All-atom modeling of anisotropic atomic fluctuations in protein crystal structures

Abstract

The accurate modeling of protein dynamics in crystalline states is essential for the development of computational techniques for simulating protein dynamics under physiological conditions. Following a previous coarse-grained modeling study of atomic fluctuations in protein crystal structures, we have refined our modeling with all-atom representation and force field. We have calculated the anisotropic atomic fluctuations of a protein structure interacting with its crystalline environment either explicitly (by including neighboring proteins into modeling) or implicitly (by adding harmonic restraints to surface atoms involved in crystal contacts). The modeling results are assessed in comparison with the experimental anisotropic displacement parameters (ADP) determined by X-ray crystallography. For a list of 40 high-resolution protein crystal structures, we have found that the optimal modeling of ADPs is achieved when the protein-environment interactions are much weaker than the internal interactions within a protein structure. Therefore, the intrinsic dynamics of a protein structure is only weakly perturbed by crystal packing. We have also found no noticeable improvement in the accuracy of ADP modeling by using all-atom over coarse-grained representation and force field, which justifies the use of coarse-grained modeling to investigate protein dynamics with both efficiency and accuracy.