Recent studies carried in our group deal with amyloid-like peptides whose importance in neuro-degenerative illnesses is recognized for a long time. Such peptides form extended β-sheets domains in bulk (amyloid fibrils) but also at an air-water interface where they can crystallize under the form of β-sheets of large coherence length which are also nicely ordered in the direction perpendicular to the hydrogen bonds [1]. These peptides were selected because β-sheets domains can be used as templates for biomimetic mineralization studies in order to model the growth of biominerals like nacre shells. These shells are nanocomposites where proteins including β-sheets domains are believed to nucleate and organize the calcium carbonate mineral phase.
This thesis work will be dedicated to elucidate such crystallographic structures of peptides in order to gain insight in the variability of the structure when external parameters (pressure, pH,...) are changed.
Fig.1 : Phase NC-AFM picture of a deposited peptide layer showing the alleged perpendicular order to the hydrogen bonds. This kind of nanostructured pattern is now used for biomimetic mineralization studies.
Grazing incidence diffraction using synchrotron radiation is one of the major techniques used for the structural determination of two-dimensional crystals. Until recently, the resolution of the technique was limited for crystals of organic molecules at the air-water or solid-water interface due to the absence of appropriate methods. We have recently developed a new method, consisting in a careful extraction of the structure factors from the diffraction data followed by fitting of molecular parameters which allowed us to reach near-atomic resolution [2,3]. The structure factor calculations are performed using the SHELX-97 program and we use the known chemical structure of the molecules by imposing atomic coordinates in a molecular model which allows us to fit relevant parameters. Sterically impossible configurations are automatically rejected by SHELX.
Molecular parameters have a marked influence on the calculated structure factors and can be determined by model fitting. Using this method, we could for example evidence a new phase of fatty acids of symmetry p2gm at high pressure, corresponding to a minimum in lattice energy, which was never observed. The use of simulated annealing technique (a Monte-Carlo method) allows a large reduction in computation time which enables the determination of conformational defects, whose statistics of conformation are estimated by considering large super-cells. The same method and the use of Patterson functions were also used to locate heavy atoms in composite organic-inorganic two-dimensional crystals. This method can now be extended to even more complicated cases like peptide or protein two-dimensional crystals where it could have a major impact.
[1] Lepère M, Chevallard C, Hernandez JF, et al., Multiscale surface self-assembly of an amyloid-like peptide, LANGMUIR 23 (15): 8150-8155 JUL 17 2007
[2] Pignat, J; Daillant, J; Leiserowitz, L; et al. Grazing incidence X-ray diffraction on Langmuir films: Toward atomic resolution JOURNAL OF PHYSICAL CHEMISTRY B, 110 (44): 22178-22184 NOV 9 2006
[3] Pignat, J; Daillant, J; Cantin, S; et al. Grazing incidence X-ray diffraction study of the tilted phases of Langmuir films: Determination of molecular conformations using simulated annealing THIN SOLID FILMS, 515 (14): 5691-5695 MAY 23 2007
Contacts : Jean Daillant (jean.daillant@cea.fr); Corinne Chevallard (corinne.chevallard@cea.fr); Patrick Guenoun (patrick.guenoun@cea.fr).