Using AlphaFold2 and Molecular Dynamics Simulation to Model Protein Recognition

Hiu Yan Wong; Kam-Bo Wong

doi:10.1007/978-1-0716-4059-3_4

Using AlphaFold2 and Molecular Dynamics Simulation to Model Protein Recognition

Methods Mol Biol. 2024:2841:49-66. doi: 10.1007/978-1-0716-4059-3_4.

Authors

Hiu Yan Wong¹, Kam-Bo Wong²

Affiliations

¹ School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
² School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China. kbwong@cuhk.edu.hk.

PMID: 39115764
DOI: 10.1007/978-1-0716-4059-3_4

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.

Keywords: Molecular modeling; Protein folding; Protein interactions; Structure prediction; Vacuolar sorting.

MeSH terms

Arabidopsis Proteins* / chemistry
Arabidopsis Proteins* / metabolism
Arabidopsis* / metabolism
Binding Sites
Molecular Dynamics Simulation*
Protein Binding
Protein Conformation
Software

Substances

Arabidopsis Proteins