Evolution of Protein Structure and Stability in Global Warming
暂无分享,去创建一个
[1] S. Barik. The Uniqueness of Tryptophan in Biology: Properties, Metabolism, Interactions and Localization in Proteins , 2020, International journal of molecular sciences.
[2] S. Akanuma,et al. Ancestral sequence reconstruction produces thermally stable enzymes with mesophilic enzyme-like catalytic properties , 2020, Scientific Reports.
[3] W. Szczuciński,et al. Temperature increase altered Daphnia community structure in artificially heated lakes: a potential scenario for a warmer future , 2020, Scientific Reports.
[4] S. Barik. Genus-specific pattern of intrinsically disordered central regions in the nucleocapsid protein of coronaviruses , 2020, Computational and Structural Biotechnology Journal.
[5] Shirisha Nagotu,et al. Chaperones and Proteostasis: Role in Parkinson’s Disease , 2020, Diseases.
[6] C. Schlötterer,et al. Long-Term Dynamics Among Wolbachia Strains During Thermal Adaptation of Their Drosophila melanogaster Hosts , 2020, Frontiers in Genetics.
[7] Ren Wei,et al. Thermophilic whole‐cell degradation of polyethylene terephthalate using engineered Clostridium thermocellum , 2020, Microbial biotechnology.
[8] S. Barik. The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them , 2020, Bioinformatics and biology insights.
[9] S. Barik,et al. Regulation of NF-kappa B and cell death by bacterial gingipains , 2020, bioRxiv.
[10] Y. Chao,et al. High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels , 2020, BMC Evolutionary Biology.
[11] I. Cristea,et al. Temporal dynamics of protein complex formation and dissociation during human cytomegalovirus infection , 2020, Nature Communications.
[12] A. S. Panja,et al. Protein stability governed by its structural plasticity is inferred by physicochemical factors and salt bridges , 2020, Scientific Reports.
[13] O. Galzitskaya,et al. How Quickly Do Proteins Fold and Unfold, and What Structural Parameters Correlate with These Values? , 2020, Biomolecules.
[14] Ren Wei,et al. Microplastic pollution in water and sediment in a textile industrial area. , 2019, Environmental pollution.
[15] S. Barik. Molecular Interactions between Pathogens and the Circadian Clock , 2019, International journal of molecular sciences.
[16] R. Isticato,et al. Bacillus subtilis builds structurally and functionally different spores in response to the temperature of growth. , 2019, Environmental microbiology.
[17] Cong T. Trinh,et al. Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables isobutyl acetate production directly from cellulose by Clostridium thermocellum at elevated temperatures , 2019, Biotechnology for Biofuels.
[18] Saurav Mallik,et al. Finding the generalized molecular principles of protein thermal stability , 2019, Proteins.
[19] S. Barik. Protein Tetratricopeptide Repeat and the Companion Non-tetratricopeptide Repeat Helices: Bioinformatic Analysis of Interhelical Interactions , 2019, Bioinformatics and biology insights.
[20] Amanda K Garcia,et al. How to resurrect ancestral proteins as proxies for ancient biogeochemistry. , 2019, Free radical biology & medicine.
[21] David Baker,et al. What has de novo protein design taught us about protein folding and biophysics? , 2019, Protein science : a publication of the Protein Society.
[22] L. Itzhaki,et al. The tetratricopeptide-repeat motif is a versatile platform that enables diverse modes of molecular recognition. , 2019, Current opinion in structural biology.
[23] C. Cardoso,et al. Effect of temperature on survival and cuticular composition of three different ant species. , 2019, Journal of thermal biology.
[24] Philippa C. Griffin,et al. Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species , 2019, BMC Genomics.
[25] C. Evilia,et al. The more adaptive to change, the more likely you are to survive: Protein adaptation in extremophiles. , 2018, Seminars in cell & developmental biology.
[26] C. Brussaard,et al. Influence of Irradiance and Temperature on the Virus MpoV-45T Infecting the Arctic Picophytoplankter Micromonas polaris , 2018, Viruses.
[27] Stefani A. Crabtree,et al. Emergent sustainability in open property regimes , 2018, Proceedings of the National Academy of Sciences.
[28] Doug Barrick,et al. Consensus sequence design as a general strategy to create hyperstable, biologically active proteins , 2018, Proceedings of the National Academy of Sciences.
[29] M. F. Khan,et al. Deciphering the rationale behind specific codon usage pattern in extremophiles , 2018, Scientific Reports.
[30] G. Procaccini,et al. Investigating cellular stress response to heat stress in the seagrass Posidonia oceanica in a global change scenario. , 2018, Marine environmental research.
[31] Anne D. Bjorkman,et al. Plant functional trait change across a warming tundra biome , 2018, Nature.
[32] J. Kim,et al. Thermophilic Proteins as Versatile Scaffolds for Protein Engineering , 2018, Microorganisms.
[33] M. Benton. Hyperthermal-driven mass extinctions: killing models during the Permian–Triassic mass extinction , 2018, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
[34] J. Overpeck,et al. Past and future global transformation of terrestrial ecosystems under climate change , 2018, Science.
[35] B. Elderd,et al. Climate change and an invasive, tropical milkweed: an ecological trap for monarch butterflies. , 2018 .
[36] M. Hilker,et al. Phenotypic Plasticity of Cuticular Hydrocarbon Profiles in Insects , 2018, Journal of Chemical Ecology.
[37] S. O’Donnell,et al. Complex body size differences in thermal tolerance among army ant workers (Eciton burchellii parvispinum). , 2018, Journal of thermal biology.
[38] U. Bastolla,et al. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. , 2017, Systematic biology.
[39] A. Airo,et al. The Adaptability of Life on Earth and the Diversity of Planetary Habitats , 2017, Front. Microbiol..
[40] Satoshi Akanuma,et al. Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere , 2017, Life.
[41] S. Barik. On the role, ecology, phylogeny, and structure of dual-family immunophilins , 2017, Cell Stress and Chaperones.
[42] Renyu Hu,et al. Exoplanet Biosignatures: A Review of Remotely Detectable Signs of Life , 2017, Astrobiology.
[43] X. Cerdá,et al. Is phenotypic plasticity a key mechanism for responding to thermal stress in ants? , 2017, The Science of Nature.
[44] M. Hansen,et al. Hormetic heat stress and HSF-1 induce autophagy to improve survival and proteostasis in C. elegans , 2017, Nature Communications.
[45] Steffen Kutter,et al. Evolutionary drivers of thermoadaptation in enzyme catalysis , 2017, Science.
[46] Antonella Rossati,et al. Global Warming and Its Health Impact , 2016, The international journal of occupational and environmental medicine.
[47] R. Cavicchioli,et al. Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function , 2016, Scientific Reports.
[48] Filipa L. Sousa,et al. The physiology and habitat of the last universal common ancestor , 2016, Nature Microbiology.
[49] J. Capelo,et al. Ocean warming alters cellular metabolism and induces mortality in fish early life stages: A proteomic approach. , 2016, Environmental research.
[50] M. Slatkin,et al. Ancient DNA and human history , 2016, Proceedings of the National Academy of Sciences.
[51] S. Akanuma,et al. Epistasis effects of multiple ancestral-consensus amino acid substitutions on the thermal stability of glycerol kinase from Cellulomonas sp. NT3060. , 2016, Journal of bioscience and bioengineering.
[52] Weontae Lee,et al. Probing the Folding-Unfolding Transition of a Thermophilic Protein, MTH1880 , 2016, PloS one.
[53] Robert M. Kelly,et al. Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals , 2015, Front. Microbiol..
[54] Lennart Nilsson,et al. Rigidity versus flexibility: the dilemma of understanding protein thermal stability , 2015, The FEBS journal.
[55] A. Yamagishi,et al. Ancestral amino acid substitution improves the thermal stability of recombinant lignin-peroxidase from white-rot fungi, Phanerochaete chrysosporium strain UAMH 3641. , 2015, Protein engineering, design & selection : PEDS.
[56] J. W. Heal,et al. Does deamidation cause protein unfolding? A top‐down tandem mass spectrometry study , 2015, Protein science : a publication of the Protein Society.
[57] U. Bastolla,et al. Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability. , 2015, Molecular biology and evolution.
[58] Yang Zhang,et al. The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.
[59] K. Bidle,et al. Temperature-Induced Viral Resistance in Emiliania huxleyi (Prymnesiophyceae) , 2014, PloS one.
[60] Soumitra Polley,et al. Inhibitor-Induced Conformational Stabilization and Structural Alteration of a Mip-Like Peptidyl Prolyl cis-trans Isomerase and Its C-Terminal Domain , 2014, PloS one.
[61] Yanrui Ding,et al. Comparison of protein-water interactions in psychrophilic, mesophilic, and thermophilic Fe-SOD. , 2014, Protein and peptide letters.
[62] A. Barkan,et al. Pentatricopeptide repeat proteins in plants. , 2014, Annual review of plant biology.
[63] Igor N. Berezovsky,et al. Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins , 2013, Nucleic acids research.
[64] P. Woo,et al. Discovery of a Novel Bottlenose Dolphin Coronavirus Reveals a Distinct Species of Marine Mammal Coronavirus in Gammacoronavirus , 2013, Journal of Virology.
[65] Haiquan Yang,et al. In Silico Rational Design and Systems Engineering of Disulfide Bridges in the Catalytic Domain of an Alkaline α-Amylase from Alkalimonas amylolytica To Improve Thermostability , 2013, Applied and Environmental Microbiology.
[66] Saurav Mallik,et al. A Comparison of Structural and Evolutionary Attributes of Escherichia coli and Thermus thermophilus Small Ribosomal Subunits: Signatures of Thermal Adaptation , 2013, PloS one.
[67] S. Kanaya,et al. Evolvability of thermophilic proteins from archaea and bacteria. , 2013, Biochemistry.
[68] S. Akanuma,et al. Experimental evidence for the thermophilicity of ancestral life , 2013, Proceedings of the National Academy of Sciences.
[69] Rita L. Wong,et al. Asparagine deamidation dependence on buffer type, pH, and temperature. , 2013, Journal of pharmaceutical sciences.
[70] Nicholas Sawyer,et al. All repeats are not equal: a module-based approach to guide repeat protein design. , 2013, Journal of molecular biology.
[71] M Michael Gromiha,et al. Hydrophobic environment is a key factor for the stability of thermophilic proteins , 2013, Proteins.
[72] Andrey V Kajava,et al. Tandem repeats in proteins: from sequence to structure. , 2012, Journal of structural biology.
[73] T. Fricaux,et al. An insect-specific P450 oxidative decarbonylase for cuticular hydrocarbon biosynthesis , 2012, Proceedings of the National Academy of Sciences.
[74] J. Carter,et al. Neoarchean deep marine paleotemperature: Evidence from turbidite successions , 2011 .
[75] Ian K. Blaby,et al. Experimental Evolution of a Facultative Thermophile from a Mesophilic Ancestor , 2011, Applied and Environmental Microbiology.
[76] E. K. Pikitch,et al. Trophic Downgrading of Planet Earth , 2011, Science.
[77] F. Miralles. Compositional and Structural Features Related to Thermal Stability in the Archaea SRP19 and SRP54 Signal Recognition Particle Proteins , 2011, Journal of Molecular Evolution.
[78] P. Kosuri,et al. Single-molecule paleoenzymology probes the chemistry of resurrected enzymes , 2011, Nature Structural &Molecular Biology.
[79] J. Buchner,et al. The heat shock response: life on the verge of death. , 2010, Molecular cell.
[80] John Orban,et al. Proteins that switch folds. , 2010, Current opinion in structural biology.
[81] S. Kanaya,et al. Open Access Research Article Evolution and Thermodynamics of the Slow Unfolding of Hyperstable Monomeric Proteins , 2022 .
[82] M. Harms,et al. Analyzing protein structure and function using ancestral gene reconstruction. , 2010, Current opinion in structural biology.
[83] R. Cheng,et al. Roles of cysteines Cys115 and Cys201 in the assembly and thermostability of grouper betanodavirus particles , 2010, Virus Genes.
[84] C. Spash. The Brave New World of Carbon Trading , 2009 .
[85] Iosif I Vaisman,et al. Discrimination of thermophilic and mesophilic proteins , 2009, 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop.
[86] Kirk R. Klausmeyer,et al. Climate Change, Habitat Loss, Protected Areas and the Climate Adaptation Potential of Species in Mediterranean Ecosystems Worldwide , 2009, PloS one.
[87] U. Arnold,et al. The effect of additional disulfide bonds on the stability and folding of ribonuclease A. , 2009, Biophysical chemistry.
[88] Jim Warwicker,et al. Stability and solubility of proteins from extremophiles. , 2009, Biochemical and biophysical research communications.
[89] S. Melchionna,et al. Key role of proximal water in regulating thermostable proteins. , 2009, The journal of physical chemistry. B.
[90] Brian F. Volkman,et al. Interconversion between two unrelated protein folds in the lymphotactin native state , 2008, Proceedings of the National Academy of Sciences.
[91] K. Mihindukulasuriya,et al. Identification of a Novel Coronavirus from a Beluga Whale by Using a Panviral Microarray , 2008, Journal of Virology.
[92] Piero Calosi,et al. Thermal tolerance, acclimatory capacity and vulnerability to global climate change , 2008, Biology Letters.
[93] S. Govindarajan,et al. Palaeotemperature trend for Precambrian life inferred from resurrected proteins , 2008, Nature.
[94] François Stricher,et al. How Protein Stability and New Functions Trade Off , 2008, PLoS Comput. Biol..
[95] C. Suttle. Marine viruses — major players in the global ecosystem , 2007, Nature Reviews Microbiology.
[96] J. Weissman,et al. A Molecular Caliper Mechanism for Determining Very Long-Chain Fatty Acid Length , 2007, Cell.
[97] M. Brunori,et al. Identification and characterization of protein folding intermediates. , 2007, Biophysical chemistry.
[98] Pernilla Turner,et al. Potential and utilization of thermophiles and thermostable enzymes in biorefining , 2007, Microbial cell factories.
[99] Kenji Mizuguchi,et al. Environment specific substitution tables for thermophilic proteins , 2007, BMC Bioinformatics.
[100] Manel Camps,et al. Genetic Constraints on Protein Evolution , 2007, Critical reviews in biochemistry and molecular biology.
[101] E. Pikuta,et al. Microbial Extremophiles at the Limits of Life , 2007, Critical reviews in microbiology.
[102] J. King,et al. Glutamine Deamidation Destabilizes Human γD-Crystallin and Lowers the Kinetic Barrier to Unfolding* , 2006, Journal of Biological Chemistry.
[103] D. P. Remeta,et al. Energetics of membrane protein folding and stability. , 2006, Archives of biochemistry and biophysics.
[104] K. Stetter. History of discovery of the first hyperthermophiles , 2006, Extremophiles.
[105] Igor N. Berezovsky,et al. Protein and DNA Sequence Determinants of Thermophilic Adaptation , 2006, PLoS Comput. Biol..
[106] J. M. Scholtz,et al. Lessons in stability from thermophilic proteins , 2006, Protein science : a publication of the Protein Society.
[107] F. Arnold,et al. Protein stability promotes evolvability. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[108] M. Porcelli,et al. The crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase II from Sulfolobus solfataricus, a thermophilic enzyme stabilized by intramolecular disulfide bonds. , 2006, Journal of molecular biology.
[109] B. Snel,et al. Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.
[110] Adam Godzik,et al. Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. , 2006, Journal of molecular biology.
[111] M. Sadeghi,et al. Effective factors in thermostability of thermophilic proteins. , 2006, Biophysical chemistry.
[112] J. Bowie. Solving the membrane protein folding problem , 2005, Nature.
[113] M. DePristo,et al. Missense meanderings in sequence space: a biophysical view of protein evolution , 2005, Nature Reviews Genetics.
[114] S. Barik,et al. A Novel Class of Dual-family Immunophilins* , 2005, Journal of Biological Chemistry.
[115] X. Xia,et al. Genetic Variation in Clones of Pseudomonas pseudoalcaligenes After Ten Months of Selection in Different Thermal Environments in the Laboratory , 2005, Current Microbiology.
[116] A. Yamagishi,et al. Thermostability of ancestral mutants of Caldococcus noboribetus isocitrate dehydrogenase. , 2005, FEMS microbiology letters.
[117] S. Pack,et al. Protein thermostability: structure-based difference of amino acid between thermophilic and mesophilic proteins. , 2004, Journal of biotechnology.
[118] A. Fersht,et al. Phi-value analysis and the nature of protein-folding transition states. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[119] David Baker,et al. Searching for folded proteins in vitro and in silico. , 2004, European journal of biochemistry.
[120] Paramvir S. Dehal,et al. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. , 2003, Genome research.
[121] M. Grubb. The Economics of the Kyoto Protocol , 2003 .
[122] Yong Xiong,et al. Design of stable alpha-helical arrays from an idealized TPR motif. , 2003, Structure.
[123] S. Schneider,et al. Fingerprints of global warming on wild animals and plants , 2003, Nature.
[124] R. Ostfeld,et al. Climate Warming and Disease Risks for Terrestrial and Marine Biota , 2002, Science.
[125] A. Karshikoff,et al. Ion pairs and the thermotolerance of proteins from hyperthermophiles: a "traffic rule" for hot roads. , 2001, Trends in biochemical sciences.
[126] T. Suzuki,et al. Ancestral residues stabilizing 3-isopropylmalate dehydrogenase of an extreme thermophile: experimental evidence supporting the thermophilic common ancestor hypothesis. , 2001, Journal of biochemistry.
[127] C. Vieille,et al. Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability , 2001, Microbiology and Molecular Biology Reviews.
[128] A F Bennett,et al. Genetic architecture of thermal adaptation in Escherichia coli. , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[129] R. Maheshwari,et al. Thermophilic Fungi: Their Physiology and Enzymes , 2000, Microbiology and Molecular Biology Reviews.
[130] A. Szilágyi,et al. Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. , 2000, Structure.
[131] Udo Heinemann,et al. Two exposed amino acid residues confer thermostability on a cold shock protein , 2000, Nature Structural Biology.
[132] C. Vieille,et al. Molecular determinants of xylose isomerase thermal stability and activity: analysis of thermozymes by site-directed mutagenesis. , 2000, Protein engineering.
[133] R. Nussinov,et al. Factors enhancing protein thermostability. , 2000, Protein engineering.
[134] Hughes,et al. Biological consequences of global warming: is the signal already apparent? , 2000, Trends in ecology & evolution.
[135] G. Olsen,et al. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[136] S. Kim,et al. Crystal structure of the β‐glycosidase from the hyperthermophile Thermosphaera aggregans: insights into its activity and thermostability , 1999, FEBS letters.
[137] H. Oki,et al. Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus. , 1998, Journal of molecular biology.
[138] R. Kelly,et al. The family 1 beta-glucosidases from Pyrococcus furiosus and Agrobacterium faecalis share a common catalytic mechanism. , 1998, Biochemistry.
[139] R. Jaenicke,et al. Recombinant phosphoglycerate kinase from the hyperthermophilic bacterium Thermotoga maritima: catalytic, spectral and thermodynamic properties. , 1998, Journal of molecular biology.
[140] R. Huber,et al. Lactate dehydrogenase from the hyperthermophilic bacterium thermotoga maritima: the crystal structure at 2.1 A resolution reveals strategies for intrinsic protein stabilization. , 1998, Structure.
[141] S. Akanuma,et al. Serial increase in the thermal stability of 3‐isopropylmalate dehydrogenase from Bacillus subtilis by experimental evolution , 1998, Protein science : a publication of the Protein Society.
[142] Seiki Kuramitsu,et al. Insights into thermal resistance of proteins from the intrinsic stability of their α‐helices , 1997 .
[143] G. Taylor,et al. The crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 A resolution,. , 1997, Biochemistry.
[144] T. Oshima,et al. Screening of stable proteins in an extreme thermophile, Thermus thermophilus , 1995, Molecular microbiology.
[145] B K Shoichet,et al. A relationship between protein stability and protein function. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[146] P. Reilly,et al. Substitution of asparagine residues in Aspergillus awamori glucoamylase by site-directed mutagenesis to eliminate N-glycosylation and inactivation by deamidation. , 1994, The Biochemical journal.
[147] A. Lesk,et al. Structural mechanisms for domain movements in proteins. , 1994, Biochemistry.
[148] N. Eldredge,et al. Punctuated equilibrium comes of age , 1993, Nature.
[149] R. Morimoto,et al. Cells in stress: transcriptional activation of heat shock genes. , 1993, Science.
[150] P. Zwickl,et al. Glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaebacterium Pyrococcus woesei: characterization of the enzyme, cloning and sequencing of the gene, and expression in Escherichia coli , 1990, Journal of bacteriology.
[151] B. Matthews,et al. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[152] C. Woese,et al. Rooting the archaebacterial tree: the pivotal role of Thermococcus celer in archaebacterial evolution. , 1988, Systematic and applied microbiology.
[153] A. Klibanov,et al. Mechanisms of irreversible thermal inactivation of Bacillus alpha-amylases. , 1988, The Journal of biological chemistry.
[154] C. Chothia,et al. Helix to helix packing in proteins. , 1981, Journal of molecular biology.
[155] A M Lesk,et al. Solvent accessibility, protein surfaces, and protein folding. , 1980, Biophysical journal.
[156] L. Excoffier,et al. Consequences of range contractions and range shifts on molecular diversity. , 2012, Molecular biology and evolution.
[157] F. Arnold,et al. How proteins adapt: lessons from directed evolution. , 2009, Cold Spring Harbor symposia on quantitative biology.
[158] I. Jonassen,et al. Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role , 2008, Extremophiles.
[159] X.-X. Zhou,et al. Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins , 2007, Amino Acids.
[160] J. Kingsolver,et al. Biophysics, physiological ecology, and climate change: does mechanism matter? , 2005, Annual review of physiology.
[161] A. Fersht,et al. Is there a unifying mechanism for protein folding? , 2003, Trends in biochemical sciences.
[162] G. Petsko. Structural basis of thermostability in hyperthermophilic proteins, or "there's more than one way to skin a cat". , 2001, Methods in enzymology.