Protein evolution speed depends on its stability and abundance and on chaperone concentrations

Proceedings of the National Academy of Sciences of the United States of America
Luca Agozzino, Ken A Dill

Abstract

Proteins evolve at different rates. What drives the speed of protein sequence changes? Two main factors are a protein's folding stability and aggregation propensity. By combining the hydrophobic-polar (HP) model with the Zwanzig-Szabo-Bagchi rate theory, we find that: (i) Adaptation is strongly accelerated by selection pressure, explaining the broad variation from days to thousands of years over which organisms adapt to new environments. (ii) The proteins that adapt fastest are those that are not very stably folded, because their fitness landscapes are steepest. And because heating destabilizes folded proteins, we predict that cells should adapt faster when put into warmer rather than cooler environments. (iii) Increasing protein abundance slows down evolution (the substitution rate of the sequence) because a typical protein is not perfectly fit, so increasing its number of copies reduces the cell's fitness. (iv) However, chaperones can mitigate this abundance effect and accelerate evolution (also called evolutionary capacitance) by effectively enhancing protein stability. This model explains key observations about protein evolution rates.

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Citations

Jun 4, 2019·PLoS Computational Biology·Alexander S Leonard, Sebastian E Ahnert
Aug 23, 2019·Molecular Biology and Evolution·Jason A Wagoner, Ken A Dill
Jun 10, 2020·Annual Review of Chemical and Biomolecular Engineering·Luca AgozzinoKen A Dill
Feb 23, 2020·Annual Review of Biophysics·Paul CampitelliS Banu Ozkan
Sep 3, 2019·Current Opinion in Genetics & Development·Cory D Dunn, Ville O Paavilainen
Feb 3, 2021·Proceedings. Biological Sciences·David BergerRichard J Walters
Mar 5, 2021·Current Opinion in Structural Biology·Martin Gruebele, Gary J Pielak
Mar 23, 2021·Evolution; International Journal of Organic Evolution·Elizabeth S DavenportJeffry L Dudycha
May 2, 2021·Biophysical Journal·Rostam M RazbanEugene I Shakhnovich
Jul 3, 2021·International Journal of Molecular Sciences·Federico Martinez-SeidelAlexandre Augusto Pereira Firmino
Jul 6, 2021·Journal of Molecular Biology·Roy NassarKen A Dill

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Methods Mentioned

BETA
protein-folding
thermal folding

Software Mentioned

GroEl

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