ArticleBiophysical journal2011
Toward a predictive understanding of slow methyl group dynamics in proteins.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer.Autophagy · 2021Article
- Simultaneous measurement ofJournal of biomolecular NMR · 2021Article
- The role of disulfide bonds in a Solanum tuberosum saposin-like protein investigated using molecular dynamics.PloS one · 2020Article
- Atomistic Insights into the Functional Instability of the Second Helix of Fatty Acid Binding Protein.Biophysical journal · 2019Article
- NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins.Journal of biomolecular NMR · 2017Article
- On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters.Protein science : a publication of the Protein Society · 2016Article
- Mechanisms of amyloid formation revealed by solution NMR.Progress in nuclear magnetic resonance spectroscopy · 2015Review
- Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.Journal of chemical theory and computation · 2015Article
- Ligand-dependent dynamics of the active-site lid in bacterial dimethylarginine dimethylaminohydrolase.Biochemistry · 2014Article
- Effect of subdomain interactions on methyl group dynamics in the hydrophobic core of villin headpiece protein.Protein science : a publication of the Protein Society · 2014Article
- Article
- Microscopic insights into the NMR relaxation-based protein conformational entropy meter.Journal of the American Chemical Society · 2013Article
- Protein dynamics elucidated by NMR technique.Protein & cell · 2013Article
- CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data.Journal of computational chemistry · 2013Article
- PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles.Journal of biomolecular NMR · 2012Article
- Article
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5 authors.
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Abstract
The development of the most recent generation of molecular mechanics force fields promises an increasingly predictive understanding of the protein dynamics-function relationship. Based on extensive validation against various types of experimental data, the AMBER force field ff99SB was benchmarked in recent years as a favorable force field for protein simulations. Recent improvements of the side chain and backbone potentials, made by different groups, led to the ff99SB-ILDN and ff99SBnmr1 force fields, respectively. The combination of these potentials into a unified force field, termed ff99SBnmr1-ILDN, was used in this study to perform a microsecond time scale molecular dynamics simulation of free ubiquitin in explicit solvent for validation against an extensive set of experimental NMR methyl group residual dipolar couplings. Our results show a high level of consistency between the experimental data and the values predicted from the molecular dynamics trajectory reflecting a systematically improved performance of ff99SBnmr1-ILDN over the original ff99SB force field. Moreover, the unconstrained ff99SBnmr1-ILDN MD ensemble achieves a similar level of agreement as the recently introduced EROS ensemble, which was constructed based on a large body of NMR data as constraints, including the methyl residual dipolar couplings. This suggests that ff99SBnmr1-ILDN provides a high-quality representation of the motions of methyl-bearing protein side chains, which are sensitive probes of protein-protein and protein-ligand interactions.
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