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EMBL Hamburg Biological
Small Angle Scattering
BioSAXS
 

Ab initio methods: how they work

Dmitri Svergun

EMBL Hamburg, 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
Envelope function, Bead models, Dummy residues model
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: Friday, 19 October 2012, 9:00


  Last modified: September 21, 2012

© BioSAXS group 2012