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Ballabio F, Paissoni C, Bollati M, de Rosa M, Capelli R, Camilloni C. Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations. J Chem Theory Comput 2023; 19:8401-8413. [PMID: 37923304 PMCID: PMC10687869 DOI: 10.1021/acs.jctc.3c00864] [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: 08/07/2023] [Revised: 10/11/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
Small-angle X-ray and neutron scattering (SAXS/SANS) provide valuable insights into the structure and dynamics of biomolecules in solution, complementing a wide range of structural techniques, including molecular dynamics simulations. As contrast-based methods, they are sensitive not only to structural properties but also to solvent-solute interactions. Their use in molecular dynamics simulations requires a forward model that should be as fast and accurate as possible. In this work, we demonstrate the feasibility of calculating SAXS and SANS intensities using a coarse-grained representation consisting of one bead per amino acid and three beads per nucleic acid, with form factors that can be corrected on the fly to account for solvation effects at no additional computational cost. By coupling this forward model with molecular dynamics simulations restrained with SAS data, it is possible to determine conformational ensembles or refine the structure and dynamics of proteins and nucleic acids in agreement with the experimental results. To assess the robustness of this approach, we applied it to gelsolin, for which we acquired SAXS data on its closed state, and to a UP1-microRNA complex, for which we used previously collected measurements. Our hybrid-resolution small-angle scattering (hySAS) implementation, being distributed in PLUMED, can be used with atomistic and coarse-grained simulations using diverse restraining strategies.
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Affiliation(s)
- Federico Ballabio
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, via Celoria 26, 20133 Milano, Italy
| | - Cristina Paissoni
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, via Celoria 26, 20133 Milano, Italy
| | - Michela Bollati
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, via Celoria 26, 20133 Milano, Italy
- Istituto
di Biofisica, Consiglio Nazionale delle
Ricerche (IBF-CNR), via
Alfonso Corti 12, 20133 Milano, Italy
| | - Matteo de Rosa
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, via Celoria 26, 20133 Milano, Italy
- Istituto
di Biofisica, Consiglio Nazionale delle
Ricerche (IBF-CNR), via
Alfonso Corti 12, 20133 Milano, Italy
| | - Riccardo Capelli
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, via Celoria 26, 20133 Milano, Italy
| | - Carlo Camilloni
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, via Celoria 26, 20133 Milano, Italy
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Bollati M, Peqini K, Barone L, Natale C, Beeg M, Gobbi M, Diomede L, Trucchi M, de Rosa M, Pellegrino S. Rational Design of a Peptidomimetic Inhibitor of Gelsolin Amyloid Aggregation. Int J Mol Sci 2022; 23:ijms232213973. [PMID: 36430461 PMCID: PMC9698219 DOI: 10.3390/ijms232213973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Gelsolin amyloidosis (AGel) is characterized by multiple systemic and ophthalmic features resulting from pathological tissue deposition of the gelsolin (GSN) protein. To date, no cure is available for the treatment of any form of AGel. More than ten single-point substitutions in the GSN gene are responsible for the occurrence of the disease and, among them, D187N/Y is the most widespread variant. These substitutions undergo an aberrant proteolytic cascade, producing aggregation-prone peptides of 5 and 8 kDa, containing the Gelsolin Amyloidogenic Core, spanning residues 182-192 (GAC182-192). Following a structure-based approach, we designed and synthesized three novel sequence-specific peptidomimetics (LB-5, LB-6, and LB-7) built on a piperidine-pyrrolidine unnatural amino acid. LB-5 and LB-6, but not LB-7, efficiently inhibit the aggregation of the GAC182-192 amyloidogenic peptides at sub-stoichiometric concentrations. These peptidomimetics resulted also effective in vivo, in a C. elegans-based assay, in counteracting the proteotoxicity of aggregated GAC182-192. These data pave the way to a novel pharmacological strategy against AGel and also validate a toolbox exploitable in other amyloidogenic diseases.
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Affiliation(s)
- Michela Bollati
- Institute of Biophysics, National Research Council (IBF-CNR), c/o Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Kaliroi Peqini
- Department of Pharmaceutical Science, “A. Marchesini” General and Organic Chemistry Section, University of Milano, Via Venezian 21, 20133 Milano, Italy
| | - Luigi Barone
- Department of Pharmaceutical Science, “A. Marchesini” General and Organic Chemistry Section, University of Milano, Via Venezian 21, 20133 Milano, Italy
| | - Carmina Natale
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Marten Beeg
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Marco Gobbi
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Luisa Diomede
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Michelangelo Trucchi
- Institute of Biophysics, National Research Council (IBF-CNR), c/o Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Matteo de Rosa
- Institute of Biophysics, National Research Council (IBF-CNR), c/o Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
- Correspondence: (M.d.R.); (S.P.)
| | - Sara Pellegrino
- Department of Pharmaceutical Science, “A. Marchesini” General and Organic Chemistry Section, University of Milano, Via Venezian 21, 20133 Milano, Italy
- Correspondence: (M.d.R.); (S.P.)
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Bollati M, Diomede L, Giorgino T, Natale C, Fagnani E, Boniardi I, Barbiroli A, Alemani R, Beeg M, Gobbi M, Fakin A, Mastrangelo E, Milani M, Presciuttini G, Gabellieri E, Cioni P, de Rosa M. A novel hotspot of gelsolin instability triggers an alternative mechanism of amyloid aggregation. Comput Struct Biotechnol J 2021; 19:6355-6365. [PMID: 34938411 PMCID: PMC8649582 DOI: 10.1016/j.csbj.2021.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 01/02/2023] Open
Abstract
Gelsolin comprises six homologous domains, named G1 to G6. Single point substitutions in this protein are responsible for AGel amyloidosis, a hereditary disease causing progressive corneal lattice dystrophy, cutis laxa, and polyneuropathy. Although several different amyloidogenic variants of gelsolin have been identified, only the most common mutants present in the G2 domain have been thoroughly characterized, leading to clarification of the functional mechanism. The molecular events underlying the pathological aggregation of 3 recently identified mutations, namely A551P, E553K and M517R, all localized at the interface between G4 and G5, are here explored for the first time. Structural studies point to destabilization of the interface between G4 and G5 due to three structural determinants: β-strand breaking, steric hindrance and/or charge repulsion, all implying impairment of interdomain contacts. Such rearrangements decrease the temperature and pressure stability of gelsolin but do not alter its susceptibility to furin cleavage, the first event in the canonical aggregation pathway. These variants also have a greater tendency to aggregate in the unproteolysed forms and exhibit higher proteotoxicity in a C. elegans-based assay. Our data suggest that aggregation of G4G5 variants follows an alternative, likely proteolysis-independent, pathway.
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Affiliation(s)
- Michela Bollati
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Luisa Diomede
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Toni Giorgino
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Carmina Natale
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Elisa Fagnani
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Irene Boniardi
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, Milano, Italy
| | - Rebecca Alemani
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Marten Beeg
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Marco Gobbi
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Eloise Mastrangelo
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Mario Milani
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | | | - Edi Gabellieri
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Patrizia Cioni
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Matteo de Rosa
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
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The structure of N184K amyloidogenic variant of gelsolin highlights the role of the H-bond network for protein stability and aggregation properties. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 49:11-19. [PMID: 31724080 DOI: 10.1007/s00249-019-01409-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/25/2019] [Accepted: 11/03/2019] [Indexed: 10/25/2022]
Abstract
Mutations in the gelsolin protein are responsible for a rare conformational disease known as AGel amyloidosis. Four of these mutations are hosted by the second domain of the protein (G2): D187N/Y, G167R and N184K. The impact of the latter has been so far evaluated only by studies on the isolated G2. Here we report the characterization of full-length gelsolin carrying the N184K mutation and compare the findings with those obtained on the wild type and the other variants. The crystallographic structure of the N184K variant in the Ca2+-free conformation shows remarkable similarities with the wild type protein. Only minimal local rearrangements can be observed and the mutant is as efficient as the wild type in severing filamentous actin. However, the thermal stability of the pathological variant is compromised in the Ca2+-free conditions. These data suggest that the N to K substitution causes a local disruption of the H-bond network in the core of the G2 domain. Such a subtle rearrangement of the connections does not lead to significant conformational changes but severely affects the stability of the protein.
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