SBNet - Publications

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  1. Xing L, Huhtala M, Pietiainen V, Kapyla J, Vuorinen K, Marjomaki V, Heino J, Johnson MS, Hyypia T, Cheng RH. (2004).
    Structural and functional analysis of integrin alpha2I domain interaction with echovirus 1.
    J Biol Chem. 279(12), 11632-11638.
  2. Ersmark K, Feierberg I, Bjelic S, Hamelink E, Hackett F, Blackman MJ, Hulten J, Samuelsson B, Åqvist J, Hallberg A (2004).
    Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity.
    J Med Chem 47(1), 110-122.
  3. Helgstrand C, Munshi S, Johnson JE, Liljas L (2004).
    The refined structure of Nudaurelia capensis omega Virus reveals control elements for a T = 4 capsid maturation.
    Virology 318(1), 192-203.
  4. Novotny M, Madsen D, Kleywegt GJ (2004).
    Evaluation of protein fold comparison servers
    Proteins 1(54), 260-270.
  5. Schafer K, Magnusson U, Scheffel F, Schiefner A, Sandgren MO, Diederichs K, Welte W, Hulsmann A, Schneider E, Mowbray SL (2004).
    X-ray structures of the maltose-maltodextrin-binding protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius provide insight into acid stability of proteins.
    J Mol Biol 335(1), 261-274.
  6. Sandmark J, Eliot AC, Famm K, Schneider G, Kirsch JF. (2004).
    Conserved and nonconserved residues in the substrate binding site of 7,8-diaminopelargonic acid synthase from Escherichia coli are essential for catalysis.
    Biochemistry. 43(5), 1213-1222.


  1. Berglund J, Knight SD (2003).
    Structural basis for bacterial adhesion in the urinary tract (Review)
    Adv Exp Med Biol 535, 33-52.
  2. Zavialov AV, Berglund J, Pudney AF, Fooks LJ, Ibrahim TM, MacIntyre S, Knight SD (2003).
    Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: preserved folding energy drives fiber formation.
    Cell 113(5), 587-596.
  3. Zavialov A, Berglund J, Knight SD (2003).
    Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of the F1 antigen Caf1M-Caf1 chaperone-subunit pre-assembly complex from Yersinia pestis.
    Acta Crystallogr D Biol Crystallogr 59(Pt 2), 359-362.
  4. Brandsdal BO, Osterberg F, Almlöf M, Feierberg I, Luzhkov VB, Åqvist J (2003).
    Free energy calculations and ligand binding (Review).
    Adv Protein Chem 66, 123-158.
  5. Ersmark K, Feierberg I, Bjelic S, Hulten J, Samuelsson B, Åqvist J, Hallberg A (2003).
    C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: synthesis and theoretical predictions.
    Bioorg Med Chem 11(17), 3723-3733.
  6. Nore BF, Mattsson PT, Antonsson P, Bäckesjö CM, Westlund A, Lennartsson J, Hansson H, Low P, Rönnstrand L, Smith CIE (2003).
    Identification of phosphorylation sites within the SH3 domains of Tec family tyrosine kinases.
    Biochim Biophys Acta 1645(2), 123-132.
  7. Helgstrand C, Wikoff WR, Duda RL, Hendrix RW, Johnson JE, Liljas L (2003).
    The refined structure of a protein catenane: the HK97 bacteriophage capsid at 3.44 A resolution.
    J Mol Biol 334(5), 885-899.
  8. Jakobsson E, Alvite G, Bergfors T, Esteves A, Kleywegt GJ (2003).
    The crystal structure of Echinococcus granulosus fatty-acid-binding protein 1.
    Biochim Biophys Acta 1649(1), 40-50.
  9. Davis AM, Teague SJ, Kleywegt GJ (2003).
    Application and limitations of X-ray crystallographic data in structure-based ligand and drug design.
    Angew Chem Int Ed Engl. 42(24), 2718-2736.
  10. Kleywegt GJ, Henrick K, Dodson EJ, van Aalten DM (2003).
    Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?
    Structure (Camb) 11(9), 1051-1059.
  11. Magnusson U, Salopek-Sondi B, Luck LA, Mowbray SL (2003).
    X-ray structures of the leucine-binding protein illustrate conformational changes and the basis of ligand specificity.
    J. Biol. Chem. Dec 12 [Epub].
  12. Muñoz IG, Mowbray SL, Ståhlberg J (2003).
    The catalytic module of Cel7D from Phanerochaete chrysosporium as a chiral selector: structural studies of its complex with the beta blocker (R)-propranolol.
    Acta Crystallogr D Biol Crystallogr 59(Pt 4), 637-643.
  13. Nikulin A, Eliseikina I, Tishchenko S, Nevskaya N, Davydova N, Platonova O, Piendl W, Selmer M, Liljas A, Drygin D, Zimmermann R, Garber M, Nikonov S (2003).
    Structure of the L1 protuberance in the ribosome.
    Nat Struct Biol 10(2), 104-108.
  14. Yankovskaya V, Horsefield R, Törnroth S, Luna-Chavez C, Miyoshi H, Leger C, Byrne B, Cecchini G, Iwata S (2003).
    Architecture of succinate dehydrogenase and reactive oxygen species generation.
    Science 299(5607), 700-704.
  15. Horsefield R, Yankovskaya V, Törnroth S, Luna-Chavez C, Stambouli E, Barber J, Byrne B, Cecchini G, Iwata S (2003).
    Using rational screening and electron microscopy to optimize the crystallization of succinate: ubiquinone oxidoreductase from Escherichia coli.
    Acta Crystallogr D Biol Crystallogr 59(Pt 3), 600-602.
  16. Xing L, Casasnovas JM, Cheng RH (2003).
    Structural analysis of human rhinovirus complexed with ICAM-1 reveals the dynamics of receptor-mediated virus uncoating.
    J Virol 77(11), 6101-6107.
  17. Li TC, Takeda N, Kato K, Nilsson J, Xing L, Haag L, Cheng RH, Miyamura T (2003).
    Characterization of self-assembled virus-like particles of human polyomavirus BK generated by recombinant baculoviruses.
    Virology 311(1), 115-124.
  18. Xing L, Huhtala M, Pietiainen V, Kapyla J, Vuorinen K, Marjomaki V, Heino J, Johnson MS, Hyypia T, Cheng RH (2003).
    Structural and functional analysis of integrin alpha2I domain interaction with echovirus 1.
    J Biol Chem Dec 29 [Epub]
  19. Benkestock K, Van Pelt CK, Åkerud T, Sterling A, Edlund PO, Roeraade J (2003).
    Automated nano-electrospray mass spectrometry for protein-ligand screening by noncovalent interaction applied to human H-FABP and A-FABP.
    J Biomol Screen. 8(3), 247-256.
  20. Bernado P, Åkerud T, Garcia de la Torre J, Akke M, Pons M (2003).
    Combined use of NMR relaxation measurements and hydrodynamic calculations to study protein association. Evidence for tetramers of low molecular weight protein tyrosine phosphatase in solution.
    J Am Chem Soc. 125(4), 916-923.


  1. Kleywegt GJ, Jones TA (2002).
    Homo crystallographicus--quo vadis?
    Structure (Camb) 10(4), 465-472.
  2. Koivula A, Ruohonen L, Wohlfahrt G, Reinikainen T, Teeri TT, Piens K, Claeyssens M, Weber M, Vasella A, Becker D, Sinnott ML, Zou JY, Kleywegt GJ, Szardenings M, Ståhlberg J, Jones TA. (2002).
    The active site of cellobiohydrolase Cel6A from Trichoderma reesei: the roles of aspartic acids D221 and D175.
    J Am Chem Soc 124(34), 10015-10024.
  3. Knight SD, Choudhury D, Hultgren S, Pinkner J, Stojanoff V, Thompson A (2002).
    Structure of the S pilus periplasmic chaperone SfaE at 2.2 A resolution.
    Acta Crystallogr D Biol Crystallogr 58(Pt 6 Pt 2), 1016-1022.
  4. Flodell S, Schleucher J, Cromsigt J, Ippel H, Kidd-Ljunggren K, Wijmenga SS (2002).
    The apical stem-loop of the hepatitis B virus encapsidation signal folds into a stable tri-loop with two underlying pyrimidine bulges.
    Nucleic Acids Res 30(21), 4803-4811.
  5. Cromsigt J, Schleucher J, Gustafsson T, Kihlberg J, Wijmenga SS (2002).
    Preparation of partially 2H/13C-labelled RNA for NMR studies. Stereo-specific deuteration of the H5" in nucleotides.
    Nucleic Acids Res 30(7), 1639-1645.
  6. Flodell S, Cromsigt J, Schleucher J, Kidd-Ljunggren K, Wijmenga SS (2002).
    Structure elucidation of the hepatitis B virus encapsidation signal by NMR on selectively labeled RNAs.
    J Biomol Struct Dyn 19(4), 627-636.
  7. Feierberg I, Åqvist J. (2002).
    The catalytic power of ketosteroid isomerase investigated by computer simulation.
    Biochemistry. 41(52), 15728-15735.
  8. Helgstrand C, Grahn E, Moss T, Stonehouse NJ, Tars K, Stockley PG, Liljas L. (2002).
    Investigating the structural basis of purine specificity in the structures of MS2 coat protein RNA translational operator hairpins.
    Nucleic Acids Res. 30(12), 2678-2685.
  9. Holm PJ, Morgenstern R, Hebert H.(2002).
    The 3-D structure of microsomal glutathione transferase 1 at 6 A resolution as determined by electron crystallography of p22(1)2(1) crystals.
    Biochim Biophys Acta. 1594(2), 276-285.
  10. Kraft L, Sprenger GA, Lindqvist Y (2002).
    Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography
    J Mol Biol 318(4), 1057-1069.
  11. Magnusson U, Chaudhuri BN, Ko J, Park C, Jones TA, Mowbray SL (2002).
    Hinge-bending motion of D-allose-binding protein from Escherichia coli: three open conformations.
    J. Biol. Chem. 277(16), 14077-14084.
  12. Xu B, Muñoz IG, Janson JC, Ståhlberg J. (2002).
    Crystallization and X-ray analysis of native and selenomethionyl beta-mannanase Man5A from blue mussel, Mytilus edulis, expressed in Pichia pastoris.
    Acta Crystallogr D Biol Crystallogr. 58(Pt 3), 542-545.
  13. Rinaldo-Matthis A, Rampazzo C, Reichard P, Bianchi V, Nordlund P.(2002).
    The crystal structure of an azide complex of the di-ferrous R2 Crystal structure of a human mitochondrial deoxyribonucleotidase.
    Nat Struct Biol. 9(10), 779-787.
  14. Eliot AC, Sandmark J, Schneider G, Kirsch JF (2002).
    The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation.
    Biochemistry. 41(42), 12582-12589.
  15. Sandmark J, Mann S, Marquet A, Schneider G (2002).
    Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin.
    J. Biol. Chem. 277(45), 43352-43358.
  16. Kristensen O, Laurberg M, Liljas A, Selmer M (2002).
    Is tRNA binding or tRNA mimicry mandatory for translation factors?
    Curr Protein Pept Sci 3(1), 133-141.
  17. Selmer M, Wilting R, Holmlund D, Su XD. (2002).
    Preparation of a crystallizable mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.
    Acta Crystallogr D Biol Crystallogr. 58(Pt 10 Pt 2),1871-1873.
  18. Selmer M, Su XD. (2002).
    Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.
    EMBO J. 21(15),4145-4153.
  19. Hirokawa G, Kiel MC, Muto A, Selmer M, Raj VS, Liljas A, Igarashi K, Kaji H, Kaji A.(2002).
    Post-termination complex disassembly by ribosome recycling factor, a functional tRNA mimic.
    EMBO J. 21(9), 2272-2281.
  20. Svensson-Ek M, Abramson J, Larsson G, Törnroth S, Brzezinski P, Iwata S. (2002).
    The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides.
    J Mol Biol. 321(2), 329-339.
  21. Jormakka M, Törnroth S, Byrne B, Iwata S. (2002).
    Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.
    Science 295(5561), 1863-1868.
  22. Törnroth S, Yankovskaya V, Cecchini G, Iwata S. (2002).
    Purification, crystallisation and preliminary crystallographic studies of succinate:ubiquinone oxidoreductase from Escherichia coli.
    Biochim Biophys Acta. 1553(1-2), 171-176.
  23. Jormakka M, Törnroth S, Abramson J, Byrne B, Iwata S. (2002).
    Purification and crystallization of the respiratory complex formate dehydrogenase-N from Escherichia coli.
    Acta Crystallogr D Biol Crystallogr. 58(Pt 1), 160-162.
  24. Bäckström S, Wolf-Watz M, Grundström C, Härd T, Grundström T, Sauer UH (2002).
    The RUNX1 Runt domain at 1.25A resolution: a structural switch and specifically bound chloride ions modulate DNA binding.
    J Mol Biol 322(2), 259-272.
  25. Haag L, Garoff H, Xing L, Hammar L, Kan ST, Cheng RH. (2002).
    Acid-induced movements in the glycoprotein shell of an alphavirus turn the spikes into membrane fusion mode.
    EMBO J. 21(17), 4402-4410.
  26. van Dongen MJ, Uppenberg J, Svensson S, Lundback T, Åkerud T, Wikström M, Schultz J. (2002).
    Structure-based screening as applied to human FABP4: a highly efficient alternative to HTS for hit generation.
    J Am Chem Soc. 124(40), 11874-11880.
  27. Åkerud T, Thulin E, Van Etten RL, Akke M (2002).
    Intramolecular dynamics of low molecular weight protein tyrosine phosphatase in monomer-dimer equilibrium studied by NMR: a model for changes in dynamics upon target binding.
    J Mol Biol. 322(1), 137-152.


  1. Cromsigt JA, Hilbers CW, Wijmenga SS (2001).
    Prediction of proton chemical shifts in RNA. Their use in structure refinement and validation.
    J Biomol NMR 21, 11-29.
  2. Cromsigt J, van Buuren B, Schleucher J, Wijmenga S (2001).
    Resonance assignment and structure determination for RNA.
    Methods Enzymol 338, 371-399.
  3. Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L (2001).
    Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.
    RNA 7, 1616-1627.
  4. Hansson H, Okoh MP, Smith CI, Vihinen M, Härd T (2001).
    Intermolecular interactions between the SH3 domain and the proline-rich TH region of Bruton's tyrosine kinase.
    FEBS Lett 489, 67-70.
  5. Hansson H, Smith CI, Härd T (2001).
    Both proline-rich sequences in the TH region of Bruton's tyrosine kinase stabilize intermolecular interactions with the SH3 domain.
    FEBS Lett 508, 11-15.
  6. Read RJ, Kleywegt GJ (2001).
    Density modification: theory and practice.
    In: Methods in Macromolecular Crystallography (D Turk & L Johnson, Eds.), IOS Press, Amsterdam, pp. 123-135.
  7. van Aalten DM, Milne KG, Zou JY, Kleywegt GJ, Bergfors T, Ferguson MA, Knudsen J, Jones TA (2001).
    Binding site differences revealed by crystal structures of Plasmodium falciparum and bovine acyl-CoA binding protein.
    J Mol Biol 309, 181-192.
  8. Becker D, Braet C, Brumer H 3rd, Claeyssens M, Divne C, Fagerström BR, Harris M, Jones TA, Kleywegt GJ, Koivula A, Mahdi S, Piens K, Sinnott ML, Ståhlberg J, Teeri TT, Underwood M, Wohlfahrt G (2001).
    Engineering of a glycosidase Family 7 cellobiohydrolase to more alkaline pH optimum: the pH behaviour of Trichoderma reesei Cel7A and its E223S/ A224H/L225V/T226A/D262G mutant.
    Biochem J 356, 19-30.
  9. Kleywegt GJ (2001).
    Validation of protein crystal structures.
    In: International Tables for Crystallography, Volume F, Crystallography of Biological Macromolecules (Rossmann, M.G. and Arnold, E., Editors). Kluwer Academic Publishers, Dordrecht (The Netherlands), Chapter 21.1, pp. 497-506, 526-528.
  10. Kleywegt GJ, Zou JY, Kjeldgaard M, Jones TA (2001).
    Around O.
    In: International Tables for Crystallography, Volume F, Crystallography of Biological Macromolecules (Rossmann, M.G. and Arnold, E., Editors). Kluwer Academic Publishers, Dordrecht (The Netherlands), Chapter 17.1, pp. 353-356, 366-367.
  11. Kraft L, Sprenger GA, Lindqvist Y (2001).
    Crystallization and preliminary X-ray crystallographic studies of recombinant thermoresistant gluconate kinase GntK from Escherichia coli.
    Acta Crystallogr D Biol Crystallogr 57, 1159-1161.
  12. Muñoz IG, Ubhayasekera W, Henriksson H, Szabo I, Pettersson G, Johansson G, Mowbray SL, Ståhlberg J (2001).
    Family 7 cellobiohydrolases from Phanerochaete chrysosporium: crystal structure of the catalytic module of Cel7D (CBH58) at 1.32 A resolution and homology models of the isozymes.
    J Mol Biol 314, 1097-1111.
  13. Fedorov R, Meshcheryakov V, Gongadze G, Fomenkova N, Nevskaya N, Selmer M, Laurberg M, Kristensen O, Al-Karadaghi S, Liljas A, Garber M, Nikonov S (2001).
    Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins.
    Acta Crystallogr D Biol Crystallogr 57, 968-976.
  14. Bennett MS, Guan Z, Laurberg M, Su XD (2001).
    Bacillus subtilis arsenate reductase is structurally and functionally similar to low molecular weight protein tyrosine phosphatases.
    Proc Natl Acad Sci U S A 98, 13577-13582.
  15. Guan Z, Hederstedt L, Li J, Su XD (2001).
    Preparation and crystallization of a Bacillus subtilis arsenate reductase.
    Acta Crystallogr D Biol Crystallogr 57, 1718-1721.
  16. Vevodova J, Marek J, Zouhar J, Brzobohaty B, Su XD (2001).
    Purification, crystallization and preliminary X-ray analysis of a maize cytokinin glucoside specific beta-glucosidase.
    Acta Crystallogr D Biol Crystallogr 57, 140-142.
  17. Zouhar J, Vevodova J, Marek J, Damborsky J, Su XD, Brzobohaty B (2001).
    Insights into the functional architecture of the catalytic center of a maize beta-glucosidase Zm-p60.1.
    Plant Physiol 127, 973-985.
  18. Bäckström S, Huang SH, Wolf-Watz M, Xie XQ, Härd T, Grundström T, Sauer UH (2001).
    Crystallization and preliminary studies of the DNA-binding runt domain of AML1.
    Acta Crystallogr D Biol Crystallogr 57, 269-271.
  19. Wolf-Watz M, Bäckström S, Grundström T, Sauer U, Härd T (2001).
    Chloride binding by the AML1/Runx1 transcription factor studied by NMR.
    FEBS Lett 488, 81-84.
  20. Wolf-Watz M, Grundström T, Härd T (2001).
    Structure and backbone dynamics of Apo-CBFbeta in solution.
    Biochemistry 40, 11423-11432.


  1. Abola EE, 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, J F G Vliegenthart (2000).
    Quality control in databanks for molecular biology.
    BioEssays 22, 1024-1034.
  2. Andersson P, Otting G (2000).
    Time-Shared X(w1)-Half-Filter for Improved Sensitivity in Subspectral Editing.
    J. Magn. Reson. 144, 168-170.
  3. Carredano E, Karlsson A, Kauppi B, Choudhury D, Parales RE, Parales JV, Lee K, Gibson DT, Eklund H, Ramaswamy S (2000).
    Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding.
    J. Mol. Biol. 296, 701-712.
  4. Carredano E, Kauppi B, Choudhury D, Ramaswamy S (2000).
    Pseudo-symmetry characterization and refinement of a trigonal crystal form of naphthalene 1,2-dioxygenase.
    Acta Crystallogr D Biol Crystallogr 56, 313-321.
  5. Chen YW, Dodson EJ, Kleywegt GJ (2000).
    Does NMR Mean "Not for Molecular Replacement"? Using NMR-Based Search Models to Solve Protein Crystal Structures.
    Structure Fold Des 8, R213-R220.
  6. Cromsigt JAMTC, Schleucher J, Kidd-Ljunggren K, Wijmenga SS (2000).
    Synthesis of specifically deuterated nucleotides for NMR studies on RNA.
    Proceedings of the 11th conversation on Biomolecular Structure & Dynamics 2, 210.
  7. Feierberg I, Luzhkov V, Åqvist J (2000).
    Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction.
    J. Biol. Chem. 275, 22657-22662.
  8. Forsell K, Xing L, Kozlovska T, Cheng RH, Garoff H (2000).
    Membrane proteins organize a symmetrical virus.
    EMBO J. 19, 5081-5091.
  9. Henriksson H, Muñoz IG, Isaksson R, Pettersson G, Johansson G (2000).
    Cellobiohydrolase 58 (P. c. Cel7D) is complementary to the homologous CBH I (T. r. Cel 7A) in enantio-separations.
    J. Chromatogr. A 898, 63-74.
  10. Kleywegt GJ (2000).
    Validation of protein crystal structures.
    Acta Crystallogr D Biol Crystallogr 56, 249-265.
  11. Knight SD (2000).
    RSPS version 4.0: a semi-interactive vector-search program for solving heavy-atom derivatives.
    Acta Crystallogr D Biol Crystallogr 56, 42-47.
  12. Knight SD, Berglund J, Choudhury D (2000).
    Bacterial adhesins: structural studies reveal chaperone function and pilus biogenesis.
    Curr Opin Chem Biol 4, 653-660.
  13. Kragelund BB, Hauenschild A, Carlström G, Pongs O, Finn BE (2000).
    1H, 13C, and 15N assignments of un-myristoylated Ca2+-frequenin, a synaptic efficacy modulator.
    J Biomol NMR 16, 85-96.
  14. Muranyi A, Evenas J, Stenberg Y, Stenflo J, Drakenberg T (2000).
    1H, 15N and (13)C assignments and secondary structure of the EGF-like module pair 3-4 from vitamin K-dependent protein S.
    FEBS Lett. 475, 135-138.
  15. Muranyi A, Evenas J, Stenberg Y, Stenflo J, Drakenberg T (2000).
    Characterization of the EGF-like module pair 3-4 from vitamin K-dependent protein S using NMR spectroscopy reveals dynamics on three separate time scales and extensive effects from calcium binding.
    Biochemistry 39, 15742-15756.
  16. Sauer FG, Barnhart M, Choudhury D, Knight SD, Waksman G, Hultgren SJ (2000).
    Chaperone-assisted pilus assembly and bacterial attachment.
    Curr Opin Struct Biol 10, 548-556.
  17. Sauer FG, Knight SD, Waksman G, Hultgren SJ (2000).
    PapD-like chaperones and pilus biogenesis.
    Semin Cell Dev Biol 11, 27-34.
  18. Stenflo J, Stenberg Y, Muranyi A (2000).
    Calcium-binding EGF-like modules in coagulation proteinases: function of the calcium ion in module interactions.
    Biochim Biophys Acta 1477, 51-63.
  19. Wu B, Hammar L, Xing L, Markarian S, Yan J, Iwasaki K, Fujiyoshi Y, Omura T, Cheng RH (2000).
    Phytoreovirus T = 1 core plays critical roles in organizing the outer capsid of T = 13 quasi-equivalence.
    Virology 271, 18-25.
  20. Xing L, Casasnovas J, Cheng H (2000).
    Distinct binding mode of cellular receptor to human poliovirus and rhinovirus.
    J. Clin. Virol. 18, 63-64.
  21. Xing L, Tjarnlund K, Lindqvist B, Kaplan GG, Feigelstock D, Cheng RH, Casasnovas JM (2000).
    Distinct cellular receptor interactions in poliovirus and rhinoviruses.
    EMBO J. 19, 1207-1216.


  1. Anderson M, Hogbom M, Rinaldo-Matthis A, Andersson K, Sjöberg BM, Nordlund P (1999).
    The crystal structure of an azide complex of the di-ferrous R2 Subunit of Ribonucleotide Reductase reveals a novel carboxylate shift with important implications for di-iron catalysed oxygen activation.
    JACS 121, 2346-2352.
  2. Chaudhuri BN, Kleywegt GJ, Björkman J, Lehman-McKeeman LD, Oliver JD, Jones TA (1999).
    The crystal structures of alpha 2u-globulin and its complex with a hyaline droplet inducer.
    Acta Cryst. D55, 753-762.
  3. Chaudhuri BN, Kleywegt GJ, Broutin-L'Hermite I, Bergfors T, Senn H, Le Motte P, Partouche O, Jones TA (1999).
    Structures of cellular retinoic acid binding proteins I and II in complex with synthetic retinoids.
    Acta Cryst. D55, 1850-1857.
  4. Choudhury D, Thompson A, Stojanoff V, Langermann S, Pinkner J, Hultgren SJ, Knight SD (1999).
    X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli.
    Science 285, 1061-1066.
  5. Feierberg I, Cameron AD, Åqvist J (1999).
    Energetics of the proposed rate-determining step of the glyoxalase I reaction.
    FEBS Lett. 453, 90-94.
  6. Finn BE, Drakenberg T (1999).
    Calcium binding proteins.
    Adv. Inorg. Chem. 46, 441-494.
  7. Hung DL, Knight SD, Hultgren SJ (1999).
    Probing conserved surfaces on PapD.
    Mol Microbiol 31, 773-783.
  8. Hung DL, Pinkner JS, Knight SD, Hultgren SJ (1999).
    Structural basis of chaperone self-capping in P pilus biogenesis.
    Proc Natl Acad Sci U S A 96, 8178-8183.
  9. Jones TA, Kleywegt GJ (1999).
    CASP3 comparative modeling evaluation.
    Proteins: Struct. Funct. Genet. Suppl. 3, 30-46.
  10. Käck H, Sandmark J, Gibson K, Schneider G, Lindqvist Y (1999).
    Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5'-phosphate-dependent enzymes.
    J. Mol. Biol. 291, 857-876.
  11. Kleywegt GJ (1999).
    Recognition of spatial motifs in protein structures.
    J. Mol. Biol. 285, 1187-1197.
  12. Kleywegt GJ (1999).
    Experimental assessment of differences between related protein crystal structures.
    Acta Cryst. D55, 1878-1884.
  13. Kleywegt GJ, Jones TA (1999).
    Software for handling macromolecular envelopes.
    Acta Cryst. D55, Acta Cryst..
  14. Marelius J, Kolmodin K, Feierberg I, Åqvist J (1999).
    Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems.
    J Mol Graph Model 16, 213-225, 261.
  15. Selmer M, Al-Karadaghi S, Hirokawa G, Kaji A, Liljas A (1999).
    Crystallization and preliminary X-ray analysis of Thermotoga maritima ribosome recycling factor.
    Acta Cryst. D55, 2049-2050.
  16. Selmer M, Al-Karadaghi S, Hirokawa G, Kaji A, Liljas A (1999).
    Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic.
    Science 286, 2349-2352.
  17. Stenberg Y, Muranyi A, Steen C, Thulin E, Drakenberg T, Stenflo J (1999).
    EGF-like module pair 3-4 in vitamin K-dependent protein S: modulation of calcium affinity of module 4 by module 3, and interaction with factor X.
    J. Mol. Biol. 293, 653-665.
  18. Wang J, Choudhury D, Chattopadhyaya J, Eriksson S (1999).
    Stereoisomeric selectivity of human deoxyribonucleoside kinases.
    Biochemistry 38, 16993-16999.
  19. Wolf-Watz M, Xie XQ, Holm M, Grundström T, Härd T (1999).
    Solution properties of the free and DNA-bound Runt domain of AML1.
    Eur J Biochem 261, 251-260.
  20. Xing L, Kato K, Li T, Takeda N, Miyamura T, Hammar L, Cheng RH (1999).
    Recombinant hepatitis E capsid protein self-assembles into a dual-domain T = 1 particle presenting native virus epitopes.
    Virology 265, 35-45.
  21. Zou JY, Kleywegt GJ, Ståhlberg J, Driguez H, Nerinckx W, Claeyssens M, Koivula A, Teeri TT, Jones TA (1999).
    Crystallographic evidence for substrate ring distortion and protein conformational changes during catalysis in cellobiohydrolase Ce16A from Trichoderma reesei.
    Structure Fold. Des. 7, 1035-1045.


  1. Andersson P, Gsell B, Wipf B, Senn H, and Otting G (1998).
    HMQC and HSQC experiments with water flip-back optimized for large proteins.
    J. Biomol. NMR 11, 279-288.
  2. Andersson P, Nordstrand K, Sunnerhagen M, Liepinsh E, Turovskis I, and Otting G (1998).
    Heteronuclear correlation experiments for the determination of one-bond coupling constants.
    J. Biomol. NMR 11, 445-450.
  3. Andersson P, Weigelt J, and Otting G (1998).
    Spin-state selection filters for the measurement of heteronuclear one-bond coupling constants.
    J. Biomol. NMR 12, 435-441.
  4. Andersson P, Annila A, and Otting G (1998).
    An alpha/beta-HSQC-alpha/beta experiment for spin-state selective editing of IS cross peaks.
    J. Magn. Reson. 133, 364-367.
  5. Axblom C, Tars K, Fridborg K, Orna L, Bundule M, and Liljas L (1998).
    Structure of phage fr capsids with a deletion in the FG loop: implications for viral assembly.
    Virology 249, 80-88.
  6. Cromsigt JAMTC, van Buuren BNM, Zdunek J, Schleucher J, Hilbers CW, and Wijmenga SS (1998).
    NMR Studies of RNA and DNA. Improved Structure Determination via Incorporation of Chemical Shift Restraints and Global Structure Information.
    D.Ziessow, W.Lubitz, F.Lendzian (Eds.): Magnetic resonance and Related Phenomena; Proc. 29th Ampere-13th ISMAR; Berlin, August 2-7, 1998, 132-133.
  7. Groves P, Finn BE, Kuznicki J, and Forsen S (1998).
    A model for target protein binding to calcium-activated S100 dimers.
    FEBS Lett. 421, 175-179.
  8. Julenius K, Thulin E, Linse S, Finn BE (1998).
    Hydrophobic core substitutions in calbindin D9k: effects on stability and structure.
    Biochemistry 37, 8915-8925.
  9. Hansson H, Mattsson PT, Allard P, Haapaniemi P, Vihinen M, Smith CI, and Härd T (1998).
    Solution structure of the SH3 domain from Bruton's tyrosine kinase.
    Biochemistry 37, 2912-2924.
  10. Hansson T, Marelius J, and Åqvist J (1998).
    Ligand binding affinity prediction by linear interaction energy methods.
    J. Comput.-Aided Mol. Des. 12, 27-35.
  11. Hultgren SJ, Hung DL, Jones CH, and Knight S (1998).
    Periplasmic PapD-Like Chaperones in Bacteria: Structure and Function.
    Molecular Biology of Chaperones (edt Bernd Bukau), Harwood Academic Publishers, Chur, ??-??.
  12. Kleywegt GJ, and Jones TA (1998).
    Databases in protein crystallography.
    Acta Crystallogr. D54, 1119-1131.
  13. Kolmodin K, Hansson T, Danielsson J, and Åqvist J (1998).
    Molecular Dynamics Simulations of Substrate Dephosphorylation by Low Molecular Weight Protein Tyrosine Phosphatase.
    ACS Symp. Ser. 721, ??-??.
  14. Kragelund BB, Jonsson M, Bifulco G, Chazin WJ, Nilsson H, Finn BE, and Linse S (1998).
    Hydrophobic core substitutions in calbindin D9k: effects on Ca2+ binding and dissociation.
    Biochemistry 37, 8926-8937.
  15. Kack H, Gibson KJ, Lindqvist Y, and Schneider G (1998).
    Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
    Proc. Natl. Acad. Sci. USA 95, 5495-5500.
  16. Kack H, Sandmark J, Gibson KJ, Schneider G, and Lindqvist Y (1998).
    Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.
    Protein Sci. 7, 2560-2566.
  17. Marelius J, Graffner-Nordberg M, Hansson T, Hallberg A, and Åqvist J (1998).
    Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases.
    J. Comput.-Aided Mol. Des. 12, 119-131.
  18. Marelius J, Hansson T, and Åqvist, J (1998).
    Calculation of Ligand Binding Free Energies from Molecular Dynamics Simulations.
    Int. J. Quantum Chem. 69, 77-??.
  19. Muranyi A, Finn BE, Gippert GP, Forsen S, Stenflo J, and Drakenberg T (1998).
    Solution structure of the N-terminal EGF-like domain from human factor VII.
    Biochemistry 37, 10605-10615.
  20. Otte K, Choudhury D, Charalambous M, Engström W, and Rozell B (1998).
    A conserved structural element in horse and mouse IGF2 genes binds a methylation sensitive factor.
    Nucleic Acids Res. 26, 1605-1612.
  21. Soto GE, Dodson KW, Ogg D, Liu C, Heuser J, Knight S, Kihlberg J, Jones CH, and Hultgren SJ (1998).
    Periplasmic chaperone recognition motif of subunits mediates quaternary interactions in the pilus.
    EMBO J. 17, 6155-6167.
  22. Åqvist J, and Hansson T (1998).
    Analysis of Electrostatic Potential Truncation Schemes in Simulations of Polar Solvents.
    J. Phys. Chem. 102, 3837-??.


Since most people funded through the Network have only just started, 1997 brought only three published papers. Naturally, we expect many more papers to appear during the next few years. A short article about SBNet was published in the October 1997 issue of the PDB Newsletter.

  1. Hansson T, Nordlund P, and Åqvist J (1997).
    Energetics of Nucleophile Activation in a Protein Tyrosine Phosphatase.
    J. Mol. Biol. 265, 118-127.
  2. Hulten J, Bonham NM, Nillroth U, Hansson T, Zuccarello G, Bouzide A, Åqvist J, Classon B, Danielson UH, Karlen A, Kvarnström I, Samuelsson B, and Hallberg A (1997).
    Cyclic HIV-1 protease inhibitors derived from mannitol: synthesis, inhibitory potencies, and computational predictions of binding affinities.
    J. Med. Chem. 40, 885-897.
  3. Kleywegt GJ, and Read RJ (1997).
    Not your average density.
    Structure 5, 1557-1569.

SBNet Latest update at 6 April, 2004.