Structural Basis of a Rationally Rewired Protein-Protein Interface Critical to Bacterial Signaling by Casino, Patricia, Marina, Alberto, Podgornaia, Anna Igorevna, Laub, Michael T

“…Our approach and conclusions have implications for studies of other protein-protein interactions and protein evolution and for the design of novel protein interfaces.…”
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Exploring the fold space preferences of ancient and newborn protein superfamilies by Edwards, H, Hannah Edwards

“…<p>Protein evolution is a complex and diverse process, yielding an incredible assortment of biological functions and pathways occurring in the cells of living organisms. …”

Drosophila dumpy is a gigantic extracellular protein required to maintain tension at epidermal-cuticle attachment sites. by Wilkin, M, Becker, M, Mulvey, D, Phan, I, Chao, A, Cooper, K, Chung, H, Campbell, I, Baron, M, MacIntyre, R

“…Dumpy represents an extreme form of modular protein evolution, containing 308 epidermal growth factor (EGF) modules, interspersed with a new module class, DPY, and terminating in a crosslinking zona pellucida domain and membrane anchor sequence. …”

High-throughput proteogenomics of <it>Ruegeria pomeroyi</it>: seeding a better genomic annotation for the whole marine <it>Roseobacter </it>clade by Christie-Oleza Joseph A, Miotello Guylaine, Armengaud Jean

“…Their discoveries point to a possible theory for protein evolution that will rely on high expression of orphans in bacteria: their putative poor efficiency could be counterbalanced by a higher level of expression. …”
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A glutamine-based single α-helix scaffold to target globular proteins by Albert Escobedo, Jonathan Piccirillo, Juan Aranda, Tammo Diercks, Borja Mateos, Carla Garcia-Cabau, Macarena Sánchez-Navarro, Busra Topal, Mateusz Biesaga, Lasse Staby, Birthe B. Kragelund, Jesús García, Oscar Millet, Modesto Orozco, Murray Coles, Ramon Crehuet, Xavier Salvatella

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PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis by Wang Huai-Chun, Susko Edward, Roger Andrew J

“…</p> <p>Results</p> <p>PROCOV (protein covarion analysis) is a software tool that implements a number of previously proposed covarion models of protein evolution for phylogenetic inference in a maximum likelihood framework. …”
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Cryptic amyloidogenic regions in intrinsically disordered proteins: Function and disease association by Jaime Santos, Irantzu Pallarès, Valentín Iglesias, Salvador Ventura

“…By exploring this function/malfunction dichotomy, we speculate that ancestral CARs might have evolved into functional interacting regions playing a significant role in protein evolution at the origins of life.…”
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An Evolution-Guided Analysis Reveals a Multi-Signaling Regulation of Fas by Tyrosine Phosphorylation and its Implication in Human Cancers. by Krittalak Chakrabandhu, Sébastien Huault, Jérôme Durivault, Kévin Lang, Ly Ta Ngoc, Angelique Bole, Eszter Doma, Benoit Dérijard, Jean-Pierre Gérard, Michel Pierres, Anne-Odile Hueber

“…Demonstrations of both pro-apoptotic and pro-survival abilities of Fas (TNFRSF6/CD95/APO-1) have led to a shift from the exclusive "Fas apoptosis" to "Fas multisignals" paradigm and the acceptance that Fas-related therapies face a major challenge, as it remains unclear what determines the mode of Fas signaling. Through protein evolution analysis, which reveals unconventional substitutions of Fas tyrosine during divergent evolution, evolution-guided tyrosine-phosphorylated Fas proxy, and site-specific phosphorylation detection, we show that the Fas signaling outcome is determined by the tyrosine phosphorylation status of its death domain. …”
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Isomin: a novel cytoplasmic intermediate filament protein from an arthropod species by Lupetti Pietro, Caroti Daniela, Ciolfi Silvia, Mencarelli Caterina, Dallai Romano

“…</p> <p>Conclusions</p> <p>Our results set a new basis for the analysis of IF protein evolution during arthropod phylogeny. In the light of this new information, the statement that the arthropod phylum lacks cytoplasmic IFs is no longer tenable.…”
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Sex-biased gene expression during head development in a sexually dimorphic stalk-eyed fly. by Gerald S Wilkinson, Philip M Johns, Jackie D Metheny, Richard H Baker

“…Genes with female-biased expression were more common on the X and less common on autosomes than expected, while male-biased genes exhibited no chromosomal pattern. Rates of protein evolution were lower for female-biased genes but higher for genes that moved on or off the novel X chromosome. …”
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Cavity architecture based modulation of ligand binding tunnels in plant START domains by Sanjeet Kumar Mahtha, Kamlesh Kumari, Vineet Gaur, Gitanjali Yadav

“…In this work, we explore the role of cavity architectural modulations in START protein evolution and functional diversity. We use deep-learning approaches to generate plant START domain models, followed by surface accessibility studies and a comprehensive structural investigation of the rice START family. …”
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Protein 3D structure computed from evolutionary sequence variation. by Debora S Marks, Lucy J Colwell, Robert Sheridan, Thomas A Hopf, Andrea Pagnani, Riccardo Zecchina, Chris Sander

“…This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures, new strategies in protein and drug design, and the identification of functional genetic variants in normal and disease genomes.…”
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Interplay between chaperones and protein disorder promotes the evolution of protein networks. by Sebastian Pechmann, Judith Frydman

“…Our results illuminate the role of chaperones in enabling protein evolution, and underline the importance of the cellular context and integrated approaches for understanding proteome evolution. …”
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Prediction of contact residue pairs based on co-substitution between sites in protein structures. by Sanzo Miyazawa

“…Besides, this excellent accuracy indicates that compensatory substitutions are significant in protein evolution.…”
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On the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture by Worth Catherine L, Blundell Tom L

“…</p> <p>Conclusions</p> <p>Conservation of buried polar residues and the hydrogen-bond interactions that they form implies an important role for maintaining protein structure, contributing strong restraints on amino acid substitutions during divergent protein evolution. Our analysis sheds light on the important stabilizing roles of these residues in protein architecture and provides further insight into factors influencing the evolution of protein families and superfamilies.…”
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Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design by Filippo Vascon, Matteo Gasparotto, Marta Giacomello, Laura Cendron, Elisabetta Bergantino, Francesco Filippini, Irene Righetto

“…Then, we provide examples of electrostatic analysis and fingerprints in natural protein evolution and in biotechnological design, in fields as diverse as biocatalysis, antibody and nanobody engineering, drug design and delivery, molecular virology, nanotechnology and regenerative medicine.…”
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Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds by Emily L. Gordon, Rebecca T. Kimball, Edward L. Braun

“…We compared those relative exchangeabilities with values calculated using a substitution matrix for transmembrane helices estimated using a variety of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. …”
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Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis. by Lukasz Huminiecki

“…Further evidence for the neo-functionalization of ROBO4 comes from the analysis of its protein interactions, the rates of protein evolution, and of positively selected sites.<h4>Conclusions</h4>The neo-functionalization model explains why ROBO4 protein acquired new context-specific biological functions in the control of angiogenesis. …”
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Full-Length Venom Protein cDNA Sequences from Venom-Derived mRNA: Exploring Compositional Variation and Adaptive Multigene Evolution. by Cassandra M Modahl, Stephen P Mackessy

“…This approach, requiring only venom, provides access to cDNA sequences in the absence of living specimens, even from commercial venom sources, to evaluate important regional differences in venom composition and to study snake venom protein evolution.…”
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Molecular determinants archetypical to the phylum Nematoda by McCarter James P, Rychlewski Leszek, Wyrwicz Lucjan, Wang Zhengyuan, Abubucker Sahar, Martin John, Yin Yong, Wilson Richard K, Mitreva Makedonka

“…</p> <p>Conclusion</p> <p>This study identified and characterized the molecular determinants that help in defining the phylum Nematoda, and therefore improved our understanding of nematode protein evolution and provided novel insights for the development of next generation parasite control strategies.…”
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