1
|
Faidon Brotzakis Z, Löhr T, Truong S, Hoff S, Bonomi M, Vendruscolo M. Determination of the Structure and Dynamics of the Fuzzy Coat of an Amyloid Fibril of IAPP Using Cryo-Electron Microscopy. Biochemistry 2023; 62:2407-2416. [PMID: 37477459 PMCID: PMC10433526 DOI: 10.1021/acs.biochem.3c00010] [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: 01/10/2023] [Revised: 06/03/2023] [Indexed: 07/22/2023]
Abstract
In recent years, major advances in cryo-electron microscopy (cryo-EM) have enabled the routine determination of complex biomolecular structures at atomistic resolution. An open challenge for this approach, however, concerns large systems that exhibit continuous dynamics. To address this problem, we developed the metadynamic electron microscopy metainference (MEMMI) method, which incorporates metadynamics, an enhanced conformational sampling approach, into the metainference method of integrative structural biology. MEMMI enables the simultaneous determination of the structure and dynamics of large heterogeneous systems by combining cryo-EM density maps with prior information through molecular dynamics, while at the same time modeling the different sources of error. To illustrate the method, we apply it to elucidate the dynamics of an amyloid fibril of the islet amyloid polypeptide (IAPP). The resulting conformational ensemble provides an accurate description of the structural variability of the disordered region of the amyloid fibril, known as fuzzy coat. The conformational ensemble also reveals that in nearly half of the structural core of this amyloid fibril, the side chains exhibit liquid-like dynamics despite the presence of the highly ordered network backbone of hydrogen bonds characteristic of the cross-β structure of amyloid fibrils.
Collapse
Affiliation(s)
- Z. Faidon Brotzakis
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Thomas Löhr
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Steven Truong
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Samuel Hoff
- Department
of Structural Biology and Chemistry, Institut
Pasteur, Université Paris Cité CNRS UMR 3528, 75015 Paris, France
| | - Massimiliano Bonomi
- Department
of Structural Biology and Chemistry, Institut
Pasteur, Université Paris Cité CNRS UMR 3528, 75015 Paris, France
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| |
Collapse
|
2
|
Wong-Benito V, de Rijke J, Dixon B. Antigen presentation in vertebrates: Structural and functional aspects. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 144:104702. [PMID: 37116963 DOI: 10.1016/j.dci.2023.104702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 06/05/2023]
Abstract
Antigen presentation is a key process of the immune system and is responsible for the activation of T cells. The main characters are the major histocompatibility complex class I (MHC-I) and class II (MHC-II) molecules, and accessory proteins that act as chaperones for these glycoproteins. Current knowledge of this process and also the elucidation of the structural features of these proteins, has been extensively reviewed in humans. Unfortunately, this is not the case for non-human species, wherein the function and structural characteristic of the antigen presentation proteins is far from being understood. The majority of previous studies in non-human species, especially in teleost fish and lower vertebrates, are limited to the transcriptomic level, which leads to gaps in the knowledge about the functional process of antigen presentation in these species. This review summarizes what is known so far about antigen presentation pathways in vertebrates from a structural and functional perspective. The focus is not only on the MHC receptors, but also, on the forgotten characters of these pathways such as the proteins of the peptide loading complex, and the MHC-II chaperone invariant chain.
Collapse
Affiliation(s)
| | - Jill de Rijke
- Department of Biology, University of Waterloo, Canada
| | - Brian Dixon
- Department of Biology, University of Waterloo, Canada.
| |
Collapse
|
3
|
Rosace A, Bennett A, Oeller M, Mortensen MM, Sakhnini L, Lorenzen N, Poulsen C, Sormanni P. Automated optimisation of solubility and conformational stability of antibodies and proteins. Nat Commun 2023; 14:1937. [PMID: 37024501 PMCID: PMC10079162 DOI: 10.1038/s41467-023-37668-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Biologics, such as antibodies and enzymes, are crucial in research, biotechnology, diagnostics, and therapeutics. Often, biologics with suitable functionality are discovered, but their development is impeded by developability issues. Stability and solubility are key biophysical traits underpinning developability potential, as they determine aggregation, correlate with production yield and poly-specificity, and are essential to access parenteral and oral delivery. While advances for the optimisation of individual traits have been made, the co-optimization of multiple traits remains highly problematic and time-consuming, as mutations that improve one property often negatively impact others. In this work, we introduce a fully automated computational strategy for the simultaneous optimisation of conformational stability and solubility, which we experimentally validate on six antibodies, including two approved therapeutics. Our results on 42 designs demonstrate that the computational procedure is highly effective at improving developability potential, while not affecting antigen-binding. We make the method available as a webserver at www-cohsoftware.ch.cam.ac.uk.
Collapse
Affiliation(s)
- Angelo Rosace
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Master in Bioinformatics for Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Anja Bennett
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Department of Mammalian Expression, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
- BRIC, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
| | - Mie M Mortensen
- Department of Purification Technologies, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
- Faculty of Engineering and Science, Department of Biotechnology, Chemistry and Environmental Engineering, University of Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Laila Sakhnini
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, 2760, Denmark
| | - Nikolai Lorenzen
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, 2760, Denmark
| | - Christian Poulsen
- Department of Mammalian Expression, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK.
| |
Collapse
|
4
|
Talian I, Laputková G, Schwartzová V. Identification of crucial salivary proteins/genes and pathways involved in pathogenesis of temporomandibular disorders. OPEN CHEM 2022. [DOI: 10.1515/chem-2022-0249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Abstract
Temporomandibular disorder (TMD) is a collective term for a group of conditions that lead to impairment of the function of the temporomandibular joint. The proteins/genes and signaling pathways associated with TMD are still poorly understood. The aim of this study was to identify key differentially expressed salivary proteins/genes (DEGs) associated with TMD progression using LC-MS/MS coupled with a bioinformatics approach. The protein–protein interaction network was obtained from the STRING database and the hub genes were identified using Cytoscape including cytoHubba and MCODE plug-ins. In addition, enrichment of gene ontology functions and the Reactome signaling pathway was performed. A total of 140 proteins/genes were differentially expressed. From cluster analysis, a set of 20 hub genes were significantly modulated: ALB, APOA1, B2M, C3, CAT, CLU, CTSD, ENO1, GSN, HBB, HP, HSPA8, LTF, LYZ, MMP9, S100A9, SERPINA1, TF, TPI1, and TXN. Two enriched signaling pathways, glycolysis and gluconeogenesis, and tryptophan signaling pathway involving the hub genes CAT, ENO1, and TPI1 have been identified. The rest of the hub genes were mainly enriched in the innate immune system and antimicrobial peptides signaling pathways. In summary, hub DEGs and the signaling pathways identified here have elucidated the molecular mechanisms of TMD pathogenesis.
Collapse
Affiliation(s)
- Ivan Talian
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P. J. Šafárik , Košice , 040 11 , Slovak Republic
| | - Galina Laputková
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P. J. Šafárik , Košice , 040 11 , Slovak Republic
| | - Vladimíra Schwartzová
- Clinic of Stomatology and Maxillofacial Surgery, Faculty of Medicine, University of P. J. Šafárik and Louis Pasteur University Hospital , Košice , 041 90 , Slovak Republic
| |
Collapse
|
5
|
Ballabio F, Broggini L, Paissoni C, Han X, Peqini K, Sala BM, Sun R, Sandalova T, Barbiroli A, Achour A, Pellegrino S, Ricagno S, Camilloni C. l- to d-Amino Acid Substitution in the Immunodominant LCMV-Derived Epitope gp33 Highlights the Sensitivity of the TCR Recognition Mechanism for the MHC/Peptide Structure and Dynamics. ACS OMEGA 2022; 7:9622-9635. [PMID: 35350306 PMCID: PMC8945122 DOI: 10.1021/acsomega.1c06964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Presentation of pathogen-derived epitopes by major histocompatibility complex I (MHC-I) can lead to the activation and expansion of specific CD8+ T cell clones, eventually resulting in the destruction of infected target cells. Altered peptide ligands (APLs), designed to elicit immunogenicity toward a wild-type peptide, may affect the overall stability of MHC-I/peptide (pMHC) complexes and modulate the recognition by T cell receptors (TCR). Previous works have demonstrated that proline substitution at position 3 (p3P) of different MHC-restricted epitopes, including the immunodominant LCMV-derived epitope gp33 and escape variants, may be an effective design strategy to increase epitope immunogenicity. These studies hypothesized that the p3P substitution increases peptide rigidity, facilitating TCR binding. Here, molecular dynamics simulations indicate that the p3P modification rigidifies the APLs in solution predisposing them for the MHC-I loading as well as once bound to H-2Db, predisposing them for TCR binding. Our results also indicate that peptide position 6, key for interaction of H-2Db/gp33 with the TCR P14, takes a suboptimal conformation before as well as after binding to the TCR. Analyses of H-2Db in complex with APLs, in which position 6 was subjected to an l- to d-amino acid modification, revealed small conformational changes and comparable pMHC thermal stability. However, the l- to d-modification reduced significantly the binding to P14 even in the presence of the p3P modification. Our combined data highlight the sensitivity of the TCR for the conformational dynamics of pMHC and provide further tools to dissect and modulate TCR binding and immunogenicity via APLs.
Collapse
Affiliation(s)
- Federico Ballabio
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
| | - Luca Broggini
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
- Institute
of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Cristina Paissoni
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
| | - Xiao Han
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Kaliroi Peqini
- DISFARM,
Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e
Organica, Università degli Studi
di Milano, Milano 20122, Italy
| | - Benedetta Maria Sala
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Renhua Sun
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Tatyana Sandalova
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Alberto Barbiroli
- Dipartimento
di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Milano 20122, Italy
| | - Adnane Achour
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Sara Pellegrino
- DISFARM,
Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e
Organica, Università degli Studi
di Milano, Milano 20122, Italy
| | - Stefano Ricagno
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
- Institute
of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Carlo Camilloni
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
| |
Collapse
|
6
|
Faravelli G, Mondani V, Mangione PP, Raimondi S, Marchese L, Lavatelli F, Stoppini M, Corazza A, Canetti D, Verona G, Obici L, Taylor GW, Gillmore JD, Giorgetti S, Bellotti V. Amyloid Formation by Globular Proteins: The Need to Narrow the Gap Between in Vitro and in Vivo Mechanisms. Front Mol Biosci 2022; 9:830006. [PMID: 35237660 PMCID: PMC8883118 DOI: 10.3389/fmolb.2022.830006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/20/2022] [Indexed: 11/15/2022] Open
Abstract
The globular to fibrillar transition of proteins represents a key pathogenic event in the development of amyloid diseases. Although systemic amyloidoses share the common characteristic of amyloid deposition in the extracellular matrix, they are clinically heterogeneous as the affected organs may vary. The observation that precursors of amyloid fibrils derived from circulating globular plasma proteins led to huge efforts in trying to elucidate the structural events determining the protein metamorphosis from their globular to fibrillar state. Whereas the process of metamorphosis has inspired poets and writers from Ovid to Kafka, protein metamorphism is a more recent concept. It is an ideal metaphor in biochemistry for studying the protein folding paradigm and investigating determinants of folding dynamics. Although we have learned how to transform both normal and pathogenic globular proteins into fibrillar polymers in vitro, the events occurring in vivo, are far more complex and yet to be explained. A major gap still exists between in vivo and in vitro models of fibrillogenesis as the biological complexity of the disease in living organisms cannot be reproduced at the same extent in the test tube. Reviewing the major scientific attempts to monitor the amyloidogenic metamorphosis of globular proteins in systems of increasing complexity, from cell culture to human tissues, may help to bridge the gap between the experimental models and the actual pathological events in patients.
Collapse
Affiliation(s)
- Giulia Faravelli
- Unit of Biochemistry, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Valentina Mondani
- Unit of Biochemistry, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - P. Patrizia Mangione
- Unit of Biochemistry, Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Wolfson Drug Discovery Unit, Division of Medicine, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, United Kingdom
| | - Sara Raimondi
- Unit of Biochemistry, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Loredana Marchese
- Unit of Biochemistry, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Francesca Lavatelli
- Unit of Biochemistry, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Monica Stoppini
- Unit of Biochemistry, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Alessandra Corazza
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy
| | - Diana Canetti
- Wolfson Drug Discovery Unit, Division of Medicine, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, United Kingdom
| | - Guglielmo Verona
- Wolfson Drug Discovery Unit, Division of Medicine, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, United Kingdom
| | - Laura Obici
- Amyloidosis Research and Treatment Centre, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Graham W. Taylor
- Wolfson Drug Discovery Unit, Division of Medicine, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, United Kingdom
| | - Julian D. Gillmore
- National Amyloidosis Centre, University College London and Royal Free Hospital, London, United Kingdom
| | - Sofia Giorgetti
- Unit of Biochemistry, Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy
| | - Vittorio Bellotti
- Unit of Biochemistry, Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Wolfson Drug Discovery Unit, Division of Medicine, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, United Kingdom
- Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy
- Scientific Direction, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- *Correspondence: Vittorio Bellotti, ,
| |
Collapse
|
7
|
Ojha VA, Bahl V, Ramachandra SC, Prashant A. Putrescence to Quintessence: An Atypical Presentation of Multiple Osteoporotic Spinal Fractures Masquerading as Multiple Myeloma. Cureus 2021; 13:e20788. [PMID: 35141056 PMCID: PMC8796275 DOI: 10.7759/cureus.20788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2021] [Indexed: 11/30/2022] Open
Abstract
A 64-year-old male patient presented with multiple osteoporotic spinal fractures of unknown origin. He was provisionally diagnosed with multiple myeloma based on biochemical and radiological findings. The patient presented in a very frail condition with a questionable outcome but showed a remarkable recovery from being frail to relatively fit. His baseline characteristics including magnetic resonance imaging of the dorsolumbar spine, beta 2 microglobulins, and C-reactive protein improved. The diagnosis was later changed to multiple spinal osteoporotic fractures. In this case report, we highlight that, although it is a good practice to have a single working diagnosis, when the diagnosis is challenging, a holistic approach should be followed to prevent medical and diagnostic miscalculations.
Collapse
|
8
|
Oliveira NFB, Rodrigues FEP, Vitorino JNM, Loureiro RJS, Faísca PFN, Machuqueiro M. Predicting stable binding modes from simulated dimers of the D76N mutant of β 2-microglobulin. Comput Struct Biotechnol J 2021; 19:5160-5169. [PMID: 34630936 PMCID: PMC8473664 DOI: 10.1016/j.csbj.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
β2m D76N mutant populates an aggregation-prone monomer (I2) with unstructured termini. MD and MM-PBSA indicate that I2 dimers are stabilized by hydrophobic interactions. The termini regions and BC- and DE-loops are prevalent in the most stable interfaces. The most stable dimer has a limited growth potential without structural rearrangement.
The D76N mutant of the β2m protein is a biologically motivated model system to study protein aggregation. There is strong experimental evidence, supported by molecular simulations, that D76N populates a highly dynamic conformation (which we originally named I2) that exposes aggregation-prone patches as a result of the detachment of the two terminal regions. Here, we use Molecular Dynamics simulations to study the stability of an ensemble of dimers of I2 generated via protein–protein docking. MM-PBSA calculations indicate that within the ensemble of investigated dimers the major contribution to interface stabilization at physiological pH comes from hydrophobic interactions between apolar residues. Our structural analysis also reveals that the interfacial region associated with the most stable binding modes are particularly rich in residues pertaining to both the N- and C-terminus, as well residues from the BC- and DE-loops. On the other hand, the less stable interfaces are stabilized by intermolecular interactions involving residues from the CD- and EF-loops. By focusing on the most stable binding modes, we used a simple geometric rule to propagate the corresponding dimer interfaces. We found that, in the absence of any kind of structural rearrangement occurring at an early stage of the oligomerization pathway, some interfaces drive a self-limited growth process, while others can be propagated indefinitely allowing the formation of long, polymerized chains. In particular, the interfacial region of the most stable binding mode reported here falls in the class of self-limited growth.
Collapse
Affiliation(s)
- Nuno F B Oliveira
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.,Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa 1749-016, Portugal
| | - Filipe E P Rodrigues
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.,Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa 1749-016, Portugal
| | - João N M Vitorino
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.,Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa 1749-016, Portugal
| | - Rui J S Loureiro
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - Patrícia F N Faísca
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.,Department of Physics, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal
| | - Miguel Machuqueiro
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.,Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa 1749-016, Portugal
| |
Collapse
|
9
|
Sala BM, Le Marchand T, Pintacuda G, Camilloni C, Natalello A, Ricagno S. Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution. Biophys J 2020; 119:978-988. [PMID: 32758421 DOI: 10.1016/j.bpj.2020.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 11/29/2022] Open
Abstract
A growing body of evidences has established that in many cases proteins may preserve most of their function and flexibility in a crystalline environment, and several techniques are today capable to characterize molecular properties of proteins in tightly packed lattices. Intriguingly, in the case of amyloidogenic precursors, the presence of transiently populated states (hidden to conventional crystallographic studies) can be correlated to the pathological fate of the native fold; the low fold stability of the native state is a hallmark of aggregation propensity. It remains unclear, however, to which extent biophysical properties of proteins such as the presence of transient conformations or protein stability characterized in crystallo reflect the protein behavior that is more commonly studied in solution. Here, we address this question by investigating some biophysical properties of a prototypical amyloidogenic system, β2-microglobulin in solution and in microcrystalline state. By combining NMR chemical shifts with molecular dynamics simulations, we confirmed that conformational dynamics of β2-microglobulin native state in the crystal lattice is in keeping with what observed in solution. A comparative study of protein stability in solution and in crystallo is then carried out, monitoring the change in protein secondary structure at increasing temperature by Fourier transform infrared spectroscopy. The increased structural order of the crystalline state contributes to provide better resolved spectral components compared to those collected in solution and crucially, the crystalline samples display thermal stabilities in good agreement with the trend observed in solution. Overall, this work shows that protein stability and occurrence of pathological hidden states in crystals parallel their solution counterpart, confirming the interest of crystals as a platform for the biophysical characterization of processes such as unfolding and aggregation.
Collapse
Affiliation(s)
| | - Tanguy Le Marchand
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon), Université de Lyon, Villeurbanne, France
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon), Université de Lyon, Villeurbanne, France
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy.
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
| |
Collapse
|