Searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis by Heng Xiang, Ruizhi Zhang, Nengzhang Li, Charles R. Vossbrinck

“…Major ecological adaptations such as flight, loss of limbs in vertebrates, pesticide resistance, adaptation to a parasitic way of life, etc., have all evolved more than once, as seen by their analogous functions in separate taxa. But what about protein evolution? Does the environment have a strong enough influence on intracellular processes that enzymes and other functional proteins play, to evolve similar functional roles separately in different organisms? …”
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Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages by Huilong Chen, Yingchao Zhang, Shuyan Feng

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The combined effects of amino acid substitutions and indels on the evolution of structure within protein families. by Zheng Zhang, Yuxiao Wang, Lushan Wang, Peiji Gao

“…BACKGROUND: In the process of protein evolution, sequence variations within protein families can cause changes in protein structures and functions. …”
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Searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis by Heng Xiang, Ruizhi Zhang, Nengzhang Li, Charles R. Vossbrinck

“…Major ecological adaptations such as flight, loss of limbs in vertebrates, pesticide resistance, adaptation to a parasitic way of life, etc., have all evolved more than once, as seen by their analogous functions in separate taxa. But what about protein evolution? Does the environment have a strong enough influence on intracellular processes that enzymes and other functional proteins play, to evolve similar functional roles separately in different organisms? …”
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The odds of duplicate gene persistence after polyploidization by Chain Frédéric JJ, Dushoff Jonathan, Evans Ben J

“…Using logistic regression, we demonstrate that the most important predictors of the odds of duplicate gene persistence in the tetraploid species are the total gene expression level and evenness of expression across tissues and development in the diploid species. Slow protein evolution and information density (fewer exons, shorter introns) in the diploid are also positively correlated with duplicate gene persistence in the tetraploid.…”
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Duplicate abalone egg coat proteins bind sperm lysin similarly, but evolve oppositely, consistent with molecular mimicry at fertilization. by Jan E Aagaard, Stevan A Springer, Scott D Soelberg, Willie J Swanson

“…We use evidence of such molecular co-evolution to target biochemical studies of fertilization in North Pacific abalone (Haliotis spp.), a model system of reproductive protein evolution. We test the evolutionary rates (d(N)/d(S)) of abalone sperm lysin and two duplicated egg coat proteins (VERL and VEZP14), and find a signal of co-evolution specific to ZP-N, a putative sperm binding motif previously identified by homology modeling. …”
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AIB1/SRC-3/NCOA3 function in estrogen receptor alpha positive breast cancer by Amber J. Kiliti, Amber J. Kiliti, Ghada M. Sharif, Mary Beth Martin, Mary Beth Martin, Anton Wellstein, Anna T. Riegel

“…Here we review the normal and pathological functions of AIB1 in regard to its ERα-dependent and ERα-independent actions, as well as its genomic conservation and protein evolution. We also outline the efforts to target AIB1 in the treatment of breast cancer.…”
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Identifying essential proteins in dynamic protein networks based on an improved h-index algorithm by Caiyan Dai, Ju He, Kongfa Hu, Youwei Ding

“…Abstract Background The essential proteins in protein networks play an important role in complex cellular functions and in protein evolution. Therefore, the identification of essential proteins in a network can help to explain the structure, function, and dynamics of basic cellular networks. …”
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Directed Chemical Evolution with an Outsized Genetic Code. by Casey J Krusemark, Nicolas P Tilmans, Patrick O Brown, Pehr B Harbury

“…Importantly, there is still no small-molecule analog of directed protein evolution, i.e. a substantiated approach for optimizing complex (≥ 10^9 diversity) populations of synthetic small molecules over successive generations. …”
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An interactive visualization tool to explore the biophysical properties of amino acids and their contribution to substitution matrices by desJardins Marie, Bulka Blazej, Freeland Stephen J

“…</p> <p>Results</p> <p>We demonstrate the three fundamental types of question that our software can address by taking as a specific example the connections between 49 measures of amino acid biophysical properties (e.g., size, charge and hydrophobicity), a generalized model of amino acid substitution (as represented by the PAM74-100 matrix), and the mutational distance that separates amino acids within the standard genetic code (i.e., the number of point mutations required for interconversion during protein evolution). We show that our software allows a user to recapture the insights from several key publications on these topics in just a few minutes.…”
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GnRH-Related Neurohormones in the Fruit Fly <i>Drosophila melanogaster</i> by David Ben-Menahem

“…Of note, while GnRH has a key role in reproduction, AKH and CRZ show pleiotropic activities in the adult fly, primarily in metabolism and stress responses. From a protein evolution standpoint, the GnRH/AKH/CRZ family nicely demonstrates the developmental process of neuropeptide signaling systems emerging from a putative common ancestor and leading to divergent activities in distal phyla.…”
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Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins by Xiaoyan Gu, Adrian Brennan, Wenbin Wei, Guangqin Guo, Keith Lindsey

“…These results provide an insight into SNARE protein evolution and functional specialization. The work provides a platform for hypothesis-building and future research into the precise functions of these proteins in plant development and responses to the environment.…”
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Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi by Huynen Leon, Subramanian Sankar, Millar Craig D, Lambert David M

“…Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes.…”
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Extracting phylogenetic dimensions of coevolution reveals hidden functional signals by Alexandre Colavin, Esha Atolia, Anne-Florence Bitbol, Kerwyn Casey Huang

“…Thus, our conceptualization of the phylogenetic separation of coevolution provides the potential to further elucidate relationships among protein evolution, function, and genetic diseases.…”
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CodonTest: modeling amino acid substitution preferences in coding sequences. by Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B Gravenor, Spencer V Muse, Sergei L Kosakovsky Pond

“…Our results suggest that current models are poor approximations of protein evolution and thus gene and organism specific multi-rate models that incorporate amino acid substitution biases are preferred. …”
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In Silico/In Vivo Insights into the Functional and Evolutionary Pathway of Pseudomonas aeruginosa Oleate-Diol Synthase. Discovery of a New Bacterial Di-Heme Cytochrome C Peroxidase... by Mónica Estupiñán, Daniel Álvarez-García, Xavier Barril, Pilar Diaz, Angeles Manresa

“…Moreover, the presence of palindromic repeats located in enzyme-coding regions, acting as protein evolution elements, is reported here for the first time in P. aeruginosa genome. …”
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A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution by Ogbunugafor, C. Brandon, Hartl, Daniel

“…Few analogies have been as successful in communicating the basics of molecular evolution as John Maynard Smith’s protein space analogy (1970), in which he compared protein evolution to the transition between the terms WORD and GENE, changing one letter at a time to yield a different, meaningful word (in his example, the preferred path was WORD → WORE → GORE → GONE → GENE). …”
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Molecular evolution of genes in avian genomes. by Nam, K, Mugal, C, Nabholz, B, Schielzeth, H, Wolf, J, Backström, N, Künstner, A, Balakrishnan, C, Heger, A, Ponting, C, Clayton, D, Ellegren, H

“…We found no evidence that selection for beneficial alleles is more efficient in regions of high recombination; in fact, there was a weak yet significant negative correlation between omega and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution. These findings set the stage for studies of functional genetics of avian genes.…”

Secreted proteins defy the expression level–evolutionary rate anticorrelation by Feyertag, F, Berninsone, P, Alvarez-Ponce, D

“…A primary factor influencing rates of protein evolution is expression. A strong negative correlation between expression levels and evolutionary rates (the so-called E–R anticorrelation) has been observed in virtually all studied organisms. …”

Pleiotropy constrains the evolution of protein but not regulatory sequences in a transcription regulatory network influencing complex social behaviours by Daria eMolodtsova, Brock A Harpur, Clement F Kent, Kajendra eSeevananthan, Amro eZayed

“…Pleiotropy and connectedness are known to constrain the general rate of protein evolution, prompting some to suggest that the evolution of complex traits, including behaviour, is fuelled by regulatory sequence evolution. …”
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