reveal how a cellulose chain is bound in the 50Å long tunnel of cellobiohydrolase 1 from Trichoderma reesei.

J. Mol. Biol.  275, 309-325.


97. JA. Sigrell, AD. Cameron, TA. Jones & SL. Mowbray (1998)

Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 Å resolution: insights into a new family of kinase structures.

Structure 6, 183-193.


98. A. Koivula, T. Kinnari, V. Harjunpaa, A. Teleman, T. Drakenberg, J. Rouvinen, T.A.Jones, & T.T. Teeri (1998)

Tryptophan 272:  essential determinant of crystalline cellulose degradation by Trichoderma reesei cellobiohydrolase Cel6A

FEBS Letters 429, 3411-346


99. G.J. Kleywegt & T.A. Jones (1998)

Databases in Protein Crystallography

Acta Cryst. D54 1119-1131


100. B. Mannervik, A.D. Cameron, E. Fernandez, A. Gustafsson, L.O. Hansson, P. Jemth, F. Jiang, T.A. Jones, A-K. Larsson, L.O. Nilsson, B. Olin, P.L. Pettersson, M. Ridderström, G. Stenberg, M. Widersten (1998)

An evolutionary approach to the design of glutathione-linked enzymes

Chemico-Biological Interactions 111-112, 15-21.


101. M.Ridderström, A.D. Cameron, T.A.Jones, B.Mannervik

Involvement of an active-site Zn2+ ligand in the catalytic mechanism of human glyoxalase I (1998)

J. Biol. Chem. 273, 21623-8


102. L.F. Mackenzie, G. Sulzenbacher, C. Divne, T.A. Jones, H.F. Woldikes, M. Schulein, S.G. Withers, G.J. Davies (1998)

Crystal structure of the family 7 endoglucanase 1 (Cel7b) from Humicola insolens at 2.2 A resolution and identification of the catalytic nucleophile by trapping of the covalent glycosyl-enzyme intermediate

Biochem. J. 335, 409-416


103. G.J. Kleywegt & T.A. Jones (1999)

Software for handling macromolecular envelopes

Acta Cryst. D55 942-944.


104. B.N. Chauduri, G.J. Kleywegt, J. Bjorkman, L.D. Lehman-McKeeman, J.D. Oliver, T.A. Jones (1999)

The crystal structure of a2u-globulin and its complex with a hyaline droplet inducer

Acta Crys.t D55 753-762


105. J. Zou, G.J. Kleywegt, J. Stahlberg, H. Driguez, W. Nerinckx, M. Claeyssens, A. Koivula, T.T. Teeri, T.A. Jones (1999)

Crystallographic evidence for substrate ring distortion and protein conformaitonal changes during catalysis in cellobiohydrolase Cel6A from Trichodema reesei

Structure 7, 1035-1045


106. B. N. Chaudhuri, J. Ko, C. Park, T.A. Jones, S.L. Mowbray (1999)

Structure of D-allose binding protein from Escherichia coli bound to D-allose at 1.8 Å resolution

J. Mol. Biol. 286, 1519-1531.


107. T.A. Jones & G.J. Kleywegt (1999)

CASP3 Comparative modelling evaluation

Proteins: Structure, Function, and Genetics Suppl. 3, 30-46


108. B.N. Chaudhuri, G.J. Kleywegt, I. Broutin-L’Hermite, T. Bergfors, H. Senn, P/ Le Motte, O. Partouche & T.A. Jones (1999)

Structures of cellular retinoic acid binding proteins I and II in complex with synthetic retinoids

Acta cryst. D55, 1850-1857


109. S.L. Mowbray, C. Helgstrand, J.A. Sigrell, A.D. Cameron& T.A. Jones (1999)

Errors and reproducibility in electron-density map interpretation

Acta cryst. D55, 1309-1319


110. J. Zou, B.M. Hallberg, T. Bergfors, F. Oesch, M. Arand, S.L. Mowbray & T.A. Jones (2000)

Structure of Aspergillus niger epoxide hydrolase at 1.8 Å resolution: implications for the structure and function of the mammalian microsomal class of epoxide hydrolases

Structure 8, 111-122


111. E E Abola, A Bairoch, W C Barker, S Beck, D A Benson, H Berman, C Cantor,  S Doubet, T J P Hubbard, T A Jones, G J Kleywegt, A S Kolaskar, A van  Kuik, A M Lesk, H W Mewes, D Neuhaus, F Pfeiffer, L F Ten Eyck, R J  Simpson, G Stoesser, J L Sussman, Y Tateno, A Tsugita, E L Ulrich and J F G Vliegenthart (2000). 

Quality control in databanks for molecular biology. 

BioEssays 22, 1024-1034


112. J. Ståhlberg, H. Henricksson, C. Divne, R. Isaksson, G. Pettersson, G. Johansson & T.A. Jones. (2001)

Structural basis for enantiomer binding and separation of a common β-blocker: crystal structure of cellobiohydrolase Cel7A with bound (S)-propranolol at 1.9 Å resolution

J. Mol. Biol 305, 79-93


113. G.J. Kleywegt, J. Zou, M. Kjeldgaard & T.A. Jones (2001)

Around O

International Tables for Crystallography Volume F, Chapter 25.2.6


114. M. Sandgren, A. Shaw, TH Ropp, S. Wu, R. Bott, AD Cameron, J. Ståhlberg, C. Mitchinson & TA Jones (2001).

The x-ray crystal structure of the Trichoderma reesei family 12 endoglucanse 3, Cel12A, at 1.9 Å resolution.

J. Mol. Biol. 308, 295-310


115. M. Harris T.A. Jones (2001).

Molray- a web interface between O and the POV-Ray ray tracer.

Acta Cryst. D57, 1201-1203


116. DMF van Aalten, KG Milne, JY Zou, GJ Kleywegt, T. Bergfors, MAJ Ferguson, J. Knudsen & T.A. Jones (2001).

Binding site differences revealed by crystal structures of Plamodium falciparum and bovine acyl-CoA binding protein.

J. Mol. Biol. 309, 181-192


117. D. Becker, C.Braet, H. Brumer, M. Claeyssens, C. Divne, BR Fagerstron, M. Harris, TA. Jones, GJ. Kleywegt, A. Koivula, S. Mahdi, K. piens, ML Sinnot, J. Stlåhlberg, TT. Teeri, M. Underwood, G. Wolfhart (2001).

Engineering of a glycosidase Family 7 cellobiohytdrolase to a more alkaline pH optimum: the pH behaviour of Trichoderma reesei Cel7A and irs E223S/ A224H/ L225V/ T226A/ D262G mutant.

Biochem. J. 356, 19-30


118. T.A. Jones (2001)

Electron density map interpretation

In ‘Methods in Macromolecular Crystallography’, Editors D. Turk & L. Johnson, IOS Press.


119. AM. Larsson, J. Ståhlberg & TA. Jones (2002)

Preparation and crystallization of selenomethionyl dextranase from Penicillium minioluteum expressed in Pichia pastoris.

Acta Crystallographica D58, 346-348.


120. GJ Kleywegt & TA. Jones (2002)

Homo Crystallographicus- Quo Vardis?

Structure 10, 465-472.


121. U.  Magnusson, B.N.  Chaudhuri, J. Ko, C. Park, T.A. Jones & SL. Mowbray (2002)

Hinge-bending motion of D-allose binding protein from Escherichia coli: three open conformations

J. Biol. Chem. 277, 14077-14084


122. A. Koivula, L. Ruohonen, G. Wohlfart, T. Reinikainen, TT Teeri, K. Piens, M.Claeyssens, M. Weber, A. Vasella, D, Becker, ML. Sinnot, J. Zou, GJ. Kleywegt, M. Szardenings, J. Ståhlberg & TA. Jones (2002)

The active site of cellobiohydrolase Cel6A from Trichoderma reesei: the roles of aspartic acids D221 and D175

J. American Chemical Society, 124, 10015-10024.


123. A Lartigue, V Campanacci, A Roussel, AM Larsson, TA Jones, M Tegoni & C Cambillau (2002)

X-ray structure and ligand binding study of a moth chemosensory protein

J. Biol. Chem. 277, 32094-32098.


124. M. Harris & TA Jones (2002)

Xtrack – a web based crystallographic notebook

Acta Crystallographica D58, 1889-1891.


125. Arand, M., Hallberg, B.M.,  Zou, J., Bergfors, T., Oesch, F., van der Werf, M.J., de Bont, J.A.M., Jones, T.A.  and Mowbray,S.L. (2003)

Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site

EMBO J. 22, 2583-2592


126. Sandgren, M.,  Guafetti, P.J., Shaw,  A., Day,  A.G., Gross, L., Saldajeno, M., Jones,T.A.  & Mitchinson, C. (2003)

Comparison of family 12 glucosyl hydrolases and recruitment of substitutions important for stability

Protein Science 12, 848-860


127.  Campanacci, V , Lartigue, A.,, Hallberg, B.M., Jones, T.A., Guidici-Orticoni, M.T., Tegoni, M. & Cambillau, C. (2003)

Moth chemosensory protein exhibits drastic conformational changes and cooperativity on ligand binding
PNAS 100, 5069-5074


128. Johansson, P., Denman, S., Brumer, H., Kallas, Å. M., Henriksson, H., Bergfors, T., Teeri, T. T.  and T. A. Jones (2003)

Crystallization and preliminary X-ray analysis of a xyloglucan endotransglycosylase from Populus tremula x tremuloides

Acta Crystallographica D59, 535-537.


129. Sandgren, M., Gualfetti, P.J., Paech, C., Paech,  S., Shaw, A., Gross, L.S., Saldajeno, M., Berglund, G.I., Jones, T.A. & Mitchinson, C. (2003)

The Humicloa grisea Cel12A enzyme structure at 1.2 Å resolution and the impact of its free cysteine  residues on thermal stability

Protein Science 12, 2782-2793


130. Larsson, A.M., Andersson, R., Ståhlberg, J., Kenne, L. and Jones. T.A. (2003)

Dextranase from Penicillium minioluteum: reaction course, crystal structure and product complex

Structure 11, 1111-1121


131. Arand, M., Cronin, A., Oesch, F., Mowbray, S. L. & Jones, T. A. (2003). The telltale structures of epoxide hydrolases. Drug Metab Rev 35, 365-83.


132. Roos, A. K., Andersson, C. E.,  Bergfors, T., Jacobsson, M., Karlén, A., Unge, T., Jones, T. A., and Mowbray, S. L. (2004)

Mycobacterium tuberculosis Ribose-5-phosphate Isomerase has a known fold, but a novel active site.

J. Mol. Biol. 335, 799-809.


133. Patrik Johansson, Harry Brumer III, Martin J. Baumann, Åsa Kallas, Hongbin Henriksson, Stuart Denman, Tuula T. Teeri and T. Alwyn Jones (2004)

Crystal structures of a xyloglucan endotransglycosylase reveal details of the transglycosylation acceptor binding

Plant Cell 16, 874-876.


134. T.A. Jones (2004) Interactive  electron-density map interpretation: from INTER to O

Acta Crystallographica  D60, 2115-2125.


135. G.J Kleywegt, M.R. Harris, J. Zou, T.C. Taylor & T.A. Jones (2004)

The Uppsala Electron Density Server (EDS)-

Acta Crystallographica  D60, 2240-2249.


136. Anna M. Larsson and T. Alwyn Jones (2007) Selenomethionine Labeling of Recombinant Proteins,  Methods Mol. Biol. 389, 165-74.


137. Adrian Suarez Covarrubias, Anna M. Larsson, Martin Högbom, Jimmy Lindberg, Terese Bergfors, Christoffer Björkelid, Sherry L. Mowbray, Torsten Unge and T. Alwyn Jones (2005) Structure and function of carbonic anhydrases from Mycobacterium tuberculosis

J. Biol. Chem. 280, 18782-18789.


138. Castell, A.,  Johansson, P.,  Unge, T.,  Jones, T.A. & Bäckbro, K. (2005) Rv0216, a conserved hypothetical protein from Mycobacterium tuberculosis that is essential for bacterial survival during infection, has a double hotdog-fold

Protein Science 14, 1850-1862.


139. Wojciech W. Krajewski1, T. Alwyn Jones1, and Sherry L. Mowbray (2005) Structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition-state mimic provides new functional insights

Proc. Nat. Acad. Sci. 102, 10499-10504


140. Patrik Johansson, Torsten Unge, Annetee Cronon, Michael Arand, Terese Bergfors, T. Alwyn Jones and Sherry L. Mowbray (2005) Structure of an atypical epoxide hydrolase from Mycobacterium tuberculosis gives insights into its function.

J. Mol. Biol (2005) 351, 1049-1056.


141. Anna M. Larsson, Terese Bergfors, Elisa Dultz, Diana C. Irwin, Annette Roos, Hugues Driguez, David B. Wilson, T. Alwyn Jones (2005) Crystal structure of Thermobifida fusca endoglucanase Cel6A in complex with substrate and inhibitor: the role of tyrosine Y73 in substrate ring distortion.

Biochemistry (2005) 44, 12915-12922.


142. Suarez Covarrubias, A., Bergfors, T., T. Jones, T.A. and Högbom, M.(2006) Structural mechanics of the pH dependent activity of β-carbonic anhydrase from Mycobacterium tuberculosis

J. Biol. Chem. (2006) 281, 4993-4999


143. Johansson, P., Castell, A., Jones, T.A. & Bäckbro, K. (2006) ‘Structure and function of Rv0130, a conserved hypothetical protein from Mycobacterium tuberculosis.’ Protein Science (2006) 15, 2300-2309.


144. M. J. Fogg, P. Alzari, M. Bahar, I. Bertini, J.-M. Betton, W. P. Burmeister, C. Cambillau, B. Canard, M. Carrondo, M. Coll, S. Daenke, O. Dym, M.-P. Egloff, F. J. Enguita, A. Geerlof, A. Haouz, T. A. Jones, Qingjun Ma, S. N. Manicka, M. Migliardi, P. Nordlund, R.J. Owens, Y. Peleg, G. Schneider, R. Schnell, D. I. Stuart, N. Tarbouriech, T. Unge, A. J. Wilkinson, M. Wilmanns, K. S. Wilson,O. Zimhonyi and J. M. Grimes.

Application of the use of high-throughput technologies to the determination of protein structures of bacterial and viral pathogens

Acta Cryst. (2006) D62, 1196-1207


145. Henriksson, L.M., Unge, T., Carlsson, J., Åqvist, J., Mowbray, S.L. and Jones, T.A. (2007) Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase provide new insights into catalysis.’ J. Biol. Chem. 282, 19905-19916.


146. Sacco, E.,. Suarez Covarrubias, A, O’Hare, H. M., Carroll, P., Eynard, N., Jones, T. A.,  Parish, T.,  Daffé, M.,Bäckbro, K. & Quémard, A. (2007)

The missing piece of the type II fatty acid synthase system from Mycobacterium tuberculosis.’ Proc. Nat. Acad. Sci. 104, 14628-14633


147. Krajewski, W., Collins, R., Holmberg-Schiavone, L., Jones, T. A., Karlberg, T. and Mowbray, S. L.. (2008)  ‘Crystal structures of mammalian glutamine synthetases illustrate substrate- induced conformational changes, and provide opportunities for drug and herbicide design.’ J. Mol. Biol.  375, 217-228.


148. Jones, T.A. & Kleywegt, G.J. (2007) ‘Experimental data for structure papers. Science 317, 194-5 (letter)


149. Suarez Covarrubias, A., Högbom, M., Bergfors, T., Carroll, P., Mannerstedt, K.,  Oscarson, S.,  Parish, T., Jones, T. A. and  Mowbray, S. L. (2008) ‘Structural, biochemical, and in vivo investigations of the threonine synthase from Mycobacterium tuberculosis.’ J. Mol. Biol. 381, 622-633.


150. Coutard, B., Gorbalenya, A. E., Snijder, E. J., Leontovich, A. M., Poupon, A., De Lamballerie, X., Charrel, R., Gould, E. A., Gunther, S., Norder, H., Klempa, B., Bourhy, H., Rohayem, J., L'Hermite, E., Nordlund, P., Stuart, D. I., Owens, R. J., Grimes, J. M., Tucker, P. A., Bolognesi, M., Mattevi, A., Coll, M., Jones, T. A., Aqvist, J., Unge, T., Hilgenfeld, R., Bricogne, G., Neyts, J., La Colla, P., Puerstinger, G., Gonzalez, J. P., Leroy, E., Cambillau, C., Romette, J. L. & Canard, B. (2008). ‘The VIZIER project: Preparedness against pathogenic RNA viruses.’ Antiviral Res. 78, 37-46.

151. Nilsson, M.T., Krajewski, W.W., Yellagunda, S., Prabhumurthy, Srinivasa, B.R, Yahiaoui, S., Larhed, M., Jones, T.A. and Mowbray, S.L. (2009)  ‘Structural basis of inhibition of Mycobacterium tuberculosis glutamine synthetase by novel ATP-competitive inhibitors.’  J. Mol. Biol. 393, 504-513.

152 Carta F,. Maresca A., Covarrubias A.S., Mowbray S.L., Jones T.A., Supuran C.T. (2009) ‘Carbonic anhydrase inhibitors. Characterization and inhibition studies of the most active beta-carbonic anhydrase from Mycobacterium tuberculosis, Rv3588c.’ Bioorg. Med. Chem. Lett. 19 6649-54.

153 Jansson, A.M., Jakobsson, E., Johansson, P., Lantez, V., Coutard, B., de Lamballerie, X., Unge,T. and Jones, T.A. (2009) ‘Structure of the methyltransferase domain from the Modoc virus, a flavivirus with no known vector.’ Acta Cryst. D65, 796–803

154 Ingvarsson, H., Jones, T. A. & Unge, T. (2009). Crystallization of Mycobacterium smegmatis methionyl-tRNA synthetase in the presence of methionine and adenosine. Acta Cryst. F65, 618-20.

155 Gorbalenya, A.E., Lieutard, P., Harris, M.R., Coutard, B., Canard, B., Kleywegt, G.J., Kravchenko, A.A., Sambordskiy, D.V., Sidorov, I.A., Leontovich, A.M., Jones, T.A. (2010) ‘Practical application of bioinformatics by the multidisciplinary VIZIER consortium ‘ Antiviral Research, 87, 95-110.

156 Björkelid, C., Bergfors, T., Henriksson, L.M., Stern. A.L., Unge, T., Mowbray, S.L., & Jones, T.A. (2011) ‘Structural and functional studies of mycobacterial IspD enzymes’, Acta Crystallographica D67, 403-414

157 Andaloussi, M., Henriksson, L.M., Więckowska, A., Lindh, M.,  Björkelid, C., Larsson, A.M.,  Surisetti, S., Iyer, H., Srinivasa, B.R., Bergfors, T., Unge, U., Mowbray, S.L., Larhed, M., Jones, T.A. and Karlén, A. (2011) ‘Design, Synthesis and X-ray Crystallographic Studies of α-Aryl Substituted Fosmidomycin Analogues as Inhibitors of Mycobacterium tuberculosis 1-Deoxy-D- xylulose-5-phosphate Reductoisomerase’, J. Med. Chem. 54, 4964-4976

158 Björkelid, C., Bergfors, T., Unge, T., Mowbray, S.L., & Jones, T.A. (2012) ‘Structural studies on Mycobacterium tuberculosis DXR in complex with the antibiotic FR-900098’, Acta Crystallographica D68, 134-143.

159 Fullam, E., Pojer, F., Bergfors, T., Jones, T.A. & Cole, S.T. (2012) ‘Structure and function of the transketolase from Mycobacterium tuberculosis and comparison with the human enzyme’, Open Biology 2, 110026

160.Björkelid, C., Bergfors, T., Kumar, A, Raichirkar, V., Mukherjee, K., Malolanarasimhan, K., Bandodkar, B. & Jones, T.A. (2013) ‘Structural and Biochemical Characterization of Compounds Inhibiting Mycobacterium tuberculosis Pantothenate Kinase’, J. Biol. Chem., 288, 18260-18270.

161.Jansson, A.M., Wiekowska, A., Björkelid, C., Yahiaoui, S., Sooriyaarachchi, S., Lindh, M., Bergfors, T., Dharavath, S., Desroses, M., Suresh, S., Andaloussi, M., Nikhil, R., Sreevali, S, Srinivasa, B.R., Larhed, M., Jones, T.A, Karlén, A., & Mowbray, S.L (2013) ‘DXR Inhibition by Potent Mono- and Disubstituted Fosmidomycin Analogues’. J. of Medicinal Chemistry, 56, 6190-6199

162. Reddy, B.K.K, Landge, S., Ravishankar, S., Pato;, V., Shinde, V., Tantry, S., Kale, M., Raichurkar, A., Menasinakai, S., Mudugal, N.V., Ambady, A., Ghosh, A., Tunduguru, R., Kaur, P., Singh, R., Kumar, N., Bharath, S., Sundaram, A., Bhat, J.,  Sambandamurthy, V.K., Björkelid, C., Jones, T.A., Das, K., Bandodkar, B., Malolanarasimhan, K., Mukherjee, K., Ramachandram V. (2014) ‘ Assessment of Mycobacterium tuberculosis Pantothenate kinase vulnerability through target knock down and mechanistically diverse inhibitors’, Antimicrobial Agents and Chemotherapy, 58, 3312-3326.

163 Chofor, R., Sooriyaarachchi, S., Risseeuw, M.D.P., Pouyez, J., Johny, C., Haymond, A., Everaert, A., Dowd, C.S., Maes, L., Coenye, T., Alex, A., Couch, R.D., Jones, T.A., Wouters, J., Mowbray*, S.L. and Van Calenbergh*, S. (2015) ‘Synthesis and bioactivity of β-substituted fosmidomycin analogues targeting 1-deoxy-d-xylulose-5-phosphate reductoisomerase.’ J. Med. Chem. (2015) 58, 2988-3001.

164 Sooriyaarachchi, S., Chofor, R.,  Risseeuw, M.D.P., Bergfors, T., Pouyez, J., Dowd, C.S., Maes, L., Wouters, J., Jones, T.A., Van Calenbergh*, S. and Mowbray*, S.L. (2016) ‘Targeting an Aromatic Hotspot in Plasmodium falciparum 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase with β-Arylpropyl Analogues of Fosmidomycin.’ Chem. Med. Chem. (2016) 11, 1-14.

Patent(s)

Quémard, A., Daffé, M., Sacco, E., Jones, T.A., Suarez Covarrubias, A., Bäckbro, K. (2007/2008) ‘(3R)-hydroxyl-ACP dehydratase enzymes used in the biosynthesis of mycolic acids and use of same for screening antibiotics’. Deposit at INPI on the 9 February, 2007, # 07 00930. International extension of priority patent # 07 00930:Deposit on the 8 February, 2008,  # PCT/FR2008/000162.