Phylogenetic Patterns of Codon Evolution in the ACTIN-DEPOLYMERIZING FACTOR/COFILIN (ADF/CFL) Gene Family. by Eileen M Roy-Zokan, Kelly A Dyer, Richard B Meagher

“…Estimating the rate of non-synonymous to synonymous mutations (dN/dS) across phylogenetic lineages revealed that the majority of ADF/CFL codon positions were under strong purifying selection, with rare episodic events of accelerated protein evolution. In both plants and animals these instances of accelerated evolution were ADF/CFL subclass specific, and all of the sites under selection were located in regions of the protein that could serve in new functional roles. …”
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Protein Biophysics Explains Why Highly Abundant Proteins Evolve Slowly by Adrian W.R. Serohijos, Zilvinas Rimas, Eugene I. Shakhnovich

“…However, other empirical findings, such as the broad distribution of evolutionary rates, suggest that additional variables determine the rate of protein evolution. Here, we report that under the global selection against the cytotoxic effects of misfolded proteins, folding stability (ΔG), simultaneous with abundance, is a causal variable of evolutionary rate. …”
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Peptide Vocabulary Analysis Reveals Ultra-Conservation and Homonymity in Protein Sequences by Derek Gatherer

“…Homonyms may be useful in detecting convergent evolution and positive selection in protein evolution. Ultra-conserved words may be useful in identifying structures intolerant to substitution over long periods of evolutionary time.…”
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Latent generative landscapes as maps of functional diversity in protein sequence space by Cheyenne Ziegler, Jonathan Martin, Claude Sinner, Faruck Morcos

“…We provide support on how the landscape helps us understand the effects of sequence variability observed in experimental data and provides insights on directed and natural protein evolution. We propose that combining generative properties and functional predictive power of variational autoencoders and coevolutionary analysis could be beneficial in applications for protein engineering and design.…”
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Energetic selection of topology in ferredoxins. by J Dongun Kim, Agustina Rodriguez-Granillo, David A Case, Vikas Nanda, Paul G Falkowski

“…Models of early protein evolution posit the existence of short peptides that bound metals and ions and served as transporters, membranes or catalysts. …”
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Gene regulation in primates evolves under tissue-specific selection pressures. by Ran Blekhman, Alicia Oshlack, Adrien E Chabot, Gordon K Smyth, Yoav Gilad

“…In addition, we found evidence for tissue-specific selection pressures, as well as lower rates of protein evolution for genes in which regulation evolves under natural selection. …”
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Epistasis as a determinant of the HIV-1 protease's robustness to mutation. by Elena Capel, Mariona Parera, Miguel Angel Martinez

“…The robustness of phenotypes to mutation is critical to protein evolution; robustness may be an adaptive trait if it promotes evolution. …”
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Predictability of evolutionary trajectories in fitness landscapes. by Alexander E Lobkovsky, Yuri I Wolf, Eugene V Koonin

“…We suggest that smoothness and the substantial deficit of peaks in the fitness landscapes of protein evolution are fundamental consequences of the physics of protein folding.…”
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Statistics of knots, geometry of conformations, and evolution of proteins. by Rhonald C Lua, Alexander Y Grosberg

“…However, the precise reason for this is unknown--for instance, if knots were removed by evolution due to their unfavorable effect on protein folding or function or due to some other unidentified property of protein evolution.…”
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MPI-PHYLIP: parallelizing computationally intensive phylogenetic analysis routines for the analysis of large protein families. by Alexander J Ropelewski, Hugh B Nicholas, Ricardo R Gonzalez Mendez

“…This paper discusses the methodology used to parallelize the PHYLIP programs and reports the performance of the parallel PHYLIP programs that are relevant to the study of protein evolution on several protein datasets.Calculations that currently take a few days on a state of the art desktop workstation are reduced to calculations that can be performed over lunchtime on a modern parallel computer. …”
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Directed evolution of aminoglycoside phosphotransferase (3') type IIIa variants that inactivate amikacin but impose significant fitness costs. by Joseph R Kramer, Ichiro Matsumura

“…The rules that govern adaptive protein evolution remain incompletely understood. Aminoglycoside aminotransferase (3') type IIIa (hereafter abbreviated APH(3')-IIIa) is a good model enzyme because it inactivates kanamycin efficiently; it recognizes other aminoglycoside antibiotics, including amikacin, but not nearly as well. …”
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Where Does the Alignment Score Distribution Shape Come from? by Philippe Ortet, Olivier Bastien

“…We investigated the possibility of deriving the main properties of sequence alignment score distributions from a basic evolutionary process: a duplication-divergence protein evolution process in a sequence space. Firstly, the distribution of sequences in this space was defined with respect to the genetic distance between sequences. …”
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A database of domain definitions for proteins with complex interdomain geometry. by Indraneel Majumdar, Lisa N Kinch, Nick V Grishin

“…We consider our domains as mobile evolutionary units, which may rearrange during protein evolution. Additionally, they may be visualized as structurally compact and possibly independently folding units. …”
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Coiled coils as possible models of protein structure evolution by Gáspári Zoltán, Nyitray László

“…In this paper, we review coiled coils in the light of protein evolution by putting our present understanding of the motif and its variants in the context of structural interconversions. …”
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Patterns of nucleotide diversity at the regions encompassing the Drosophila insulin-like peptide (dilp) genes: demography vs. positive selection in Drosophila melanogaster. by Sara Guirao-Rico, Montserrat Aguadé

“…The comparison of polymorphism in D. melanogaster and divergence from D. simulans at different functional classes of the dilp genes provided no evidence of adaptive protein evolution after the split of the D. melanogaster and D. simulans lineages. …”
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Evidence for divergent evolution of growth temperature preference in sympatric Saccharomyces species. by Paula Gonçalves, Elisabete Valério, Cláudia Correia, João M G C F de Almeida, José Paulo Sampaio

“…In order to contribute to explain the occurrence in sympatry of Saccharomyces species, we screened Saccharomyces genomic data for protein divergence that might be correlated to distinct growth temperature preferences of the species, using the dN/dS ratio as a measure of protein evolution rates and pair-wise species comparisons. …”
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Peptide Vocabulary Analysis Reveals Ultra-Conservation and Homonymity in Protein Sequences by Derek Gatherer

“…Homonyms may be useful in detecting convergent evolution and positive selection in protein evolution. Ultra-conserved words may be useful in identifying structures intolerant to substitution over long periods of evolutionary time.…”
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Language Models Predict Drug Resistance from Complex Sequence Variation by Tso, Andy

“…In this thesis, we show that language modeling of protein evolution can also predict mutations that confer drug resistance. …”
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N‐glycoproteins exhibit a positive expression level–evolutionary rate correlation by Feyertag, F, Berninsone, P, Alvarez-Ponce, D

“…One of the primary factors influencing rates of protein evolution is expression level, with highly expressed proteins tending to evolve at slow rates. …”

Insight into the RssB-Mediated Recognition and Delivery of σ^s to the AAA+ Protease, ClpXP by Dimce Micevski, Kornelius Zeth, Terrence D. Mulhern, Verena J. Schuenemann, Jessica E. Zammit, Kaye N. Truscott, David A. Dougan

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