ArticleBiochemistry2008
Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex.
Article in Biochemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 52 citations in OpenAlex.
- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- LAWS: Local alignment for water sites-Tracking ordered water in simulations.Biophysical journal · 2023Article
- Article
- Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure.Nucleic acids research · 2022Article
- Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.Acta crystallographica. Section D, Structural biology · 2020Article
- Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations.Biophysical journal · 2019Article
- Slow conformational exchange and overall rocking motion in ubiquitin protein crystals.Nature communications · 2017Article
- X-ray Scattering Studies of Protein Structural Dynamics.Chemical reviews · 2017Review
- Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.Protein science : a publication of the Protein Society · 2016Article
- High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Observing the overall rocking motion of a protein in a crystal.Nature communications · 2015Article
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- Article
- Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics.Protein science : a publication of the Protein Society · 2014Article
- Dependence of protein crystal stability on residue charge states and ion content of crystal solvent.Biophysical journal · 2014Article
- Peptide modulation of class I major histocompatibility complex protein molecular flexibility and the implications for immune recognition.The Journal of biological chemistry · 2013Article
- Peptide crystal simulations reveal hidden dynamics.Journal of the American Chemical Society · 2013Article
- Streptavidin and its biotin complex at atomic resolution.Acta crystallographica. Section D, Biological crystallography · 2011Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
A 250 ns molecular dynamics simulation of the biotin-liganded streptavidin crystal lattice, including cryoprotectant molecules and crystallization salts, is compared to a 250 ns simulation of the lattice solvated with pure water. The simulation using detailed crystallization conditions preserves the initial X-ray structure better than the simulation using pure water, even though the protein molecules display comparable mobility in either simulation. Atomic fluctuations computed from the simulation with crystallization conditions closely reproduce fluctuations derived from experimental temperature factors (correlation coefficient of 0.88, omitting two N-terminal residues with very high experimental B-factors). In contrast, fluctuations calculated from the simulation with pure water were less accurate, particularly for two of the streptavidin loops exposed to solvent in the crystal lattice. Finally, we obtain good agreement between the water and cryoprotectant densities obtained from the simulated crystallization conditions and the electron density due to solvent molecules in the X-ray structure. Our results suggest that detailed lattice simulations with realistic crystallization conditions can be used to assess potential function parameters, validate simulation protocols, and obtain valuable insights that solution-phase simulations do not easily provide. We anticipate that this will prove to be a powerful strategy for molecular dynamics simulations of biomolecules.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.