On the potential of normal-mode analysis for solving difficult molecular-replacement problems.

Abstract

Molecular replacement (MR) is the method of choice for X-ray crystallographic data phasing when structural data of suitable homologues are available. However, MR may fail even in cases of high sequence homology when conformational changes arising for example from ligand binding or different crystallogenic conditions come into play. In this work, the potential of normal-mode analysis as an extension to MR to allow recovery from such drawbacks is demonstrated. Three examples are presented in which screening for MR solutions with templates perturbed in the direction of one or two normal modes allows a valid MR solution to be found where MR using the original template failed to yield a model that could ultimately be refined. It has been shown recently that half of the known protein movements can be modelled by displacing the studied structure using at most two low-frequency normal modes. This suggests that normal-mode analysis has the potential to break tough MR problems in up to 50% of cases. Moreover, even in cases where an MR solution is available, this method can be used to further improve the starting model prior to refinement, eventually reducing the time spent on manual model construction (in particular for low-resolution data sets).