Department of Crystal and Structural Chemistry

Padualaan 8 (H.R. Kruytgebouw), 3584 CH Utrecht, the Netherlands
phone: +31-30-2533502 (secr.) fax: +31-30-2533940, e-mail: science.secr.ks@uu.nl
 

Research group of Loes Kroon-Batenburg

Current research projects

Accurate data collection from X-ray diffraction : the EVAL method

EVAL14: summation integration based on accurate prediction of reflection contours

The EVAL14 method is used for summation integration of reflections from X-ray diffraction experiments. Ab initio reflection boundaries are calculated, within which summation-integration is performed. Since the contours are based on physical principles their shapes are realistic on include effects due crystal properties and the geometrical set-up of the diffraction experiments. It is particularly well designed for handeling aniostropic reflections and reflections from twin lattices. The method is widely used in chemical crystallography, in particular the version implemented in COLLECT (Nonius, 1999).
• A.J.M. Duisenberg, L.M.J. Kroon-Batenburg and A.M.M. Schreurs, J. Appl. Cryst. 36 (2003) 220-229
  An intensity evaluation method: EVAL-14
  Copyright © International Union of Crystallography
  J. Appl. Cryst. 36, 220---229



EVAL15: a profile prediction method for the accurate integration of diffraction data

EVAL15 is based on general impacts as introduced in EVAL14. Building on that experience EVAL15 calculates a complete standard reflection profile from general impacts, i.e. impacts originating from different parts of the crystal, focus, wavelength spectrum and mosaic orientations. The method and algorithm of EVAL15, the details of its implementation and the quality of the profiles is described in a recent paper. The improvement of the integration of weak reflections by using profile fitting with EVAL15 data is clearly proven. The EVAL15 data quality for small molecule and protein crystals is further explored and integration of difficult cases as well as overlap deconvolution is studied.

• A.M.M. Schreurs, X. Xian and L.M.J. Kroon-Batenburg, J. Appl. Cryst., accepted for publication
  EVAL15: a diffraction data integration method based on ab initio predicted profiles
  Copyright © International Union of Crystallography
  J. Appl. Cryst.,
  
• X. Xian, thesis: Accurate diffraction data integration by the EVAL15 profile prediction method.
  Application in chemical and biological crystallography
  Utrecht University (2009).



Fibre diffraction data integrated with EVAL

The EVAL14 method was extended from single crystal diffraction to fibre diffraction of para-crystalline fibres. The method has been applied to cellulose polymorphs.
• L.M.J. Kroon-Batenburg and J. Kroon, Glycoconjugate Journal 14 (1997) 677-690
  The crystal and molecular structures of cellulose I and II

Structural basis for the binding of amyloid peptides and proteins to multiligand receptors

Under denaturing or stress conditions and when partially degraded, proteins have the tendency to misfold into so-called cross-beta structure. In the body the consequence is that misfolded proteins aggregate and accumulate in amyloid plaques. Amyloid plaque formation is associated with well known diseases like Alzheimer's disease, light-chain amyloidosis, type II diabetes, prion-diseases and Parkinson's disease. Recently more and more evidence is found for the hypothesis that in early stages of aggregation small soluble oligomeric species are formed, which are toxic to cells in the disease-specific tissue. A class of proteins have been found that recognize cross-beta structure independent of the amino acid sequence of the protein/peptide, which suggest that in the body regulation mechanism exist directed at misfolded proteins. One such a protein is tissue-type plasminogen activator (tPA), an enzyme that is involved in the fibrinolytic system. It converts the inactive zymogen plaminogen into the active protease plamin, which degrades fibrin which serves as a co-factor to tPA. Since tPA is also activated by amyloid, an intriguing role emerges for tPA as an enzyme that could remove unwanted amyloids. A small domain within tPA is responsible for the binding of the amyloid cross-beta structure: the finger domain. It is our goal to acquire a detailed structural picture of the interaction of amyloid peptides with tPA. This knowledge will be an essential part of understanding how amyloids signal their presence so that regulation mechanisms may become effective.
• O. Kranenburg, B. Bouma, L.M.J. Kroon-Batenburg, A. Reijerkerk, Y.P. Wu, E.E. Voest and M.F.B.G. Gebbink, Current Biology 12 (2002) 1833-1839
  Tissue-type plasmonogen avtivator is a multiligand cross beta structure receptor
• B. Bouma, L.M.J. Kroon-Batenburg, Y.P. Wu, B. Brunjes, G. Postuma, O. Kranenburg. P.G. de Groot, E.E. Voest and M.F.B.G. Gebbink, J. Biol. Chem. 278 (2003) 41810-41819
  Glycation induces formation of Amyloid Cross-beta structure in Albumin

Earlier research projects

Cellulose Structural Studies

Celluose polymorphs have been extensively studied by diffraction methods. Conformational and packing difference between the native and regenerated forms of cellulose are notible.
• L.M.J. Kroon-Batenburg, S.A.H. Spieser, M. Ramzi, G.J. Vroege and J. Kroon, IPW Das Papier 4 (2001), 3-8
  New insights in the structure of cellulose. Solid state, Accessibility and solvent interactions
• L.M.J. Kroon-Batenburg, P.H. Kruiskamp, J.F.G. Vliegenthart and J. Kroon, J. Phys. Chem. B 101 (1997) 8454-8459
  Estimation of the persistence length of polymers by MD simulations on small fragments in solution. Application to cellulose
• S.A.H. Spieser, J.A. van Kuik, L.M.J. Kroon-Batenburg and J. Kroon
  Carbohydr. Res. 322 (1999) 264-273
  Improved carbohydrate force field for GROMOS: ring and hydroxymethyl group conformations and exo-anomeric effect
• L.M.J. Kroon-Batenburg, B. Bouma and J. Kroon, Macromolecules 29 (1996) 5695
  Stability of cellulose structures studied by MD simulations. Could mercerized cellulose II be parallel?
• S.A.H. Spieser, J.A. van Kuik, L.M.J. Kroon-Batenburg and J. Kroon, Carbohydr. Res. 322 (1999) 264-273
  Improved carbohydrate force field for GROMOS: ring and hydroxymethyl group conformations and exo-anomeric effect
• S.A.H. Spieser, B.R. Leeflang, L.M.J. Kroon-Batenburg and J. Kroon, J. Phys. Chem. A104 (2000) 7333-7338
  A force field for phosphoric acid: comparison of simulated with experimental data in the solid and liquid state