Biophys J, December 2002, p. 3113-3125, Vol. 83, No. 6

Addition of Missing Loops and Domains to Protein Models by X-Ray Solution Scattering

Maxim V. Petoukhov,^* Nigel A. J. Eady, Katherine A. Brown, and Dmitri I. Svergun^*§

 ^*European Molecular Biology Laboratory, Hamburg Outstation, D-22603 Hamburg, Germany;  Physics Department, Moscow State University, 117234 Moscow, Russia;  Department of Biological Sciences, Centre for Molecular Microbiology and Infection, Imperial College of Science, Technology and Medicine, London SW7 2AY, United Kingdom; and  ^§Institute of Crystallography, Russian Academy of Sciences, 117333 Moscow, Russia

Inherent flexibility and conformational heterogeneity in proteins can often result in the absence of loops and even entire domains in structures determined by x-ray crystallographic or NMR methods. X-ray solution scattering offers the possibility of obtaining complementary information regarding the structures of these disordered protein regions. Methods are presented for adding missing loops or domains by fixing a known structure and building the unknown regions to fit the experimental scattering data obtained from the entire particle. Simulated annealing was used to minimize a scoring function containing the discrepancy between the experimental and calculated patterns and the relevant penalty terms. In low-resolution models where interface location between known and unknown parts is not available, a gas of dummy residues represents the missing domain. In high-resolution models where the interface is known, loops or domains are represented as interconnected chains (or ensembles of residues with spring forces between the C atoms), attached to known position(s) in the available structure. Native-like folds of missing fragments can be obtained by imposing residue-specific constraints. After validation in simulated examples, the methods have been applied to add missing loops or domains to several proteins where partial structures were available.

Biophys J, December 2002, p. 3113-3125, Vol. 83, No. 6
© 2002 by the Biophysical Society   0006-3495/02/12/3113/13  $2.00

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