TORSION ANGLE DYNAMICS FOR NMR STRUCTURE CALCULATION WITH THE NEW PROGRAM DYANA

The new program DYANA (DYnamics Algorithm for Nmr Applications) for ef ficient calculation of three-dimensional protein and nucleic acid stru ctures from distance constraints and torsion angle constraints collect ed by nuclear magnetic resonance (NMR) experiments performs simulated annealing by molecular dynamics in torsion angle space and uses a fast recursive algorithm to integrate the equations of motions. Torsion an gle dynamics can be more efficient than molecular dynamics in Cartesia n coordinate space because of the reduced number of degrees of freedom and the concomitant absence of high-frequency bond and angle vibratio ns, which allows for the use of longer time-steps and/or higher temper atures in the structure calculation. It also represents a significant advance over the variable target function method in torsion angle spac e with the REDAC strategy used by the predecessor program DIANA. DYANA computation times per accepted conformer in the ''bundle'' used to re present the NMR structure compare favorably with those of other presen tly available structure calculation algorithms, and are of the order o f 160 seconds for a protein of 165 amino acid residues when using a DE C Alpha 8400 5/300 computer. Test calculations starting from conformer s with random torsion angle values further showed that DYANA is capabl e of efficient calculation of high-quality protein structures with up to 400 amino acid residues, and of nucleic acid structures. (C) 1997 A cademic Press Limited.