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This paper demonstrates that a biophysics-based fitness landscape of an essential central metabolism enzyme (DHFR) can provide an accurate prediction of the antibiotic resistant phenotypes. Specifically, a kinetic flux model was used to predict, with high accuracy, the IC50 of trimethoprim resistance from a unique combination of the molecular (activity, binding, and folding stability) and cellular (intracellular abundance) parameters of the mutant and orthologous forms of DHFR. Further, this work established the role of PQC in the evolution of antibiotic resistance.
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4•• Rodrigues, J.V., Bershtein, S., Li, A., Lozovsky, E.R., Hartl, D.L., Shakhnovich, E.I., Biophysical principles predict fitness landscapes of drug resistance. Proc Natl Acad Sci U S A 113 (2016), E1470–E1478 This paper demonstrates that a biophysics-based fitness landscape of an essential central metabolism enzyme (DHFR) can provide an accurate prediction of the antibiotic resistant phenotypes. Specifically, a kinetic flux model was used to predict, with high accuracy, the IC50 of trimethoprim resistance from a unique combination of the molecular (activity, binding, and folding stability) and cellular (intracellular abundance) parameters of the mutant and orthologous forms of DHFR. Further, this work established the role of PQC in the evolution of antibiotic resistance.
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This work uses computational models of thermodynamic stability and simulations of protein sequence evolution by sequential fixation of nearly neutral mutations to study epistasis, contingency, and entrenchment under long-term purifying selection on protein stability. Importantly, the paper demonstrates that fixed mutations often become entrenched by epistasis — substitutions that were nearly neutral upon fixation become increasingly deleterious to revert as subsequent substitutions accumulate.
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By applying a biophysical and evolutionary model, the paper examines how the inherent structural coupling between protein stability and binding gives rise to an evolutionary coupling between them. The authors conclude that these traits can co-evolve even though their coevolution does not confer a fitness advantage per se (so-called, evolutionary ‘spandrels’).
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8• Manhart, M., Morozov, A.V., Protein folding and binding can emerge as evolutionary spandrels through structural coupling. Proc Natl Acad Sci U S A 112 (2015), 1797–1802 By applying a biophysical and evolutionary model, the paper examines how the inherent structural coupling between protein stability and binding gives rise to an evolutionary coupling between them. The authors conclude that these traits can co-evolve even though their coevolution does not confer a fitness advantage per se (so-called, evolutionary ‘spandrels’).
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A comprehensive insight into the molecular mechanisms shaping the evolution of functional specificity in protein-protein interactions. The sequence space encompassing the interface formed by PhoQ-PhoP proteins (constituting bacterial two-component signaling system) was mapped via a saturated mutagenesis of four key residues of PhoQ followed by a functional selection. The authors found that degeneracy and epistasis shape the connectivity pattern in sequence space of the identified functional variants.
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An important work that provides a comprehensive insight into the role of intra-molecular and inter-molecular epistasis in the evolution of molecular interfaces. The joint sequence space connecting the evolutionary transition in specificity of a transcription factor (TF) and a corresponding DNA response element (RE) was experimentally mapped, and it was concluded that epistasis was essential for the evolution of TF–RE complexes with unique specificity.
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