Applications of sequence coevolution in membrane protein biochemistry
By J. Nicoludis, R. Gaudet. 2017
32 citations recorded by the source corpus.
Recently, protein sequence coevolution analysis has matured into a predictive powerhouse for protein structure and function. Direct Coupling Analysis, a method that uses a global statistical model of sequence coevolution, has enabled the prediction of membrane and disordered protein structures, protein complex architectures, and the functional effects of mutations in proteins. The field of membrane protein biochemistry and structural biology has embraced these computational techniques, which provide functional and structural information in an otherwise experimentally-challenging field. Here we review recent applications of protein sequence coevolution analysis to membrane protein structure and function and highlight the promising directions and future obstacles in these fields. We provide insights and guidelines for membrane protein biochemists who wish to apply sequence coevolution analysis to a given experimental system.
Subfields: Genetics, Molecular Biology
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Citations in the corpus
- Sampling alternative conformational states of transporters and receptors with AlphaFold2 (2022, background): “The resulting models are unnaturally compact and frequently distorted, preventing critical questions about ligand and/or drug binding modes from being addressed ( Ovchinnikov et al., 2015 ; Nicoludis and Gaudet, 2018 ).”
- AlphaFold2 predicts the inward-facing conformation of the multidrug transporter LmrP (2021, background): “Occluded models result from methodological biases that favor compactness.(12) Therefore, the success of AlphaFold2 in modeling IF LmrP suggests that these biases may finally have been overcome.”