Selected publications by SARomics Biostructures managing group and employees:

2015
•A. Badarau, H. Rouha, S. Malafa, D. T. Logan, M. Håkansson, L. Stulik, I. Dolezilkova, A. Teubenbacher, K. Gross, B. Maierhofer, S. Weber, M. Jägerhofer, D. Hoffmann, · E. Nagy. (2015). Structure-Function Analysis of Heterodimer Formation, Oligomerization, and Receptor Binding of the Staphylococcus aureus Bi-component Toxin LukGH.
J. Biol. Chem. 290, 142-156.
•Rodrigues T. Reker D.,Welin M.,Caldera M.,Brunner C., Gabernet G.,Schneider P.,Walse B. and Schneider G. (2015). De Novo Fragment Design for Drug Discovery and Chemical Biology.
Angewandte Chemie International Edition, 2015, published online: 21 OCT 2015, DOI: 10.1002/anie.201508055.
•Fisher SZ, von Schantz L, Håkansson M, Logan DT, Ohlin M. (2015). Neutron Crystallographic Studies Reveal Hydrogen Bond and Water-Mediated Interactions between a Carbohydrate-Binding Module and Its Bound Carbohydrate Ligand.
Biochemistry, Oct 13. [Epub ahead of print].


2014
•von Schantz, L., Håkansson, M., Logan, D.T., Nordberg-Karlsson, E. and Ohlin, M., (2014). Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH-π interactions. Proteins, 82, 3466-75.
•Turnbull, A.P., Boyd,. S.M. & Walse, B. (2014). Fragment-based drug discovery and protein-protein interactions. Res. Rep Biochem. 4, 13-26.
•Marco L. Lolli, Alex Ducime, Antonella Federico, Agnese Chiara Pippione, Stefano Sainas, Alessandro Barge, Katia Martina, Donatella Boschi, Elisa Lupino, Marco Piccinini, Michael Kubbutat, Christoph Schächtele, Jean Marie Contreras, Christophe Morice, Joel Sussman, Yoav Peleg, Bjorn Walse, Salam Kadaraghi (2014).
TOWARD A BIOISOSTERIC ALKAEST – APPLICATION TO THE BIOISOSTERIC MODULATION OF IMD-0354. In: Book of Abstracts. p. 234, Lisbon, Portugal, September 7-11, 2014. See poster…
•Lolli Marco L., Federico Antonella, Ducime Alex, Pippione Agnese, Sainas Stefano, Barge Alessandro, Martina Katia, Boschi Donatella, Lupino Elisa, Piccinini Marco, Kubbutat Michael, Contreras Jean Marie, Morice Christophe, Sussman Joel, Peleg Yoav, Walse Bjorn, Al-Kadaraghi Salam (2014).
Towards a Bioisosteric Alkaest: application to the bioisosteric modulation of IMD-0354. In: Book of Abstracts. p. 100, San Diego, USA, April 23-25. See poster…
•Jean-Marie Contreras, Bo Svensson, Bjorn Walse, Salam Al-Karadaghi, Frank Totzke, Michael H.G. Kubbutat, Christophm Schächtele, Marco Lolli, Donatella Boschi, Marco Piccinini, Elisa Lupino, Joel Sussmann, Israel Silman, Yoav Peleg, Christophe Morice, and Thierry Langer
Structure-based discovery of novel NIK inhibitors, Presented at International Conference on Medicinal Chemistry Rouen, Normandy, France - July 2-4, 2014. See poster…
•Jean-Marie Contreras, Bo Svensson, Bjorn Walse, Salam Al-Karadaghi,2Frank Totzke, Michael H.G., Kubbutat, Christoph Schächtele, Christophe Morice, and Thierry Langer
Comparison of hit discovery approaches case study: NIK inhibitors, presented at EFMC-ISMC 2014, XXIII International Symposium on Medicinal Chemistry, Lisbon, Portugal - September 7-11, 2014. See poster...


2013
•Söderberg CA, Rajan S, Shkumatov AV, Gakh O, Schaefer S, Ahlgren EC, Svergun DI, Isaya G, Al-Karadaghi S. (2013). The molecular basis of iron-induced oligomerization of frataxin and the role of the ferroxidation reaction in oligomerization.
J Biol Chem., 288, 8156-67.
•Danielsson J, Awad W, Saraboji K, Kurnik M, Lang L, Leinartaite L, Marklund SL, Logan DT, Oliveberg M (2013). Global structural motions from the strain of a single hydrogen bond.
Proc Natl Acad Sci U S A, 110, 3829-34.


2012
• Saraboji K, Håkansson M, Genheden S, Diehl C, Qvist J, Weininger U, Nilsson UJ, Leffler H, Ryde U, Akke M, Logan DT. (2012). The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics. Biochemistry 2012, 51:296-306.
•Humble, M.S., Cassimjee, K.E., Håkansson, M., Kimbung, Y.R., Walse, B., Abedi, V., Federsel, H-J., Berglund, P. and Logan, D.T. (2012). Crystal structures of the Chromobacterium violaceum ω-transaminase reveal major structural rearrangements upon binding of coenzyme PLP.
FEBS J., 279, 779-792.
•von Schantz, L., Håkansson, M., Logan, D.T., Walse, B., Osterlin, J., Nordberg-Karlsson, E. and Ohlin, M. (2012). Structural basis for carbohydrate-binding specificity -a comparative assessment of two engineered carbohydrate-binding modules.
Glycobiology, 22, 948-961.
•Akke M.(2012). Conformational dynamics and thermodynamics of protein-ligand binding studied by NMR relaxation.
Biochem Soc Trans., 40, 419-23.
•Boyd, S.M., Turnbull, A.P. and Walse, B. (2012). Fragment library design considerations.
WIREs Comput. Mol. Sci., 2, 868-885.
•Weininger U, Liu Z, McIntyre DD, Vogel HJ, Akke M.(2012). Specific 12CβD(2)12CγD(2)S13CεHD(2) isotopomer labeling of methionine to characterize protein dynamics by 1H and 13C NMR relaxation dispersion.
J Am Chem Soc., 134, 18562-5.


2011
• Söderberg CA, Shkumatov AV, Rajan S, Gakh O, Svergun DI, Isaya G, Al-Karadaghi S. Oligomerization Propensity and Flexibility of Yeast Frataxin Studied by X-ray Crystallography and Small-Angle X-ray Scattering.
J Mol Biol. 2011, 414:783-797.
• Liljas A, Ehrenberg M, Åqvist J. Comment on "The mechanism for activation of GTP hydrolysis on the ribosome".
Science. 2011, 333:37.
• Wang E, Ikonen TP, Knaapila M, Svergun D, Logan DT, von Wachenfeldt C. Small-angle X-ray scattering study of a Rex family repressor: conformational response to NADH and NAD+ binding in solution.
J Mol Biol. 2011, 408:670-683.
• Kasetty G, Papareddy P, Kalle M, Rydengård V, Walse B, Svensson B, Mörgelin M, Malmsten M, Schmidtchen A. The C-terminal sequence of several human serine proteases encodes host defense functions.
J Innate Immun. 2011, 3:471-482.
• Logan DT. Closing the circle on ribonucleotide reductases.
Nat Struct Mol Biol. 2011, 18:251-253.

2010
• Svensson SL, Pasupuleti M, Walse B, Malmsten M, Mörgelin M, Sjögren C, Olin AI, Collin M, Schmidtchen A, Palmer R, Egesten A. Midkine and pleiotrophin have bactericidal properties: preserved antibacterial activity in a family of heparin-binding growth factors during evolution.
J Biol Chem. 2010, 285:16105-16115.
• Bernadó P, Modig K, Grela P, Svergun DI, Tchorzewski M, Pons M, Akke M. Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation. Biophys J. 2010, 98:2374-2382.
• Diehl C, Engström O, Delaine T, Håkansson M, Genheden S, Modig K, Leffler H, Ryde U, Nilsson UJ, Akke M. Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3. J Am Chem Soc. 2010, 132:14577-1489.
• Lundqvist, J., Elmlund, H., Peterson Wulff, R., Berglund, L., Elmlund, D., Emanuelsson, C., Hebert, H., Willows, R.D., Hansson, M., Lindahl, M. and Al-Karadaghi, S. ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase.
Structure 2010, 18:354-365.
• Fritzson I, Svensson B, Al-Karadaghi S, Walse B, Wellmar U, Nilsson UJ, da Graça Thrige D, Jönsson S. Inhibition of human DHODH by 4-hydroxycoumarins, fenamic acids, and N-(alkylcarbonyl)anthranilic acids identified by structure-guided fragment selection.
ChemMedChem. 2010, 5:608-617.


2009
• Teilum K, Smith MH, Schulz E, Christensen LC, Solomentsev G, Oliveberg M, Akke M. Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization.
Proc Natl Acad Sci USA. 2009, 106:18273-18278.
•Nordlund A, Leinartaite L, Saraboji K, Aisenbrey C, Gröbner G, Zetterström P, Danielsson J, Logan DT, Oliveberg M. Functional features cause misfolding of the ALS-provoking enzyme SOD1.
Proc Natl Acad Sci USA. 2009, 106:9667-9672.