NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements

[Display omitted] •NMMD: new method for flexible fitting of atomic structures into cryo-EM maps.•NMMD efficiently combines normal mode analysis and molecular dynamics simulation.•NMMD was tested using synthetic and experimental cryo-EM maps.•Adding normal modes to molecular dynamics makes the fittin...

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Vydáno v:Journal of molecular biology Ročník 434; číslo 7; s. 167483
Hlavní autoři: Vuillemot, Rémi, Miyashita, Osamu, Tama, Florence, Rouiller, Isabelle, Jonic, Slavica
Médium: Journal Article
Jazyk:angličtina
Vydáno: Netherlands Elsevier Ltd 15.04.2022
Elsevier
Témata:
Biochemistry, Molecular Biology
Biophysics
Computer Science
cryo electron microscopy (cryo-EM)
cryo-electron microscopy
Cryoelectron Microscopy - methods
Crystallography, X-Ray
flexible fitting
Life Sciences
molecular biology
Molecular Conformation
molecular dynamics
Molecular Dynamics Simulation
molecular modeling
normal mode analysis
Protein Conformation
Signal and Image Processing
Structural Biology
X-ray diffraction
cryo electron microscopy (cryo-EM)
normal mode analysis
flexible fitting
molecular modeling
molecular dynamics simulation
replica exchange umbrella sampling
Molecular modeling
EMfit
GENESIS
ISSN:0022-2836, 1089-8638, 1089-8638
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Shrnutí:[Display omitted] •NMMD: new method for flexible fitting of atomic structures into cryo-EM maps.•NMMD efficiently combines normal mode analysis and molecular dynamics simulation.•NMMD was tested using synthetic and experimental cryo-EM maps.•Adding normal modes to molecular dynamics makes the fitting faster and more accurate. Atomic models of cryo electron microscopy (cryo-EM) maps of biomolecular conformations are often obtained by flexible fitting of the maps with available atomic structures of other conformations (e.g., obtained by X-ray crystallography). This article presents a new flexible fitting method, NMMD, which combines normal mode analysis (NMA) and molecular dynamics simulation (MD). Given an atomic structure and a cryo-EM map to fit, NMMD simultaneously estimates global atomic displacements based on NMA and local displacements based on MD. NMMD was implemented by modifying EMfit, a flexible fitting method using MD only, in GENESIS 1.4. As EMfit, NMMD can be run with replica exchange umbrella sampling procedure. The new method was tested using a variety of EM maps (synthetic and experimental, with different noise levels and resolutions). The results of the tests show that adding normal modes to MD-based fitting makes the fitting faster (40% in average) and, in the majority of cases, more accurate.
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ISSN:0022-2836
1089-8638
1089-8638
DOI:10.1016/j.jmb.2022.167483