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Publications Derek Logan

Logan group publications

ResearcherID: http://www.researcherid.com/rid/A-1114-2011

Google Scholar: http://scholar.google.com/citations?user=7Um2bwQAAAAJ&hl=en

In refereed journals

      2017

  1. 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
  2. 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
  3. Rämisch S, Tillgren V, Aspberg A & Logan DT (2017) Crystal structure of chondroadherin: solving a difficult molecular replacement problem using de novo models. Acta Crystallogr. D. Biol. Crystallogr., 73, 53–63. doi: 10.1107/S205979831601980X
  4. 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 (2017) 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.M116.74643.

    2016

  5. Manzoni F, Saraboji K, Sprenger J, Kumar R, Noresson AL, Nilsson UJ, Leffler H, Fisher SZ, Schrader TE, Ostermann A, Coates L, Blakeley MP, Oksanen E, Logan DT (2016) Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C. Acta Crystallogr D Struct Biol. 72, 1194-1202. doi:10.1107/S2059798316015540
  6. Wang H, Lang L, Logan DT, Danielsson J & Oliveberg M (2016) Tricking a protein to swap strands. J. Am. Chem. Soc., 38, 15571-15579. doi:10.1021/jacs.6b05151
  7. 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 dimerisation-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralising antibodies. mAbs 8, 1347–1360 doi:10.1080/19420862.2016.1215791
  8. Lizatovic R, Aurelius O, Stenström O, Drakenberg T, Akke M, Logan DT & André I (2016)  A de novo designed coiled-coil peptide with a reversible pH-induced oligomerization switch. Structure 24, 946–55. doi:10.1016/j.str.2016.03.027
  9. Johansson R, Jonna VR, Kumar R, Nayeri N, Lundin D, Sjöberg B-M, Hofer A & Logan DT (2016) A novel mode of allosteric activity regulation in a ribonucleotide reductase with double ATP cones. Structure 24, 906–17. doi:10.1016/j.str.2016.03.025
  10. Nilsson LM, Green LC, Muralidharan SV, Demir D, Welin M, Bhadury J, Logan DT, Walse B & Nilsson JA (2016) Cancer differentiation agent hexametylene bisacetamide inhibits BET bromodomain proteins. Cancer Research 76, 2376–2383 doi: 10.1158/0008-5472.CAN-15-2721

    2015

  11. 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
  12. Danielsson J, Mu X, Lang L, Wang H, Binolfi A, Theillet FX, Bekei B, Logan DT, Selenko P, Wennerström H & Oliveberg M (2015) Thermodynamics of protein destabilisation in live cells. Proc. Natl. Acad. Sci. USA 112, 12402–12407. doi: 10.1073/pnas.1511308112
  13. Ohlin M, von Schantz L, Schrader TE, Ostermann A Logan DT & Fisher SZ (2015) Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase. Acta Crystallogr. F Struct. Biol. Commun. 71, 1072-1077. doi:10.1107/S2053230X15011383
  14. Awad W, Adamczyk B, Örnros J, Karlsson NG, Mani K & Logan DT (2015) Structural aspects of N-glycosylations and the C-terminal region in human glypican-1. J. Biol. Chem., doi:10.1075/jbc.M115.660878
  15. Aurelius O, Johansson R, Bågenholm V, Lundin D, Tholander F, Balhuizen A, Beck T, Sahlin M, Sjöberg B.-M., Mulliez E & Logan DT (2015) The crystal structure of Thermotoga maritima class III ribonucleotide reductase lacks a radical cysteine pre-positioned in the active site. PLoS ONE 10, e0128199.
  16. Logan DT, Appio R, Fredslund F, Haase D, Martínez Casado FJ, Nan J, Nardella A, Norén K, Sigfridsson KGV, Thomas D, Unge J, Balmes O, Carlson S, Ursby T & Thunnissen MMGM (2015)  Status of the crystallography beamlines at the MAX IV Laboratory. European Physical Journal Plus 130, 49.

    2014

  17. von Schantz L, Håkansson M, Logan DT, Nordberg-Karlsson E & Ohlin M (2014) Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH-Π interactions. Proteins 82, 3466-3475
  18. Badarau A, Rouha H, Malafa H, Logan DT, Håkansson M, Stulik L, Dolezilkova I, Teubenbacher A, Gross K, Maierhofer B, Weber S, Jägerhofer M, Hoffmann D & Nagy E (2014) Structure-function analysis of heterodimer formation, oligomerization and receptor binding of the Staphylococcus aureus bi-component toxin LukGH. J. Biol. Chem. 290, 142-156.
  19. Rosengren A, Reddy SK, Svantesson Sjöberg J, Aurelius O, Logan DT, Kolenová K & Stålbrand H (2014)  An Aspergillus nidulans β-mannanase with high transglycosylation capacity revealed through comparative studies within glycosidase family 5. Appl. Microbiol. Biotechnol. 98, 10091-10104 

    2013

  20. Awad W, Svensson Birkedal G, Thunnissen MMGM, Mani K & Logan DT (2013) Improvements of the order, isotropy and electron density of glypican-1 crystals by controlled dehydration. Acta Crystallogr. D Biol. Crystallogr., 69 (12), 2524-2533
  21. Ursby T, Unge J, Appio R, Logan DT, Fredslund F, Svensson C, Larsson K, Labrador A & Thunnissen M (2013) The macromolecular crystallography beamline I911-3 at the MAX IV Laboratory. J. Synchr. Rad. 20, 648-653.
  22. Danielsson J, Awad W, Saraboji K, Kurnik M, Lang L, Leinartaité L, Marklund SL, Logan DT & Oliveberg M (2013) Global motions from the strain of a single hydrogen bond. Proc. Natl. Acad. Sci. USA. 110, 3829-34.

    2012

  23. von Schantz L, Håkansson M, Logan DT, Walse B, Österlin J, Nordberg Karlsson E & Ohlin M (2012) Structural basis for carbohydrate binding specificity - a comparative assessment of two engineered carbohydrate binding modules. Glycobiology 22, 948-61.
  24. Svensson G, Awad W, Håkansson M, Mani K & Logan DT (2012) Crystal structure of N-glycosylated human glypican-1 core protein: structure of two loops evolutionarily conserved in vertebrate glypican-1. J. Biol. Chem. 287, 14040-51. PDF
  25. Svedendahl Humble M, Engelmark Cassimjee K, Håkansson M, Kimbung YR, Walse B, Abedi V, Federsel HJ, 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.
  26. Haglund E, Danielsson D, K Saraboji, Lindberg MO, Logan DT & Oliveberg M (2012) Trimming down a protein structure to its bare foldons: spatial organisation of the cooperative unit. J. Biol. Chem. 287, 2731-2738.
  27. 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 pre-organized to recognize a sugar-like framework of oxygens: ultra-high resolution structures and water dynamics. Biochemistry 51, 296-306.

    2011

  28. Ofer A, Kreft J, Logan DT, Cohen G, Borovok I & Aharonowitz Y (2011) Implications of the inability of Listeria monocytogenes EGD-e to grow anaerobically due to a deletion in the class III NrdD ribonucleotide reductase for its use as a model laboratory strain. J. Bacteriol. 193, 2931–40.
  29. 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. 408, 670–683.

    2010

  30. Leinartaité L, Saraboji K, Nordlund A, Logan DT & Oliveberg M (2010) Folding catalysis by transient coordination of Zn2+ to the Cu ligands of the ALS-associated enzyme Cu/Zn superoxide dismutase 1. J. Am. Chem. Soc. 132, 13495-13504.
  31. Johansson R, Torrents E, Lundin D, Sprenger J, Sahlin M, Sjöberg B-M & Logan DT (2010) High resolution crystal structures of flavoprotein NrdI in oxidised and reduced states: an unusual flavodoxin. FEBS J. 277, 4265-4277. 
  32. Larsson KM, Logan DT & Nordlund P (2010) Structural basis for adenosylcobalamin activation in AdoCbl-dependent ribonucleotide reductases. ACS Chem. Biol. 5, 933-942.
  33. Pozzo T, Linares-Pasten J, Nordberg Karlsson E & Logan DT (2010) Structural and functional analysis of β-glucosidase 3B from Thermotoga neapolitana: a thermostable 3-domain representative of glycosyl hydrolase family 3. J. Mol. Biol. 397, 724-39.

    2005-2009

  34. Krintel C, Mörgelin M, Logan DT & Holm C (2009) Phosphorylation of hormone-sensitive lipase by protein kinase A in vitro promotes an increase in its hydrophobic surface area. FEBS J 276, 4752-4762.
  35. Nordlund A, Leinartaité L, Saraboji K, Aisenbrey C, Gröbner G, Danielsson J, Logan DT & Oliveberg M (2009) Functional features cause misfolding of the ALS-provoking enzyme SOD1: non-native metal coordination obstructs active-site packing. Proc. Natl. Acad. Sci. U.S.A. 106, 9667-9672. 
  36. Krintel C, Osmark P, Larsen MR, Resjö S, Logan DT & Holm C (2008) Ser 649 and Ser650 are the major determinants of protein kinase A-mediated activation of human hormone-sensitive lipase against lipid substrates. PLoS ONE 3:e3756.
  37. Pramhed A, Addis L, Tillgren V, Wenglén C, Heinegård D & Logan DT (2008) Purification, crystallisation and preliminary diffraction analysis of human chondroadherin. Acta Crystallogr. F 64, 516-9.
  38. Wang E, Bauer M, Rogstam A, Linse S, Logan DT & von Wachenfeldt C (2008) Structure and functional properties of the Bacillus subtilis transcriptional repressor Rex. Mol. Microbiol. 69, 466-78.
  39. Turner P, Pramhed A, Kanders E, Hedström M, Nordberg-Karlsson E & Logan DT (2007) Expression, purification, crystallization and preliminary X-ray diffraction analysis of Thermotoga maritima β-glucosidase B. Acta Crystallogr. F 63, 702-706.
  40. Olofsson M, Hansson S, Hedberg L, Logan DT & Oliveberg M (2007) Folding of S6 structures with divergent amino-acid composition:  pathway flexibility within the bounds of partly overlapping foldons. J. Mol. Biol. 365, 237-248
  41. Hörnberg A, Logan DT, Marklund SL & Oliveberg M (2007) The coupling between disulphide status, metallation and dimer interface strength in Cu/Zn superoxide dismutase. J. Mol. Biol. 365, 333-342.
  42. Hansson S, Singh R, Gudkov AT, Liljas A & Logan DT (2005) Structure of elongation factor G trapped with a GTP analogue. FEBS Lett. 579, 4492-4497
  43. Hansson S, Singh R, Gudkov AT, Liljas A & Logan DT (2005) Structural insights into fusidic acid sensitivity and resistance in EF-G. J. Mol. Biol. 348, 939-949
  44. Poole AM & Logan DT (2005): Modern mRNA proofreading and repair: proof that the last universal common ancestor (LUCA) had an RNA genome? Mol. Biol. Evol. 22, 1444-1455
  45. Kolberg M, Logan DT, Bleifuss G, Potsch S, Sjöberg BM, Gräslund A, Lubitz W, Lassmann G & Lendzian F (2005) A new tyrosyl radical on F208 as ligand to the diiron center in E. coli ribonucleotide reductase, mutant R2-Y122H: Combined X-ray diffraction, and EPR/ENDOR studies. J. Biol. Chem. 280, 11233-11246.

    2000-2004

  46. Ursby T, Mammen CB, Cerenius Y, Svensson C, Sommarin B, Fodje, MN, Kvick, Å,  Logan DT, Als-Nielsen J, Thunnissen, MMGM, Larsen S. & Liljas A. (2004) The new macromolecular crystallography stations at MAX-lab: The MAD Station. AIP Conference Proceedings 705, 1241-1246.
  47. Larsson K-M, Eliasson R, Jordan A, Reichard P, Logan DT & Nordlund P (2004) Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase. Nat. Struct. Mol. Biol. 11, 1142-1149
  48. Lundell A, Olin AI, al-Karadaghi S, Mörgelin M, Aspberg A & Logan DT (2004) Structural basis for the interactions between tenascins and lectican C-type lectin domains: evidence for a cross-linking role for tenascins. Structure 12, 1495-1506.
  49. Logan DT, Mulliez E, Larsson K-M, Bodevin S, Atta M, Garnaud PE, Sjöberg BM & Fontecave M (2003) A metal binding site in the catalytic subunit of anaerobic ribonucleotide reductase. Proc. Natl. Acad. Sci. U.S.A. 100, 3826–3831
  50. Poole AM, Logan DT & Sjöberg B-M (2002) Evolution of the ribonucleotide reductases: much ado about oxygen. J. Mol. Evol. 55, 180-96
  51. Larsson K-M, Andersson J, Sjöberg B-M, Nordlund P & Logan, DT (2001) Structural basis for allosteric substrate specificity regulation in class III ribonucleotide reductases. Structure 9, 739-750.

    1995-1999

  52. Logan DT, Andersson J, Sjöberg, BM & Nordlund P1 (1999) A glycyl radical site in the crystal structure of a class III anaerobic ribonucleotide reductase. Science 283, 1499–1504.
  53. Logan DT, Persson BO, deMaré F, Slaby A, & Nordlund P. (1998) Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: Structural basis for the oxygen insertion step of hydroxylation reactions catalysed by diiron proteins. Biochemistry 37, 10798-10807.
  54. Mazauric M-H, Keith G, Logan DT, Kreutzer R, Giegé R & Kern D (1998) Glycyl-tRNA synthetase from Thermus thermophilus. Wide structural divergence with other prokaryotic glycyl-tRNA synthetases and functional inter-relation with prokaryotic and eukaryotic glycylation systems. Eur. J. Biochem. 251, 744-757
  55. Katterle B, Sahlin M, Schmidt PP, Pötsch S, Logan D, Gräslund A & Sjöberg B-M (1997) Kinetics of transient radicals in Escherichia coli ribonucleotide reductase: Formation of a new tyrosyl radical in mutant protein R2 J. Biol. Chem. 27, 10414-10421
  56. Gauss D, Logan DT & Freist, W (1996) Glycyl-tRNA synthetase. Biological Chemistry Hoppe-Seyler 377, 343-356
  57. Logan DT, Su XD, Åberg A, Regnström K, Hajdu J, Eklund H & Nordlund P. (1996) Structure of the reduced protein R2 of ribonucleotide reductase: structural basis for activation at a di-iron site. Structure 4, 1053-1064.
  58. Logan DT, Mazauric MH, Kern D & Moras D (1995) Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus. EMBO J. 14, 4145-4167
  59. Lea S, Abu-Ghazaleh R, Blakemore W, Curry S, Fry E, Jackson T, King A, Logan D, Newman J & Stuart D (1995) Structural comparison of two strains of foot-and-mouth disease virus subtype O1 and a laboratory antigenic variant, G67. Structure 3, 571-580

    1990-1994

  60. Logan DT, Cura V, Touzel  JP, Kern D & Moras D (1994)  Crystallisation of the glycyl-tRNA synthetase from Thermus thermophilus and preliminary crystallographic data. J. Mol. Biol. 241, 732-735
  61. Logan D, Abu-Ghazaleh R, Blakemore W, Curry S, Jackson T, King A, Lea S, Lewis R, Newman J, Parry N, Rowlands D, Stuart D & Fry E (1993) Structure of a major immunogenic site on foot-and-mouth disease virus. Nature 362, 566-568
  62. Curry S, Abu-Ghazaleh R, Blakemore W, Fry E, Jackson T, King A, Lea S, Logan D, Newman J &  Stuart D (1992) Crystallization and preliminary X-ray analysis of three serotypes of foot-and-mouth disease virus. J. Mol. Biol. 228, 1263-1268
  63. Davey RJ, Black SN, Logan D, Maginn SJ, Fairbrother JE & Grant DJW (1992) Structural and kinetic features of crystal-growth inhibition - adipic acid growing in the presence of n-alkanoic acids. J. Chem. Soc Faraday Trans. 88, 3461-3466
  64. Parry N, Fox G, Rowlands D, Brown F, Fry E, Acharya R, Logan D & Stuart D (1990) Structural and serological evidence for a novel mechanism of antigenic variation in foot-and-mouth disease virus. Nature 347, 569-572

 

Reviews/proceedings

  1. Lundin D, Berggren G, Logan DT & Sjöberg B.-M. (2015) The origin and evolution of ribonucleotide reduction. Life 5, 604-636.
  2. Thunnissen MMGM, Sondhauss PM, Wallén E, Theodor K, Logan DT, Labrador A, Unge J, Appio R, Fredslund F & Ursby T (2013) BIOMAX: The future macromolecular crystallography beamline at MAX IV. Journal of Physics: Conference Series 425, 072012.
  3. Hofer A, Crona M, Logan DT & Sjöberg B-M (2012) DNA building blocks: keeping control of manufacture. Crit. Rev. Biochem. Mol. Biol. 47, 50–63.
  4. Logan DT (2011) Closing the circle on ribonucleotide reductases. Nature Struct. Mol. Biol. 18, 251-253.
  5. Fontecave M, Mulliez E & Logan DT (2002) Deoxyribonucleotide synthesis in anaerobic organisms: the class III ribonucleotide reductase. Progress in Nucleic Acids Research and Molecular Biology 72, 95-127
  6. Eklund H, Faernegårdh M, Uhlin U, Logan DT & Nordlund  P (2001) Structure and function of the radical enzyme ribonucleotide reductase. Prog. Biochem. Biophys. 77, 177-268
  7. Andersson ME, Högbom M, Logan D, Andersson KK & Nordlund P (1999) Studies of the oxygen activation mechanism in RNR R2 using x-ray crystallographic techniques. J. Inorg. Biochem. 74, 64
  8. Eklund H, Eriksson M, Uhlin U, Nordlund P & Logan D. (1997) Ribonucleotide reductase - structural studies of a radical enzyme. Biological Chemistry 378, 821-825
  9. Rowlands, D, Logan D, Abu-Ghazaleh R, Blakemore W, Curry S, Jackson T, King A, Lea S, Lewis R, Newman J, Parry N, Stuart D & Fry E (1994) The structure of an immunodominant loop on foot-and-mouth disease virus, serotype O1, determined under reducing conditions. Arch. Virol. 9, 51-58
  10. Fry E, Logan D, Acharya R, Fox G, Rowlands D, Brown F & Stuart D (1990) Architecture and topography of an aphthovirus. Seminars in Virology 1, 439-451
  11. Acharya R, Fry E, Logan D, Stuart D, Fox G, Rowlands D & Brown F (1990) The structure of foot-and-mouth disease virus, in The use of X-ray Crystallography in the design of anti-viral agents, ed. W.G. Laver & G. Air, Academic Press, Inc.
  12. Acharya R, Fry E, Logan D, Stuart D, Brown F, Fox G & Rowlands D (1990) Some observations on the three-dimensional structure of foot-and-mouth disease virus, in New Aspects of Positive-strand RNA Viruses, ed. MA Brinton & FX Heinz, American Society for Microbiology.

  

Book chapters

  1. Logan DT (2008) Anaerobic ribonucleotide reductases: recent progress in understanding. In "Ribonucleotide reductase (ed. K.K. Andersson), "Molecular Anatomy and Physiology of Proteins" series, Nova Science Publishers, Hauppauge, NY. 
  2. Fry E, Logan D & Stuart D (1996) Virus Crystallography, in Methods in Molecular Biology, Volume 56 – Crystallographic methods and protocols, ed. C. Jones, B. Mulloy & M.A. Sanderson. New Jersey: Humana Press Inc.