Publications co-authored by SARomics Biostructures

2018

  • Peterson K, Kumar R, Stenström O, Verma P, Verma PR, Håkansson M, Kahl-Knutsson B, Zetterberg F, Leffler H, Akke M, Logan DT, Nilsson UJ (2018). Systematic tuning of fluoro-galectin-3 interactions provides thiodigalactoside derivatives with single digit nM affinity and high selectivity. J Med Chem 61, 1164–1175. DOI: 10.1021/acs.jmedchem.7b01626.

  • Zetterberg FR, Peterson K, Johnsson R, Brimert T, Håkansson M, Logan DT, Leffler H, Nilsson UJ (2018). Monosaccharide derivatives with low nM lectin affinity and high selectivity based on combined fluorine-amide, phenyl-arginine, sulfur-π, and halogen bond interactions. ChemMedChem 13, 133-137. DOI: 10.1002/cmdc.201700744.

  • Takemoto Y, Slough DP, Meinke G, Katnik C, Graziano ZA, Chidipi B, Reiser M, Alhadidy MM, Ramirez R, Salvador-Montañés O, Ennis S, Guerrero-Serna G, Haburcak M, Diehl C, Cuevas J, Jalife J, Bohm A, Lin YS, Noujaim SF (2017). Structural basis for the antiarrhythmic blockade of a potassium channel with a small molecule. FASEB J pii: fj.201700349R. DOI: 10.1096/fj.201700349R.


2017

  • Anderson LC, Håkansson M, Walse B and Nilsson CL (2017). Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2). J Am Soc Mass Spectrom 28, 1796-1804. DOI: 10.1007/s13361-017-1705-0

  • Walse B, Turnbull AP and Boyd SM (2017). Tailoring Hit Identification and Qualification Methods for Targeting Protein–Protein Interactions. In Applied Biophysics for Drug Discovery (Huddler, D. and Zartler, E.R., ed.) pp. 29-59, John Wiley & Sons, Inc, Hoboken, NJ, USA.

  • Linares-Pastén JA, Falck P, Albasri K, Kjellström S, Adlercreutz P, Logan DT & Nordberg Karlsson E (2017) Three-dimensional structures and functional studies of two GH43 arabinofuranosidases from Weissella sp. strain 142 and Lactobacillus brevis. FEBS J, May 9. DOI: 10.1111/febs.14101

  • Pippione AC, Federico A, Ducime A, Sainas S, Boschi D, Barge A, Lupino L, Piccinini M, Kubbutat M, Contreras J-M, Morice C, Al-Karadaghi S and Lolli ML. (2017). 4-Hydroxy-N-[3,5-bis(trifluoromethyl)phenyl]-1,2,5-thiadiazole-3-carboxamide: a novel inhibitor of the canonical NF-κB cascade. Med. Chem. Commun. 8, 1850–1855. DOI: 10.1039/c7md00278e

  • Sainas S, Pippione AC, Giorgis M, Lupino E, Goyal P, Ramondetti C, Buccinnà B, Piccinini M, Braga RC, Andrade CH, Andersson M, Moritzer AC, Friemann R, Mensa S, Al-Karadaghi S, Boschi D & Lolli ML (2017). Design, synthesis, biological evaluation and X-ray structural studies of potent human dihydroorotate dehydrogenase inhibitors based on hydroxylated azole scaffolds. Eur J Med Chem 129, 287-302. https://doi.org/10.1016/j.ejmech.2017.02.017

  • Kulkarni TS ,Khan S, Villagomez R, Mahmood T, Lindahl S, Logan DT, Linares-Pastén JA & Nordberg Karlsson E (2017) Crystal structure of β-glucosidase 1A from Thermotoga neapolitana and comparison of active site mutants for hydrolysis of flavonoid glucosides (2017) Proteins 85, 872-884. DOI:10.1002/prot.25256


2016

  • Nilsson LM, Green LC, Veppil Muralidharan S, Demir D, Welin M, Bhadury J, Logan D, Walse B and Nilsson JA (2016). Cancer differentiating agent hexamethylene bisacetamide inhibits BET bromodomain proteins. Cancer Res. 76, 2376-2383. DOI: 10.1158/0008-5472.CAN-15-2721

  • Badarau A, Rouha H, Malafa S, Battles MB, Walker L, Nielson N, Dolezilkova I, Teubenbacher A, Banerjee S, Maierhofer B, Weber S, Stulik L, Logan DT, Welin M, Mirkina I, Pleban C, Zauner G, Gross K, Jägerhofer M, Magyarics Z & Nagy E (2016). Context matters: The importance of dimerization-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralizing antibodies. MAbs. 8, 1347-1360. DOI: 10.1080/19420862.2016.1215791

  • Wang H, Lang L, Logan DT, Danielsson J & Oliveberg M (2016) Tricking a protein to swap strands. J. Am. Chem. Soc. 138, 15571-15579. DOI: 10.1021/jacs.6b05151

  • Manzoni F, Saraboji K, Sprenger J, Noresson A-L, Nilsson U, Leffler H, Fisher Z, Schrader T, Ostermann A, Coates L, Blakeley MP, Oksanen O & Logan DT (2016) Perdeuteration, crystallisation, data collection and comparison of five neutron diffraction datasets of human galectin-3C. Acta Crystallogr. D. Biol. Crystallogr. 72, 1194-1202. DOI:10.1107/S2059798316015540

  • Bågenholm V, Reddy SK, Bouraoui H, Morrill J, Kulcinskaja E, Bahr CM, Aurelius O, Rogerts T, Xiao Y, Logan DT, Martens EC, Koropatkin NM & Stålbrand H (2016) Galactomannan catabolism conferred by a polysaccharide utilisation locus of Bacteroides ovatus: enzyme synergy and crystal structure of a β-mannanase. J. Biol. Chem. 292, 229-243. DOI: jbc.M116.746438

  • Sprenger J, Carey J, Svensson B, Wengel V, Persson L (2016). Binding and Inhibition of Spermidine Synthase from Plasmodium falciparum and Implications for In Vitro Inhibitor Testing. PLoS One. 11:e0163442. DOI: 10.1371/journal.pone.0163442.


2015

  • Badarau A, Rouha H, Malafa S, Logan DT, Håkansson M, Stulik L, Dolezilkova I, Teubenbacher A, Gross K, Maierhofer B, Weber S, Jägerhofer M, Hoffmann D, Nagy E (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. DOI: 10.1074/jbc.M114.598110

  • 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, 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 54, 6435-6438. DOI: 10.1021/acs.biochem.5b01058

  • Sprenger J, Svensson B, Hålander J, Carey J, Persson L & Al-Karadaghi S (2015). Three-dimensional structures of Plasmodium falciparum spermidine synthase with bound inhibitors suggest new strategies for drug design. Acta Cryst. D Biol Crystallogr. 71, 484-493. DOI: 10.1107/S1399004714027011


2014

  • von Schantz L, Håkansson M, Logan DT, 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.


  • Lolli ML, Ducime A, Federico, A Pippione AC, Sainas S, Barge A, Martina K, Boschi D, Lupino E, Piccinini M, Kubbutat M, Schächtele C, Contreras JM, Morice C, Sussman J, Peleg J, Walse B and Al-Kadaraghi S (2014). Towards a Bioisosteric Alkaest: application to the bioisosteric modulation of IMD-0354. In: Book of Abstracts. p. 234, Lisbon, Portugal, September 7-11. See poster…

  • Lolli ML, Ducime A, Federico A, Pippione AC, Sainas S, Barge A, Martina K, Boschi D, Lupino E, Piccinini M, Kubbutat M, Schächtele C, Contreras JM, Morice C, Sussman J, Peleg J, Walse B, Al-Kadaraghi S (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…

  • Contreras JM, Svensson B, Walse B, Al-Karadaghi S, Totzke F, Kubbutat M, Schächtele C, Lolli M, Boschi D, Piccinini M, Lupino E, Sussmann J, Silman I, Peleg Y, Morice C and Langer T (2014). Structure-based discovery of novel NIK inhibitors. International Conference on Medicinal Chemistry Rouen, Normandy, France - July 2-4. See poster…

  • Contreras JM, Svensson B, Walse B, Al-Karadaghi S, Totzke F, Kubbutat M, Schächtele C, Morice C, and Langer T. (2014). Comparison of hit discovery approaches case study: NIK inhibitors. EFMC-ISMC 2014, XXIII International Symposium on Medicinal Chemistry, Lisbon, Portugal - September 7-11. 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 MS, Cassimjee KE, Håkansson, M, Kimbung YR, Walse B, Abedi V, Federsel H-J, Berglund P & Logan DT (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.



  • 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. (2011). 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 (2011). The C-terminal sequence of several human serine proteases encodes host defense functions. J Innate Immun. 3, 471-482.


2010

  • Svensson SL, Pasupuleti M, Walse B, Malmsten M, Mörgelin M, Sjögren C, Olin AI, Collin M, Schmidtchen A, Palmer R & Egesten A (2010). Midkine and pleiotrophin have bactericidal properties: preserved antibacterial activity in a family of heparin-binding growth factors during evolution. J Biol Chem. 285, 16105-16115.

  • Bernadó P, Modig K, Grela P, Svergun DI, Tchorzewski M, Pons M & Akke M (2010). Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation. Biophys J. 98, 2374-2382.

  • Diehl C, Engström O, Delaine T, Håkansson M, Genheden S, Modig K, Leffler H, Ryde U, Nilsson UJ & Akke M (2010). Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3. J Am Chem Soc. 132, 14577-1489.

  • Lundqvist J, Elmlund H, Peterson Wulff R, Berglund L, Elmlund D, Emanuelsson C, Hebert H, Willows RD, Hansson M, Lindahl M & Al-Karadaghi S (2010). ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase. Structure 18, 354-365.

  • Fritzson I, Svensson B, Al-Karadaghi S, Walse B, Wellmar U, Nilsson UJ, da Graça Thrige D & Jönsson S. (2010). Inhibition of human DHODH by 4-hydroxycoumarins, fenamic acids, and N-(alkylcarbonyl)anthranilic acids identified by structure-guided fragment selection. ChemMedChem. 5, 608-617.


2009

  • Teilum K, Smith MH, Schulz E, Christensen LC, Solomentsev G, Oliveberg M & Akke M (2009). Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization. Proc Natl Acad Sci USA. 106, 18273-18278.

  • Nordlund A, Leinartaite L, Saraboji K, Aisenbrey C, Gröbner G, Zetterström P, Danielsson J, Logan DT & Oliveberg M (2009). Functional features cause misfolding of the ALS-provoking enzyme SOD1. Proc Natl Acad Sci USA. 106, 9667-9672.