Please use this identifier to cite or link to this item: http://hdl.handle.net/10668/3218
Título : A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2
Autor : Karathanou, Konstantina
Lazaratos, Michalis
Bertalan, Éva
Siemers, Malte
Buzar, Krzysztof
Schertler, Gebhard F.X.
del Val, Coral
Bondar, Ana-Nicoleta
Filiación: [Karathanou,K; Lazaratos,M; Bertalan,E; Siemers,M; Buzar,K; Bondar,AN] Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Berlin, Germany. [Schertler,GFX] Paul Scherrer Institut, Department of Biology and Chemistry, Laboratory of Biomolecular Research, Villigen-PSI, Switzerland. [Schertler,GFX] ETH Zürich, Department of Biology, Zürich, Switzerland. [del Val,C] University of Granada, Department of Computer Science and Artificial Intelligence, Granada, Spain. [del Val,C] Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain. [del Val,C] Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI Institute), Granada, Spain.
Palabras clave : Bimolecular structure
Hydrogen bonding
Dynamic hydrogen-bond clusters
Conformational plasticity
SARS-CoV-2 protein S
ACE2
Enlace de hidrógeno
MeSH: Medical Subject Headings::Information Science::Information Science::Computing Methodologies::Algorithms
Medical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Computational Biology
Medical Subject Headings::Phenomena and Processes::Chemical Phenomena::Chemical Processes::Physicochemical Processes::Hydrogen Bonding
Medical Subject Headings::Information Science::Information Science::Computing Methodologies::Computer Graphics
Medical Subject Headings::Diseases::Virus Diseases::RNA Virus Infections::Nidovirales Infections::Coronaviridae Infections::Coronavirus Infections
Medical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans
Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Models, Theoretical::Models, Molecular
Medical Subject Headings::Health Care::Environment and Public Health::Public Health::Disease Outbreaks::Epidemics::Pandemics
Medical Subject Headings::Chemicals and Drugs::Enzymes and Coenzymes::Enzymes::Hydrolases::Peptide Hydrolases::Exopeptidases::Dipeptidyl-Peptidases and Tripeptidyl-Peptidases::Peptidyl-Dipeptidase A
Medical Subject Headings::Diseases::Virus Diseases::Pneumonia, Viral
Medical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Protein Binding
Medical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Molecular Structure::Molecular Conformation::Protein Conformation::Protein Structure, Tertiary::Protein Interaction Domains and Motifs
Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Molecular Probe Techniques::Protein Interaction Mapping
Medical Subject Headings::Phenomena and Processes::Metabolic Phenomena::Metabolism::Metabolic Networks and Pathways::Protein Interaction Maps
Medical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Molecular Structure::Molecular Conformation::Protein Conformation::Protein Structure, Quaternary
Medical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Molecular Structure::Molecular Conformation::Protein Conformation::Protein Structure, Secondary
Medical Subject Headings::Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Membrane Proteins::Membrane Fusion Proteins::Viral Fusion Proteins::Spike Glycoprotein, Coronavirus
Medical Subject Headings::Phenomena and Processes::Microbiological Phenomena::Microbiological Processes::Virus Physiological Processes::Virus Internalization
Fecha de publicación : 10-Sep-2020
Editorial : Elsevier Inc.
Cita Bibliográfica: Karathanou K, Lazaratos M, Bertalan É, Siemers M, Buzar K, Schertler GFX. A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2. J Struct Biol. 2020 Nov 1;212(2):107617.
Abstract: Corona virus spike protein S is a large homo-trimeric protein anchored in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into the host cell. The structural elements that govern conformational plasticity of the spike protein are largely unknown. Here, we present a methodology that relies upon graph and centrality analyses, augmented by bioinformatics, to identify and characterize large H-bond clusters in protein structures. We apply this methodology to protein S ectodomain and find that, in the closed conformation, the three protomers of protein S bring the same contribution to an extensive central network of H-bonds, and contribute symmetrically to a relatively large H-bond cluster at the receptor binding domain, and to a cluster near a protease cleavage site. Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. From analyses of spike protein sequences we identify patches of histidine and carboxylate groups that could be involved in transient proton binding.
URI: http://hdl.handle.net/10668/3218
Versión del editor : https://www.sciencedirect.com/science/article/pii/S1047847720301908?via%3Dihub
DOI: 10.1016/j.jsb.2020.107617
ISSN : 1047-8477 (Print)
Appears in Collections:01- Artículos - ibsGRANADA. Instituto de Investigación Biosanitaria de Granada

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