Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis

Abstract

Normal‐mode analysis (NMA) can be used to generate multiple structural variants of a given template model, thereby increasing the chance of finding the molecular‐replacement solution. Here, it is shown that it is also possible to directly refine the amplitudes of the normal modes against experimental data (X‐ray or cryo‐EM), generalizing rigid‐body refinement methods by adding just a few additional degrees of freedom that sample collective and large‐amplitude movements. It is also argued that the situation where several (conformations of) models are present simultaneously in the crystal can be studied with adjustable occupancies using techniques derived from statistical thermodynamics and already used in molecular modelling.

Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes

“…AMBER includes a framework to perform refinement via an interface with the Crystallography and NMR System (CNS) software suite (22). Other notable recent developments include normal mode refinement (36), the Rosetta implementation of physical energy functions (41) and its combination with reciprocal space X-ray refinement in Phenix (39), torsional optimization protocols (58), external structural restraints or jelly body refinement in REFMAC (97), and xMDFF (92). …”

BALBES: a molecular-replacement pipeline

“…Despite the high productivity of the molecular-replacement technique, until recently it was not applied in automation procedures. Nevertheless, several automated molecular-replacement pipelines have already been made available to the user community, including NORMA (Delarue, 2008), MrBUMP (Keegan & Winn, 2008) and part of the JSCS structure-solution pipeline (Schwarzenbacher et al, 2008). All of these approaches are built around one or more of the popular molecular-replacement programs AMoRe (Navaza, 1987), MOLREP (Vagin & Teplyakov, 1997;Lebedev et al, 2008) and Phaser (Storoni et al, 2004).…”

Improving the Accuracy of Macromolecular Structure Refinement at 7 Å Resolution

“…New refinement methods based on physical energy functions such as Rosetta (DiMaio et al, 2011), are complementary to DEN refinement, and are expected to further improve the accuracy of low-resolution crystal structures. Other recent methods may also be useful at low resolution, including LSSR in Buster (Smart et al, 2008), external structure restraints or jelly body refinement in REFMAC (Murshudov et al, 2011), restraints in torsion angle space based on a reference model (Headd et al, 2012), and normal mode refinement (Kidera and Go, 1992; Delarue, 2008). It should be noted that the principle of achieving higher accuracy of positional information than the diffraction limit is referred to as “super-resolution” in optical microscopy (Moerner, 2007; Pertsinidis et al, 2010).…”