Using AlphaFold2 and Molecular Dynamics Simulation to Model Protein Recognition.
Methods Mol Biol
; 2841: 49-66, 2024.
Article
en En
| MEDLINE
| ID: mdl-39115764
ABSTRACT
In this chapter, we predict the structure of the Arabidopsis receptor-homology-transmembrane-RING-H2 isoform 1 (RMR1) in complex with the C-terminal sorting determinant of cruciferin (CRU1) by AlphaFold2 using the ColabFold web interface and to perform molecular dynamics simulation to probe the dynamics of the predicted structures. Our results predict that the C-terminal carboxylate group of ctVSD of CRU1 is recognized by the conserved Arg89 of the cargo-binding loop of RMR1 and Arg468 of CRU1 by negative charge residues in the cargo-binding pocket of RMR1. The procedures described here are useful for modeling of other protein complexes.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Arabidopsis
/
Proteínas de Arabidopsis
/
Simulación de Dinámica Molecular
Idioma:
En
Revista:
Methods Mol Biol
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2024
Tipo del documento:
Article
País de afiliación:
China
Pais de publicación:
Estados Unidos