ArticleBiophysical journal2005
Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search.Journal of chemical information and modeling · 2024Article
- Explicit versus implicit consideration of binding partners in protein-protein complex to elucidate intrinsic dynamics.Biophysical reviews · 2022Review
- State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.Progress in biophysics and molecular biology · 2021Article
- A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs.Frontiers in molecular biosciences · 2020Article
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Normal mode analysis and beyond.Biophysics and physicobiology · 2019Review
- Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.Biophysical journal · 2017Article
- Bayesian Modeling of Biomolecular Assemblies with Cryo-EM Maps.Frontiers in molecular biosciences · 2017Article
- Deformable elastic network refinement for low-resolution macromolecular crystallography.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Cross-validation in cryo-EM-based structural modeling.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Developing advanced X-ray scattering methods combined with crystallography and computation.Methods (San Diego, Calif.) · 2013Review
- Modeling, docking, and fitting of atomic structures to 3D maps from cryo-electron microscopy.Methods in molecular biology (Clifton, N.J.) · 2013Article
- Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Putting structure into context: fitting of atomic models into electron microscopic and electron tomographic reconstructions.Current opinion in cell biology · 2012Review
- Consensus among flexible fitting approaches improves the interpretation of cryo-EM data.Journal of structural biology · 2012Article
- Accurate flexible fitting of high-resolution protein structures to small-angle x-ray scattering data using a coarse-grained model with implicit hydration shell.Biophysical journal · 2011Article
- Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization.Biophysical journal · 2011Article
- Anisotropic elastic network modeling of entire microtubules.Biophysical journal · 2010Article
- Vibrational entropy and the structural organization of proteins.The European physical journal. E, Soft matter · 2010Article
- Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.Chemical reviews · 2010Review
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Authors and funding
5 authors.
Funding
Abstract
A method for the flexible docking of high-resolution atomic structures into lower resolution densities derived from electron microscopy is presented. The atomic structure is deformed by an iterative process using combinations of normal modes to obtain the best fit of the electron microscopical density. The quality of the computed structures has been evaluated by several techniques borrowed from crystallography. Two atomic structures of the SERCA1 Ca-ATPase corresponding to different conformations were used as a starting point to fit the electron density corresponding to a different conformation. The fitted models have been compared to published models obtained by rigid domain docking, and their relation to the known crystallographic structures are explored by normal mode analysis. We find that only a few number of modes contribute significantly to the transition. The associated motions involve almost exclusively rotation and translation of the cytoplasmic domains as well as displacement of cytoplasmic loops. We suggest that the movements of the cytoplasmic domains are driven by the conformational change that occurs between nonphosphorylated and phosphorylated intermediate, the latter being mimicked by the presence of vanadate at the phosphorylation site in the electron microscopy structure.
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