Amino acid coevolution induces an evolutionary Stokes shift

By D. Pollock, Grant Thiltgen, Richard A. Goldstein. 2012

208 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Genetics, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Atomic and Molecular Physics, and Optics

1. Martin Weigt
2. L. Gong
3. Orr Ashenberg
4. Jesse D. Bloom

In Genetics

1. Jesse D. Bloom
2. Adrian W. R. Serohijos
3. Martin Weigt
4. Matteo Figliuzzi
5. Alexander Schug
6. David M. McCandlish
7. Joshua B. Plotkin
8. Orr Ashenberg

In Molecular Biology

1. Martin Weigt
2. Matteo Figliuzzi
3. Jesse D. Bloom
4. Joshua B. Plotkin
5. Alexander Schug
6. L. Gong
7. Orr Ashenberg
8. Eugene I. Shakhnovich

Citations in the corpus

• Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1 (2015, background): “There are ample proofs of the existence of epistasis and condition dependent effects [12, 14–17].”
• Epistasis and the Dynamics of Reversion in Molecular Evolution (2016, background): “The first factor is co-evolution between sites as suggested by, e.g., Pollock et al. (2012).”
• Mutational effects on stability are largely conserved during protein evolution (2013, methodology): “(2) constrain a destabilizing substitution to remain fixed during evolution, and then monitor the effect of reverting this substitution as the rest of the sequence evolves.”
• Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding (2020, unknown): “This shift in the effects of mutations between more distantly related RBDs is consistent with studies of protein evolution demonstrating that epistastic entrenchment causes amino acid preferences to change as proteins diverge (Hilton and Bloom, 2018; Lee et al., 2018; Pollock et al., 2012; Povolotsk”
• Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics (2014, background): “For example, some groups are now examining the validity of some central assumptions in molecular evolution such as the site-independence of substitution models [83,84].”
• Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding (2020, unknown): “This shift in the effects of mutations between more distantly related RBDs is consistent with other studies of protein evolution demonstrating that epistastic entrenchment causes amino-acid preferences to change as homologous proteins become increasingly diverged (Hilton and Bloom, 2018; Lee et al.,”