Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force

It is often the case that a substantial number of torsion angles (both back bone and sidechain) in structures of proteins and nucleic acids determined by NMR are found in physically unlikely and energetically unfavorable confo rmations. We have previously proposed a database-derived potential of mean force comprising one-, two-, three-, and four-dimensional potential surface s which describe the likelihood of various torsion angle combinations to bi as conformational sampling during simulated annealing refinement toward tho se regions that are populated in very high resolution (less than or equal t o 1.75 Angstrom) crystal structures. We now note a shortcoming of our origi nal implementation of this approach: namely, the forces it places on atoms are very rough. When the density of experimental restraints is low, this ro ughness can both hinder convergence to commonly populated regions of torsio n angle space and reduce overall conformational sampling, In this paper we describe a modification that completely eliminates these problems by replac ing the original potential surfaces by a sum of multidimensional Gaussian f unctions. Structures refined with the new Gaussian implementation now simul taneously enjoy excellent global sampling and excellent local choices of to rsion angles.