Publications

Daan van Aalten Laboratory

1995

  1. D.M.F. van Aalten, A. Amadei, A.B.M. Linssen, V.G.H. Eijsink, G. Vriend, and H.J.C. Berendsen, "The essential dynamics of thermolysin - confirmation of the hinge-bending motion and comparison of simulations in vacuum and water", Proteins (1995), 22, 45-54.
  2. D.M.F. van Aalten, J.B.C. Findlay, A. Amadei, and H.J.C. Berendsen, "Essential dynamics of the cellular retinol-binding protein - evidence for ligand-induced conformational changes", Prot. Engng. (1995), 8, 1129-1135.

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    1996

  3. D.M.F. van Aalten, A. Amadei, R. Bywater, J.B.C. Findlay, H.J.C. Berendsen, C. Sander, and P.F.W. Stouten, "A comparison of structural and dynamic properties of different simulation methods applied to SH3", Biophys. J. (1996), 70, 684-692.
  4. A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten, and H.J.C. Berendsen, "An efficient method for sampling the essential subspace of proteins", J. Biomol. Str. Dyn. (1996), 13, 615-625.
  5. B.L. de Groot, A. Amadei, D.M.F. van Aalten, and H.J.C. Berendsen, "Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin", J. Biomol. Str. Dyn. (1996), 13, 741-751.
  6. D.M.F. van Aalten, R. Bywater, J.B.C. Findlay, M. Hendlich, R.W.W. Hooft, and G. Vriend, "PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules", JCAMD (1996), 10, 255-262. Postscript
  7. B.L. de Groot, D.M.F. van Aalten, A. Amadei, and H.J.C. Berendsen, "The consistency of large concerted motions in proteins in molecular dynamics simulations", Biophys. J. (1996), 71, 1707-1713. PDF
  8. D.M.F. van Aalten, B.L. de Groot, H.J.C. Berendsen, and J.B.C. Findlay, "Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins", Biochem. J. (1996), 319, 543-550. PDF
  9. G.H. Peters, D.M.F. van Aalten, O. Edholm, S. Toxvaerd, and R. Bywater, "Dynamics of proteins in different solvent systems: Analysis of essential motion in lipases", Biophys. J. (1996), 71, 2245-2255.

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    1997

  10. D.M.F. van Aalten, B.L. de Groot, J.B.C. Findlay, H.J.C. Berendsen, and A. Amadei, "A comparison of techniques for calculating protein essential dynamics", J. Comp. Chem. (1997), 18, 169-181. PDF
  11. D.M.F. van Aalten, P.C. Jones, M. de Sousa, and J.B.C. Findlay, "Engineering protein mechanics: inhibition of concerted motions of the cellular retinol binding protein by site-directed mutagenesis", Prot. Engng. (1997), 10, 31-37. PDF
  12. G.H. Peters, D.M.F. van Aalten, A. Svendsen, and R. Bywater, "Essential dynamics of lipase binding sites: the effect of inhibitors of different chain length", Prot. Engng. (1997), 10, 149-158. PDF
  13. L.V. Mello, D.M.F. van Aalten, and J.B.C. Findlay, "Comparison of ras-p21 bound to GDP and GTP: differences in protein and ligand dynamics", Prot. Engng. (1997), 10, 381-387. PDF
  14. B.L. de Groot, D.M.F. van Aalten, R.M. Scheek, A. Amadei, G. Vriend, and H.J.C. Berendsen, "Prediction of protein conformational freedom from distance constraints", Proteins (1997), 29, 240-251. PDF
  15. D.M.F. van Aalten, D.A. Conn, B.L. de Groot, H.J.C. Berendsen, J.B.C. Findlay, and A. Amadei, "Protein dynamics derived from clusters of crystal structures", Biophys. J. (1997), 73, 2891-2896. PDF

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    1998

  16. L.V. Mello, D.M.F. van Aalten, and J.B.C. Findlay, "Dynamic properties of the guanine nucleotide binding protein alpha subunit and comparison of its guanosine triphosphate hydrolase domain with that of ras-p21", Biochemistry (1998), 37, 3137-3142. PDF
  17. B.L. de Groot, S. Hayward, D.M.F. van Aalten, A. Amadei, and H.J.C. Berendsen, "Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data", Proteins (1998), 31, 116-127. PDF
  18. H. Yamaguchi, D.M.F. van Aalten, M. Pinak, A. Furukawa, and R. Osman, "Essential dynamics of DNA containing a cis.syn cyclobutane thymine dimer lesion", Nucl. Acids Res. (1998), 26, 1939-1946. PDF
  19. D.M.F. van Aalten, E. Grotewold, and L. Joshua-Tor, "Essential dynamics from NMR clusters: dynamic properties of the Myb DNA-binding domain and a hinge-bending enhancing variant", Methods (1998), 14, 318-328. PDF
  20. R. Kort, M.K. Phillips-Jones, D.M.F. van Aalten, A. Haker, S.M. Hoffer, K.J. Hellingwerf, and W. Crielaard, "Sequence, chromophore extraction and 3-D model of the photoactive yellow protein from Rhodobacter sphaeroides", Biochim. Biophys. Acta (1998), 1385, 1-6. PDF
  21. M. Sundaram, A. Sivaprasadarao, D.M.F. van Aalten, and J.B.C. Findlay, "Expression, characterization and engineered specificity of rat epididymal retinoic acid-binding protein", Biochem. J. (1998), 334, 155-160. PDF
  22. D.M.F. van Aalten, W.D. Hoff, J.B.C. Findlay, W. Crielaard, and K.J. Hellingwerf, "Concerted motions in the photoactive yellow protein", Prot. Engng. (1998), 11, 873-879. PDF

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    1999

  23. P.-L. Chau, D.M.F. van Aalten, J.B.C. Findlay, and R.P. Bywater, "Functional concerted motions in the bovine serum retinol-binding protein", JCAMD (1999), 13, 11-20.
  24. D.M.F. van Aalten, D.A. Erlanson, G.L. Verdine, and L. Joshua-Tor, "A structural snapshot of base-pair opening in DNA", Proc. Natl. Acad. Sci. USA (1999), 96, 11809-1814. PDF

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    2000

  25. D.M.F. van Aalten, W. Crielaard, K.J. Hellingwerf, and L. Joshua-Tor, "Conformational substates in different crystal forms of the photoactive yellow protein - correlation with theoretical and experimental flexibility", Protein Science (2000), 9, 64-72. PDF
  26. P.J.L. Werten, B. Roll, D.M.F. van Aalten, and W.W. de Jong, "Gecko iota-crystallin: How cellular retinol-binding protein became an eye lens ultraviolet filter", Proc. Natl. Acad. Sci. USA (2000), 97, 3282-3287. PDF
  27. D.M.F. van Aalten, J.Knudsen, C.C. DiRusso, T. Kokko, and R. Wierenga, "Crystallization and X-ray diffraction studies of the fatty acid responsive transcription factor FadR from Escherichia coli", Acta Cryst. (2000), D56, 469-471. PDF
  28. D.M.F. van Aalten, B. Synstad, M.B. Brurberg, E. Hough, B.W. Riise, V.G.H. Eijsink, and R.K. Wierenga, "Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9 Å resolution", Proc. Natl. Acad. Sci. USA (2000), 97, 5842-5847. PDF
  29. A.M. Mursula, D.M.F. van Aalten, Y. Modis, J. K. Hiltunen, and R.K. Wierenga, "Crystallization and X-ray diffraction analysis of peroxisomal D3-D2-enoyl-CoA isomerase from Saccharomyces cerevisiae", Acta Cryst. (2000), D56, 1020-1023. PDF
  30. D.M.F. van Aalten, C.R. Chong, and L. Joshua-Tor, "Crystal structure of carboxypeptidase A complexed with D-cysteine at 1.75 Å - Inhibitor-induced conformational changes", Biochemistry (2000), 39, 10082-10089. PDF
  31. D.M.F. van Aalten, C.C. DiRusso, J. Knudsen, and R.K. Wierenga, "Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold", EMBO J. (2000), 19, 5167-5177. PDF

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    2001

  32. D.M.F. van Aalten, K.G. Milne, J. Y. Zou, G.J. Kleywegt, T. Bergfors, M.A.J. Ferguson, J. Knudsen, and T.A. Jones, "Binding site differences revealed by crystal structures of Plasmodium falciparum and bovine acyl-CoA binding protein", J. Mol. Biol. (2001), 309, 181-192. PDF
  33. D.M.F. van Aalten, C.C. DiRusso, and J. Knudsen, "The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR", EMBO J. (2001), 20, 2041-2050. PDF
  34. M.A.M. van Boekel, D.M.F. van Aalten, G.-J. Caspers, B. Roll, and W.W. de Jong, "Evolution of the aldose reductase-related gecko eye lens protein rho-B-crystallin: a sheep in wolf's clothing", J. Mol. Evol. (2001), 52, 239-248. PDF
  35. A.M. Mursula, D.M.F. van Aalten, J.K. Hiltunen, and R.K. Wierenga, "The crystal structure of D3-D2-enoyl-CoA isomerase", J. Mol. Biol. (2001), 309, 845-853. PDF
  36. D.M.F. van Aalten, D. Komander, B. Synstad, S. Gåseidnes, M.G. Peter, and V.G.H. Eijsink, "Structural insights into the catalytic mechanism of a family 18exo-chitinase", Proc. Natl. Acad. Sci. USA (2001), 98, 8979-8984. PDF
  37. M.B. Brurberg, B. Synstad, S.S. Klemsdal, D.M.F. van Aalten, L. Sundheim, and V.G.H. Eijsink, "Chitinases from Serratia marcescens", Recent Res. Devel. Microbiology (2001), 5, 187-204. PDF
  38. C.C. Thomas, S.J. Dowler, M. Deak, D.R. Alessi, and D.M.F. van Aalten, "Crystal structure of the phosphatidylinositol (3,4)-bisphosphatebinding PH domain of TAPP1 - molecular basis of lipid specificity", Biochem. J. (2001), 358, 287-294. PDF
  39. A.M. Haapalainen, D.M.F. van Aalten, G. Meriläinen, J.E. Jalonen, R.K. Wierenga, J.K. Hiltunen, and T. Glumoff, "Crystal structure of the liganded SCP-2 like domain of humanperoxisomal multifunctional enzyme type 2 at 1.75 Å resolution", J. Mol. Biol. (2001), 313, 1127-1138. PDF

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    2002

  40. G. Kolstad, B. Synstad, V.G.H. Eijsink, and D.M.F. van Aalten, "Crystal structure of the D140N mutant of chitinase B from Serratia marcescens at 1.45 Å resolution", Acta Cryst. (2002), D58, 377-379. PDF
  41. J.N. Tabudravu, V.G.H. Eijsink, G.W. Gooday, M. Jaspars, D.Komander, M. Legg, B. Synstad, and D.M.F. van Aalten, "Psammaplin A, a chitinase inhibitor isolated from the Fijian marinesponge Aplysinella rhax", Bioorg. Med. Chem. (2002), 10, 1123-1128. PDF
  42. D.M.F. van Aalten, A. Haker, J. Hendriks, K.J. Hellingwerf, L. Joshua-Tor, and W. Crielaard, "Engineering photocycle dynamics - crystal structures and kinetics of three photoactive yellow protein hinge-bending mutants", J. Biol. Chem. (2002), 277, 6463-6468. PDF
  43. M. Sundaram, D.M.F. van Aalten, J.B.C. Findlay, and A. Sivaprasadarao, "The transfer of transthyretin and receptor-binding properties from the plasma retinol-binding protein to the epididymal retinoic acid-binding protein", Biochem. J. (2002), 362, 265-271. PDF
  44. D.M.F. van Aalten, W. Crielaard, K.J. Hellingwerf, and L. Joshua-Tor, "Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 Å resolution", Acta Cryst. (2002), D58, 585-590. PDF
  45. D.R. Houston, K. Shiomi, N. Arai, S. Omura, M.G. Peter, A. Turberg, B. Synstad, V.G.H. Eijsink, and D.M.F. van Aalten, "High-resolution structures of a chitinase complexed with natural product cyclopentapeptide inhibitors: Mimicry of carbohydrate substrate", Proc. Natl. Acad. Sci. USA (2002), 99, 9127-9132. PDF + Commentary PDF
  46. F. Fusetti, H. von Moeller, D. Houston, H.J. Rozeboom, B.W. Dijkstra, R.G. Boot, J.M.F.G. Aerts, and D.M.F. van Aalten, "Structure of human chitotriosidase - implications for specific inhibitor design and function of mammalian chitinase-like lectins", J. Biol. Chem. (2002), 277, 25537-25544. PDF
  47. C.C. Thomas, M. Deak, D.R. Alessi, and D.M.F. van Aalten, "High-resolution structure of the pleckstrin homology domain of protein kinaseB/Akt bound to phosphatidylinositol (3,4,5)-trisphosphate", Curr. Biol. (2002), 12, 1256-1262. PDF
  48. R.M. Biondi, D. Komander, C.C. Thomas, J.M. Lizcano, M. Deak, D.R. Alessi, and D.M.F. van Aalten, "High resolution crystal structure of the human PDK1 catalytic domain defines the regulatory phosphopeptide docking site", EMBO J. (2002), 21, 4219-4228. PDF
  49. D.R. Houston, I. Eggleston, B. Synstad, V.G.H. Eijsink, and D.M.F. van Aalten, "The cyclic dipeptide CI-4 inhibits family 18 chitinases by structural mimicry of a reaction intermediate", Biochem. J. (2002), 368, 23-27. PDF

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    2003

  50. M.S. Alphey, H. Attrill, P.R. Crocker, and D.M.F. van Aalten, "High resolution crystal structures of Siglec-7 - insights into ligand specificity in the Siglec family", J. Biol. Chem. (2003), 278, 3372-3377. PDF
  51. F.V. Rao, D.R. Houston, R.G. Boot, J.M.F.G. Aerts, S. Sakuda, and D.M.F. van Aalten, "Crystal structures of allosamidin derivatives in complex with human macrophage chitinase", J. Biol. Chem. (2003), 278, 20110-20116. PDF
  52. J. Vreede, M.A. van der Horst, K.J. Hellingwerf, W. Crielaard, and D.M.F. van Aalten, "PAS domains - common structure, common flexibility?", J. Biol. Chem. (2003), 278, 18434-18439. PDF
  53. D.R. Houston, A.D. Recklies, J.C. Krupa, and D.M.F. van Aalten, "Structure and ligand-induced conformational change of the 39 kD glycoprotein from human articular chondrocytes", J. Biol. Chem. (2003), 278, 30206-30212. PDF
  54. G.J. Kleywegt, K. Henrick, E.J. Dodson, and D.M.F. van Aalten, "Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?", Structure (2003), 11, 1051-1059. PDF
  55. D. Komander, G.S. Kular, J. Bain, M. Elliott, D.R. Alessi, and D.M.F. van Aalten, "Structural basis for UCN-01 (7-hydroxystaurosporine) specificity and PDK1 (3-phosphoinositide-dependent protein kinase-1) inhibition", Biochem. J. (2003), 375, 255-262. PDF
  56. C.C. Milburn, M. Deak, S.M. Kelly, N.C. Price, D.R. Alessi, and D.M.F. van Aalten, "Binding of phosphatidylinositol 3,4,5-trisphosphate to the Pleckstrin Homology domain of protein kinase B induces a conformational change", Biochem. J. (2003), 375, 531-538. PDF

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    2004

  57. G. Vaaje-Kolstad, D.R. Houston, F.V. Rao, M.G. Peter, B. Synstad, D.M.F. van Aalten, and V.G.H. Eijsink, "Structure of the D142N mutant of the family 18 chitinase ChiB from Serratia marcescens and its complex with allosamidin", Biochim. Biophys. Acta (2004), 1696, 103-111. PDF
  58. C.C. Milburn, J. Boudeau, M. Deak, D.R. Alessi, and D.M.F. van Aalten, "Crystal structure of MO25α in complex with the C terminus of the pseudo kinase STE20-related adaptor", Nature Struct. Mol. Biol. (2004),11, 192-200. PDF
  59. D. Komander, G.S. Kular, A.W. Schüttelkopf, M. Deak, K.R.C. Prakash, J. Bain, M. Elliott, M. Garrido-Franco, A.P. Kozikowski, D.R. Alessi, and D.M.F. van Aalten, "Interactions of LY333531 and other bisindolyl maleimide inhibitors with PDK1", Structure (2004), 12, 215-226. PDF
  60. G. Vaaje-Kolstad, A. Vasella, M.G. Peter, C. Netter, D.R. Houston, B. Westereng, B. Synstad, V.G.H. Eijsink, and D.M.F. van Aalten, "Interactions of a family 18 chitinase with the designed inhibitor HM508 and its degradation product, chitobiono-δ-lactone", J. Biol. Chem. (2004), 279, 3612-3619. PDF
  61. B. Synstad, S. Gåseidnes, D.M.F. van Aalten, G. Vriend, J.E. Nielsen, and V.G.H. Eijsink, "Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase", Eur.J.Biochem. (2004), 271, 253-262. PDF
  62. D. Komander, M. Deak, N. Morrice, and D.M.F. van Aalten, "Purification, crystallisation and preliminary X-ray diffraction of aproteolytic fragment of PDK1 containing the pleckstrin homology domain", Acta Cryst. (2004), D60, 314-316. PDF
  63. A. Mora, D. Komander, D.M.F. van Aalten, and D.R. Alessi, "PDK1, the master regulator of AGC kinase signal transduction", Semin. Cell Dev. Biol. (2004), 15, 161-170. PDF
  64. N. Dimasi, H. Attrill, D.M.F. van Aalten, A. Moretta, L. Moretta, R. Biassoni, and R. Mariuzza, "Structure of the saccharide-binding domain of the human natural killer cell inhibitory receptor p75/AIRM1", Acta Cryst. (2004), D60, 620. PDF
  65. A.W. Schuettelkopf and D.M.F. van Aalten, "PRODRG: a tool for high-throughput crystallography of protein-ligandcomplexes", Acta Cryst. (2004), D60, 1355-1363. PDF
  66. D.E. Blair and D.M.F. van Aalten, "Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine", FEBS Lett. (2004), 570, 13-19. PDF
  67. D. Komander, A. Fairservice, M. Deak, G.S. Kular, A.R. Prescott, C.P. Downes, S.T. Safrany, D.R. Alessi, and D.M.F. van Aalten, "Structural insights into the regulation of PDK1 by phosphoinositides and inositol phosphates", EMBO J. (2004), 23, 3918-3928. PDF
  68. D.R. Houston, B. Synstad, V.G.H. Eijsink, M.J.R. Stark, I.M. Eggleston, and D.M.F. van Aalten, "Structure-based exploration of cyclic dipeptide chitinase inhibitors", J. Med. Chem. (2004), 47, 5713-5720. PDF
  69. J. Boudeau, J.W. Scott, N. Resta, M. Deak, A. Kieloch, D. Komander, D.G. Hardie, A.R. Prescott, D.M.F. van Aalten, and D.R. Alessi, "Analysis of the LKB1:STRAD:MO25 complex", J. Cell. Sci. (2004), 117, 6365-6375. PDF

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    2005

  70. F.V. Rao, D.R. Houston, R.G. Boot, J.M.F.G. Aerts, M. Hodkinson, D.J. Adams, K. Shiomi, S. Omura, and D.M.F. van Aalten, "Specificity and affinity of natural product cyclopentapeptide inhibitors against Aspergillus fumigatus, human and bacterial chitinases", Chem. Biol. (2005), 12, 65-76. PDF + Commentary PDF
  71. F. Villa, M. Deak, G.B. Bloomberg, D.R. Alessi, and D. M.F. van Aalten, "Crystal structure of the PTPL1/FAP-1 human tyrosine phosphatase mutated in colorectal cancer: evidence for a second phosphotyrosine substrate recognition pocket", J. Biol. Chem. (2005), 280, 8180-8187. PDF
  72. G. Vaaje-Kolstad, D.R. Houston, A.H.K. Riemen, V.G.H. Eijsink, and D.M.F. van Aalten, "Crystal structure and binding properties of the Serratia marcescens chitin-binding protein CBP21", J. Biol. Chem. (2005), 280, 11313-11319. PDF
  73. D. Komander, G. Kular, M. Deak, D.R. Alessi, and D.M.F. van Aalten, "Role of T-loop phosphorylation in PDK1 activation, stability and substrate binding", J. Biol. Chem. (2005), 280, 18797-11802. PDF
  74. M.D. Urbaniak, A. Crossman, T. Chang, T.K. Smith, D.M.F. van Aalten, and M.A.J. Ferguson, "The N-acetyl-D-glucosaminylphosphatidylinositol de-N-acetylase of glycosylphosphatidylinositol biosynthesis is a zinc metalloenzyme",J. Biol. Chem. (2005), 280, 22831-22838. PDF
  75. G. Vaaje-Kolstad, S.J. Horn, D.M.F. van Aalten, B. Synstad, and V.G.H. Eijsink, "The non-catalytic chitin-binding protein CBP21 from Serratiamarcescens is essential for chitin degradation", J. Biol. Chem. (2005), 280, 28492-28497. PDF + Commentary PDF
  76. F.V. Rao, O.A. Andersen, K.A. Vora, J.A. DeMartino, and D.M.F. van Aalten, "Methylxanthine drugs are chitinase inhibitors: investigation of inhibition and binding modes", Chem. Biol. (2005), 12, 973-980. PDF
  77. M.J. Dixon, O.A. Andersen, D.M.F. van Aalten, and I.M. Eggleston, "An efficient synthesis of argifin: A natural product chitinase inhibitor with chemotherapeutic potential", Bioorg. Med. Chem. Lett. (2005), 15, 4717-4721. PDF
  78. O.A. Andersen, M.J. Dixon, I.M. Eggleston, and D.M.F. van Aalten, "Natural product family 18 chitinase inhibitors", Nat. Prod. Rep. (2005), 22, 563-579. PDF
  79. D.E. Blair, A.W. Schuettelkopf, J.I. MacRae, and D.M.F. van Aalten, "Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor", Proc. Natl. Acad. Sci. USA (2005), 102, 15429-15434. PDF

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    2006

  80. S.R. Wickramasinghe, K.A. Inglis, J.E. Urch, S. Mueller, D.M.F. van Aalten, and A.H. Fairlamb, "Kinetic, inhibition and structural studies on 3-oxoacyl-ACP reductase from Plasmodium falciparum, a key enzyme in fatty acid biosynthesis", Biochem. J. (2006), 393, 447-457. PDF
  81. M. Jaleel, F. Villa, M. Deak, R. Toth, A.R. Prescott, D.M.F. van Aalten, and Dario R. Alessi, "The ubiquitin-associated domain of AMPK-related kinases regulates conformation and LKB1-mediated phosphorylation and activation", Biochem. J. (2006), 394, 545-555. PDF + Commentary PDF
  82. F.V. Rao, H.C. Dorfmueller, F. Villa, M. Allwood, I.M. Eggleston, and D.M.F. van Aalten, "Structural insights into mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis", EMBO J. (2006), 25, 1569-1578. PDF + Commentary PDF
  83. H. Attrill, H. Takazawa, S. Witt, S. Kelm, R. Isecke, R. Brossmer, T. Ando, H. Ishida, M. Kiso, P.R. Crocker, and D.M.F. van Aalten, "The structure of Siglec-7 in complex with sialosides: leads for rational structure-based inhibitor design", Biochem. J. (2006), 397, 271-278. PDF
  84. A.W. Schuettelkopf, G. Hamilton, C. Watts, and D.M.F. van Aalten, "Structural basis of reduction-dependent activation of human Cystatin F", J. Biol. Chem. (2006), 281, 16570-16575. PDF
  85. D.E. Blair, O. Hekmat, A.W. Schuettelkopf, B. Shrestha, K. Tokuyasu, S.G.Withers, and D.M.F. van Aalten, "Structure and mechanism of chitin deacetylase from the fungal pathogen Colletotrichum lindemuthianum", Biochemistry (2006), 45, 9416-9426. PDF
  86. A.W. Schuettelkopf, O.A. Andersen, F.V. Rao, M. Allwood, C. Lloyd, I.M.Eggleston, and D.M.F. van Aalten, "Screening-based discovery and structural dissection of a novel family 18 chitinase inhibitor", J. Biol. Chem. (2006), 281, 27278-27285. PDF
  87. S.H. Conner, G. Kular, M. Peggie, S. Shepherd, A.W. Schuettelkopf, P. Cohen, and D.M.F. van Aalten, "TAK1-binding protein 1 is a pseudophosphatase", Biochem. J. (2006), 399, 427-434. PDF
  88. M.J. Dixon, O.A. Andersen, D.M.F. van Aalten, and Ian M. Eggleston, "First synthesis of argadin: a nanomolar inhibitor of family-18 chitinases", Eur. J. Org. Chem. (2006), 22, 5002-5006. PDF
  89. H. Attrill, A. Imamura, R.S. Sharma, M. Kiso, P.R. Crocker, and D.M.F. van Aalten, "Siglec-7 undergoes a major conformational change when complexed with the α2,8-disialylganglioside GT1b", J. Biol. Chem. (2006), 281, 32774-32783. PDF
  90. H.C. Dorfmueller, V.S. Borodkin, M. Schimpl, S.M. Shepherd, N.A. Shpiro, and D.M.F. van Aalten, "GlcNAcstatin: a picomolar, selective O-GlcNAcase inhibitor that modulates intracellular O-GlcNAcylation levels", J. Am. Chem. Soc. (2006), 128, 16484-16485. PDF + Commentary PDF

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    2007

  91. J. Taskinen, D.M.F. van Aalten, J. Knudsen, and R.K. Wierenga, "High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand", Proteins (2007), 66, 220-238. PDF
  92. S.J. Mills, D. Komander, M.N. Trusselle, S.T. Safrany, D.M.F. van Aalten, and B.L.V. Potter, "Novel inositol phospholipid headgroup surrogate crystallized in the pleckstrin homology domain of protein kinase Bα", ACS Chem. Biol. (2007), 2, 242-246. PDF
  93. R. Hurtado-Guerrero and D.M.F. van Aalten, "Structure of Saccharomyces cerevisiae chitinase 1 and screening-based discovery of potent inhibitors", Chem. Biol. (2007), 14, 589-599. PDF
  94. F. Villa, J. Goebel, F.H. Rafiqi, M. Deak, J. Thastrup, D.R. Alessi, and D.M.F. van Aalten, "Structural insights into the recognition of substrates and activators by the OSR1 kinase", EMBO Rep. (2007), 8, 839-845. PDF
  95. M.B. Allwood, B. Cannan, D.M.F. van Aalten, and I.E. Eggleston, "Efficient synthesis of 1,3,7-substituted xanthines by a safety-catch protection strategy", Tetrahedron (2007), 50, 12294-12302. PDF
  96. R. Hurtado-Guerrero, O. Raimi, S. Shepherd, and D.M.F. van Aalten, "Glucose-6-phosphate as a probe for the glucosamine-6-phosphate N-acetyltransferase Michaelis complex", FEBS Lett. (2007), 581, 5597-5600. PDF
    97. Back to top

    2008

  97. O.A. Andersen, A. Nathubhai, M.J. Dixon, I.M. Eggleston, and D.M.F. van Aalten, "Structure-based dissection of the natural product cyclopentapeptide chitinase inhibitor argifin", Chem. Biol. (2008), 15, 295-301. PDF + Commentary PDF
  98. J.R. Bayascas, S. Wullschleger, K. Sakamoto, J.M. Garcia-Martinez, C. Clacher, D. Komander, D.M.F. van Aalten, K.M. Boini, F. Lang, C. Lipina, L. Logie, C. Sutherland, J.A. Chudek, J. van Diepen, P.J. Voshol, J.M. Lucocq, and D.R. Alessi, "Mutation of PDK1 PH domain inhibits PKB/Akt leading to small size and insulin-resistance", Mol. Cell. Biol. (2008), 28, 3258-3272. PDF
  99. S. Pathak, H.C. Dorfmueller, V.S. Borodkin, and D.M.F. van Aalten, "Chemical dissection of the link between streptozotocin, O-GlcNAc and pancreatic cell death", Chem. Biol. (2008), 15, 799-807. PDF
  100. R. Hurtado-Guerrero, O.G. Raimi, J. Min, H. Zeng, L. Vallius, S.M. Shepherd, A.F.M. Ibrahim, H. Wu, A.N. Plotnikov, and D.M.F. van Aalten, "Structural and kinetic differences between human and Aspergillus fumigatus D-glucosamine-6-phosphate N-acetyltransferase", Biochem. J. (2008), 415, 217-223. PDF
  101. D. Lamb, A.W. Schuettelkopf, D.M.F. van Aalten, and D.W. Brighty, "Highly specific inhibition of leukaemia virus membrane fusion by interaction of peptide antagonists with a conserved region of the coiled coil ofenvelope", Retrovirology (2008), 5, 70. PDF
  102. F. Villa, M. Deak, D.R. Alessi, and D.M.F. van Aalten, "Structure of the OSR1 kinase, a hypertension drug target", Proteins (2008), 73, 1082-1087. PDF
  103. A. Clarke, R. Hurtado-Guerrero, S. Pathak, A.W. Schuettelkopf, V. Borodkin, S.M. Shepherd, A.F.M. Ibrahim, and D.M.F. van Aalten, "Structural insights into mechanism and specificity of O-GlcNAc transferase", EMBO J. (2008), 27, 2780-2788. PDF + Commentary PDF
  104. R. Hurtado-Guerrero, H.C. Dorfmueller, and D.M.F. van Aalten, "Molecular mechanisms of O-GlcNAcylation", Curr. Opin. Struct. Biol. (2008), 18, 551-557. PDF
  105. D.M.F. van Aalten and N.C.J. Strynadka,"Putting glycobiology on a structural footing", Curr. Opin. Struct. Biol. (2008), 18, 525-526. PDF

    106. Back to top

    2009

  106. M.J. Dixon, A. Nathubhai, O.A. Andersen, D.M.F. van Aalten, and I.M. Eggleston, "Solid-phase synthesis of cyclic peptide chitinase inhibitors: SAR of the argifin scaffold", Org. Biomol. Chem. (2009), 7, 259-268. PDF Pubmed
  107. D.M. Deng, J.E. Urch, J.M. ten Cate, V.A. Rao, D.M.F. van Aalten, and W. Crielaard, "Streptococcus mutans SMU.623c codes for a functional, metal-dependent polysaccharide deacetylase that modulates interactions with salivary agglutinin", J. Bact. (2009), 191, 392-402. PDF Pubmed
  108. R. Hurtado-Guerrero, A.W. Schuettelkopf, I. Mouyna, A.F.M. Ibrahim, S. Shepherd, T. Fontaine, J.P. Latge, and D.M.F. van Aalten, "Molecular mechanisms of yeast cell wall glucan remodeling", J.Biol.Chem. (2009), 284, 8461-8469. PDF  Pubmed
  109. H.C. Dorfmueller, V.S. Borodkin, M Schimpl, and D.M.F. van Aalten, "GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular hyper-O-GlcNAcylation", Biochem.J. (2009), 420, 221-227. PDF  Pubmed
  110. J.E. Urch, R. Hurtado-Guerrero, D. Brosson, Z. Liu, V.G.H. Eijsink, C. Texier, and D.M.F. van Aalten, "Structural and functional characterization of a putative polysaccharide deacetylase of the human parasite Encephalitozoon cuniculi", Prot. Sci. (2009), 18, 1197-1209. PDF  Pubmed
  111. E. Zeqiraj, B.M. Filippi, S. Goldie, I. Navratilova, J. Boudeau, M. Deak, D.R. Alessi, and D.M.F. van Aalten, "ATP and MO25α regulate the conformational state of the STRADα pseudokinase and activation of the LKB1 tumour suppressor", PLoS Biol. (2009), 7, e1000126. PDF  Pubmed
  112. E. Zeqiraj, B.M. Filippi, M. Deak, D.R. Alessi and D.M.F. van Aalten, "Structure of the LKB1-STRAD-MO25 complex reveals an allosteric mechanism of kinase activation", Science (2009), 326, 1707-1711. PDF  Pubmed

    113. Back to top

    2010

  113. H.C. Dorfmueller and D.M.F. van Aalten, "Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds", FEBS Lett. (2010), 584, 694-700. PDF  Pubmed
  114. R. Hurtado-Guerrero, T. Zusman, S. Pathak, A.F.M. Ibrahim, S. Shepherd, A. Prescott, G. Segal and D.M.F. van Aalten, "Molecular mechanism of elongation factor 1A inhibition by a Legionella pneumophila glycosyltransferase", Biochem.J. (2010), 426, 281-292. PDF  Pubmed
  115. J.A. Frearson, S. Brand, S.P. McElroy, L.A.T. Cleghorn, O. Smid, L. Stojanovski, H.P. Price, M.L.S. Guther, L.S. Torrie, D.A. Robinson, I. Hallyburton, C.P. Mpamhanga, J.A. Brannigan, A.J. Wilkinson, M. Hodgkinson, R. Hui, W. Qiu, O.G. Raimi, D.M.F. van Aalten, R. Brenk, I.H. Gilbert, K.D. Read, A.H. Fairlamb, M.A.J. Ferguson, D.F. Smith and P.G. Wyatt, "N-myristoyltransferase inhibitors as new leads to treat sleeping sickness", Nature (2010), 464, 728-732. PDF +  Commentary PDF  Pubmed
  116. V.S. Borodkin and D,M.F. van Aalten, "An efficient and versatile synthesis of GlcNAcstatins - potent and selective O-GlcNAcase inhibitors built on the tetrahydroimidazo[1,2-a]pyridine scaffold", Tetrahedron (2010), 66, 7838-7849. PDF  Pubmed
  117. C.L. Rush, A.W. Schuettelkopf, R. Hurtado-Guerrero, D.E. Blair, A.F.M. Ibrahim, S. Desvergnes, I.M. Eggleston and D.M.F. van Aalten, "Natural product-guided discovery of a fungal chitinase inhibitor", Chem.Biol. (2010), 17, 1275-1281. PDF  Pubmed
  118. H.C. Dorfmueller, V.S. Borodkin, M. Schimpl, X. Zheng, R. Kime, K. D. Read and D.M.F. van Aalten, "Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases", Chem.Biol. (2010), 17, 1250-1255. PDF  Pubmed
  119. A.W. Schuettelkopf, L. Gros, D.E Blair, J.A. Frearson, D.M.F. van Aalten and I. Gilbert, "Acetazolamide-based fungal chitinase inhibitors", Bioorg.Med.Chem. (2010), 18, 8334-8340. PDF  Pubmed
  120. M. Schimpl, A.W. Schuettelkopf, V.S. Borodkin and D.M.F. van Aalten, "Human O-GlcNAcase binds substrates in a conserved peptide recognition groove", Biochem.J. (2010), 432, 1-7. PDF  Pubmed
  121. E. Zeqiraj and D.M.F. van Aalten, "Pseudokinases - remnants of evolution or key allosteric regulators?", Curr.Opin.Struct.Biol. (2010), 20, 772-781. PDF  Pubmed

    122. Back to top

    2011

  122. D. Lamb, A.W. Schuettelkopf, D.M.F. van Aalten and D.W. Brighty, "Charge-surrounded pockets and electrostatic interactions with small ions modulate the activity of retroviral fusion proteins", PLOS Pathog. (2011), 7, e1001268. PDF  Pubmed
  123. H.C. Dorfmueller, V.S. Borodkin, D.E. Blair, S. Pathak, I. Navratilova and D.M.F. van Aalten, "Substrate and product analogues as human O-GlcNAc transferase inhibitors", Amino Acids (2011), 40, 781-792. PDF  Pubmed
  124. L.M. Gay, X. Zheng and D.M.F. van Aalten, "O-GlcNAc transfer : size matters", Nature Chem.Biol. (2011), 7, 134-135. PDF  Pubmed
  125. A.W. Schuettelkopf, O.A. Andersen, F.V. Rao, M. Allwood, C.L. Rush, I.M. Eggleston and D.M.F. van Aalten, "Bisdionin C – a rationally designed, submicromolar inhibitor of family 18 chitinases", ACS Med.Chem.Lett. (2011), 2, 428-432. PDF
  126. T.E. Sutherland, O.A. Andersen, M. Betou, I.M. Eggleston, R.M. Maizels, D.M.F. van Aalten* and J.E. Allen*, "Analysing airway inflammation with chemical biology: dissection of acidic mammalian chitinase function with a selective drug-like inhibitor", Chem.Biol. (2011), 18, 569-579. (* co-corresponding authors). PDF  Pubmed
  127. D. Mariappa, K. Sauert, K. Mariño, D. Turnock, R. Webster, D.M.F. van Aalten, M.A.J. Ferguson and H.A.J. Mueller, "Protein O-GlcNAcylation is required for Fibroblast Growth Factor signaling in Drosophila", Sci.Signal. (2011), 4, ra89. PDF + Commentary PDF  Pubmed
  128. H.I. Woodroof, J.H. Pogson, M. Begley, L.C. Cantley, M. Deak, D.G. Campbell, D.M.F. van Aalten, A.J. Whitworth, D.R. Alessi and M.M.K. Muqit, "Discovery of catalytically active orthologues of the Parkinson’s disease kinase PINK1: analysis of substrate specificity and impact of mutations", Open Biol. (2011), 1, 110012. PDF Pubmed

    129. Back to top

    2012

  129. E. Wong, G. Vaaje-Kolstad, A. Ghosh, R. Hurtado-Guerrero, P.V. Konarev, A.F.M. Ibrahim, D.I. Svergun, V.G.H. Eijsink, N.S. Chatterjee and D.M.F. van Aalten, “The Vibrio cholerae colonization factor GbpA possesses a modular structure that governs binding to different host surfaces”, PLOS Pathog. (2012), 8, e1002373. PDF  Pubmed
  130. M. Schimpl, V.S. Borodkin, L.J. Gray and D.M.F. van Aalten, "Synergy of peptide and sugar in O-GlcNAcase substrate recognition", Chem.Biol. (2012), 19, 173-176. PDF  Pubmed
  131. S. Pathak, V.S. Borodkin, O. Albarbarawi, D.G. Campbell, A. Ibrahim and D.M.F. van Aalten, "O-GlcNAcylation of TAB1 modulates TAK1-mediated cytokine release", EMBO J. (2012), 31, 1394-1404. PDF  Pubmed
  132. M.J. Dixon, A. Gray, M. Schenning, M. Agacan, W. Tempel, Y. Tong, L. Nedyalkova, H.-W. Park, N.R. Leslie, D.M.F. van Aalten, C.P. Downes and I.H. Batty, "IQGAP proteins reveal an atypical phosphoinositide (aPI) binding domain with a pseudo C2 domain fold", J.Biol.Chem. (2012), 287, 22483-22496. PDF  Pubmed
  133. G.A. Penman, D.E.A. Lockhart, A. Ferenbach and D.M.F. van Aalten, "Purification, crystallization and preliminary X-ray diffraction data of UDP-galactopyranose mutase from Aspergillus fumigatus", Acta Cryst. F (2012), F68, 705-708. PDF  Pubmed
  134. H.C. Dorfmueller, W. Fang, F.V. Rao, D.E. Blair, H. Attrill and D.M.F van Aalten, "Structural and biochemical characterization of a trapped coenzyme A adduct of Caenorhabditis elegans glucosamine-6-phosphate N-acetyltransferase", Acta Cryst. D (2012), D68, 1019-1029. PDF  Pubmed
  135. M. Schimpl, C.L. Rush, M. Betou, I.M. Eggleston, A.D. Recklies and D.M.F van Aalten, "Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide-binding properties", Biochem.J. (2012), 446, 149-157. PDF  Pubmed
  136. M. Schimpl, X. Zheng, V.S. Borodkin, D.E. Blair, A.T. Ferenbach, A.W. Schuettelkopf, I. Navratilova, T. Aristotelous, O. Albarbarawi, D.A. Robinson, M.A. MacNaughtan and D.M.F. van Aalten, "O-GlcNAc transferase invokes nucleotide sugar pyrophosphate participation in catalysis", Nature Chem.Biol. (2012), 8, 969-974. PDF + Commentary PDF  Pubmed

    137. 2013

  137. H. Hahne, N. Sobotzki, T. Nyberg, D. Helm, V.S. Borodkin, D.M.F. van Aalten, B. Agnew and B. Kuster, "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry", J.Proteome Res. (2013), 12, 927-936. PDF  Pubmed
  138. D. Mariappa, S. Pathak and D.M.F. van Aalten, "A sweet TET-à-tête - synergy of TET proteins and O-GlcNAc transferase in transcription", EMBO J. (2013), 32, 612-613. PDF  Pubmed
  139. W. Fang, T. Du, O.G. Raimi, R. Hurtado-Guerrero, M.D. Urbaniak, A.F.M. Ibrahim, M.A.J. Ferguson, C. Jin and D.M.F. van Aalten, "Genetic and structural validation of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase as an antifungal target", Mol.Microbiol. (2013), in press.
  140. W. Fang, T. Du, O.G. Raimi, R. Hurtado-Guerrero, K. Mariño, A.F.M. Ibrahim, O. Albarbarawi, M.A.J. Ferguson, C. Jin and D.M.F. van Aalten "Genetic and structural validation of Aspergillus fumigatus N-acetylphosphoglucosamine mutase as an antifungal target", Biosci.Rep. (2013), accepted.

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