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  • 1
    ISSN: 0020-1693
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Publication Date: 2014-06-17
    Description: Understanding how chance historical events shape evolutionary processes is a central goal of evolutionary biology. Direct insights into the extent and causes of evolutionary contingency have been limited to experimental systems, because it is difficult to know what happened in the deep past and to characterize other paths that evolution could have followed. Here we combine ancestral protein reconstruction, directed evolution and biophysical analysis to explore alternative 'might-have-been' trajectories during the ancient evolution of a novel protein function. We previously found that the evolution of cortisol specificity in the ancestral glucocorticoid receptor (GR) was contingent on permissive substitutions, which had no apparent effect on receptor function but were necessary for GR to tolerate the large-effect mutations that caused the shift in specificity. Here we show that alternative mutations that could have permitted the historical function-switching substitutions are extremely rare in the ensemble of genotypes accessible to the ancestral GR. In a library of thousands of variants of the ancestral protein, we recovered historical permissive substitutions but no alternative permissive genotypes. Using biophysical analysis, we found that permissive mutations must satisfy at least three physical requirements--they must stabilize specific local elements of the protein structure, maintain the correct energetic balance between functional conformations, and be compatible with the ancestral and derived structures--thus revealing why permissive mutations are rare. These findings demonstrate that GR evolution depended strongly on improbable, non-deterministic events, and this contingency arose from intrinsic biophysical properties of the protein.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447330/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447330/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harms, Michael J -- Thornton, Joseph W -- F32-GM090650/GM/NIGMS NIH HHS/ -- R01 GM081592/GM/NIGMS NIH HHS/ -- R01 GM104397/GM/NIGMS NIH HHS/ -- R01-GM081592/GM/NIGMS NIH HHS/ -- R01-GM104397/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Aug 14;512(7513):203-7. doi: 10.1038/nature13410. Epub 2014 Jun 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institute of Molecular Biology and Department of Chemistry &Biochemistry, University of Oregon, Eugene, Oregon 97403, USA [2] Departments of Human Genetics and Ecology &Evolution, University of Chicago, Chicago, Illinois 60637, USA. ; 1] Departments of Human Genetics and Ecology &Evolution, University of Chicago, Chicago, Illinois 60637, USA [2] Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24930765" target="_blank"〉PubMed〈/a〉
    Keywords: Biophysics ; *Evolution, Molecular ; Genotype ; Mutation/genetics ; Protein Conformation ; Protein Stability ; Receptors, Glucocorticoid/*chemistry/*genetics ; Saccharomyces cerevisiae ; Substrate Specificity ; Two-Hybrid System Techniques
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2012-01-11
    Description: Many cellular processes are carried out by molecular 'machines'-assemblies of multiple differentiated proteins that physically interact to execute biological functions. Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking. Here we use ancestral gene resurrection and manipulative genetic experiments to determine how the complexity of an essential molecular machine--the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump--increased hundreds of millions of years ago. We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3979732/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3979732/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Finnigan, Gregory C -- Hanson-Smith, Victor -- Stevens, Tom H -- Thornton, Joseph W -- R01 GM038006/GM/NIGMS NIH HHS/ -- R01-GM081592/GM/NIGMS NIH HHS/ -- R01-GM38006/GM/NIGMS NIH HHS/ -- T32-GM007257/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Jan 9;481(7381):360-4. doi: 10.1038/nature10724.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22230956" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Computational Biology ; *Evolution, Molecular ; Extinction, Biological ; Fungi/classification/*enzymology/genetics ; Gene Duplication ; *Models, Biological ; Mutagenesis ; Phylogeny ; Protein Conformation ; Saccharomyces cerevisiae/enzymology ; Vacuolar Proton-Translocating ATPases/*chemistry/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2016-04-29
    Description: The regulation of water content in polymeric membranes is important in a number of applications, such as reverse electrodialysis and proton-exchange fuel-cell membranes. External thermal and water management systems add both mass and size to systems, and so intrinsic mechanisms of retaining water and maintaining ionic transport in such membranes are particularly important for applications where small system size is important. For example, in proton-exchange membrane fuel cells, where water retention in the membrane is crucial for efficient transport of hydrated ions, by operating the cells at higher temperatures without external humidification, the membrane is self-humidified with water generated by electrochemical reactions. Here we report an alternative solution that does not rely on external regulation of water supply or high temperatures. Water content in hydrocarbon polymer membranes is regulated through nanometre-scale cracks ('nanocracks') in a hydrophobic surface coating. These cracks work as nanoscale valves to retard water desorption and to maintain ion conductivity in the membrane on dehumidification. Hydrocarbon fuel-cell membranes with surface nanocrack coatings operated at intermediate temperatures show improved electrochemical performance, and coated reverse-electrodialysis membranes show enhanced ionic selectivity with low bulk resistance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Chi Hoon -- Lee, So Young -- Hwang, Doo Sung -- Shin, Dong Won -- Cho, Doo Hee -- Lee, Kang Hyuck -- Kim, Tae-Woo -- Kim, Tae-Wuk -- Lee, Mokwon -- Kim, Deok-Soo -- Doherty, Cara M -- Thornton, Aaron W -- Hill, Anita J -- Guiver, Michael D -- Lee, Young Moo -- England -- Nature. 2016 Apr 28;532(7600):480-3. doi: 10.1038/nature17634.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Energy Engineering, College of Engineering, Hanyang University, Seoul 133-791, South Korea. ; Department of Life Science, College of Natural Science, Hanyang University, Seoul 133-791, South Korea. ; School of Mechanical Engineering, College of Engineering, Hanyang University, Seoul 133-791, South Korea. ; Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Clayton, Victoria 3168, Australia. ; State Key Laboratory of Engines, Tianjin University, Tianjin 300072, China. ; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27121841" target="_blank"〉PubMed〈/a〉
    Keywords: Biomimetic Materials/chemistry ; Biomimetics ; Cactaceae/metabolism ; Desiccation ; Dialysis ; Electrochemistry ; Humidity ; Hydrophobic and Hydrophilic Interactions ; *Membranes, Artificial ; *Nanotechnology ; Plant Stomata/metabolism ; Polymers/*chemistry ; Protons ; Surface Properties ; Temperature ; Water/*analysis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2018-04-25
    Description: Interactions among mutations within a protein have the potential to make molecular evolution contingent and irreversible, but the extent to which epistasis actually shaped historical evolutionary trajectories is unclear. To address this question, we experimentally measured how the fitness effects of historical sequence substitutions changed during the billion-year evolutionary history...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 6
    ISSN: 1618-2650
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Industrial & engineering chemistry 3 (1911), S. 419-420 
    ISSN: 1520-5045
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1618-2650
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1618-2650
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1618-2650
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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