A new default restraint library for the protein backbone inPhenix: a conformation-dependent geometry goes mainstream

Abstract

Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriartyet al.(2014),FEBS J.281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used byPhenixis described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries.

Bond distances in polypeptide backbones depend on the local conformation

“…A broader awareness among scientists of bond-distance variations with local conformation together with an improved understanding of the electronic origins of these structural effects may spur new efforts to incorporate these subtle features into molecular modelling, protein-folding calculations and crystallographic refinement. In the latter field, recent attempts (Berkholz et al, 2009(Berkholz et al, , 2010Tronrud et al, 2010;Tronrud & Karplus, 2011;Moriarty et al, 2014) to use a restraint library including conformational dependences seems to be very encouraging for future developments. Finally, the good performance of present QM calculations hints at the possibility of highlighting specific features by reiterating this procedure on other types of amino acids.…”

“…It is important to mention that the notion of peptide geometry variability has attracted the attention of the protein crystallography community, as it can be used both in protein structure refinement and validation (EU 3-D Validation Network, 1998;Kleywegt, 2009). In particular, the develop-ment of specific conformational-dependent libraries (CDL) by Karplus and coworkers (Berkholz et al, 2009(Berkholz et al, , 2010Tronrud et al, 2010;Tronrud & Karplus, 2011;Moriarty et al, 2014) represents a promising novel approach in protein refinement.…”

Strategies for carbohydrate model building, refinement and validation

“…Currently, the accuracy with which protein models are determined from low-resolution data sets is, thanks to a new generation of context-dependent restraints (Moriarty et al, 2014(Moriarty et al, , 2016Tronrud & Karplus, 2011;Tronrud et al, 2010), much higher than that of carbohydrates . With cryo-EM now routinely venturing into the 2.0-4.0 Å resolution range, it is becoming increasingly clear that sugar chemistry will need to find its way into the current refinement methods: new dictionaries will have to be produced with accurate torsion restraints, force fields may have to be introduced in order to keep conformations and contacts within chemical expectations, and new combined validation approaches will be needed to assess and support distortion in active sites.…”

Real-space quantum-based refinement for cryo-EM: Q|R#3

“…Classic refinement (also referred here to as CCTBX refinement) used geometry restraints as implemented in CCTBX and used in Phenix refinement programs such as phenix.refine and phenix.real_space_refine . Classic refinement used only a standard set of geometry restraints: restraints on covalent bond lengths and bond angles, dihedral angles, chiralities, planarities and non-bonded repulsion (Engh & Huber, 1991, Grosse-Kunstleve et al, 2002Moriarty et al, 2016). TeraChem refinement was performed using the Hartree-Fock (Slater, 1951) method with Grimme's dispersion correction D3 (Grimme et al, 2010) in conjunction with the 6-31G basis set (Hehre et al, 1972) accounting for the polar (water, e=78) environment by means of the COSMO polarizable continuum model (Liu et al, 2015, Barone & Cossi, 1998, Truong & Stefanovich, 1995.…”