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Wang MF, Wang J, Wang XB, Zhu XC, Wang YP, Wang W. Effect of SPoT-mediated Stringent Response on Biofilm Formation, Stress Resistance and Quorum Sensing in Pseudomonas protegens SN15-2. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822040172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Karathanou K, Lazaratos M, Bertalan É, Siemers M, Buzar K, Schertler GFX, Del Val C, Bondar AN. A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2. J Struct Biol 2020; 212:107617. [PMID: 32919067 PMCID: PMC7481144 DOI: 10.1016/j.jsb.2020.107617] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/03/2020] [Accepted: 09/06/2020] [Indexed: 02/07/2023]
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.
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Affiliation(s)
- Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Éva Bertalan
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Krzysztof Buzar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Gebhard F X Schertler
- Paul Scherrer Institut, Department of Biology and Chemistry, Laboratory of Biomolecular Research, CH-5303 Villigen-PSI, Switzerland; ETH Zürich, Department of Biology, 8093 Zürich, Switzerland
| | - Coral Del Val
- University of Granada, Department of Computer Science and Artificial Intelligence, E-18071 Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain; Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI Institute), 18014 Granada, Spain
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany.
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Lemieux MJ, Overduin M. Structure and function of proteins in membranes and nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183445. [PMID: 32841614 PMCID: PMC7443088 DOI: 10.1016/j.bbamem.2020.183445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The field of membrane structural biology represents a fast-moving field with exciting developments including native nanodiscs that allow preparation of complexes of post-translationally modified proteins bound to biological lipids. This has led to conceptual advances including biological membrane:protein assemblies or “memteins” as the fundamental functional units of biological membranes. Tools including cryo-electron microscopy and X-ray crystallography are maturing such that it is becoming increasingly feasible to solve structures of large, multicomponent complexes, while complementary methods including nuclear magnetic resonance spectroscopy yield unique insights into interactions and dynamics. Challenges remain, including elucidating exactly how lipids and ligands are recognized at atomic resolution and transduce signals across asymmetric bilayers. In this special volume some of the latest thinking and methods are gathered through the analysis of a range of transmembrane targets. Ongoing work on areas including polymer design, protein labelling and microfluidic technologies will ensure continued progress on improving resolution and throughput, providing deeper understanding of this most important group of targets.
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Affiliation(s)
- M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Michael Overduin
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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