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Castelli M, Magni A, Bonollo G, Pavoni S, Frigerio F, Oliveira ASF, Cinquini F, Serapian SA, Colombo G. Molecular mechanisms of chaperone-directed protein folding: Insights from atomistic simulations. Protein Sci 2023; 33:e4880. [PMID: 38145386 PMCID: PMC10895457 DOI: 10.1002/pro.4880] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Molecular chaperones, a family of proteins of which Hsp90 and Hsp70 are integral members, form an essential machinery to maintain healthy proteomes by controlling the folding and activation of a plethora of substrate client proteins. This is achieved through cycles in which Hsp90 and Hsp70, regulated by task-specific co-chaperones, process ATP and become part of a complex network that undergoes extensive compositional and conformational variations. Despite impressive advances in structural knowledge, the mechanisms that regulate the dynamics of functional assemblies, their response to nucleotides, and their relevance for client remodeling are still elusive. Here, we focus on the glucocorticoid receptor (GR):Hsp90:Hsp70:co-chaperone Hop client-loading and the GR:Hsp90:co-chaperone p23 client-maturation complexes, key assemblies in the folding cycle of glucocorticoid receptor (GR), a client strictly dependent upon Hsp90/Hsp70 for activity. Using a combination of molecular dynamics simulation approaches, we unveil with unprecedented detail the mechanisms that underpin function in these chaperone machineries. Specifically, we dissect the processes by which the nucleotide-encoded message is relayed to the client and how the distinct partners of the assemblies cooperate to (pre)organize partially folded GR during Loading and Maturation. We show how different ligand states determine distinct dynamic profiles for the functional interfaces defining the interactions in the complexes and modulate their overall flexibility to facilitate progress along the chaperone cycle. Finally, we also show that the GR regions engaged by the chaperone machinery display peculiar energetic signatures in the folded state, which enhance the probability of partial unfolding fluctuations. From these results, we propose a model where a dynamic cross-talk emerges between the chaperone dynamics states and remodeling of client-interacting regions. This factor, coupled to the highly dynamic nature of the assemblies and the conformational heterogeneity of their interactions, provides the basis for regulating the functions of distinct assemblies during the chaperoning cycle.
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Affiliation(s)
| | - Andrea Magni
- Dipartimento di Chimica, Università di Pavia, Pavia, Italy
| | | | - Silvia Pavoni
- Department of Physical Chemistry, R&D Eni SpA, San Donato Milanese, Italy
| | - Francesco Frigerio
- Department of Physical Chemistry, R&D Eni SpA, San Donato Milanese, Italy
| | - A Sofia F Oliveira
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Fabrizio Cinquini
- Upstream & Technical Services - TECS/STES - Eni Spa, San Donato Milanese, Italy
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Triveri A, Casali E, Frasnetti E, Doria F, Frigerio F, Cinquini F, Pavoni S, Moroni E, Marchetti F, Serapian SA, Colombo G. Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences. J Chem Theory Comput 2023; 19:2120-2134. [PMID: 36926878 PMCID: PMC10029694 DOI: 10.1021/acs.jctc.3c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
SARS-CoV-2 has evolved rapidly in the first 3 years of pandemic diffusion. The initial evolution of the virus appeared to proceed through big jumps in sequence changes rather than through the stepwise accumulation of point mutations on already established variants. Here, we examine whether this nonlinear mutational process reverberates in variations of the conformational dynamics of the SARS-CoV-2 Spike protein (S-protein), the first point of contact between the virus and the human host. We run extensive microsecond-scale molecular dynamics simulations of seven distinct variants of the protein in their fully glycosylated state and set out to elucidate possible links between the mutational spectrum of the S-protein and the structural dynamics of the respective variant, at global and local levels. The results reveal that mutation-dependent structural and dynamic modulations mostly consist of increased coordinated motions in variants that acquire stability and in an increased internal flexibility in variants that are less stable. Importantly, a limited number of functionally important substructures (the receptor binding domain, in particular) share the same time of movements in all variants, indicating efficient preorganization for functional regions dedicated to host interactions. Our results support a model in which the internal dynamics of the S-proteins from different strains varies in a way that reflects the observed random and non-stepwise jumps in sequence evolution, while conserving the functionally oriented traits of conformational dynamics necessary to support productive interactions with host receptors.
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Affiliation(s)
- Alice Triveri
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Emanuele Casali
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Elena Frasnetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Filippo Doria
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Francesco Frigerio
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | - Fabrizio Cinquini
- Upstream & Technical
Services—TECS/STES—Eni Spa, via Emilia 1, 20097 San Donato
Milanese (Mi), Italy
| | - Silvia Pavoni
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | | | - Filippo Marchetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Stefano A. Serapian
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Giorgio Colombo
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
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Triveri A, Serapian SA, Marchetti F, Doria F, Pavoni S, Cinquini F, Moroni E, Rasola A, Frigerio F, Colombo G. SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. J Chem Inf Model 2021; 61:4687-4700. [PMID: 34468141 PMCID: PMC8479857 DOI: 10.1021/acs.jcim.1c00857] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 12/30/2022]
Abstract
The SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments and raises concerns for their consequences on vaccine efficacy. To develop a model able to predict the potential impact of S-protein mutations on antibody binding sites, we performed unbiased multi-microsecond molecular dynamics of several glycosylated S-protein variants and applied a straightforward structure-dynamics-energy based strategy to predict potential changes in immunogenic regions on each variant. We recover known epitopes on the reference D614G sequence. By comparing our results, obtained on isolated S-proteins in solution, to recently published data on antibody binding and reactivity in new S variants, we directly show that modifications in the S-protein consistently translate into the loss of potentially immunoreactive regions. Our findings can thus be qualitatively reconnected to the experimentally characterized decreased ability of some of the Abs elicited against the dominant S-sequence to recognize variants. While based on the study of SARS-CoV-2 spike variants, our computational epitope-prediction strategy is portable and could be applied to study immunoreactivity in mutants of proteins of interest whose structures have been characterized, helping the development/selection of vaccines and antibodies able to control emerging variants.
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Affiliation(s)
- Alice Triveri
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Stefano A. Serapian
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Filippo Doria
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Silvia Pavoni
- Department
of Physical Chemistry, R&D Eni SpA, Via Maritano 27, San Donato Milanese, Milan 20097, Italy
| | - Fabrizio Cinquini
- Upstream
& Technical Services—TECS/STES—Eni Spa, Via Emilia 1, San
Donato Milanese, Milan 20097, Italy
| | - Elisabetta Moroni
- Istituto
di Scienze e Tecnologie Chimiche “Giulio Natta”—SCITEC, CNR Via Mario Bianco 9, Milano 20131, Italy
| | - Andrea Rasola
- Department
of Biomedical Sciences, University of Padua, Viale G. Colombo 3, Padova 35131, Italy
| | - Francesco Frigerio
- Department
of Physical Chemistry, R&D Eni SpA, Via Maritano 27, San Donato Milanese, Milan 20097, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
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Armbrüster M, Behrens M, Cinquini F, Föttinger K, Grin Y, Haghofer A, Klötzer B, Knop-Gericke A, Lorenz H, Ota A, Penner S, Prinz J, Rameshan C, Révay Z, Rosenthal D, Rupprechter G, Sautet P, Schlögl R, Shao L, Szentmiklósi L, Teschner D, Torres D, Wagner R, Widmer R, Wowsnick G. How to Control the Selectivity of Palladium-based Catalysts in Hydrogenation Reactions: The Role of Subsurface Chemistry. ChemCatChem 2012. [DOI: 10.1002/cctc.201200100] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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de Smit E, van Schooneveld MM, Cinquini F, Bluhm H, Sautet P, de Groot FMF, Weckhuysen BM. On the Surface Chemistry of Iron Oxides in Reactive Gas Atmospheres. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005282] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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de Smit E, van Schooneveld MM, Cinquini F, Bluhm H, Sautet P, de Groot FMF, Weckhuysen BM. On the Surface Chemistry of Iron Oxides in Reactive Gas Atmospheres. Angew Chem Int Ed Engl 2011; 50:1584-8. [DOI: 10.1002/anie.201005282] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 10/09/2010] [Indexed: 11/06/2022]
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de Smit E, Cinquini F, Beale AM, Safonova OV, van Beek W, Sautet P, Weckhuysen BM. Stability and Reactivity of ϵ−χ−θ Iron Carbide Catalyst Phases in Fischer−Tropsch Synthesis: Controlling μC. J Am Chem Soc 2010; 132:14928-41. [PMID: 20925335 DOI: 10.1021/ja105853q] [Citation(s) in RCA: 356] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emiel de Smit
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Université de Lyon, Institut de Chimie de Lyon, Laboratoire de Chimie, École Normale Supérieure de Lyon and CNRS, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France, Swiss-Norwegian Beamlines, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP220, F-38043 Grenoble Cedex, France, and Dipartimento di Scienze e Tecnologie Avanzate and Nano-SiSTeMI
| | - Fabrizio Cinquini
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Université de Lyon, Institut de Chimie de Lyon, Laboratoire de Chimie, École Normale Supérieure de Lyon and CNRS, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France, Swiss-Norwegian Beamlines, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP220, F-38043 Grenoble Cedex, France, and Dipartimento di Scienze e Tecnologie Avanzate and Nano-SiSTeMI
| | - Andrew M. Beale
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Université de Lyon, Institut de Chimie de Lyon, Laboratoire de Chimie, École Normale Supérieure de Lyon and CNRS, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France, Swiss-Norwegian Beamlines, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP220, F-38043 Grenoble Cedex, France, and Dipartimento di Scienze e Tecnologie Avanzate and Nano-SiSTeMI
| | - Olga V. Safonova
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Université de Lyon, Institut de Chimie de Lyon, Laboratoire de Chimie, École Normale Supérieure de Lyon and CNRS, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France, Swiss-Norwegian Beamlines, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP220, F-38043 Grenoble Cedex, France, and Dipartimento di Scienze e Tecnologie Avanzate and Nano-SiSTeMI
| | - Wouter van Beek
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Université de Lyon, Institut de Chimie de Lyon, Laboratoire de Chimie, École Normale Supérieure de Lyon and CNRS, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France, Swiss-Norwegian Beamlines, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP220, F-38043 Grenoble Cedex, France, and Dipartimento di Scienze e Tecnologie Avanzate and Nano-SiSTeMI
| | - Philippe Sautet
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Université de Lyon, Institut de Chimie de Lyon, Laboratoire de Chimie, École Normale Supérieure de Lyon and CNRS, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France, Swiss-Norwegian Beamlines, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP220, F-38043 Grenoble Cedex, France, and Dipartimento di Scienze e Tecnologie Avanzate and Nano-SiSTeMI
| | - Bert M. Weckhuysen
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Université de Lyon, Institut de Chimie de Lyon, Laboratoire de Chimie, École Normale Supérieure de Lyon and CNRS, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France, Swiss-Norwegian Beamlines, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP220, F-38043 Grenoble Cedex, France, and Dipartimento di Scienze e Tecnologie Avanzate and Nano-SiSTeMI
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Cinquini F, Delbecq F, Sautet P. A DFT comparative study of carbon adsorption and diffusion on the surface and subsurface of Ni and Ni3Pd alloy. Phys Chem Chem Phys 2009; 11:11546-56. [DOI: 10.1039/b914418h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ferrari AM, Pisani C, Cinquini F, Giordano L, Pacchioni G. Cationic and anionic vacancies on the NiO(100) surface: DFT+U and hybrid functional density functional theory calculations. J Chem Phys 2007; 127:174711. [DOI: 10.1063/1.2796154] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Wörz AS, Heiz U, Cinquini F, Pacchioni G. Charging of Au Atoms on TiO2 Thin Films from CO Vibrational Spectroscopy and DFT Calculations. J Phys Chem B 2005; 109:18418-26. [PMID: 16853371 DOI: 10.1021/jp054093o] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Au atoms have been deposited on oxidized and reduced TiO2 thin films grown on Mo(110). The gold binding sites and the occurrence of Au-TiO2 charge transfer were identified by measuring infrared spectra as a function of temperature and substrate preparation. The results have been interpreted by slab model DFT calculations. Au binds weakly to regular TiO2 sites (De < 0.5 eV) where it remains neutral, and diffuses easily even at low temperature until it gets trapped at strong binding sites such as oxygen vacancies (De = 1.7 eV). Here, a charge transfer from TiO2 to Au occurs. Au(delta-)CO complexes formed on oxygen vacancies easily lose CO (De = 0.4 eV), and the CO stretching frequency is red-shifted. On nondefective surfaces, CO adsorption induces a charge transfer from Au to TiO2 with formation of strongly bound Audelta+CO complexes (De = 2.4 eV); the corresponding CO frequency is blue-shifted with respect to free CO. We propose possible mechanisms to reconcile the observed CO desorption around 380 K with the unusually high stability of Au-CO complexes formed on regular sites predicted by the calculations. This implies: (a) diffusion of AuCO complexes above 150 K; (b) formation of gold dimers when the diffusing AuCO complex encounters a Au atom bound to an oxygen vacancy (reduced TiO2) or a second AuCO unit (oxidized TiO2); and (c) CO desorption from the resulting dimer, occurring around 350-400 K.
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Affiliation(s)
- Anke S Wörz
- Lehrstuhl für Physikalische Chemie 1, Technische Universität München, D-85747 Garching, Germany
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