Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome.
J Chem Theory Comput
; 19(21): 7924-7933, 2023 Nov 14.
Article
en En
| MEDLINE
| ID: mdl-37856311
For the first time, a complete all-atom molecular dynamics (MD) model of a virus, bacteriophage MS2, in its entirety, including a protein outer shell, native genomic RNA with necessary divalent ions, and surrounding explicit aqueous solution with ions at physiological concentration, was built. The model is based on an experimentally measured cryo-EM structure, which was substantially augmented by reconstructing missing or low-resolution parts of the measured density (where the atomistic structure cannot be fit unambiguously). The model was tested by a quarter of a microsecond MD run, and various biophysical characteristics are obtained and analyzed. The developed methodology of building the model can be used for reconstructing other large biomolecular structures when experimental data are fragmented and/or of varying resolution, while the model itself can be used for studying the biology of MS2, including the dynamics of its interaction with the host bacteria.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Levivirus
/
Simulación de Dinámica Molecular
Idioma:
En
Revista:
J Chem Theory Comput
Año:
2023
Tipo del documento:
Article
País de afiliación:
Ucrania
Pais de publicación:
Estados Unidos