Dmitri Svergun
EMBL, Hamburg Outstation, Germany

Principles of ab initio shape determination in small-angle scattering are explained and different approached proposed to reconstruct three-dimensional models out of one-dimensional scattering data are presented. The question of informational content in the small-angle scattering data is related to the possibility of ab initio shape analysis. Several methods are discussed including the angular envelope function based on spherical harmonics (Stuhrmann, 1970; Svergun & Stuhrmann, 1991; Svergun et al., 1996), and Monte-Carlo type approaches using models consisting of densely packed fixed beads (Chacon et al., 1998; Svergun, 1999; Walther, Cohen & Doniach, 2000) or condensation of a gas of dummy residues (Svergun, Petoukhov & Koch, 2001). The possibilities (and necessity) of the use of a priori information are discussed and advantages and limitations of ab initio methods are illustrated in practical applications.

Models used in ab initio methods

All the methods minimize Discrepancy[Data] + Penalty[Additional info]

Chacon, P., Moran, F., Diaz, J. F., Pantos, E. & Andreu, J. M. (1998). Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophys J 74, 2760-75.
Stuhrmann, H. B. (1970). Ein neues Verfahren zur Bestimmung der Oberflaechenform und der inneren Struktur von geloesten globularen Proteinen aus Roentgenkleinwinkelmessungen. Zeitschr. Physik. Chem. Neue Folge 72, 177-198.
Svergun, D. I. (1999). Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76, 2879-86.
Svergun, D. I., Petoukhov, M. V. & Koch, M. H. J. (2001). Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80, 2946-53.
Svergun, D. I. & Stuhrmann, H. B. (1991). New developments in direct shape determination from small-angle scattering 1. Theory and model calculations. Acta Crystallogr. A47, 736-744.
Svergun, D. I., Volkov, V. V., Kozin, M. B. & Stuhrmann, H. B. (1996). New developments in direct shape determination from small-angle scattering 2. Uniqueness. Acta Crystallogr. A52, 419-426.
Walther, D., Cohen, F. E. & Doniach, S. (2000). Reconstruction of low-resolution three-dimensional density maps from one-dimensional small-angle X-ray solution scattering data for biomolecules. J. Appl. Crystallogr. 33, 350-363.

Date/time: Tuesday, 21 October, 9:00