SBNet

SBNet - People funded by the Network

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Between 1996 and 2002, SBNet has been funding the positions of 27 structural biologists (14 female, 13 male) in Sweden. Of these, 20 were PhD students, 4 research associates, and 3 held other positions. In terms of fields, 15 were X-ray crystallographers, 7 NMR spectroscopists, two electron-microscopists, one modeller, and two worked in the expression laboratory in Uppsala. The distribution of the 27 positions over the various universities is shown in the following table.

Item Nr of students Nr of researchers Other
Lund University, LU 3 2 -
Swedish University of Agricultural Sciences, SLU 3 2 -
Karolinska Institute, KI 5 - -
Uppsala University, UU 5 - Network Coordinator and two people in the Expression Facility
Royal Institute of Technology, KTH 2 - -
Stockholm University, SU 1 - -
Umeå University, UmU 1 - -


Researchers

  1. Name: Bryan Finn
    PI: (Forsén)
    Position: Researcher (FoAss)
    Project: Protein structure and dynamics
    E-mail: bryan.finn@fkem2.lth.se
    Gender: M
    Home page: http://www.fkem2.lth.se/~bryan/
    Actual starting date: 1 January, 1997
    Administrative starting date: 1 July, 1996
    Funding ends: 31 December, 2000
    Research reports: 1997 1998 1999 2000
    Continued career: SLU
    1. 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.
      (PubMed)
    2. Finn BE, Drakenberg T (1999).
      Calcium binding proteins.
      Adv. Inorg. Chem. 46, 441-494.
    3. 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.
      (MEDLINE)
    4. Julenius K, Thulin E, Linse S, Finn BE (1998).
      Hydrophobic core substitutions in calbindin D9k: effects on stability and structure.
      Biochemistry 37, 8915-8925.
      (MEDLINE)
    5. 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.
      (MEDLINE)
    6. 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.
      (MEDLINE)


  2. Name: Stefan Knight
    PI: (Eklund)
    Position: Researcher (FoAss)
    Project: Structure/function studies of virulence associated adhesion organelles from pathogenic Gram-negative bacteria
    E-mail: stefan@xray.bmc.uu.se
    Gender: M
    Home page: http://xray.bmc.uu.se/~stefan/
    Actual starting date: 1 January, 1997
    Administrative starting date: 1 January, 1997
    Funding ends: 31 December, 2000
    Research reports: 1997 1998 1999 2000
    Continued career: Associate professor ("lektor") at the Swedish University of Agricultural Sciences in Uppsala
    Professor at the Swedish University of Agricultural Sciences in Uppsala

    1. 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.
      (PubMed)
    2. Knight SD, Berglund J, Choudhury D (2000).
      Bacterial adhesins: structural studies reveal chaperone function and pilus biogenesis.
      Curr Opin Chem Biol 4, 653-660.
      (PubMed)
    3. 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.
      (PubMed)
    4. Sauer FG, Knight SD, Waksman G, Hultgren SJ (2000).
      PapD-like chaperones and pilus biogenesis.
      Semin Cell Dev Biol 11, 27-34.
      (PubMed)
    5. 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.
      (PubMed)
    6. Hung DL, Knight SD, Hultgren SJ (1999).
      Probing conserved surfaces on PapD.
      Mol Microbiol 31, 773-783.
      (PubMed)
    7. 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.
      (PubMed)
    8. 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, ??-??.
    9. 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.
      (MEDLINE)


  3. Name: Jan Saras
    PI: Mowbray/Jones
    Position: Researcher (FoAss)
    Project: Structural studies on membrane protein receptors
    E-mail: saras@xray.bmc.uu.se
    Gender: M
    Home page: ?
    Actual starting date: 1 August, 1997
    Administrative starting date: 1 July, 1997
    Funding ends: 30 June, 2001
    Research reports: 1997 1998 1999 2000
    Continued career: ?
    1. No publications yet


  4. Name: Xiao-Dong Su
    PI: (A. Liljas)
    Position: Researcher (FoAss)
    Project: Protein Crystallography at MAX II and Lund University
    E-mail: xiao-dong.su@mbfys.lu.se
    Gender: M
    Home page: ?
    Actual starting date: 23 April, 1998
    Administrative starting date: 1 July, 1997
    Funding ends: 31 December, 2001
    Research reports: 1998 1999 2000 2001
    Continued career: Professor in Beijing, China
    1. 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.
      (PubMed)
    2. 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.
      (PubMed)
    3. 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.
      (PubMed)
    4. 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.
      (PubMed)


  5. Name: Gerard Kleywegt
    Position: Network Coordinator/Researcher
    Project: Structural Neurobiology / Protein Crystallography / Structural Bioinformatics
    E-mail: gerard@xray.bmc.uu.se
    Gender: M
    Home page: http:xray.bmc.uu.se/gerard/
    Actual starting date: 1 June, 1997
    Administrative starting date: 1 June, 1997
    Funding ends: 31 December, 2001
    Research reports: 1997 1998 1999 2000 2001
    Continued career: Research Fellow of the Royal Swedish Academy of Sciences (KVA)
    1. Novotny M, Madsen D, Kleywegt GJ. (2004).
      Evaluation of protein fold comparison servers
      Proteins 1(54), 260-270.
      (PubMed)
    2. 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.
      (PubMed)
    3. 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.
      (PubMed)
    4. 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.
      (PubMed)
    5. Kleywegt GJ, Jones TA (2002).
      Homo crystallographicus--quo vadis?
      Structure (Camb) 10(4), 465-472.
      (PubMed)
    6. 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.
      (PubMed)
    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.
      (PubMed)
    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.
      (PubMed)
    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. 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.
    12. 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.
    13. 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.
      (PubMed)
    14. Kleywegt GJ (2000).
      Validation of protein crystal structures.
      Acta Crystallogr D Biol Crystallogr 56, 249-265.
      (PubMed)
    15. 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.
      (PubMed)
    16. 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.
      (PubMed)
    17. Jones TA, Kleywegt GJ (1999).
      CASP3 comparative modeling evaluation.
      Proteins: Struct. Funct. Genet. Suppl. 3, 30-46.
      (PubMed)
    18. Kleywegt GJ (1999).
      Recognition of spatial motifs in protein structures.
      J. Mol. Biol. 285, 1187-1197.
      (PubMed)
    19. Kleywegt GJ (1999).
      Experimental assessment of differences between related protein crystal structures.
      Acta Cryst. D55, 1878-1884.
      (PubMed)
    20. Kleywegt GJ, Jones TA (1999).
      Software for handling macromolecular envelopes.
      Acta Cryst. D55, Acta Cryst..
      (PubMed)
    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.
      (PubMed)
    22. Kleywegt GJ, and Jones TA (1998).
      Databases in protein crystallography.
      Acta Crystallogr. D54, 1119-1131.
    23. Kleywegt GJ, and Read RJ (1997).
      Not your average density.
      Structure 5, 1557-1569.
      (MEDLINE)


  6. Name: Henrik Hansson
    PI: (Kleywegt)
    Position: Network coordinator/Researcher
    Project: Structure validation
    E-mail: henke@xray.bmc.uu.se
    Gender: M
    Home page: ?
    Actual starting date: 1 May, 2002
    Administrative starting date: 1 May, 2002
    Funding ends: 31 December, 2003
    Research reports: 2002
    Continued career:Resaercher at the Swedish University of Agricultural Sciences
    1. No publications yet


Expression Lab

  1. Name: Eva Davey
    PI: (Expression Lab Uppsala)
    Position: Lab Assistant
    Project: n/a
    E-mail: eva@xray.bmc.uu.se
    Gender: F
    Home page: ?
    Actual starting date: 1 July, 1996
    Administrative starting date: 1 July, 1996
    Funding ends: 31 December, 2001
    Research reports: 1997 1998 2000 2001
    Continued career: ?


  2. Name: Petra Franzén
    PI: (Expression Lab Uppsala)
    Position: Lab Engineer
    Project: n/a
    E-mail: petra@xray.bmc.uu.se
    Gender: F
    Home page: ?
    Actual starting date: 1 July, 1996
    Administrative starting date: 1 July, 1996
    Funding ends: 31 December, 2000
    Research reports: 1997 1998 2000 2001
    Continued career: ?


PhD Students


PhD Awarded


  1. Name: Emma Jakobsson
    PI: Gerard Kleywegt
    Position: PhD student
    Project: Crystallographic studies of monoamine oxidase, a drug target in the treatment of clinical depression and Parkinson's disease
    E-mail: emma@xray.bmc.uu.se
    Gender: F
    Mentors: Knight, Norin
    Home page: http:xray.bmc.uu.se/~emma/
    Actual starting date: 1 January, 1999
    Administrative starting date: 1 January, 1999
    Funding ends: 31 December, 2002
    PhD awarded: 23 September, 2005
    Research reports: 1997 1998 2000 2001
    Continued career: Post-doc at CIC bioGUNE, Bilbao, Spain
    1. 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.
      (PubMed)


  2. Name: Peter Holm
    PI: Hebert
    Position: PhD student
    Project: Electron crystallography of microsomal glutathione transferase
    E-mail: pjh@bioxray.dk
    Gender: M
    Mentors: Jones, Eklund
    Home page: http://www.biosci.ki.se/em/
    Actual starting date: 1 August, 1999
    Administrative starting date: 1 January, 1997
    Funding ends: 30 June, 2002
    PhD awarded: 3 June, 2005
    Research reports: 1997 1998 2000 2001
    Continued career: Post Doc in the lab of Poul Nissen, University of Aarhus, Denmark. Patent officer, National Patent Office, Copenhagen
    1. 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.
      (PubMed)


  3. Name: Agnes Rinaldo-Matthis
    PI: Nordlund
    Position: PhD student
    Project: Structural studies on protein phosphatases
    E-mail: arinaldo@medusa.bioc.aecom.yu.edu
    Gender: F
    Mentors: A. Liljas, Ladenstein
    Home page: ?
    Actual starting date: 1 February, 1997
    Administrative starting date: 1 January, 1997
    Funding ends: 31 December, 2000
    PhD awarded: 29 May, 2004
    Research reports: 1997 1998 2000 2001
    Continued career: Post Doc in the lab of Vern Schramm, Albert Einstein School of Medicine. Post-doc at MBB, Karolinska Institutet.
    1. 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.
      (PubMed)
    2. 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.


  4. Name: Tomas Åkerud
    PI: Mikael Akke
    Position: PhD student
    Project: Protein structural dynamics, interactions and drug design
    E-mail: tomas.akerud@fkem2.lth.se
    Gender: M
    Mentors: Kraulis, Åberg
    Home page: ?
    Actual starting date: 1 January, 1999
    Administrative starting date: 1 January, 1999
    Funding ends: 31 December, 2002
    PhD awarded: 16 April, 2004
    Research reports: 1997 1998 2000 2001
    Continued career: AstraZeneca SCL, Mölndal
    1. Åkerud T. (2004)
      Protein Dynamics Studied by NMR. Kinetics of the Adipocyte Fatty Acid-Binding Protein and Oligomerisation of the Low Molecular Weight Protein Tyrosine Phosphatase.
      Ph. D. Thesis, Lund University
    2. 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.
      (PubMed)
    3. 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.
      (PubMed)
    4. 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.
      (PubMed)
    5. van Dongen MJ, Uppenberg J, Svensson S, Lundbäck 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.
      (PubMed)


  5. Name: Jenny Berglund
    PI: Stefan Knight
    Position: PhD student
    Project: Structure/function studies of virulence associated adhesion organelles from pathogenic Gram negative bacteria
    E-mail: jb@xray.bmc.uu.se
    Gender: F
    Mentors: Ståhlberg, Ogg
    Home page: ?
    Actual starting date: 1 September 1998,
    Administrative starting date: 1 July, 1997
    Funding ends: 30 June, 2002
    PhD awarded: 16 April, 2004
    Research reports: 1997 1998 2000 2001
    Continued career: Post Doc at Carlsberg Laboratories, Copenhagen. Post-doc with Prof. Ute Krengel at University of Oslo
    1. Berglund J. (2004)
      Structure-function Studies of Organelle Assembly and Receptor Recognition in Organelles Assembled via the Bacterial Chaperone/user Pathway.
      Ph. D. Thesis, Swedish University for Agricultural Sciences
    2. Berglund J, Knight SD (2003).
      Structural basis for bacterial adhesion in the urinary tract (Review)
      Adv Exp Med Biol 535, 33-52.
      (PubMed)
    3. 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.
      (PubMed)
    4. 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.
      (PubMed)
    5. Knight SD, Berglund J, Choudhury D (2000).
      Bacterial adhesins: structural studies reveal chaperone function and pilus biogenesis.
      Curr Opin Chem Biol 4, 653-660.
      (PubMed)
  6. Name: Ulrika Magnusson
    PI: Jones/Mowbray
    Position: PhD student
    Project: Structural studies of the platelet-derived growth-factor receptors
    E-mail:ulrika.magnusson@xray.bmc.uu.se
    Gender: F
    Mentors: Lindqvist, Hebert
    Home page: ?
    Actual starting date: 1 July, 1996
    Administrative starting date: 1 July, 1996
    Funding ends: 30 June, 2001
    PhD awarded: 21 November, 2003
    Research reports: 1997 1998 2000 2001
    Continued career: AstraZeneca, Södertälje
    1. Magnusson U. (2003)
      Structural Studies of Binding Proteins: Investigations of Flexibility, Specificity and Stability
      Ph. D. Thesis, Uppsala University
    2. 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.
      (PubMed)
    3. 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].
      (PubMed)
    4. 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.
      (PubMed)

  7. Name: Jenny Sandmark
    PI: Schneider
    Position: PhD student
    Project: Time-resolved crystallographic studies of an ATP-dependent carboxylase: dethiobiotin synthetase
    E-mail: jenny@alfa.mbb.ki.se
    Gender: F
    Mentors: Mowbray, Andersson
    Home page: ?
    Actual starting date: 1 July, 1996
    Administrative starting date: 1 July, 1996
    Funding ends: 30 June, 2000
    PhD awarded: 5 September, 2003
    Research reports: 1997 1998 2000 2001
    Continued career: AstraZeneca, Lund
    1. Sandmark J. (2003)
      Enzymatic mechanisms in biotin synthesis: vitamin B6 catalysis and phosphoryl transfer
      Ph. D. Thesis, Karolinska Institute
    2. 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.
      (PubMed)
    3. 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.
      (PubMed)
    4. 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.
      (PubMed)
    5. 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.
      (PubMed)
    6. Käck 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.
      (MEDLINE)


  8. Name: Isabella Feierberg
    PI: Åqvist
    Position: PhD student
    Project: Computer modelling of enzyme catalysis
    E-mail: isabella@xray.bmc.uu.se
    Gender: F
    Mentors: L. Nilsson, Schneider
    Actual starting date: 1 July, 1998
    Administrative starting date: 1 July, 1996 (Tomas Hansson)
    Funding ends: 30 June, 2000
    PhD awarded: 4 April, 2003
    Research reports: 1997 1998 2000 2001
    Continued career: AstraZeneca, Mölndal
    1. Feierberg I. (2003)
      Computational Studies of Enzymatic Enolization Reactions and Inhibitor Binding to a Malarial Protease
      Ph. D. Thesis, Uppsala University
    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.
      (PubMed)
    3. 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.
      (PubMed)
    4. 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.
      (PubMed)
    5. Feierberg I, Åqvist J. (2002).
      The catalytic power of ketosteroid isomerase investigated by computer simulation.
      Biochemistry. 41(52), 15728-15735.
      (PubMed)
    6. 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.
      (PubMed)
    7. Feierberg I, Cameron AD, Åqvist J (1999).
      Energetics of the proposed rate-determining step of the glyoxalase I reaction.
      FEBS Lett. 453, 90-94.
      (PubMed)
    8. 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.
      (PubMed)

  9. Name: Charlotte Helgstrand
    PI: L. Liljas
    Position: PhD student
    Project: Structure of viruses and viral components
    E-mail: lotta@xray.bmc.uu.se
    Gender: F
    Mentors: Schneider, Hebert
    Home page: ?
    Actual starting date: 1 March, 1997
    Administrative starting date: 1 January, 1997
    Funding ends: 31 December, 2000
    PhD awarded: 15 November, 2002
    Research reports: 1997 1998 2000 2001
    Continued career: Post doc in the lab of Leyla Lo-Leggio, University of Copenhagen
    1. Helgstrand C. (2002)
      Control of Quasi-Equivalence in Virus Capsids
      Ph. D. Thesis, Uppsala University
    2. 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.
      (PubMed)
    3. 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.
      (PubMed)
    4. 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.
      (PubMed)
    5. 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.
      (PubMed)
    6. 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.
      (MEDLINE)


  10. Name: Susanna Törnroth
    PI: So Iwata
    Position: PhD student
    Project:Structural studies of human multidrug resistance protein (MDR) and multidrug resistance-associated protein (MRP)
    E-mail: susanna@xray.bmc.uu.se
    Gender: F
    Mentors: Cheng, Medina
    Home page: http://zorn.bmc.uu.se/~susanna/
    Actual starting date: 1 September, 1997
    Administrative starting date: ?
    Funding ends: 30 June, 2001
    PhD awarded: 4 October, 2002
    Research reports: 1997 1998 2000 2001
    Continued career: Research engineer within the SweGene project at Chalmers University
    1. Törnroth S (2002).
      Structural studies on aerobic and anaerobic respiratory complexes
      Ph. D. Thesis, Uppsala University
    2. 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.
      (MEDLINE)
    3. 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.
      (MEDLINE)
    4. 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.
      (MEDLINE)
    5. 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.
      (MEDLINE)
    6. 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.
      (MEDLINE)
    7. 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.
      (MEDLINE)


  11. Name:Li Xing
    PI: Holland Cheng
    Position: PhD student
    Project: Structural studies on virus-host interactions
    E-mail: lix@csb.ki.se
    Gender: F
    Mentors: Iwata, Sauer-Eriksson
    Home page: ?
    Actual starting date: 1 January, 1998
    Administrative starting date: 1 January, 1998
    Funding ends: 31 December, 2001
    PhD awarded: 2 Sept, 2002
    Research reports: 1997 1998 2000 2001
    Continued career: ?
    1. Xing L (2002).
      Non-enveloped virus infection probed with host cellular molecules: a structural study
      Ph. D. thesis. Karolinska Institute
    2. 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]
      (PubMed)
    3. 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.
      (PubMed)
    4. 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.
      (PubMed)
    5. 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.
      (PubMed)
    6. Forsell K, Xing L, Kozlovska T, Cheng RH, Garoff H (2000).
      Membrane proteins organize a symmetrical virus.
      EMBO J. 19, 5081-5091.
      (PubMed)
    7. 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.
      (PubMed)
    8. Xing L, Casasnovas J, Cheng H (2000).
      Distinct binding mode of cellular receptor to human poliovirus and rhinovirus.
      J. Clin. Virol. 18, 63-64.
    9. 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.
      (PubMed)
    10. 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.
      (PubMed)


  12. Name: Inés Muñoz
    PI: Jerry Ståhlberg
    Position: PhD student
    Project: Structural studies of cellulases and other enzymes with potential for use in the cellulose industry and bio-organic synthesis
    E-mail: imunoz@cnio.e
    Gender: F
    Mentors: Kleywegt, Sauer
    Home page: ?
    Actual starting date: 1 October, 1997
    Administrative starting date: 1 January, 1998
    Funding ends: 31 December, 2001
    PhD awarded: 17 May, 2002
    Research reports: 1997 1998 2000 2001
    Continued career: Reseacher within the Structural Biology and Biocomputing Programme at the Spanish National Cancer Centre (CNIO)
    1. Muñoz I (2002).
      Structural and functional studies of cellobiohydrolase Cel7D from the white-rot fungus Phanerochaete chrysosporium.
      Ph. D. Thesis, Swedish University of Agricultural Sciences.
    2. 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.
      (PubMed)
    3. Xu B, Muñoz I IG, Janson JC, StåhlbergStåhlberg 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.
      (PubMed)
    4. 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.
      (PubMed)
    5. 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.


  13. Name: Maria Selmer
    PI: A. Liljas
    Position: PhD student
    Project: Structural studies on ribosomal proteins and RNA and their complexes
    E-mail: Maria.Selmer@mbfys.lu.se
    Gender: F
    Mentors: Nordlund, Unge
    Home page: ?
    Actual starting date: 1 July, 1996
    Administrative starting date: 1 July, 1996
    Funding ends: 30 June, 2000
    PhD awarded: 22 February, 2002
    Research reports: 1997 1998 2000 2001
    Continued career: Post-doc with Venki Ramakrishnan at the MRC Laboratory of Molecular Biology, Cambridge, England (2002). Research Assistant at Department for Cell and Molecular Biology, Uppsala Unviersity (2006)
    1. Selmer M (2002).
      Protein-RNA interplay in translation. Structural studies of RRF, SelB and L1.
      Ph. D thesis. Lund University.
    2. 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.
      (PubMed)
    3. 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.
      (PubMed)
    4. Selmer M, Su XD. (2002).
      Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.
      EMBO J. 21(15),4145-4153.
      (PubMed)
    5. 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.
      (PubMed)
    6. 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.
      (PubMed)
    7. 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.
      (PubMed)
    8. 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.
      (PubMed)
    9. 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.
      (PubMed)


  14. Name: Henrik Hansson
    PI: Härd
    Position: PhD student
    Project: Protein-protein interactions
    E-mail: henrik.hansson@biochem.kth.se
    Gender: M
    Mentors: Wijmenga, Hård
    Home page: http://www.csb.ki.se/users/nmr/henrik.html
    Actual starting date: 1 December, 1996
    Administrative starting date: 1 January, 1997
    Funding ends: 31 December, 2000
    PhD awarded: 25 January, 2002
    Research reports: 1997 1998 2000 2001
    Continued career: SBNet Coordinator (2002) Post-doc at the Swedish University of Agricultural Sciences (2004)
    1. Hansson H (2002).
      Structure and function of the SH3 domain from Bruton's tyrosine kinase.
      Ph. D. Thesis, Royal Institute of Technology.
    2. 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.
      (PubMed)
    3. Hansson H, Okoh MP, Smith CIE, 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.
      (PubMed)
    4. Hansson H, Smith CIE, 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.
      (PubMed)
    5. Hansson H, Mattsson PT, Allard P, Haapaniemi P, Vihinen M, Smith CIE, and Härd T (1998).
      Solution structure of the SH3 domain from Bruton's tyrosine kinase.
      Biochemistry 37, 2912-2924.
      (MEDLINE)
    6. Lundbäck, T, Hansson H, Knapp S, Ladenstein R, and Härd T (1998).
      Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus.
      J Mol Biol. 276(4), 775-786.
      (MEDLINE)


  15. Name: Louise Kraft
    PI: Lindqvist
    Position: PhD student
    Project: Structural studies of vesicle-transport proteins
    E-mail: louise@alfa.mbb.ki.se
    Gender: F
    Mentors: L. Liljas, Åqvist
    Home page: ?
    Actual starting date: 1 October, 1996
    Administrative starting date: 1 July, 1996
    Funding ends: 30 June, 2000
    PhD awarded: 14 December, 2001
    Research reports: 1997 1998 2000 2001
    Continued career: AstraZeneca SCL, Mölndal
    1. Kraft L (2001).
      Crystallographic studies of gluconate kinase.
      Ph. D. Thesis, Karolinska Institute.
    2. 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.
      (PubMed)
    3. 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.
      (PubMed)


  16. Name: Jenny Cromsigt
    PI: Sybren Wijmenga
    Position: PhD student
    Project: Development of methods for improved structure determination of larger systems by means of NMR
    E-mail: Jenny.Cromsigt@medchem.umu.se
    Gender: F
    Mentors: Akke, Wikström
    Home page: http://rambo.chem.umu.se/jenny.html
    Actual starting date: 1 July, 1997
    Administrative starting date: 1 July, 1997
    Funding ends: 30 June, 2001
    PhD awarded: 27 September, 2001
    Research reports: 1997 1998 2000 2001
    Continued career: IP Manager, Galapagos Genomics BV, Leiden, The Netherlands
    1. Cromsigt J (2001).
      New techniques for NMR structural studies on RNA.
      Ph. D. Thesis, Umeå University.
    2. 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.
      (PubMed)
    3. 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.
      (PubMed)
    4. 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.
      (PubMed)
    5. 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.
      (PubMed)
    6. Cromsigt J, van Buuren B, Schleucher J, Wijmenga S (2001).
      Resonance assignment and structure determination for RNA.
      Methods Enzymol 338, 371-399.
      (PubMed)
    7. 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.
    8. 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.


  17. Name: Devapriya Choudhury
    PI: Eklund
    Position: PhD student
    Project: Ribonucleotide reductase holoenzyme complexes
    E-mail: deva@xray.bmc.uu.se
    Gender: M
    Mentors: A. Liljas, Lundqvist
    Home page: ?
    Actual starting date: 1 March, 1997
    Administrative starting date: 1 January, 1997
    Funding ends: 31 December, 2000
    PhD awarded: 18 May, 2001
    Research reports: 1997 1998 2000
    Continued career: AstraZeneca SCL, Mölndal (2001); Associate professor, Centre for Biotechnology, Jawaharlal Nehru University, New Delhi, India (2002)
    1. Choudhury D (2001).
      Functional implications of macromolecular recognition: assembly of adhesive pili and enzyme substrate interactions.
      Ph. D. Thesis, Swedish University of Agricultural Sciences.
    2. 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.
      (PubMed)
    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.
      (PubMed)
    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.
      (PubMed)
    5. Knight SD, Berglund J, Choudhury D (2000).
      Bacterial adhesins: structural studies reveal chaperone function and pilus biogenesis.
      Curr Opin Chem Biol 4, 653-660.
      (PubMed)
    6. 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.
      (PubMed)
    7. Wang J, Choudhury D, Chattopadhyaya J, Eriksson S (1999).
      Stereoisomeric selectivity of human deoxyribonucleoside kinases.
      Biochemistry 38, 16993-16999.
      (PubMed)
    8. 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.
      (MEDLINE)


  18. Name: Magnus Wolf-Watz
    PI: Härd
    Position: PhD student
    Project: Structure and dynamics of proteins in solution
    E-mail: magnus.wolf-watz@csb.ki.se
    Gender: M
    Mentors: Forsén, Kördel
    Home page: http://www.csb.ki.se/users/nmr/magnus.html
    Actual starting date: 1 February, 1997
    Administrative starting date: 1 January, 1997
    Funding ends: 31 December, 2000
    PhD awarded: 1 June, 2001
    Research reports: 1997 1998 2000 2001
    Continued career: Post-doctoral fellow in Dr. Dorothee Kern's lab, Brandeis University (2001), Research Assistant at Umeå University (20034
    1. Wolf-Watz M (2001).
      Structure-function relationships of the human Runx1 transcription factor.
      Ph. D. Thesis, Royal Institute of Technology.
    2. 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.
      (PubMed)
    3. 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.
      (PubMed)
    4. Wolf-Watz M, Grundström T, Härd T (2001).
      Structure and backbone dynamics of Apo-CBFbeta in solution.
      Biochemistry 40, 11423-11432.
      (PubMed)
    5. 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.
      (PubMed)
    6. 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.
      (PubMed)


  19. Name: Patrik Andersson
    PI: Otting
    Position: PhD student
    Project: NMR spectroscopy of large proteins
    E-mail: patrik@mfn.ki.se
    Gender: M
    Mentors: Härd, Finn
    Home page: ?
    Actual starting date: 15 April, 1996
    Administrative starting date: 1 July, 1996
    Funding ends: 30 June, 2000
    PhD awarded: October, 2000
    Research reports: 1997 1998 2000
    Continued career: Ericsson Radio Systems in Kista (near Stockholm)
    1. Andersson P (2000).
      Development of new NMR techniques and Structural characterization of complexes between the N-terminal domain of the E. coli arginine repressor and operator DNA.
      Ph. D. Thesis, Karolinska Institute.
    2. Andersson P, Otting G (2000).
      Time-Shared X(ω-1)-Half-Filter for Improved Sensitivity in Subspectral Editing.
      J. Magn. Reson. 144, 168-170.
      (PubMed)
    3. 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.
      (MEDLINE)
    4. 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.
      (MEDLINE)
    5. 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.
      (MEDLINE)
    6. 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.
      (MEDLINE)


  20. Name: Andreas Muranyi
    PI: Forsén
    Position: PhD student
    Project: Solution structures of blood coagulation protein domains
    E-mail: andreas.muranyi@fkem2.lth.se
    Gender: M
    Mentors: Otting, Härd
    Home page: ?
    Actual starting date: 1 July, 1996
    Administrative starting date: 1 July, 1996
    Funding ends: 30 June, 2000
    PhD awarded: 19 May, 2000
    Research reports: 1997 1998 2000
    Continued career: Post-doc with Kristy Downing at the Oxford Centre for Molecular Sciences (2000) Amersham Biosciences in Uppsala (2002)
    1. Muranyi A (2000).
      EGF-like Modules in Blood Coagulation Proteins. Ca2+ binding, module interactions, structure and dynamics as studied by NMR spectroscopy.
      Ph. D. Thesis, Lund University.
    2. 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.
      (PubMed)
    3. 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.
      (PubMed)
    4. 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.
      (PubMed)
    5. 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.
      (PubMed)
    6. 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.
      (MEDLINE)


  21. Name: Tomas Hansson
    PI: Åqvist
    Project: Computational approaches to ligand design and enzyme catalysis
    E-mail: toha@xray.bmc.uu.se
    Mentors: L. Nilsson, Schneider
    Actual starting date: 1 July, 1996
    Administrative starting date: 1 July, 1996
    Funding ends: n/a (continued by Feierberg)
    PhD awarded: 16 May, 1998
    Research reports: 1997 1998
    Continued career: post-doc with Wilfred van Gunsteren at the ETH in Zürich. Researcher at KaroBio, Stockholm (2003).
    1. Hansson T (1998).
      Ligand Binding and Enzyme Catalysis Studied by Molecular Dynamics Simulations.
      Ph. D. Thesis, Uppsala University.
    2. 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.
      (MEDLINE)
    3. 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, ??-??.
    4. 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.
      (MEDLINE)
    5. Marelius J, Hansson T, and Åqvist, J (1998).
      Calculation of Ligand Binding Free Energies from Molecular Dynamics Simulations.
      Int. J. Quantum Chem. 69, 77-??.
    6. Åqvist J, and Hansson T (1998).
      Analysis of Electrostatic Potential Truncation Schemes in Simulations of Polar Solvents.
      J. Phys. Chem. 102, 3837-??.
    7. Hansson T, Nordlund P, and Åqvist J (1997).
      Energetics of Nucleophile Activation in a Protein Tyrosine Phosphatase.
      J. Mol. Biol. 265, 118-127.
      (MEDLINE)
    8. 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.
      (MEDLINE)


SBNet Latest update at 23 November, 2007.