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Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber.

Oleg Mikhailovskii^1,2, Yi Xue^3,4,5, Nikolai R Skrynnikov^1,2

¹Laboratory of Biomolecular NMR, St Petersburg State University, St Petersburg 199034, Russian Federation.

|January 21, 2022

Summary

A new Amber-based molecular dynamics method refines protein crystal structures, achieving lower R-free values and better MolProbity scores than standard programs. This approach realistically models crystal environments and improves refinement of low-accuracy models.

Keywords:

Amber Phenix Rfree X-ray crystallography computational modeling ensemble model intracrystalline water maximum likelihood molecular dynamics molecular replacement protein crystals protein structure determination protein structure refinement restrained simulations

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Published on: May 13, 2020

Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Crystallographic protein structure refinement is crucial for understanding biological function.
Existing refinement methods may struggle with low-accuracy models or poorly diffracting regions.
Accurate modeling of crystal lattice environments, including water and protein-protein interactions, is essential.

Purpose of the Study:

To develop and validate a novel protein crystal structure refinement procedure using biomolecular simulation.
To improve the accuracy and reliability of crystallographic structure refinement, particularly for challenging cases.
To leverage molecular dynamics simulations for a more realistic representation of protein crystals.

Main Methods:

Developed a refinement procedure using the Amber biomolecular simulation program.
Constructed hydrated crystal unit cell models with periodic boundary conditions.
Employed a short molecular dynamics run with the ff14SB force field and maximum-likelihood potential for refinement.
Tested the procedure on 84 protein structures, including low-accuracy and molecular replacement models.

Main Results:

Achieved lower R-free values compared to PDB depositions and phenix.refine for most structures.
Demonstrated superior performance in refining low-accuracy scrambled and molecular replacement models.
Amber-refined structures consistently yielded better MolProbity scores.
Provided realistic modeling of protein-protein, protein-water interactions, and crystal dynamics.

Conclusions:

The new Amber-based refinement procedure offers a significant advancement in protein crystallography.
The method effectively integrates diffraction data with molecular dynamics for improved structure determination.
It provides a realistic and computationally efficient approach to refining complex protein crystal structures.
The protocol is parameter-free and accessible via desktop GPUs or a web service.