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Klyshko E, Kim JSH, McGough L, Valeeva V, Lee E, Ranganathan R, Rauscher S. Functional protein dynamics in a crystal. Nat Commun 2024; 15:3244. [PMID: 38622111 PMCID: PMC11018856 DOI: 10.1038/s41467-024-47473-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Proteins are molecular machines and to understand how they work, we need to understand how they move. New pump-probe time-resolved X-ray diffraction methods open up ways to initiate and observe protein motions with atomistic detail in crystals on biologically relevant timescales. However, practical limitations of these experiments demands parallel development of effective molecular dynamics approaches to accelerate progress and extract meaning. Here, we establish robust and accurate methods for simulating dynamics in protein crystals, a nontrivial process requiring careful attention to equilibration, environmental composition, and choice of force fields. With more than seven milliseconds of sampling of a single chain, we identify critical factors controlling agreement between simulation and experiments and show that simulated motions recapitulate ligand-induced conformational changes. This work enables a virtuous cycle between simulation and experiments for visualizing and understanding the basic functional motions of proteins.
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Affiliation(s)
- Eugene Klyshko
- Department of Physics, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Justin Sung-Ho Kim
- Department of Physics, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Victoria Valeeva
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Ethan Lee
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Rama Ranganathan
- Center for Physics of Evolving Systems and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Sarah Rauscher
- Department of Physics, University of Toronto, Toronto, ON, Canada.
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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Klyshko E, Sung-Ho Kim J, McGough L, Valeeva V, Lee E, Ranganathan R, Rauscher S. Functional Protein Dynamics in a Crystal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.06.548023. [PMID: 37461732 PMCID: PMC10350071 DOI: 10.1101/2023.07.06.548023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Proteins are molecular machines and to understand how they work, we need to understand how they move. New pump-probe time-resolved X-ray diffraction methods open up ways to initiate and observe protein motions with atomistic detail in crystals on biologically relevant timescales. However, practical limitations of these experiments demands parallel development of effective molecular dynamics approaches to accelerate progress and extract meaning. Here, we establish robust and accurate methods for simulating dynamics in protein crystals, a nontrivial process requiring careful attention to equilibration, environmental composition, and choice of force fields. With more than seven milliseconds of sampling of a single chain, we identify critical factors controlling agreement between simulation and experiments and show that simulated motions recapitulate ligand-induced conformational changes. This work enables a virtuous cycle between simulation and experiments for visualizing and understanding the basic functional motions of proteins.
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Affiliation(s)
- Eugene Klyshko
- Department of Physics, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Justin Sung-Ho Kim
- Department of Physics, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Victoria Valeeva
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Ethan Lee
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Rama Ranganathan
- Center for Physics of Evolving Systems and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Sarah Rauscher
- Department of Physics, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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Pennacchietti V, Toto A. Different electrostatic forces drive the binding kinetics of SARS-CoV, SARS-CoV-2 and MERS-CoV Envelope proteins with the PDZ2 domain of ZO1. Sci Rep 2023; 13:7906. [PMID: 37193746 DOI: 10.1038/s41598-023-35079-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/12/2023] [Indexed: 05/18/2023] Open
Abstract
The Envelope protein (E) is a structural protein encoded by the genome of SARS-CoV, SARS-CoV-2 and MERS-CoV Coronaviruses. It is poorly present in the virus but highly expressed in the host cell, with prominent role in virus assembly and virulence. The E protein possesses a PDZ-binding motif (PBM) at its C terminus that allows it to interact with host PDZ domain containing proteins. ZO1 is a key protein in assembling the cytoplasmic plaque of epithelial and endothelial Tight Junctions (TJs) as well as in determining cell differentiation, proliferation and polarity. The PDZ2 domain of ZO1 is known to interact with the Coronaviruses Envelope proteins, however the molecular details of such interaction have not been established. In this paper we directly measured, through Fluorescence Resonance Energy Transfer and Stopped-Flow methodology, the binding kinetics of the PDZ2 domain of ZO1 with peptides mimicking the C-terminal portion of the Envelope protein from SARS-CoV, SARS-CoV-2 and MERS-CoV in different ionic strength conditions. Interestingly, the peptide mimicking the E protein from MERS-CoV display much higher microscopic association rate constant with PDZ2 compared to SARS-CoV and SARS-CoV-2 suggesting a stronger contribution of electrostatic forces in the early events of binding. A comparison of thermodynamic and kinetic data obtained at increasing ionic strengths put in evidence different contribution of electrostatics in the recognition and complex formation events for the three peptides. Our data are discussed under the light of available structural data of PDZ2 domain of ZO1 and of previous works about these protein systems.
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Affiliation(s)
- Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy.
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Santos-Mendoza T. The Envelope (E) Protein of SARS-CoV-2 as a Pharmacological Target. Viruses 2023; 15:v15041000. [PMID: 37112980 PMCID: PMC10143767 DOI: 10.3390/v15041000] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus is still a global health concern. Several spike (S) protein-based vaccines have been developed that efficiently protect the human population against severe forms of COVID-19. However, some SARS-CoV-2 variants of concern (VOCs) have emerged that evade the protective effect of vaccine-induced antibodies. Therefore, efficient and specific antiviral treatments to control COVID-19 are indispensable. To date, two drugs have been approved for mild COVID-19 treatment; nevertheless, more drugs, preferably broad-spectrum and ready-to-use therapeutic agents for new pandemics, are needed. Here, I discuss the PDZ-dependent protein-protein interactions of the viral E protein with host proteins as attractive alternatives for the development of antivirals against coronavirus.
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Affiliation(s)
- Teresa Santos-Mendoza
- Laboratory of Transcriptomics and Molecular Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico
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Schoeman D, Cloete R, Fielding BC. The Flexible, Extended Coil of the PDZ-Binding Motif of the Three Deadly Human Coronavirus E Proteins Plays a Role in Pathogenicity. Viruses 2022; 14:v14081707. [PMID: 36016329 PMCID: PMC9416557 DOI: 10.3390/v14081707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
The less virulent human (h) coronaviruses (CoVs) 229E, NL63, OC43, and HKU1 cause mild, self-limiting respiratory tract infections, while the more virulent SARS-CoV-1, MERS-CoV, and SARS-CoV-2 have caused severe outbreaks. The CoV envelope (E) protein, an important contributor to the pathogenesis of severe hCoV infections, may provide insight into this disparate severity of the disease. We, therefore, generated full-length E protein models for SARS-CoV-1 and -2, MERS-CoV, HCoV-229E, and HCoV-NL63 and docked C-terminal peptides of each model to the PDZ domain of the human PALS1 protein. The PDZ-binding motif (PBM) of the SARS-CoV-1 and -2 and MERS-CoV models adopted a more flexible, extended coil, while the HCoV-229E and HCoV-NL63 models adopted a less flexible alpha helix. All the E peptides docked to PALS1 occupied the same binding site and the more virulent hCoV E peptides generally interacted more stably with PALS1 than the less virulent ones. We hypothesize that the increased flexibility of the PBM in the more virulent hCoVs facilitates more stable binding to various host proteins, thereby contributing to more severe disease. This is the first paper to model full-length 3D structures for both the more virulent and less virulent hCoV E proteins, providing novel insights for possible drug and/or vaccine development.
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Affiliation(s)
- Dewald Schoeman
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
| | - Burtram C. Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
- Correspondence:
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Genomic surveillance of SARS-CoV-2 in patients presenting neurological manifestations. PLoS One 2022; 17:e0270024. [PMID: 35771751 PMCID: PMC9246207 DOI: 10.1371/journal.pone.0270024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/02/2022] [Indexed: 11/19/2022] Open
Abstract
During the first wave of infections, neurological symptoms in Coronavirus Disease 2019 (COVID-19) patients raised particular concern, suggesting that, in a subset of patients, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could invade and damage cells of the central nervous system (CNS). Indeed, up to date several in vitro and in vivo studies have shown the ability of SARS-CoV-2 to reach the CNS. Both viral and/or host related features could explain why this occurs only in certain individuals and not in all the infected population. The aim of the present study was to evaluate if onset of neurological manifestations in COVID-19 patients was related to specific viral genomic signatures. To this end, viral genome was extracted directly from nasopharyngeal swabs of selected SARS-CoV-2 positive patients presenting a spectrum of neurological symptoms related to COVID-19, ranging from anosmia/ageusia to more severe symptoms. By adopting a whole genome sequences approach, here we describe a panel of known as well as unknown mutations detected in the analyzed SARS-CoV-2 genomes. While some of the found mutations were already associated with an improved viral fitness, no common signatures were detected when comparing viral sequences belonging to specific groups of patients. In conclusion, our data support the notion that COVID-19 neurological manifestations are mainly linked to patient-specific features more than to virus genomic peculiarities.
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Ashour L. Roles of the ACE/Ang II/AT1R pathway, cytokine release, and alteration of tight junctions in COVID-19 pathogenesis. Tissue Barriers 2022; 11:2090792. [PMID: 35726726 PMCID: PMC10161962 DOI: 10.1080/21688370.2022.2090792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This paper shows how SARS-CoV-2 alters tight junctions (TJs) in human organs. The effect of SARS-CoV-2 on the ACE/Ang II/AT1R pathway and immune cells culminates in the release of numerous pro-inflammatory mediators, leading to the presence of certain symptoms in COVID-19, such as acute lung injury (ALI), pulmonary hypertension, and pulmonary fibrosis. Furthermore, the cytokines released alter different TJs components. The study shows how the irregular release of pro-inflammatory cytokines leads to claudin disruption in various tissues of the body, resulting in different symptoms, such as alveolar fibrosis, pulmonary edema, conjunctivitis, altered fertility in males, gastrointestinal symptoms, Covid toes, and others. SARS-CoV-2 also alters occludin expression in the endothelial and blood-testis barriers (BTB) resulting in edema and altered fertility. Viral disruption of JAM-A leads to activation of the RhoA GTPase, which leads to ALI. Taken together, these results define ACE/Ang II/AT1R pathway receptors and tight junctional components as potential therapeutic targets in COVID-19.
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Affiliation(s)
- Laith Ashour
- Faculty of Medicine, Al-Balqa Applied University, Al-Salt, Jordan
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