NMR structure calculation methods for large proteins Application of torsion angle dynamics and distance geometry/simulated annealing to the 269-residue protein serine protease PB92

Abstract

Molecular dynamics in torsion angle space together with the well established combination of metric matrix distance geometry and simulated annealing in Cartesian space have been applied to the solution structure determination of serine protease PB92, a 269-residue monomeric protein from Bacillus alcalophilus. The input data set comprised distance restraints and a combination of distance and angular restraints derived from NMR data. A number of different modifications of the two calculation strategies were studied with respect to their convergence behaviour. The resulting structural ensembles were evaluated according to several criteria for protein structure quality. Improved protocols for both methods have been developed from these analyses. A comparison of the structures obtained with these protocols demonstrates the superior convergence behaviour of the torsion angle dynamics method. Although both methods are able to fold up the protein correctly, the torsion angle dynamics protocol scores slightly better with respect to measures of structural quality, especially when dihedral angle restraints are available. Torsion angle molecular dynamics presents a simple and robust method for the NMR structure calculations of large proteins.