Molecular evolution of cytochrome C oxidase-I protein of insects living in Saudi Arabia. by Jamal S M Sabir, Samar Rabah, Haitham Yacoub, Nahid H Hajrah, Ahmed Atef, Mohammed Al-Matary, Sherif Edris, Mona G Alharbi, Magdah Ganash, Jazem Mahyoub, Rashad R Al-Hindi, Khalid M Al-Ghamdi, Neil Hall, Ahmed Bahieldin, Majid R Kamli, Irfan A Rather

“…The study underpins barcode characterization of insect species collected from Saudi Arabia and explored functional constraints during evolution at the DNA and protein levels to expect the possible mechanisms of protein evolution in insects. Codon structure designated AT-biased insect barcode of the cytochrome C oxidase I (COI). …”
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Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. by Noah Ollikainen, René M de Jong, Tanja Kortemme

“…The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.…”
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The trouble with sliding windows and the selective pressure in BRCA1. by Karl Schmid, Ziheng Yang

“…Instead, likelihood ratio tests provide a more rigorous framework for detecting signals of natural selection affecting protein evolution. We demonstrate that a previous finding that a particular region of the BRCA1 gene experienced a synonymous rate reduction driven by purifying selection is likely an artifact of the sliding window analysis. …”
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Ancestral sequence reconstruction as a tool to study the evolution of wood decaying fungi by Iván Ayuso-Fernández, Gonzalo Molpeceres, Susana Camarero, Francisco Javier Ruiz-Dueñas, Angel T. Martínez

“…However, these tools provide scarce biochemical information of the organisms and systems of interest and are therefore very limited when they come to explain protein evolution. In the past decade, this limitation has been overcome by the development of ancestral sequence reconstruction (ASR) methods. …”
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Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis by Klingenspor Martin, Stoneking Mark, Jastroch Martin, Hughes David A

“…</p> <p>Results</p> <p>Models of adaptive evolution through phylogenetic analysis of amino acid sequences by maximum likelihood were implemented to determine the mode of UCP1 protein evolution in Eutherians. An increase in the rate of amino acid substitutions on the branch leading to Eutherians is observed, but is best explained by relaxed constraints, not positive selection. …”
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Structure and stability of the designer protein WRAP-T and its permutants by Bram Mylemans, Xiao Yin Lee, Ina Laier, Christine Helsen, Arnout R. D. Voet

“…These proteins are useful tools to study protein evolution of this very diverse fold. While the 7-bladed architecture is the most common, no symmetric 7-bladed monomer has been created and characterized so far. …”
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Functional determinants of protein assembly into homomeric complexes by L. Therese Bergendahl, Joseph A. Marsh

“…Overall we demonstrate a clear relationship between protein function and homomer symmetry that has important implications for understanding protein evolution, as well as for predicting protein function and quaternary structure.…”
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Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins by Tsoka Sophia, Hazelwood Lee, Espinosa Octavio, Freilich Shiri, Simon Michelle, Ainali Chrysanthi, Ouzounis Christos A, Hancock John M

“…We find evidence for two coalitions of proteins and the role of co-adaptation in protein evolution is identified and could be used in future research within a functional context.…”
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Evolutionary and physiological importance of hub proteins. by Nizar N Batada, Laurence D Hurst, Mike Tyers

“…In contrast, local connectivity does not correlate with the rate of protein evolution even in reliable datasets. This perhaps surprising lack of correlation with evolutionary rate appears in part to arise from the fact that hub proteins do not have a higher density of residues associated with binding. …”
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Usefulness of a Darwinian system in a biotechnological application: evolution of optical window fluorescent protein variants under selective pressure. by Ulrike Schoetz, Nikolaos C Deliolanis, David Ng, Jutta Pauli, Ute Resch-Genger, Enrico Kühn, Steffen Heuer, Wolfgang Beisker, Reinhard W Köster, Horst Zitzelsberger, Randolph B Caldwell

“…One particularly striking exception in the case of protein evolution is in the natural production of antibodies. …”
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Comparative analysis of the <it>Saccharomyces cerevisiae </it>and <it>Caenorhabditis elegans </it>protein interaction networks by Butcher Sarah, Huntley Derek, Abbott James, Swire Jonathan, Agrafioti Ino, Stumpf Michael PH

“…The signature of protein evolution is shaped by a protein's abundance in the organism and its function and the biological process it is involved in. …”
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Efficient translation initiation dictates codon usage at gene start by Kajetan Bentele, Paul Saffert, Robert Rauscher, Zoya Ignatova, Nils Blüthgen

“…The genetic code is degenerate; thus, protein evolution does not uniquely determine the coding sequence. …”
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Long non-coding RNAs as a source of new peptides by Jorge Ruiz-Orera, Xavier Messeguer, Juan Antonio Subirana, M Mar Alba

“…The patterns of ribosome protection are consistent with the translation of short peptides. lncRNAs show similar coding potential and sequence constraints than evolutionary young protein coding sequences, indicating that they play an important role in de novo protein evolution.…”
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How structural and physicochemical determinants shape sequence constraints in a functional enzyme. by Luciano A Abriata, Timothy Palzkill, Matteo Dal Peraro

“…These findings provide fundamental insights into the chemistry underlying protein evolution and design, by quantitating links between sequence and different protein traits, illuminating subtle and unexpected sequence-trait relationships and pinpointing what traits are sacrificed upon gain-of-function mutation.…”
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GC content across insect genomes: phylogenetic patterns, causes and consequences by Holland, P, Mulhair, P, Kyriacou, R

“…Despite dramatic AT-biased codon usage, we find no evidence that this has driven divergent protein evolution. We argue that the GC landscape of Lepidoptera, Diptera and Coleoptera genomes is influenced by GC-biased gene conversion, strongest in Lepidoptera, with some outlier taxa affected drastically by counteracting processes.…”

Exploring fold space preferences of new-born and ancient protein superfamilies by Edwards, H, Abeln, S, Deane, C

“…While we tend to define protein evolution in terms of sequence level mutations, insertions and deletions, it is hard to translate these processes to a more complete picture incorporating a polypeptide's structure and function. …”

A unified analysis of evolutionary and population constraint in protein domains highlights structural features and pathogenic sites by Stuart A. MacGowan, Fábio Madeira, Thiago Britto-Borges, Geoffrey J. Barton

“…Abstract Protein evolution is constrained by structure and function, creating patterns in residue conservation that are routinely exploited to predict structure and other features. …”
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Comparison of the frequency of functional SH3 domains with different limited sets of amino acids using mRNA display. by Junko Tanaka, Hiroshi Yanagawa, Nobuhide Doi

“…Application of this approach to various combinations of codons in protein sequences may be useful not only for clarifying the precise order of the amino acid expansion in the early stages of protein evolution but also for efficiently creating novel functional proteins in the laboratory.…”
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The role of local backrub motions in evolved and designed mutations. by Daniel A Keedy, Ivelin Georgiev, Edward B Triplett, Bruce R Donald, David C Richardson, Jane S Richardson

“…These results support the hypothesis that backrubs participate in natural protein evolution and validate their continued use for design of synthetic proteins.…”
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Estudio computacional de las relaciones evolutivas de los receptores ionotrópicos NMDA, AMPA y kainato en cuatro especies de primates by Francy Johanna Moreno-Pedraza, Leonardo Rene Lareo, Edgar Antonio Reyes-Montaño

“…We identified 91sequences for NMDA, AMPA and kainate receptors and analyzed with software for predicting secondary structure, phosphorylation sites,multiple alignments, selection of protein evolution models and phylogenetic prediction. Results. …”
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