Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates. by Christoffer Norn, Ingemar André

“…Thermodynamic stability is a crucial fitness constraint in protein evolution and is a central factor in shaping the sequence landscapes of proteins. …”
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Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp by Sarah Farhat, Phuong Le, Ehsan Kayal, Benjamin Noel, Estelle Bigeard, Erwan Corre, Florian Maumus, Isabelle Florent, Adriana Alberti, Jean-Marc Aury, Tristan Barbeyron, Ruibo Cai, Corinne Da Silva, Benjamin Istace, Karine Labadie, Dominique Marie, Jonathan Mercier, Tsinda Rukwavu, Jeremy Szymczak, Thierry Tonon, Catharina Alves-de-Souza, Pierre Rouzé, Yves Van de Peer, Patrick Wincker, Stephane Rombauts, Betina M. Porcel, Laure Guillou

“…Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. …”
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Position matters: metwork centrality considerably impacts rates of protein evolution in the human protein–protein interaction network by Alvarez-Ponce, D, Feyertag, F, Chakraborty, S

“…A long list of factors affecting rates of protein evolution have been identified. However, the relative importance of each factor in determining rates of protein evolution remains unresolved. …”

Inference on coat protein evolution of Lily symptomless carlavirus in India and abroad based on motifs study and phylogenetic analysis by Huddone, S, Bhardwaj, S, Rattan, R, Kanwar, K, Zinta, G, Handa, A

Stability-mediated epistasis constrains the evolution of an influenza protein by Lizhi Ian Gong, Marc A Suchard, Jesse D Bloom

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Evolution of an Iron-Detoxifying Protein: Eukaryotic and <i>Rickettsia</i> Frataxins Contain a Conserved Site Which Is Not Present in Their Bacterial Homologues by Rui Alves, Maria Pazos-Gil, Marta Medina-Carbonero, Arabela Sanz-Alcázar, Fabien Delaspre, Jordi Tamarit

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Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis by Etai Jacob, Ron Unger, Amnon Horovitz

Subjects: “…protein evolution…”
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Influenza evolution navigates stability valleys by Mary M Rorick, Mercedes Pascual

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Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy by Andreina Baj, Federica Novazzi, Francesca Drago Ferrante, Angelo Genoni, Elena Tettamanzi, Giuseppe Catanoso, Daniela Dalla Gasperina, Francesco Dentali, Daniele Focosi, Fabrizio Maggi

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Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (<it>Melampsora </it>spp.) by Tanguay Philippe, Feau Nicolas, Joly David L, Hamelin Richard C

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Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp by Sarah Farhat, Phuong Le, Ehsan Kayal, Benjamin Noel, Estelle Bigeard, Erwan Corre, Florian Maumus, Isabelle Florent, Adriana Alberti, Jean-Marc Aury, Tristan Barbeyron, Ruibo Cai, Corinne Da Silva, Benjamin Istace, Karine Labadie, Dominique Marie, Jonathan Mercier, Tsinda Rukwavu, Jeremy Szymczak, Thierry Tonon, Catharina Alves-de-Souza, Pierre Rouzé, Yves Van de Peer, Patrick Wincker, Stephane Rombauts, Betina M. Porcel, Laure Guillou

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The insights into calcium ion selectivity provided by ancestral prokaryotic ion channels by Katsumasa Irie

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Tweaking the structure to radically change the function: the evolution of transthyretin from 5-hydroxyisourate hydrolase to triiodothyronine distributor to thyroxine distributor. by Samantha J. Richardson

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New β-Propellers Are Continuously Amplified From Single Blades in all Major Lineages of the β-Propeller Superfamily by Joana Pereira, Andrei N. Lupas

Subjects: “…protein evolution…”
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Correction: No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly by Koonin Eugene V, Wolf Yuri I, Jordan I King

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The Repertoire of Tissue Inhibitors of Metalloproteases: Evolution, Regulation of Extracellular Matrix Proteolysis, Engineering and Therapeutic Challenges by Salvatore Costa, Maria Antonietta Ragusa, Gabriele Lo Buglio, Simone Dario Scilabra, Aldo Nicosia

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BALCONY: an R package for MSA and functional compartments of protein variability analysis by Alicja Płuciennik, Michał Stolarczyk, Maria Bzówka, Agata Raczyńska, Tomasz Magdziarz, Artur Góra

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Self-analysis of repeat proteins reveals evolutionarily conserved patterns by Matthew Merski, Krzysztof Młynarczyk, Jan Ludwiczak, Jakub Skrzeczkowski, Stanisław Dunin-Horkawicz, Maria W. Górna

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Protein aggregation profile of the human kinome by Ricardo eGraña-Montes, Ricardo eSant'anna de Oliveira, Salvador eVentura

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Relative evolutionary rate inference in HyPhy with LEISR by Stephanie J. Spielman, Sergei L. Kosakovsky Pond

Subjects: “…Protein evolution…”
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