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Molecular-dynamics simulation methods for macromolecular crystallography
- Source :
- Acta crystallographica. Section D, Structural biology, vol 79, iss Pt 1
- Publication Year :
- 2023
- Publisher :
- International Union of Crystallography (IUCr), 2023.
-
Abstract
- To assess the potential benefits of molecular-dynamics (MD) simulations for macromolecular crystallography (MX), we performed room-temperature X-ray diffraction studies of the catalytic subunit of mouse protein kinase A (PKA-C). We then performed crystalline MD simulations of PKA-C, computed simulated electron densities from the water, protein, and ion components of the MD simulations, and carefully compared them to the initial crystal structure. The results led to the development of an MD-MX analysis procedure and several associated methods: 1) density comparison to evaluate consistency between the MD and the initial crystal structure model; 2) water building to generate alternative solvent models; and 3) protein remodeling to improve the crystal structure where interpretation of density is unclear. This procedure produced a revised structure of PKA with a new ordered water model and a modified protein structure. The revisions yield new insights into PKA mechanisms, including: a sensitivity of the His294 conformation to protonation state, with potential consequences for regulation of substrate binding; a remodeling of the Lys217 side chain along with a bound phosphate; an alternative conformation for Lys213 associated with binding to the regulatory subunit; and an alternative conformation for catalytic base Asp166 and nearby waters, suggesting a mechanism of progression of the phosphotransfer reaction via changes in Mg2+ coordination. Based on the benefits seen applying these methods to PKA, we recommend incorporating our MD-MX procedure into MX studies, to decide among ambiguous interpretations of electron density that occur, inevitably, as part of standard model refinement.
- Subjects :
- protein kinases
Crystallography
Protein Conformation
1.1 Normal biological development and functioning
conformational ensembles
Biophysics
Proteins
Molecular Dynamics Simulation
Biological Sciences
1.4 Methodologies and measurements
molecular-dynamics simulations
water structure
Underpinning research
Structural Biology
Physical Sciences
Chemical Sciences
Solvents
X-Ray
Generic health relevance
Subjects
Details
- ISSN :
- 20597983
- Volume :
- 79
- Database :
- OpenAIRE
- Journal :
- Acta Crystallographica Section D Structural Biology
- Accession number :
- edsair.doi.dedup.....9db1e7851b62c5df5ea86abc7df068a9