QM/MM X-ray refinement of zinc metalloenzymes

Abstract

Zinc metalloenzymes play an important role in biology. However, due to the limitation of molecular force field energy restraints used in X-ray refinement at medium or low resolutions, the precise geometry of the zinc coordination environment can be difficult to distinguish from ambiguous electron density maps. Due to the difficulties involved in defining accurate force fields for metal ions, the QM/MM (Quantum-Mechanical /Molecular-Mechanical) method provides an attractive and more general alternative for the study and refinement of metalloprotein active sites. Herein we present three examples that indicate that QM/MM based refinement yields a superior description of the crystal structure based on R and R free values and on the inspection of the zinc coordination environment. It is concluded that QM/MM refinement is a useful general tool for the improvement of the metal coordination sphere in metalloenzyme active sites.

QM methods in structure based design: Utility in probing protein–ligand interactions

“…While this work is not representative due to the focus on small numbers of structures from a single target class, from a more general consideration of the literature [21,20,[24][25][26][27]51] it does appear that the atomic coordinates derived from X-ray analyses, while capable of demonstrating the overall ligand binding modes, should not necessarily be taken as a "perfect" reference given the intrinsic errors that arise from protein mobility and choices made during structural refinement [21]. This is particularly important for the validation of ligand docking methods since the X-ray coordinates are often used in quantitative way to assess the performance of software [51].…”

“…This is because repulsive interactions, either real or due to sub-optimal refinement, can be unrealistically dissipated into the wider protein by very small changes in the overall protein conformation following MM optimization. This could arise due to the limitations of MM forcefields [8,9,[24][25][26] or the coupling between QM and MM regions in QM/MM calculations [46].…”

“…This might also be pertinent in light of research that show the ligand density associated with relatively weak binding inhibitors can be less distinct, even for protein structures of good overall resolution [20], which can complicate their application to SBD [21]. Indeed classical molecular mechanical (MM) [22,23] and QM based methods [24,25] have been specifically developed to help improve the active site placement of ligands and co-factors. MM techniques are widely used in the pharmaceutical industry as they are both fast and the results are easily interpretable due to the relatively simple terms used in the derivation of their forcefields.…”

Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

“…While restrained dynamics methods that utilize NMR data (RD-NMR) have been successfully utilized to fold protein structures using MD platforms, QM/MM methods have been previously used to study metal ion coordination, and refine the metal binding site of zinc and copper bound metalloproteins (Case 2002; Chen et al 2005; Robustelli et al 2010; Chen et al 2004; Bertini et al 2011; Calhoun et al 2008; Montalvao et al 2012; Boehr et al 2009; Showalter et al 2007; Li et al 2010; Markwick et al 2010; Long and Bruschweiler 2011; Sgrignani and Pierattelli 2012). Using the approach described here, we implement a metal ion inclusive restrained dynamics NMR structure refinement method, denoted as MRD-NMR, in which the metal ions are modeled using specially developed force field parameters that accurately describe the metal ion coordination and electrostatics in NMR-data restrained MD simulations that sample on biologically relevant time-scales on the order of hundreds of nanoseconds (Chakravorty et al 2012b; Pierce et al 2012).…”

Simulation with quantum mechanics/molecular mechanics for drug discovery

“…A force-field equation requires empirical parameters for defining bonds, angles, and dihedrals (see equation 1). The fact that experimental structures of bioinorganic complexes are rare lead to a weakness of molecular mechanics strategy in the studies of these systems [43]. Even the hapticity, that is, the number of atoms attached to the metal, is hard to define with metals.…”