FRETsg: Biomolecular structure model building from multiple FRET experiments

Abstract

Fluorescence energy transfer (FRET) experiments of site-specifically labelled proteins allow one to determine distances between residues at the single molecule level, which provide information on the three-dimensional structural dynamics of the biomolecule. To systematically extract this information from the experimental data, we describe a program that generates an ensemble of configurations of residues in space that agree with the experimental distances between these positions. Furthermore, a fluctuation analysis allows to determine the structural accuracy from the experimental error. Program summary Title of program: FRETsg Catalogue identifier: ADTU Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADTU Computer: SGI Octane, Pentium II/III, Athlon MP, DEC Alpha Operating system: Unix, Linux, Windows98/NT/XP Programming language used: ANSI C No. of bits in a word: 32 or 64 No. of processors used: 1 No. of bytes in distributed program, including test data, etc.: 11407 No. of lines in distributed program, including test data, etc.: 1647 Distribution format: gzipped tar file Nature of the physical problem: Given an arbitrary number of distance distributions between an arbitrary number of points in three-dimensional space, find all configurations (set of coordinates) that obey the given distances. Method of solution: Each distance is described by a harmonic potential. Starting from random initial configurations, their total energy is minimized by steepest descent. Fluctuations of positions are chosen to generate distance distribution widths that best fit the given values.