ArticleJournal of the American Chemical Society2013
Peptide crystal simulations reveal hidden dynamics.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Functional protein dynamics in a crystal.Nature communications · 2024Article
- gmXtal: Cooking Crystals with GROMACS.The protein journal · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- LAWS: Local alignment for water sites-Tracking ordered water in simulations.Biophysical journal · 2023Article
- Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography.Journal of the American Chemical Society · 2023Article
- Simulations of Amyloid-Forming Peptides in the Crystal State.The protein journal · 2023Article
- Article
- Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.Acta crystallographica. Section D, Structural biology · 2020Article
- Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein.Structural dynamics (Melville, N.Y.) · 2019Article
- Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation.The journal of physical chemistry. B · 2019Article
- Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.Journal of the American Chemical Society · 2019Article
- Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations.Biophysical journal · 2019Article
- Fluorescence enhancement of a ligand-activated fluorescent protein induced by collective noncovalent interactions.Chemical science · 2018Article
- Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics.International journal of molecular sciences · 2018Review
- Bringing diffuse X-ray scattering into focus.Current opinion in structural biology · 2018Review
- Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.IUCrJ · 2018Article
- Article
- Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines.Chemistry (Weinheim an der Bergstrasse, Germany) · 2017Article
- Measuring and modeling diffuse scattering in protein X-ray crystallography.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation.Journal of the American Chemical Society · 2016Article
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4 authors.
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Abstract
Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in X-ray diffraction data. We present here 9.6 μs of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom RMSD; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom RMSD. The R-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The B-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but B-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 310 helical propensity and a gauche(-) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data as well as to validate computational chemistry methods.
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