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Maritan M. Immersive structure exploration with virtual reality. Acta Crystallogr A Found Adv 2022. [DOI: 10.1107/s2053273322097686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Maritan M, Autin L, Karr J, Covert MW, Olson AJ, Goodsell DS. Building Structural Models of a Whole Mycoplasma Cell. J Mol Biol 2022; 434:167351. [PMID: 34774566 PMCID: PMC8752489 DOI: 10.1016/j.jmb.2021.167351] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/01/2023]
Abstract
Building structural models of entire cells has been a long-standing cross-discipline challenge for the research community, as it requires an unprecedented level of integration between multiple sources of biological data and enhanced methods for computational modeling and visualization. Here, we present the first 3D structural models of an entire Mycoplasma genitalium (MG) cell, built using the CellPACK suite of computational modeling tools. Our model recapitulates the data described in recent whole-cell system biology simulations and provides a structural representation for all MG proteins, DNA and RNA molecules, obtained by combining experimental and homology-modeled structures and lattice-based models of the genome. We establish a framework for gathering, curating and evaluating these structures, exposing current weaknesses of modeling methods and the boundaries of MG structural knowledge, and visualization methods to explore functional characteristics of the genome and proteome. We compare two approaches for data gathering, a manually-curated workflow and an automated workflow that uses homologous structures, both of which are appropriate for the analysis of mesoscale properties such as crowding and volume occupancy. Analysis of model quality provides estimates of the regularization that will be required when these models are used as starting points for atomic molecular dynamics simulations.
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Affiliation(s)
- Martina Maritan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA. https://twitter.com/MartinaMaritan
| | - Ludovic Autin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA. https://twitter.com/grinche
| | - Jonathan Karr
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA; RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
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Russo R, Romeo M, Schulte T, Maritan M, Oberti L, Barzago MM, Barbiroli A, Pappone C, Anastasia L, Palladini G, Diomede L, Ricagno S. Cu(II) Binding Increases the Soluble Toxicity of Amyloidogenic Light Chains. Int J Mol Sci 2022; 23:ijms23020950. [PMID: 35055136 PMCID: PMC8780072 DOI: 10.3390/ijms23020950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 11/16/2022] Open
Abstract
Light chain amyloidosis (AL) is caused by the aberrant overproduction of immunoglobulin light chains (LCs). The resulting abnormally high LC concentrations in blood lead to deposit formation in the heart and other target organs. Organ damage is caused not only by the accumulation of bulky amyloid deposits, but extensive clinical data indicate that circulating soluble LCs also exert cardiotoxic effects. The nematode C. elegans has been validated to recapitulate LC soluble toxicity in vivo, and in such a model a role for copper ions in increasing LC soluble toxicity has been reported. Here, we applied microscale thermophoresis, isothermal calorimetry and thermal melting to demonstrate the specific binding of Cu2+ to the variable domain of amyloidogenic H7 with a sub-micromolar affinity. Histidine residues present in the LC sequence are not involved in the binding, and yet their mutation to Ala reduces the soluble toxicity of H7. Copper ions bind to and destabilize the variable domains and induce a limited stabilization in this domain. In summary, the data reported here, elucidate the biochemical bases of the Cu2+-induced toxicity; moreover, they also show that copper binding is just one of the several biochemical traits contributing to LC soluble in vivo toxicity.
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Affiliation(s)
- Rosaria Russo
- Dipartimento di Fisiopatologia Medico-Chirurgica e Dei Trapianti, Università Degli Studi di Milano, 20090 Segrate, Italy;
| | - Margherita Romeo
- Dipartimento di Biochimica e Farmacologia Molecolare, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (M.R.); (M.M.B.)
| | - Tim Schulte
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; (T.S.); (C.P.); (L.A.)
| | - Martina Maritan
- Dipartimento di Bioscienze, Università Degli Studi di Milano, 20133 Milano, Italy; (M.M.); (L.O.)
| | - Luca Oberti
- Dipartimento di Bioscienze, Università Degli Studi di Milano, 20133 Milano, Italy; (M.M.); (L.O.)
| | - Maria Monica Barzago
- Dipartimento di Biochimica e Farmacologia Molecolare, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (M.R.); (M.M.B.)
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, La Nutrizione e L’Ambiente, Università Degli Studi di Milano, 20133 Milan, Italy;
| | - Carlo Pappone
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; (T.S.); (C.P.); (L.A.)
- Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, San Donato, 20097 Milan, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Luigi Anastasia
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; (T.S.); (C.P.); (L.A.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Giovanni Palladini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, 27100 Pavia, Italy;
| | - Luisa Diomede
- Dipartimento di Biochimica e Farmacologia Molecolare, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (M.R.); (M.M.B.)
- Correspondence: (L.D.); (S.R.)
| | - Stefano Ricagno
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; (T.S.); (C.P.); (L.A.)
- Dipartimento di Bioscienze, Università Degli Studi di Milano, 20133 Milano, Italy; (M.M.); (L.O.)
- Correspondence: (L.D.); (S.R.)
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Abstract
CellPAINT is an interactive digital tool that allows non-expert users to create illustrations of the molecular structure of cells and viruses. We present a new release with several key enhancements, including the ability to generate custom ingredients from structure information in the Protein Data Bank, and interaction, grouping, and locking functions that streamline the creation of assemblies and illustration of large, complex scenes. An example of CellPAINT as a tool for hypothesis generation in the interpretation of cryoelectron tomograms is presented. CellPAINT is freely available at http://ccsb.scripps.edu/cellpaint.
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Affiliation(s)
- Adam Gardner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Ludovic Autin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Daniel Fuentes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Martina Maritan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Benjamin A. Barad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Michaela Medina
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Arthur J. Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Danielle A. Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - David S. Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- *Correspondence: David S. Goodsell
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Jewett AI, Stelter D, Lambert J, Saladi SM, Roscioni OM, Ricci M, Autin L, Maritan M, Bashusqeh SM, Keyes T, Dame RT, Shea JE, Jensen GJ, Goodsell DS. Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics. J Mol Biol 2021; 433:166841. [PMID: 33539886 DOI: 10.1016/j.jmb.2021.166841] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 02/01/2023]
Abstract
Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them. Consequently, the use of coarse-grained models has remained challenging. Moltemplate is a file format for storing coarse-grained molecular models and the forces that act on them, as well as a program that converts moltemplate files into input files for LAMMPS, a popular molecular dynamics engine. Moltemplate has broad scope and an emphasis on generality. It accommodates new kinds of forces as they are developed for LAMMPS, making moltemplate a popular tool with thousands of users in computational chemistry, materials science, and structural biology. To demonstrate its wide functionality, we provide examples of using moltemplate to prepare simulations of fluids using many-body forces, coarse-grained organic semiconductors, and the motor-driven supercoiling and condensation of an entire bacterial chromosome.
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Affiliation(s)
- Andrew I Jewett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | | | - Jason Lambert
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Shyam M Saladi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Ludovic Autin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Martina Maritan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Saeed M Bashusqeh
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Tom Keyes
- Department of Chemistry, Boston University, MA, USA
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Joan-Emma Shea
- Departments of Chemistry and Biochemistry and Physics, University of California, Santa Barbara, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA; RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
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Nguyen N, Strnad O, Klein T, Luo D, Alharbi R, Wonka P, Maritan M, Mindek P, Autin L, Goodsell DS, Viola I. Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models. IEEE Trans Vis Comput Graph 2021; 27:722-732. [PMID: 33055034 PMCID: PMC8642830 DOI: 10.1109/tvcg.2020.3030415] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/31/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
We present a new technique for the rapid modeling and construction of scientifically accurate mesoscale biological models. The resulting 3D models are based on a few 2D microscopy scans and the latest knowledge available about the biological entity, represented as a set of geometric relationships. Our new visual-programming technique is based on statistical and rule-based modeling approaches that are rapid to author, fast to construct, and easy to revise. From a few 2D microscopy scans, we determine the statistical properties of various structural aspects, such as the outer membrane shape, the spatial properties, and the distribution characteristics of the macromolecular elements on the membrane. This information is utilized in the construction of the 3D model. Once all the imaging evidence is incorporated into the model, additional information can be incorporated by interactively defining the rules that spatially characterize the rest of the biological entity, such as mutual interactions among macromolecules, and their distances and orientations relative to other structures. These rules are defined through an intuitive 3D interactive visualization as a visual-programming feedback loop. We demonstrate the applicability of our approach on a use case of the modeling procedure of the SARS-CoV-2 virion ultrastructure. This atomistic model, which we present here, can steer biological research to new promising directions in our efforts to fight the spread of the virus.
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Affiliation(s)
- Ngan Nguyen
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Ondřej Strnad
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | | | - Deng Luo
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Ruwayda Alharbi
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Peter Wonka
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | | | | | | | | | - Ivan Viola
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
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Autin L, Maritan M, Barbaro BA, Gardner A, Olson AJ, Sanner M, Goodsell DS. Mesoscope: A Web-based Tool for Mesoscale Data Integration and Curation. MolVa (2020) 2020; 2020:23-31. [PMID: 37928321 PMCID: PMC10624244 DOI: 10.2312/molva.20201098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Interest is growing for 3D models of the biological mesoscale, the intermediate scale between the nanometer scale of molecular structure and micrometer scale of cellular biology. However, it is currently difficult to gather, curate and integrate all the data required to define such models. To address this challenge we developed Mesoscope (mesoscope.scripps.edu/beta), a web-based data integration and curation tool. Mesoscope allows users to begin with a listing of molecules (such as data from proteomics), and to use resources at UniProt and the PDB to identify, prepare and validate appropriate structures and representations for each molecule, ultimately producing a portable output file used by CellPACK and other modeling tools for generation of 3D models of the biological mesoscale. The availability of this tool has proven essential in several exploratory applications, given the high complexity of mesoscale models and the heterogeneity of the available data sources.
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Affiliation(s)
- L Autin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - M Maritan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - B A Barbaro
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - A Gardner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - A J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - M Sanner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - D S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- RCSB Protein Data Bank and Center for Integrative Proteomics Research, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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Swuec P, Lavatelli F, Tasaki M, Paissoni C, Rognoni P, Maritan M, Brambilla F, Milani P, Mauri P, Camilloni C, Palladini G, Merlini G, Ricagno S, Bolognesi M. Cryo-EM structure of cardiac amyloid fibrils from an immunoglobulin light chain AL amyloidosis patient. Nat Commun 2019; 10:1269. [PMID: 30894521 PMCID: PMC6427027 DOI: 10.1038/s41467-019-09133-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/15/2019] [Indexed: 11/09/2022] Open
Abstract
Systemic light chain amyloidosis (AL) is a life-threatening disease caused by aggregation and deposition of monoclonal immunoglobulin light chains (LC) in target organs. Severity of heart involvement is the most important factor determining prognosis. Here, we report the 4.0 Å resolution cryo-electron microscopy map and molecular model of amyloid fibrils extracted from the heart of an AL amyloidosis patient with severe amyloid cardiomyopathy. The helical fibrils are composed of a single protofilament, showing typical 4.9 Å stacking and cross-β architecture. Two distinct polypeptide stretches (total of 77 residues) from the LC variable domain (Vl) fit the fibril density. Despite Vl high sequence variability, residues stabilizing the fibril core are conserved through different cardiotoxic Vl, highlighting structural motifs that may be common to misfolding-prone LCs. Our data shed light on the architecture of LC amyloids, correlate amino acid sequences with fibril assembly, providing the grounds for development of innovative medicines.
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Affiliation(s)
- Paolo Swuec
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.,Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Francesca Lavatelli
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy
| | - Masayoshi Tasaki
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy.,Department of Morphological and Physiological Sciences, Graduate School of Health Sciences,, Kumamoto University, 4-24-1 Kuhonji, Kumamoto, 862-0976, Japan.,Department of Neurology, Graduate School of Medical Sciences, 1-1-1, Honjo, Kumamoto, 860-0811, Japan
| | - Cristina Paissoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Paola Rognoni
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy
| | - Martina Maritan
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Francesca Brambilla
- Institute for Biomedical Technologies-CNR, Via Fratelli Cervi 93, 20090, Segrate, Italy
| | - Paolo Milani
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy
| | - Pierluigi Mauri
- Institute for Biomedical Technologies-CNR, Via Fratelli Cervi 93, 20090, Segrate, Italy
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Giovanni Palladini
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy
| | - Giampaolo Merlini
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy. .,Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
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Maritan M, Ambrosetti A, Oberti L, Barbiroli A, Diomede L, Romeo M, Lavatelli F, Sormanni P, Palladini G, Bolognesi M, Merlini G, Ricagno S. Modulating the cardiotoxic behaviour of immunoglobulin light chain dimers through point mutations. Amyloid 2019; 26:105-106. [PMID: 31343361 DOI: 10.1080/13506129.2019.1583185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Martina Maritan
- a Department of Bioscience, University of Milan , Milan , Italy
| | | | - Luca Oberti
- a Department of Bioscience, University of Milan , Milan , Italy
| | - Alberto Barbiroli
- b Department of Nutritional Science, University of Milan , Milan , Italy
| | - Luisa Diomede
- c IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Milano , Italy
| | - Margherita Romeo
- c IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Milano , Italy
| | - Francesca Lavatelli
- d Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo , Pavia , Italy
| | - Pietro Sormanni
- e Department of Chemistry, University of Cambridge , Cambridge , UK
| | - Giovanni Palladini
- d Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo , Pavia , Italy
| | | | - Giampaolo Merlini
- d Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo , Pavia , Italy
| | - Stefano Ricagno
- a Department of Bioscience, University of Milan , Milan , Italy
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10
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Oberti L, Maritan M, Rognoni P, Barbiroli A, Lavatelli F, Russo R, Palladini G, Bolognesi M, Merlini G, Ricagno S. The concurrency of several biophysical traits links immunoglobulin light chains with toxicity in AL amyloidosis. Amyloid 2019; 26:107-108. [PMID: 31343357 DOI: 10.1080/13506129.2019.1583187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Luca Oberti
- a Department of Bioscience, University of Milan , Milan , Italy
| | - Martina Maritan
- a Department of Bioscience, University of Milan , Milan , Italy
| | - Paola Rognoni
- b Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, University of Pavia , Pavia , Italy
| | - Alberto Barbiroli
- c DeFENS - Department of Food, Environmental and Nutritional Sciences, University of Milan , Milan , Italy
| | - Francesca Lavatelli
- b Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, University of Pavia , Pavia , Italy
| | - Rosaria Russo
- d Department of Physiopathology and Transplantation, University of Milan , Milan , Italy
| | - Giovanni Palladini
- b Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, University of Pavia , Pavia , Italy
| | | | - Giampaolo Merlini
- b Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, University of Pavia , Pavia , Italy
| | - Stefano Ricagno
- a Department of Bioscience, University of Milan , Milan , Italy
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Maritan M, Veggi D, Cozzi R, Dello Iacono L, Bartolini E, Lo Surdo P, Maruggi G, Spraggon G, Bottomley MJ, Malito E. Structures of NHBA elucidate a broadly conserved epitope identified by a vaccine induced antibody. PLoS One 2018; 13:e0201922. [PMID: 30133484 PMCID: PMC6104945 DOI: 10.1371/journal.pone.0201922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 06/28/2018] [Indexed: 11/18/2022] Open
Abstract
Neisserial heparin binding antigen (NHBA) is one of three main recombinant protein antigens in 4CMenB, a vaccine for the prevention of invasive meningococcal disease caused by Neisseria meningitidis serogroup B. NHBA is a surface-exposed lipoprotein composed of a predicted disordered N-terminal region, an arginine-rich region that binds heparin, and a C-terminal domain that folds as an anti-parallel β-barrel and that upon release after cleavage by human proteases alters endothelial permeability. NHBA induces bactericidal antibodies in humans, and NHBA-specific antibodies elicited by the 4CMenB vaccine contribute to serum bactericidal activity, the correlate of protection. To better understand the structural bases of the human antibody response to 4CMenB vaccination and to inform antigen design, we used X-ray crystallography to elucidate the structures of two C-terminal fragments of NHBA, either alone or in complex with the Fab derived from the vaccine-elicited human monoclonal antibody 5H2, and the structure of the unbound Fab 5H2. The structures reveal details on the interaction between an N-terminal β-hairpin fragment and the β-barrel, and explain how NHBA is capable of generating cross-reactive antibodies through an extensive conserved conformational epitope that covers the entire C-terminal face of the β-barrel. By providing new structural information on a vaccine antigen and on the human immune response to vaccination, these results deepen our molecular understanding of 4CMenB, and might also aid future vaccine design projects.
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Affiliation(s)
| | | | | | | | | | | | | | - Glen Spraggon
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, United States of America
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Maritan M, Cozzi R, Lo Surdo P, Veggi D, Bottomley MJ, Malito E. Crystal structures of human Fabs targeting the Bexsero meningococcal vaccine antigen NHBA. Acta Crystallogr F Struct Biol Commun 2017; 73:305-314. [PMID: 28580917 PMCID: PMC5458386 DOI: 10.1107/s2053230x17006021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/20/2017] [Indexed: 11/10/2022]
Abstract
The crystal structures and functional characterization of two anti-NHBA human Fabs provide insight into the recognition by human antibodies of one of the main components of the first vaccine against serogroup B N. meningitidis (Bexsero). Neisserial heparin-binding antigen (NHBA) is a surface-exposed lipoprotein from Neisseria meningitidis and is a component of the meningococcus B vaccine Bexsero. As part of a study to characterize the three-dimensional structure of NHBA and the molecular basis of the human immune response to Bexsero, the crystal structures of two fragment antigen-binding domains (Fabs) isolated from human monoclonal antibodies targeting NHBA were determined. Through a high-resolution analysis of the organization and the amino-acid composition of the CDRs, these structures provide broad insights into the NHBA epitopes recognized by the human immune system. As expected, these Fabs also show remarkable structural conservation, as shown by a structural comparison of 15 structures of apo Fab 10C3 which were obtained from crystals grown in different crystallization conditions and were solved while searching for a complex with a bound NHBA fragment or epitope peptide. This study also provides indirect evidence for the intrinsically disordered nature of two N-terminal regions of NHBA.
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Abate F, Cozzi R, Maritan M, Lo Surdo P, Maione D, Malito E, Bottomley MJ. Crystal structure of FhuD at 1.6 Å resolution: a ferrichrome-binding protein from the animal and human pathogen Staphylococcus pseudintermedius. Acta Crystallogr F Struct Biol Commun 2016; 72:214-9. [PMID: 26919525 DOI: 10.1107/s2053230x16002272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 02/05/2016] [Indexed: 11/10/2022]
Abstract
Staphylococcus pseudintermedius is a leading cause of disease in dogs, and zoonosis causes human infections. Methicillin-resistant S. pseudintermedius strains are emerging, resembling the global health threat of S. aureus. Therefore, it is increasingly important to characterize potential targets for intervention against S. pseudintermedius. Here, FhuD, an S. pseudintermedius surface lipoprotein implicated in iron uptake, was characterized. It was found that FhuD bound ferrichrome in an iron-dependent manner, which increased the thermostability of FhuD by >15 °C. The crystal structure of ferrichrome-free FhuD was determined via molecular replacement at 1.6 Å resolution. FhuD exhibits the class III solute-binding protein (SBP) fold, with a ligand-binding cavity between the N- and C-terminal lobes, which is here occupied by a PEG molecule. The two lobes of FhuD were oriented in a closed conformation. These results provide the first detailed structural characterization of FhuD, a potential therapeutic target of S. pseudintermedius.
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Affiliation(s)
| | - Roberta Cozzi
- Research Centre, GSK Vaccines Srl, Via Fiorentina 1, 53100 Siena, Italy
| | - Martina Maritan
- Research Centre, GSK Vaccines Srl, Via Fiorentina 1, 53100 Siena, Italy
| | - Paola Lo Surdo
- Research Centre, GSK Vaccines Srl, Via Fiorentina 1, 53100 Siena, Italy
| | - Domenico Maione
- Research Centre, GSK Vaccines Srl, Via Fiorentina 1, 53100 Siena, Italy
| | - Enrico Malito
- Research Centre, GSK Vaccines Srl, Via Fiorentina 1, 53100 Siena, Italy
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