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Original Articles

Comparative Molecular Dynamics of Mesophilic and Psychrophilic Protein Homologues Studied by 1.2 ns Simulations

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Pages 493-506 | Received 31 May 1999, Published online: 21 May 2012

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Xing Du, Peng Sang, Yuan-Ling Xia, Yi Li, Jing Liang, Shi-Meng Ai, Xing-Lai Ji, Yun-Xin Fu & Shu-Qun Liu. (2017) Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics 35:7, pages 1500-1517.
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D. Benrezkallah, M. Dauchez & A.M. Krallafa. (2015) Molecular dynamics of the salt dependence of a cold-adapted enzyme: endonuclease I. Journal of Biomolecular Structure and Dynamics 33:11, pages 2511-2521.
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Articles from other publishers (28)

Jens Guðmundur Hjörleifsson, Ronny Helland, Manuela Magnúsdóttir & Bjarni Ásgeirsson. (2020) The high catalytic rate of the cold‐active Vibrio alkaline phosphatase requires a hydrogen bonding network involving a large interface loop . FEBS Open Bio 11:1, pages 173-184.
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Gislaine Fongaro, Guilherme Augusto Maia, Paula Rogovski, Rafael Dorighello Cadamuro, Joana Camila Lopes, Renato Simões Moreira, Aline Frumi Camargo, Thamarys Scapini, Fábio Spitza Stefanski, Charline Bonatto, Doris Sobral Marques Souza, Patrícia Hermes Stoco, Rubens Tadeu Delgado Duarte, Ariadne Cristiane Cabral da Cruz, Glauber Wagner & Helen Treichel. (2020) Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools. Current Genomics 21:4, pages 240-252.
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Yuan-Ling Xia, Jian-Hong Sun, Shi-Meng Ai, Yi Li, Xing Du, Peng Sang, Li-Quan Yang, Yun-Xin Fu & Shu-Qun Liu. (2018) Insights into the role of electrostatics in temperature adaptation: a comparative study of psychrophilic, mesophilic, and thermophilic subtilisin-like serine proteases. RSC Advances 8:52, pages 29698-29713.
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Jun Hyuck Lee, Jin Myung Choi & Hak Jun Kim. (2017) Crystal structure of 5-enolpyruvylshikimate-3-phosphate synthase from a psychrophilic bacterium, Colwellia psychrerythraea 34H. Biochemical and Biophysical Research Communications 492:3, pages 500-506.
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Davide Michetti, Bjørn Olav Brandsdal, Davide Bon, Geir Villy Isaksen, Matteo Tiberti & Elena Papaleo. (2017) A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations. PLOS ONE 12:2, pages e0169586.
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Elena Papaleo, Matteo Tiberti & Gaetano Invernizzi. 2016. Biotechnology of Extremophiles:. Biotechnology of Extremophiles: 675 698 .
Yong-Geun Choi, Chin-Ju Park, Hee-Eun Kim, Yeo-Jin Seo, Ae-Ree Lee, Seo-Ree Choi, Shim Sung Lee & Joon-Hwa Lee. (2015) Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase. Journal of Biomolecular NMR 61:2, pages 137-150.
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Geir Villy Isaksen, Johan Åqvist & Bjørn Olav Brandsdal. (2014) Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin. PLoS Computational Biology 10:8, pages e1003813.
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So Yeon Hong, Hyun June Park & Young Je Yoo. (2014) Flexibility analysis of activity-enhanced mutants of bacteriophage T4 lysozyme. Journal of Molecular Catalysis B: Enzymatic 106, pages 95-99.
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Georges Feller. (2013) Psychrophilic Enzymes: From Folding to Function and Biotechnology. Scientifica 2013, pages 1-28.
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Deeptak Verma, Donald J. Jacobs & Dennis R. Livesay. (2012) Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged. PLoS Computational Biology 8:3, pages e1002409.
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Michael C. FlickingerSandeep Kumar, Satish K. Singh & M. Michael Gromiha. 2009. Encyclopedia of Industrial Biotechnology. Encyclopedia of Industrial Biotechnology 1 22 .
Sangeeta Kundu & Debjani Roy. (2009) Comparative structural studies of psychrophilic and mesophilic protein homologues by molecular dynamics simulation. Journal of Molecular Graphics and Modelling 27:8, pages 871-880.
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Helga Margrét Pálsdóttir & Ágústa Gudmundsdóttir. (2008) The novel trypsin Y from Atlantic cod (Gadus morhua) – isolation, purification and characterisation. Food Chemistry 111:2, pages 408-414.
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Inger Lin Uttakleiv Ræder, Ingar Leiros, Nils Peder Willassen, Arne O. Smalås & Elin Moe. (2008) Uracil-DNA N-glycosylase (UNG) from the marine, psychrophilic bacterium Vibrio salmonicida shows cold adapted features. Enzyme and Microbial Technology 42:7, pages 594-600.
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Elena Papaleo, Marco Pasi, Laura Riccardi, Ilaria Sambi, Piercarlo Fantucci & Luca De Gioia. (2008) Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases. FEBS Letters 582:6, pages 1008-1018.
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Magne Olufsen, Arne O. Smalås & Bjørn O. Brandsdal. (2008) Electrostatic interactions play an essential role in DNA repair and cold-adaptation of Uracil DNA glycosylase. Journal of Molecular Modeling 14:3, pages 201-213.
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Tony Collins, Frédéric Roulling, Florence Piette, Jean-Claude Marx, Georges Feller, Charles Gerday & Salvino D'Amico. 2008. Psychrophiles: from Biodiversity to Biotechnology. Psychrophiles: from Biodiversity to Biotechnology 211 227 .
Sandeep Kumar, Sunil Arya & Ruth Nussinov. 2007. Physiology and Biochemistry of Extremophiles. Physiology and Biochemistry of Extremophiles 75 85 .
Tony Collins, Salvino D'Amico, Jean-Claude Marx, Georges Feller & Charles Gerday. 2007. Physiology and Biochemistry of Extremophiles. Physiology and Biochemistry of Extremophiles 165 179 .
Vojtěch Spiwok, Petra Lipovová, Tereza Skálová, Jarmila Dušková, Jan Dohnálek, Jindřich Hašek, Nicholas J. Russell & Blanka Králová. (2007) Cold-active enzymes studied by comparative molecular dynamics simulation. Journal of Molecular Modeling 13:4, pages 485-497.
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Bjarni Ásgeirsson & Pavol Cekan. (2006) Microscopic rate-constants for substrate binding and acylation in cold-adaptation of trypsin I from Atlantic cod. FEBS Letters 580:19, pages 4639-4644.
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Elena Papaleo, Laura Riccardi, Chiara Villa, Piercarlo Fantucci & Luca De Gioia. (2006) Flexibility and enzymatic cold-adaptation: A comparative molecular dynamics investigation of the elastase family. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1764:8, pages 1397-1406.
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Khawar Sohail SiddiquiRicardo Cavicchioli. (2006) Cold-Adapted Enzymes. Annual Review of Biochemistry 75:1, pages 403-433.
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Elena Papaleo, Piercarlo Fantucci & Luca De Gioia. (2005) Effects of Calcium Binding on Structure and Autolysis Regulation in Trypsins. A Molecular Dynamics Investigation. Journal of Chemical Theory and Computation 1:6, pages 1286-1297.
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Bjarni Ásgeirsson & Ólafur S. Andrésson. (2001) Primary structure of cold-adapted alkaline phosphatase from a Vibrio sp. as deduced from the nucleotide gene sequence. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1549:1, pages 99-111.
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Bjørn Olav Brandsdal, Arne O. Smalås & Johan Åqvist. (2001) Electrostatic effects play a central role in cold adaptation of trypsin. FEBS Letters 499:1-2, pages 171-175.
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Thierry Lonhienne, Charles Gerday & Georges Feller. (2000) Psychrophilic enzymes: revisiting the thermodynamic parameters of activation may explain local flexibility. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1543:1, pages 1-10.
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