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Li B, Ustyugova IV, Szymkowicz L, Zhu S, Ming M, Fung KYY, Cortés G, James DA, Hrynyk M, Rahman N, Brookes RH, Ausar SF. Formulation development of a stable influenza recombinant neuraminidase vaccine candidate. Hum Vaccin Immunother 2024; 20:2304393. [PMID: 38497413 PMCID: PMC10950269 DOI: 10.1080/21645515.2024.2304393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/09/2024] [Indexed: 03/19/2024] Open
Abstract
Current influenza vaccines could be augmented by including recombinant neuraminidase (rNA) protein antigen to broaden protective immunity and improve efficacy. Toward this goal, we investigated formulation conditions to optimize rNA physicochemical stability. When rNA in sodium phosphate saline buffer (NaPBS) was frozen and thawed (F/T), the tetrameric structure transitioned from a "closed" to an "open" conformation, negatively impacting functional activity. Hydrogen deuterium exchange experiments identified differences in anchorage binding sites at the base of the open tetramer, offering a structural mechanistic explanation for the change in conformation and decreased functional activity. Change to the open configuration was triggered by the combined stresses of acidic pH and F/T. The desired closed conformation was preserved in a potassium phosphate buffer (KP), minimizing pH drop upon freezing and including 10% sucrose to control F/T stress. Stability was further evaluated in thermal stress studies where changes in conformation were readily detected by ELISA and size exclusion chromatography (SEC). Both tests were suitable indicators of stability and antigenicity and considered potential critical quality attributes (pCQAs). To understand longer-term stability, the pCQA profiles from thermally stressed rNA at 6 months were modeled to predict stability of at least 24-months at 5°C storage. In summary, a desired rNA closed tetramer was maintained by formulation selection and monitoring of pCQAs to produce a stable rNA vaccine candidate. The study highlights the importance of understanding and controlling vaccine protein structural and functional integrity.
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Affiliation(s)
- Bing Li
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
| | | | | | | | - Marin Ming
- Sanofi Analytical Sciences, Toronto, ON, Canada
| | - Karen Y. Y. Fung
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
| | - Guadalupe Cortés
- Sanofi mRNA & Translational Medicine COVID Franchise, Global Clinical Development, Waltham, MA, USA
| | - D. Andrew James
- Sanofi External Research and Development, Toronto, ON, Canada
| | | | - Nausheen Rahman
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
| | - Roger H. Brookes
- Sanofi Global Vaccine Drug Product Development, Toronto, ON, Canada
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2
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Peter AS, Hoffmann DS, Klier J, Lange CM, Möller J, Most V, Wüst CK, Beining M, Gülesen S, Junker H, Brumme B, Schiffner T, Meiler J, Schoeder CT. Strategies of rational and structure-driven vaccine design for Arenaviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024:105626. [PMID: 38908736 DOI: 10.1016/j.meegid.2024.105626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/16/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024]
Abstract
The COVID-19 outbreak has highlighted the importance of pandemic preparedness for the prevention of future health crises. One virus family with high pandemic potential are Arenaviruses, which have been detected almost worldwide, particularly in Africa and the Americas. These viruses are highly understudied and many questions regarding their structure, replication and tropism remain unanswered, making the design of an efficacious and molecularly-defined vaccine challenging. We propose that structure-driven computational vaccine design will contribute to overcome these challenges. Computational methods for stabilization of viral glycoproteins or epitope focusing have made progress during the last decades and particularly during the COVID-19 pandemic, and have proven useful for rational vaccine design and the establishment of novel diagnostic tools. In this review, we summarize gaps in our understanding of Arenavirus molecular biology, highlight challenges in vaccine design and discuss how structure-driven and computationally informed strategies will aid in overcoming these obstacles.
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Affiliation(s)
- Antonia Sophia Peter
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Dieter S Hoffmann
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Johannes Klier
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Christina M Lange
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Johanna Möller
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany
| | - Victoria Most
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Christina K Wüst
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Molecular Medicine Studies, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Max Beining
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; SECAI, School of Embedded Composite Artificial Intelligence, Dresden/Leipzig, Germany
| | - Sevilay Gülesen
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Hannes Junker
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Birke Brumme
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Torben Schiffner
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; The Scripps Research Institute, Department for Immunology and Microbiology, La Jolla, CA, United States
| | - Jens Meiler
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany; Department of Chemistry, Vanderbilt University, Nashville, TN, United States; Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Clara T Schoeder
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany.
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3
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Cornet J, Coulonges N, Pezeshkian W, Penissat-Mahaut M, Desgrez-Dautet H, Marrink SJ, Destainville N, Chavent M, Manghi M. There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning. SOFT MATTER 2024. [PMID: 38884641 DOI: 10.1039/d4sm00089g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
We describe a complete methodology to bridge the scales between nanoscale molecular dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species are furthermore embedded. To go from the molecular to the mesoscale, we notably appeal to physical renormalization arguments enabling us to rigorously infer the mesoscale interaction parameters from its molecular counterpart. We also explain how to deal with the physical timescales at stake at the mesoscale. Simulating the as-obtained mesoscale system enables us to equilibrate the long wavelengths of the vesicles of interest, up to the vesicle size. Conversely, we then backmap from the meso- to the nano-scale, which enables us to equilibrate in turn the short wavelengths down to the molecular length-scales. By applying our approach to the specific situation of patterning a vesicle membrane, we show that macroscopic membranes can thus be equilibrated at all length-scales in achievable computational time offering an original strategy to address the fundamental challenge of timescale in simulations of large bio-membrane systems.
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Affiliation(s)
- Julie Cornet
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
| | - Nelly Coulonges
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Maël Penissat-Mahaut
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Hermes Desgrez-Dautet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | | | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
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4
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Lederhofer J, Tsybovsky Y, Nguyen L, Raab JE, Creanga A, Stephens T, Gillespie RA, Syeda HZ, Fisher BE, Skertic M, Yap C, Schaub AJ, Rawi R, Kwong PD, Graham BS, McDermott AB, Andrews SF, King NP, Kanekiyo M. Protective human monoclonal antibodies target conserved sites of vulnerability on the underside of influenza virus neuraminidase. Immunity 2024; 57:574-586.e7. [PMID: 38430907 PMCID: PMC10962683 DOI: 10.1016/j.immuni.2024.02.003] [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: 03/27/2023] [Revised: 12/02/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Continuously evolving influenza viruses cause seasonal epidemics and pose global pandemic threats. Although viral neuraminidase (NA) is an effective drug and vaccine target, our understanding of the NA antigenic landscape still remains incomplete. Here, we describe NA-specific human antibodies that target the underside of the NA globular head domain, inhibit viral propagation of a wide range of human H3N2, swine-origin variant H3N2, and H2N2 viruses, and confer both pre- and post-exposure protection against lethal H3N2 infection in mice. Cryo-EM structures of two such antibodies in complex with NA reveal non-overlapping epitopes covering the underside of the NA head. These sites are highly conserved among N2 NAs yet inaccessible unless the NA head tilts or dissociates. Our findings help guide the development of effective countermeasures against ever-changing influenza viruses by identifying hidden conserved sites of vulnerability on the NA underside.
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Affiliation(s)
- Julia Lederhofer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Lam Nguyen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julie E Raab
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Z Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian E Fisher
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michelle Skertic
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christina Yap
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Schaub
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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5
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Beck TL, Carloni P, Asthagiri DN. All-Atom Biomolecular Simulation in the Exascale Era. J Chem Theory Comput 2024; 20:1777-1782. [PMID: 38382017 DOI: 10.1021/acs.jctc.3c01276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Exascale supercomputers have opened the door to dynamic simulations, facilitated by AI/ML techniques, that model biomolecular motions over unprecedented length and time scales. This new capability holds the potential to revolutionize our understanding of fundamental biological processes. Here we report on some of the major advances that were discussed at a recent CECAM workshop in Pisa, Italy, on the topic with a primary focus on atomic-level simulations. First, we highlight examples of current large-scale biomolecular simulations and the future possibilities enabled by crossing the exascale threshold. Next, we discuss challenges to be overcome in optimizing the usage of these powerful resources. Finally, we close by listing several grand challenge problems that could be investigated with this new computer architecture.
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Affiliation(s)
- Thomas L Beck
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Paolo Carloni
- INM-9/IAS-5 Computational Biomedicine, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-54245 Jülich, Germany
- Department of Physics, RWTH Aachen University, D-52078 Aachen, Germany
| | - Dilipkumar N Asthagiri
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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6
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Hsieh CL, Leist SR, Miller EH, Zhou L, Powers JM, Tse AL, Wang A, West A, Zweigart MR, Schisler JC, Jangra RK, Chandran K, Baric RS, McLellan JS. Prefusion-stabilized SARS-CoV-2 S2-only antigen provides protection against SARS-CoV-2 challenge. Nat Commun 2024; 15:1553. [PMID: 38378768 PMCID: PMC10879192 DOI: 10.1038/s41467-024-45404-x] [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: 08/25/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Ever-evolving SARS-CoV-2 variants of concern (VOCs) have diminished the effectiveness of therapeutic antibodies and vaccines. Developing a coronavirus vaccine that offers a greater breadth of protection against current and future VOCs would eliminate the need to reformulate COVID-19 vaccines. Here, we rationally engineer the sequence-conserved S2 subunit of the SARS-CoV-2 spike protein and characterize the resulting S2-only antigens. Structural studies demonstrate that the introduction of interprotomer disulfide bonds can lock S2 in prefusion trimers, although the apex samples a continuum of conformations between open and closed states. Immunization with prefusion-stabilized S2 constructs elicits broadly neutralizing responses against several sarbecoviruses and protects female BALB/c mice from mouse-adapted SARS-CoV-2 lethal challenge and partially protects female BALB/c mice from mouse-adapted SARS-CoV lethal challenge. These engineering and immunogenicity results should inform the development of next-generation pan-coronavirus therapeutics and vaccines.
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Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Emily Happy Miller
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Medicine-Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - John M Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexandra L Tse
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Albert Wang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mark R Zweigart
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jonathan C Schisler
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rohit K Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, 71103, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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7
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McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 2024; 187:563-584. [PMID: 38306982 DOI: 10.1016/j.cell.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
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Affiliation(s)
| | - Sven Klumpe
- Research Group CryoEM Technology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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8
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Samsudin F, Zuzic L, Marzinek JK, Bond PJ. Mechanisms of allostery at the viral surface through the eyes of molecular simulation. Curr Opin Struct Biol 2024; 84:102761. [PMID: 38142635 DOI: 10.1016/j.sbi.2023.102761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/13/2023] [Accepted: 12/04/2023] [Indexed: 12/26/2023]
Abstract
The outermost surface layer of any virus is formed by either a capsid shell or envelope. Such layers have traditionally been thought of as immovable structures, but it is becoming apparent that they cannot be viewed exclusively as static architectures protecting the viral genome. A limited number of proteins on the virion surface must perform a multitude of functions in order to orchestrate the viral life cycle, and allostery can regulate their structures at multiple levels of organization, spanning individual molecules, protomers, large oligomeric assemblies, or entire viral surfaces. Here, we review recent contributions from the molecular simulation field to viral surface allostery, with a particular focus on the trimeric spike glycoprotein emerging from the coronavirus surface, and the icosahedral flaviviral envelope complex. As emerging viral pathogens continue to pose a global threat, an improved understanding of viral dynamics and allosteric regulation will prove crucial in developing novel therapeutic strategies.
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Affiliation(s)
- Firdaus Samsudin
- Bioinformatics Institute (A∗STAR), 30 Biopolis Street, 07-01 Matrix, 138671, Singapore
| | - Lorena Zuzic
- Department of Chemistry, Langelandsgade 140, Aarhus University, Aarhus 8000, Denmark
| | - Jan K Marzinek
- Bioinformatics Institute (A∗STAR), 30 Biopolis Street, 07-01 Matrix, 138671, Singapore
| | - Peter J Bond
- Bioinformatics Institute (A∗STAR), 30 Biopolis Street, 07-01 Matrix, 138671, Singapore; Department of Biological Sciences, 16 Science Drive 4, National University of Singapore, 117558, Singapore.
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9
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Beltrán D, Hospital A, Gelpí JL, Orozco M. A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort. Nucleic Acids Res 2024; 52:D393-D403. [PMID: 37953362 PMCID: PMC10767965 DOI: 10.1093/nar/gkad991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
Molecular dynamics (MD) simulations are keeping computers busy around the world, generating a huge amount of data that is typically not open to the scientific community. Pioneering efforts to ensure the safety and reusability of MD data have been based on the use of simple databases providing a limited set of standard analyses on single-short trajectories. Despite their value, these databases do not offer a true solution for the current community of MD users, who want a flexible analysis pipeline and the possibility to address huge non-Markovian ensembles of large systems. Here we present a new paradigm for MD databases, resilient to large systems and long trajectories, and designed to be compatible with modern MD simulations. The data are offered to the community through a web-based graphical user interface (GUI), implemented with state-of-the-art technology, which incorporates system-specific analysis designed by the trajectory providers. A REST API and associated Jupyter Notebooks are integrated into the platform, allowing fully customized meta-analysis by final users. The new technology is illustrated using a collection of trajectories obtained by the community in the context of the effort to fight the COVID-19 pandemic. The server is accessible at https://bioexcel-cv19.bsc.es/#/. It is free and open to all users and there are no login requirements. It is also integrated into the simulations section of the BioExcel-MolSSI COVID-19 Molecular Structure and Therapeutics Hub: https://covid.molssi.org/simulations/ and is part of the MDDB effort (https://mddbr.eu).
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Affiliation(s)
- Daniel Beltrán
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Josep Lluís Gelpí
- Department of Biochemistry and Biomedicine. University of Barcelona, Barcelona, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biochemistry and Biomedicine. University of Barcelona, Barcelona, Spain
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10
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Wu NC, Ellebedy AH. Targeting neuraminidase: the next frontier for broadly protective influenza vaccines. Trends Immunol 2024; 45:11-19. [PMID: 38103991 PMCID: PMC10841738 DOI: 10.1016/j.it.2023.11.001] [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: 10/24/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 12/19/2023]
Abstract
Current seasonal influenza vaccines, which mainly target hemagglutinin (HA), require annual updates due to the continuous antigenic drift of the influenza virus. Developing an influenza vaccine with increased breadth of protection will have significant public health benefits. The recent discovery of broadly protective antibodies to neuraminidase (NA) has provided important insights into developing a universal influenza vaccine, either by improving seasonal influenza vaccines or designing novel immunogens. However, further in-depth molecular characterizations of NA antibody responses are warranted to fully leverage broadly protective NA antibodies for influenza vaccine designs. Overall, we posit that focusing on NA for influenza vaccine development is synergistic with existing efforts targeting HA, and may represent a cost-effective approach to generating a broadly protective influenza vaccine.
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Affiliation(s)
- Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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11
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Olmedillas E, Rajamanickam RR, Avalos RD, Sosa FA, Zandonatti MA, Harkins SS, Shresta S, Hastie KM, Saphire EO. Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571764. [PMID: 38168261 PMCID: PMC10760097 DOI: 10.1101/2023.12.14.571764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The 800 million human infections with SARS-CoV-2 and the likely emergence of new variants and additional coronaviruses necessitate a better understanding of the essential spike glycoprotein and the development of immunogens that foster broader and more durable immunity. The S2 fusion subunit is more conserved in sequence, is essential to function, and would be a desirable immunogen to boost broadly reactive antibodies. It is, however, unstable in structure and in its wild-type form, cannot be expressed alone without irreversible collapse into a six-helix bundle. In addition to the irreversible conformational changes of fusion, biophysical measurements indicate that spike also undergoes a reversible breathing action. However, spike in an open, "breathing" conformation has not yet been visualized at high resolution. Here we describe an S2-only antigen, engineered to remain in its relevant, pre-fusion viral surface conformation in the absence of S1. We also describe a panel of natural human antibodies specific for S2 from vaccinated and convalescent individuals. One of these mAbs, from a convalescent individual, afforded a high-resolution cryo-EM structure of the prefusion S2. The structure reveals a complex captured in an "open" conformation with greater stabilizing intermolecular interactions at the base and a repositioned fusion peptide. Together, this work provides an antigen for advancement of next-generation "booster" immunogens and illuminates the likely breathing adjustments of the coronavirus spike.
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Affiliation(s)
- Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Roshan R. Rajamanickam
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Ruben Diaz Avalos
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Fernanda A. Sosa
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Michelle A. Zandonatti
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Stephanie S. Harkins
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kathryn M. Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
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12
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Simmons HC, Finney J, Kotaki R, Adachi Y, Moseman AP, Watanabe A, Song S, Robinson-McCarthy LR, Sage VL, Kuraoka M, Moseman EA, Kelsoe G, Takahashi Y, McCarthy KR. A broad antibody class engages the influenza virus hemagglutinin head at its stem interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571543. [PMID: 38168412 PMCID: PMC10760138 DOI: 10.1101/2023.12.13.571543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Influenza infection and vaccination impart strain-specific immunity that fails to protect against both seasonal antigenic variants and the next pandemic. However, antibodies directed to conserved sites can confer broad protection. We identify and characterize a class of human antibodies that engage a previously undescribed, conserved, epitope on the influenza hemagglutinin protein (HA). Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizing in vitro but protect against lethal infection in mice. Their breadth of binding extends across most influenza A serotypes and seasonal human variants. Antibodies to the head-stem interface epitope are present at low frequency in the memory B cell populations of multiple donors. The immunogenicity of the epitope warrants its consideration for inclusion in improved or "universal" influenza vaccines.
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Affiliation(s)
- Holly C. Simmons
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joel Finney
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Ryutaro Kotaki
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Yu Adachi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Annie Park Moseman
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Akiko Watanabe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Shengli Song
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
| | - Lindsey R. Robinson-McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Valerie Le Sage
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Masayuki Kuraoka
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - E. Ashley Moseman
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Garnett Kelsoe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kevin R. McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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13
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Colombo G. Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design. Curr Opin Struct Biol 2023; 83:102702. [PMID: 37716095 DOI: 10.1016/j.sbi.2023.102702] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The concept of allostery has become a central tenet in the study of biological systems. In parallel, the discovery of allosteric drugs is generating new opportunities to selectively modulate difficult targets involved in pathologic mechanisms. Molecular simulations can provide atomistically detailed insight into the processes involved in allosteric regulation and signaling, and at the same time, they have the potential to unveil regulatory hotspots or cryptic sites that are not immediately evident from the analysis of static structures. In this context, computational approaches should be able to connect the study of allosteric regulation at different scales to the possibility of leveraging this knowledge to expand the chemical space of new, active drugs. Here, we will discuss recent advances in the study of allosteric regulation via computational methods and connect the mechanistic knowledge generated to the possibility of designing new small molecules that can tweak the functions of their receptors.
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Affiliation(s)
- Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy.
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14
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Lei R, Kim W, Lv H, Mou Z, Scherm MJ, Schmitz AJ, Turner JS, Tan TJC, Wang Y, Ouyang WO, Liang W, Rivera-Cardona J, Teo C, Graham CS, Brooke CB, Presti RM, Mok CKP, Krammer F, Dai X, Ellebedy AH, Wu NC. Leveraging vaccination-induced protective antibodies to define conserved epitopes on influenza N2 neuraminidase. Immunity 2023; 56:2621-2634.e6. [PMID: 37967533 PMCID: PMC10655865 DOI: 10.1016/j.immuni.2023.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 07/19/2023] [Accepted: 10/10/2023] [Indexed: 11/17/2023]
Abstract
There is growing appreciation for neuraminidase (NA) as an influenza vaccine target; however, its antigenicity remains poorly characterized. In this study, we isolated three broadly reactive N2 antibodies from the plasmablasts of a single vaccinee, including one that cross-reacts with NAs from seasonal H3N2 strains spanning five decades. Although these three antibodies have diverse germline usages, they recognize similar epitopes that are distant from the NA active site and instead involve the highly conserved underside of NA head domain. We also showed that all three antibodies confer prophylactic and therapeutic protection in vivo, due to both Fc effector functions and NA inhibition through steric hindrance. Additionally, the contribution of Fc effector functions to protection in vivo inversely correlates with viral growth inhibition activity in vitro. Overall, our findings advance the understanding of NA antibody response and provide important insights into the development of a broadly protective influenza vaccine.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wooseob Kim
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Microbiology, Korea University College of Medicine, Seoul 02841, Korea
| | - Huibin Lv
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zongjun Mou
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Michael J Scherm
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aaron J Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jackson S Turner
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wenhao O Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weiwen Liang
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Joel Rivera-Cardona
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chuyun Teo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Claire S Graham
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rachel M Presti
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chris K P Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; S.H. Ho Research Centre for Infectious Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Xinghong Dai
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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15
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. J Phys Chem Lett 2023; 14:9926-9934. [PMID: 37903229 PMCID: PMC10641874 DOI: 10.1021/acs.jpclett.3c02524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023]
Abstract
All protein simulations are conducted with varying degrees of simplification, oftentimes with unknown ramifications about how these simplifications affect the interpretability of the results. In this work, we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: (1) glycosylated neuraminidase in a whole virion (i.e., crowded membrane) environment, (2) glycosylated neuraminidase in its own lipid bilayer, and (3) unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting the solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large-scale conformational change, while making the protein structure more compact. Understanding these effects informs what factors one must consider in attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - İlker Deveci
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
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16
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Johnson GT, Agmon E, Akamatsu M, Lundberg E, Lyons B, Ouyang W, Quintero-Carmona OA, Riel-Mehan M, Rafelski S, Horwitz R. Building the next generation of virtual cells to understand cellular biology. Biophys J 2023; 122:3560-3569. [PMID: 37050874 PMCID: PMC10541477 DOI: 10.1016/j.bpj.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/19/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023] Open
Abstract
Cell science has made significant progress by focusing on understanding individual cellular processes through reductionist approaches. However, the sheer volume of knowledge collected presents challenges in integrating this information across different scales of space and time to comprehend cellular behaviors, as well as making the data and methods more accessible for the community to tackle complex biological questions. This perspective proposes the creation of next-generation virtual cells, which are dynamic 3D models that integrate information from diverse sources, including simulations, biophysical models, image-based models, and evidence-based knowledge graphs. These virtual cells would provide statistically accurate and holistic views of real cells, bridging the gap between theoretical concepts and experimental data, and facilitating productive new collaborations among researchers across related fields.
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Affiliation(s)
| | - Eran Agmon
- Center for Cell Analysis and Modeling, University of Connecticut Health, Farmington, Connecticut
| | - Matthew Akamatsu
- Department of Biology, University of Washington, Seattle, Washington
| | - Emma Lundberg
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Bioengineering, Stanford University, Stanford, California; Department of Pathology, Stanford University, Stanford, California; Chan Zuckerberg Biohub, San Francisco, California
| | - Blair Lyons
- Allen Institute for Cell Science, Seattle, Washington
| | - Wei Ouyang
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | | | | | - Rick Horwitz
- Allen Institute for Cell Science, Seattle, Washington.
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17
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.556910. [PMID: 37745347 PMCID: PMC10515755 DOI: 10.1101/2023.09.10.556910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
All protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - İlker Deveci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
- Department of Pharmacology, University of California, San Diego, La Jolla, California
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18
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Guarra F, Colombo G. Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens. J Chem Theory Comput 2023; 19:5315-5333. [PMID: 37527403 PMCID: PMC10448727 DOI: 10.1021/acs.jctc.3c00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 08/03/2023]
Abstract
The design of new biomolecules able to harness immune mechanisms for the treatment of diseases is a prime challenge for computational and simulative approaches. For instance, in recent years, antibodies have emerged as an important class of therapeutics against a spectrum of pathologies. In cancer, immune-inspired approaches are witnessing a surge thanks to a better understanding of tumor-associated antigens and the mechanisms of their engagement or evasion from the human immune system. Here, we provide a summary of the main state-of-the-art computational approaches that are used to design antibodies and antigens, and in parallel, we review key methodologies for epitope identification for both B- and T-cell mediated responses. A special focus is devoted to the description of structure- and physics-based models, privileged over purely sequence-based approaches. We discuss the implications of novel methods in engineering biomolecules with tailored immunological properties for possible therapeutic uses. Finally, we highlight the extraordinary challenges and opportunities presented by the possible integration of structure- and physics-based methods with emerging Artificial Intelligence technologies for the prediction and design of novel antigens, epitopes, and antibodies.
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Affiliation(s)
- Federica Guarra
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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19
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Lynch DL, Pavlova A, Fan Z, Gumbart JC. Understanding Virus Structure and Dynamics through Molecular Simulations. J Chem Theory Comput 2023. [PMID: 37192279 DOI: 10.1021/acs.jctc.3c00116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn benefits from a detailed understanding of both viral structure and dynamics. While great strides have been made in characterizing these systems experimentally, molecular simulations have proven to be an essential, complementary approach. In this work, we review the contributions of molecular simulations to the understanding of viral structure, functional dynamics, and processes related to the viral life cycle. Approaches ranging from coarse-grained to all-atom representations are discussed, including current efforts at modeling complete viral systems. Overall, this review demonstrates that computational virology plays an essential role in understanding these systems.
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Affiliation(s)
- Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zixing Fan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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20
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Mészáros B, Park E, Malinverni D, Sejdiu BI, Immadisetty K, Sandhu M, Lang B, Babu MM. Recent breakthroughs in computational structural biology harnessing the power of sequences and structures. Curr Opin Struct Biol 2023; 80:102608. [PMID: 37182396 DOI: 10.1016/j.sbi.2023.102608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
Recent advances in computational approaches and their integration into structural biology enable tackling increasingly complex questions. Here, we discuss several key areas, highlighting breakthroughs and remaining challenges. Theoretical modeling has provided tools to accurately predict and design protein structures on a scale currently difficult to achieve using experimental approaches. Molecular Dynamics simulations have become faster and more precise, delivering actionable information inaccessible by current experimental methods. Virtual screening workflows allow a high-throughput approach to discover ligands that bind and modulate protein function, while Machine Learning methods enable the design of proteins with new functionalities. Integrative structural biology combines several of these approaches, pushing the frontiers of structural and functional characterization to ever larger systems, advancing towards a complete understanding of the living cell. These breakthroughs will accelerate and significantly impact diverse areas of science.
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Affiliation(s)
- Bálint Mészáros
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Electa Park
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Duccio Malinverni
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/DucMalinverni
| | - Besian I Sejdiu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/bisejdiu
| | - Kalyan Immadisetty
- Department of Bone Marrow Transplantation & Cellular Therapy, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/k_immadisetty
| | - Manbir Sandhu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/M5andhu
| | - Benjamin Lang
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/langbnj
| | - M Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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21
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Prakaash D, Khalid S. All-Atom Mesoscale Simulations Predict the Conformational Dynamics of Influenza Virus Surface Glycoproteins. ACS CENTRAL SCIENCE 2023; 9:10-13. [PMID: 36712489 PMCID: PMC9881196 DOI: 10.1021/acscentsci.3c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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22
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Corey RA, Baaden M, Chavent M. A brief history of visualizing membrane systems in molecular dynamics simulations. FRONTIERS IN BIOINFORMATICS 2023; 3:1149744. [PMID: 37213533 PMCID: PMC10196259 DOI: 10.3389/fbinf.2023.1149744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/13/2023] [Indexed: 05/23/2023] Open
Abstract
Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.
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Affiliation(s)
- R. A. Corey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - M. Baaden
- Centre Nationale de la Recherche Scientifique, Laboratoire de Biochimie Théorique, Université Paris Cité, Paris, France
| | - M. Chavent
- Institut de Pharmacologie et Biologie Structurale, CNRS, Université de Toulouse, Toulouse, France
- *Correspondence: M. Chavent,
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