Refinement of protein structures in explicit solvent

Abstract

We present a CPU efficient protocol for refinement of protein structures in a thin layer of explicit solvent and energy parameters with completely revised dihedral angle terms. Our approach is suitable for protein structures determined by theoretical (e.g., homology modeling or threading) or experimental methods (e.g., NMR). In contrast to other recently proposed refinement protocols, we put a strong emphasis on consistency with widely accepted covalent parameters and computational efficiency. We illustrate the method for NMR structure calculations of three proteins: interleukin-4, ubiquitin, and crambin. We show a comparison of their structure ensembles before and after refinement in water with and without a force field energy term for the dihedral angles; crambin was also refined in DMSO. Our results demonstrate the significant improvement of structure quality by a short refinement in a thin layer of solvent. Further, they show that a dihedral angle energy term in the force field is beneficial for structure calculation and refinement. We discuss the optimal weight for the energy constant for the backbone angle omega and include an extensive discussion of meaning and relevance of the calculated validation criteria, in particular root mean square Z scores for covalent parameters such as bond lengths.

Three-Dimensional Structure of the Water-Insoluble Protein Crambin in Dodecylphosphocholine Micelles and Its Minimal Solvent-Exposed Surface

“…Crambin has been also used widely in developing methodology for the determination of protein structure from NMR data. 14, [16][17][18][19] Here we report the system we developed for producing crambin in good yield from Escherichia coli. This system enabled us to prepare the first samples of this protein labeled with stable isotopes ( 15 N and 13 C) for multinuclear magnetic resonance investigations.…”

Rapid, robotic, small‐scale protein production for NMR screening and structure determination

“…Of the final 100 structures calculated, the 20 conformers with the lowest target function values were selected and subjected to a molecular-dynamics protocol in explicit solvent using XPLOR-NIH. 27 All time-domain NMR data and chemical shift assignments have been deposited in BioMagResBank (accession code: 16520) and the Protein Data Bank (accession code: 2kom).…”

Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes

“…The NOE originates from cross-relaxation between dipolar-coupled spins through space spin-spin interactions that involve a transfer of magnetization from one spin to another. The NOE approximately scales with the distance r between the two spins as 1/r 6 . Because of this 1/r 6 dependency, NOEs are only detected between protons less than 5 to 6Å away in space.…”

“…The experimental NMR parameters are then typically used in restrained molecular dynamics simulations following some kind of simulated annealing scheme (MD/SA) to generate 3D structures [5]. These are nowadays usually refined in explicit solvent (water), which has been shown to significantly improve the quality of the structures [6,7]. The resulting ensembles of structures should satisfy as many restraints as possible, together with general chemical properties of proteins (such as bond lengths and angles).…”