Structural heterogeneity in protein crystals

Abstract

Extensive conformational heterogeneity is reported in highly refined crystallographic models for the proteins crambin, erabutoxin, myohemerythrin, and lamprey hemoglobin. From 6% to 13% of the amino acid side chains of these four proteins are seen in multiple, discrete conformations. Most common are flexible side chains on the molecular surface, but structural heterogeneity occasionally extends to buried side chains or to the polypeptide backbone. A few instances of sequence heterogeneity are also very clear. Numerous solvent sites are multiplets, and at high resolution, multiple, mutually exclusive solvent networks are observed. The proteins have been studied with X-ray diffraction data extending to spacings of from 0.945 to 2.0 A. The extensive heterogeneity observed here provides detailed, accurate structures for conformational substates of these molecules and sets a lower bound on the number of substates accessible to each protein molecule in solution. Electron density is missing or very weak for only a few side chains in these protein crystals, revealing a strong preference for discrete over continuous conformational perturbations. The results at very high resolution further suggest that even rather small conformational fluctuations produce discrete substates and that unresolved conformers are accommodated in increased atomic thermal parameters.