Chasing long-range evolutionary couplings in the AlphaFold era.

ABSTRACT: Coevolution between protein residues is normally interpreted as direct contact. However, the evolutionary record of a protein sequence contains rich information that may include long-range functional couplings, couplings that report on homo-oligomeric states or even conformational changes. Due to the complexity of the sequence space and the lack of structural information on various members of a protein family, it has been difficult to effectively mine the additional information encoded in a multiple sequence alignment (MSA). Here, taking advantage of the recent release of the AlphaFold (AF) database we attempt to identify coevolutionary couplings that cannot be explained simply by spatial proximity. We propose a simple computational method that performs direct coupling analysis on a MSA an

SUBMITTER: Karamanos TK 

PROVIDER: S-EPMC10909459 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature