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2 results on '"Suncheon National University [Suncheon, Corée du Sud]"'

1. Surface-based protein domains retrieval methods from a SHREC2021 challenge

Author

Florent Langenfeld, Tunde Aderinwale, Charles Christoffer, Woong-Hee Shin, Genki Terashi, Xiao Wang, Daisuke Kihara, Halim Benhabiles, Karim Hammoudi, Adnane Cabani, Feryal Windal, Mahmoud Melkemi, Ekpo Otu, Reyer Zwiggelaar, David Hunter, Yonghuai Liu, Léa Sirugue, Huu-Nghia H. Nguyen, Tuan-Duy H. Nguyen, Vinh-Thuyen Nguyen-Truong, Danh Le, Hai-Dang Nguyen, Minh-Triet Tran, Matthieu Montès, Laboratoire Génomique, bioinformatique et chimie moléculaire (GBCM), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Department of Computer Science [Purdue], Purdue University [West Lafayette], Suncheon National University [Suncheon, Corée du Sud], Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Bio-Micro-Electro-Mechanical Systems - IEMN (BIOMEMS - IEMN), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), JUNIA (JUNIA), Université catholique de Lille (UCL), Institut de Recherche en Informatique Mathématiques Automatique Signal - IRIMAS - UR 7499 (IRIMAS), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), Université de Strasbourg (UNISTRA), École Supérieure d’Ingénieurs en Génie Électrique (ESIGELEC), Aberystwyth University, Edge Hill University, Vietnam National University - Ho Chi Minh City (VNU-HCM), and Léa Sirugue, Matthieu Montès and Florent Langenfeld are supported by the European Research Council Executive Agency under the research grant number 640,283. Daisuke Kihara acknowledges supports from the National Institutes of Health (R01GM133840, R01GM123055) and the National Science Foundation (DBI2003635, CMMI1825941, and MCB1925643). Charles Christoffer is supported by NIGMS-funded pre–doctoral fellowship (T32 GM132024). Huu-Nghia H. Nguyen, Tuan-Duy H. Nguyen, Vinh-Thuyen Nguyen-Truong, Danh Le, Hai-Dang Nguyen, and Minh-Triet Tran are supported by National University Ho Chi Minh City (VNU-HCM) (DS2020-42-01).

Subjects
Models, Molecular, Static Electricity, Proteins, Ligands, Computer Graphics and Computer-Aided Design, Article, Proteins surface, [SPI]Engineering Sciences [physics], SHREC2021, Protein Domains, Materials Chemistry, Physical and Theoretical Chemistry, Spectroscopy, 2000 MSC: 92-08
Abstract

publication dans une revue suite à la communication hal-03467479 (SHREC 2021: surface-based protein domains retrieval); International audience; Proteins are essential to nearly all cellular mechanism and the effectors of the cells activities. As such, they often interact through their surface with other proteins or other cellular ligands such as ions or organic molecules. The evolution generates plenty of different proteins, with unique abilities, but also proteins with related functions hence similar 3D surface properties (shape, physico-chemical properties, …). The protein surfaces are therefore of primary importance for their activity. In the present work, we assess the ability of different methods to detect such similarities based on the geometry of the protein surfaces (described as 3D meshes), using either their shape only, or their shape and the electrostatic potential (a biologically relevant property of proteins surface). Five different groups participated in this contest using the shape-only dataset, and one group extended its pre-existing method to handle the electrostatic potential. Our comparative study reveals both the ability of the methods to detect related proteins and their difficulties to distinguish between highly related proteins. Our study allows also to analyze the putative influence of electrostatic information in addition to the one of protein shapes alone. Finally, the discussion permits to expose the results with respect to ones obtained in the previous contests for the extended method. The source codes of each presented method have been made available online.

Published
2022
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2. Hot mitochondria?

Author

Howard T. Jacobs, Pierre Rustin, Malgorzata Rak, Riyad El-Khoury, Hyung-Ho Ha, Paule Bénit, Young-Tae Chang, Martin Jastroch, Dominique Chretien, Susanne Keipert, Neuroprotection du Cerveau en Développement / Promoting Research Oriented Towards Early Cns Therapies (PROTECT), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), College of Pharmacy [Suncheon, Corée du Sud], Suncheon National University [Suncheon, Corée du Sud], Institute for Diabetes and Obesity [Neuherberg, Allemagne], German Research Center for Environmental Health - Helmholtz Center München (GmbH), Neuromuscular Diagnostic Laboratory [Beyrouth, Liban], Department of Pathology & Laboratory Medicine [Beyrouth, Liban], American University of Beirut Medical Center [Beyrouth, Liban] (AUBMC), American University of Beirut [Beyrouth] (AUB)-American University of Beirut [Beyrouth] (AUB)-American University of Beirut Medical Center [Beyrouth, Liban] (AUBMC), American University of Beirut [Beyrouth] (AUB)-American University of Beirut [Beyrouth] (AUB), Department of Chemistry [Pohang, Corée du Sud], Pohang University of Science and Technology (POSTECH), Institute of Biosciences and Medical Technology [Tampere, Finlande] (BioMediTech), University of Tampere [Finland], Tampere University Hospital, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Centre National de la Recherche Scientifique (CNRS), European Research Council (grant number 232738). Received by HTJ. Academy Professorship (grant number 256615). Received by HTJ. Academy of Finland (grant number FinMIT CoE 272376). Received by HTJ. Ouvrir Les Yeux (OLY). Received by PB and PR. Association Française contre l'Ataxie de Friedreich (AFAF). Received by PB and PR. Association contre les Maladies Mitochondriales (AMMi). Received by DC, PB, MR, and PR. Association d'Aide aux Jeunes Infirmes (AAJI). Received by PB and PR. E-Rare (grant number E-rare Genomit). Received by DC, PB, MR, and PR. ANR (grant number ANR MITOXDRUGS-DS0403). Received by DC, PB, MR, and PR. ANR (grant number ANR FIFA2-12-BSV1-0010). Received by DC, PB, MR, and PR., ANR-12-BSV1-0010,FiFA2,Combattre l'Ataxie de Friedreich: utilisation de modèles biologiques complémentaires pour le criblage et l'optimisation de nouvelles molécules thérapeutiques(2012), European Project: 232738,EC:FP7:ERC,ERC-2008-AdG,MITO BY-PASS(2009), University of Helsinki-University of Helsinki, Bodescot, Myriam, BLANC - Combattre l'Ataxie de Friedreich: utilisation de modèles biologiques complémentaires pour le criblage et l'optimisation de nouvelles molécules thérapeutiques - - FiFA22012 - ANR-12-BSV1-0010 - BLANC - VALID, and Molecular by-pass therapy for mitochondrial dysfunction - MITO BY-PASS - - EC:FP7:ERC2009-04-01 - 2015-03-31 - 232738 - VALID

Subjects
Hot Temperature, Luminescence, Physiology, Respiratory chain, Mitochondrion, Toxicology, Pathology and Laboratory Medicine, Biochemistry, 0302 clinical medicine, Cytosol, Short Reports, Animal Cells, Medicine and Health Sciences, Uncoupling protein, Biology (General), Uncoupling Protein 1, Energy-Producing Organelles, Plant Proteins, Skin, Connective Tissue Cells, chemistry.chemical_classification, 0303 health sciences, ATP synthase, biology, Physics, Electromagnetic Radiation, Temperature, Thermogenesis, Mitochondria, Electrophysiology, Chemistry, Connective Tissue, Mitochondrial Membranes, Physical Sciences, Cellular Structures and Organelles, Anatomy, Cellular Types, Oxidoreductases, Chemical Elements, Alternative oxidase, QH301-705.5, Primary Cell Culture, Toxic Agents, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Bioenergetics, Membrane Potential, Fluorescence, Mitochondrial Proteins, 03 medical and health sciences, Humans, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, 030304 developmental biology, Fluorescent Dyes, Cyanides, HEK 293 cells, Chemical Compounds, Biology and Life Sciences, Kidneys, Metabolism, Cell Biology, Renal System, Fibroblasts, Oxygen, Enzyme, HEK293 Cells, Biological Tissue, chemistry, biology.protein, Biophysics, Salts, 030217 neurology & neurosurgery
Abstract

In endothermic species, heat released as a product of metabolism ensures stable internal temperature throughout the organism, despite varying environmental conditions. Mitochondria are major actors in this thermogenic process. Part of the energy released by the oxidation of respiratory substrates drives ATP synthesis and metabolite transport, but a substantial proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured mitochondrial temperature in situ under different physiological conditions. At a constant external temperature of 38 °C, mitochondria were more than 10 °C warmer when the respiratory chain (RC) was fully functional, both in human embryonic kidney (HEK) 293 cells and primary skin fibroblasts. This differential was abolished in cells depleted of mitochondrial DNA or treated with respiratory inhibitors but preserved or enhanced by expressing thermogenic enzymes, such as the alternative oxidase or the uncoupling protein 1. The activity of various RC enzymes was maximal at or slightly above 50 °C. In view of their potential consequences, these observations need to be further validated and explored by independent methods. Our study prompts a critical re-examination of the literature on mitochondria., Author summary To ensure a stable internal temperature, endothermic species make use of the heat released during the final steps of food burning by the mitochondria present in all cells of the organism. Indeed, only a fraction of the energy released by the oxidation of respiratory substrates is used to generate ATP, while a substantial proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured the temperature of active mitochondria in cultured intact human cells. Mitochondria were found to be more than 10 °C warmer when the respiratory chain was functional. This differential was abolished in cells depleted of mitochondrial DNA or by respiratory inhibitors but preserved or enhanced by the expression of thermogenic enzymes such as Ciona alternative oxidase or by uncoupling protein 1. The activity of various respiratory chain enzymes was found to be maximal near 50 °C. Note that in view of their potential consequences, the observations reported here need to be validated and explored further by independent methods.

Published
2018
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