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Vickers S, Irving J, Lomas DA, Thalassinos K. Native and Ion Mobility Mass Spectrometry Characterization of Alpha 1 Antitrypsin Variants and Oligomers. Methods Mol Biol 2024; 2750:41-55. [PMID: 38108966 DOI: 10.1007/978-1-0716-3605-3_5] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
In this chapter, we describe a method for analyzing both recombinant and plasma-derived alpha 1 antitrypsin and its oligomers by means of native ion mobility mass spectrometry. Our experimental workflow can be applied to other variants of alpha 1 antitrypsin and its oligomers as well as being used to probe their interactions with small molecules in the gas phase.
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Affiliation(s)
- Sarah Vickers
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - James Irving
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
- UCL Respiratory, University College London, London, UK
| | - David A Lomas
- UCL Respiratory, University College London, London, UK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK.
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK.
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Felline A, Schiroli D, Comitato A, Marigo V, Fanelli F. Structure network-based landscape of rhodopsin misfolding by mutations and algorithmic prediction of small chaperone action. Comput Struct Biotechnol J 2021; 19:6020-6038. [PMID: 34849206 PMCID: PMC8605067 DOI: 10.1016/j.csbj.2021.10.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/09/2021] [Accepted: 10/31/2021] [Indexed: 11/28/2022] Open
Abstract
Failure of a protein to achieve its functional structural state and normal cellular location contributes to the etiology and pathology of heritable human conformational diseases. The autosomal dominant form of retinitis pigmentosa (adRP) is an incurable blindness largely linked to mutations of the membrane protein rod opsin. While the mechanisms underlying the noxious effects of the mutated protein are not completely understood, a common feature is the functional protein conformational loss. Here, the wild type and 39 adRP rod opsin mutants were subjected to mechanical unfolding simulations coupled to the graph theory-based protein structure network analysis. A robust computational model was inferred and in vitro validated in its ability to predict endoplasmic reticulum retention of adRP mutants, a feature linked to the mutation-caused misfolding. The structure-based approach could also infer the structural determinants of small chaperone action on misfolded protein mutants with therapeutic implications. The approach is exportable to conformational diseases linked to missense mutations in any membrane protein.
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Affiliation(s)
- Angelo Felline
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
| | - Davide Schiroli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy
| | - Antonella Comitato
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy
| | - Valeria Marigo
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy.,Center for Neuroscience and Neurotechnology, Italy
| | - Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy.,Center for Neuroscience and Neurotechnology, Italy
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Fanelli F, Felline A, Marigo V. Structural aspects of rod opsin and their implication in genetic diseases. Pflugers Arch 2021; 473:1339-1359. [PMID: 33728518 DOI: 10.1007/s00424-021-02546-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 01/04/2023]
Abstract
Vision in dim-light conditions is triggered by photoactivation of rhodopsin, the visual pigment of rod photoreceptor cells. Rhodopsin is made of a protein, the G protein coupled receptor (GPCR) opsin, and the chromophore 11-cis-retinal. Vertebrate rod opsin is the GPCR best characterized at the atomic level of detail. Since the release of the first crystal structure 20 years ago, a huge number of structures have been released that, in combination with valuable spectroscopic determinations, unveiled most aspects of the photobleaching process. A number of spontaneous mutations of rod opsin have been found linked to vision-impairing diseases like autosomal dominant or autosomal recessive retinitis pigmentosa (adRP or arRP, respectively) and autosomal congenital stationary night blindness (adCSNB). While adCSNB is mainly caused by constitutive activation of rod opsin, RP shows more variegate determinants affecting different aspects of rod opsin function. The vast majority of missense rod opsin mutations affects folding and trafficking and is linked to adRP, an incurable disease that awaits light on its molecular structure determinants. This review article summarizes all major structural information available on vertebrate rod opsin conformational states and the insights gained so far into the structural determinants of adCSNB and adRP linked to rod opsin mutations. Strategies to design small chaperones with therapeutic potential for selected adRP rod opsin mutants will be discussed as well.
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Affiliation(s)
- Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125, Modena, Italy. .,Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via Campi 287, Modena, 41125, Italy.
| | - Angelo Felline
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125, Modena, Italy
| | - Valeria Marigo
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via Campi 287, Modena, 41125, Italy.,Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125, Modena, Italy
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Alaei L, Ashengroph M, Moosavi-Movahedi AA. The concept of protein folding/unfolding and its impacts on human health. Adv Protein Chem Struct Biol 2021; 126:227-78. [PMID: 34090616 DOI: 10.1016/bs.apcsb.2021.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Proteins have evolved in specific 3D structures and play different functions in cells and determine various reactions and pathways. The newly synthesized amino acid chains once depart ribosome must crumple into three-dimensional structures so can be biologically active. This process of protein that makes a functional molecule is called protein folding. The protein folding is both a biological and a physicochemical process that depends on the sequence of it. In fact, this process occurs more complicated and in some cases and in exposure to some molecules like glucose (glycation), mistaken folding leads to amyloid structures and fatal disorders called conformational diseases. Such conditions are detected by the quality control system of the cell and these abnormal proteins undergo renovation or degradation. This scenario takes place by the chaperones, chaperonins, and Ubiquitin-proteasome complex. Understanding of protein folding mechanisms from different views including experimental and computational approaches has revealed some intermediate ensembles such as molten globule and has been subjected to biophysical and molecular biology attempts to know more about prevalent conformational diseases.
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Soya N, Roldan A, Lukacs GL. Differential Scanning Fluorimetry and Hydrogen Deuterium Exchange Mass Spectrometry to Monitor the Conformational Dynamics of NBD1 in Cystic Fibrosis. Methods Mol Biol 2019; 1873:53-67. [PMID: 30341603 DOI: 10.1007/978-1-4939-8820-4_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cystic fibrosis (CF) is one of the most common, lethal autosomal recessive diseases in Caucasians with a life expectancy of 37-47 years. The CF transmembrane conductance regulator (CFTR) is a plasma membrane ion channel, confined to apical membrane of epithelia, and ensures transepithelial water and solute movement across secretory epithelia in several organs. Numerous CF mutations, including the most prevalent deletion of F508 (ΔF508) in the nucleotide binding domain 1 (NBD1) leads to CFTR global misfolding and premature intracellular degradation at the endoplasmic reticulum (ER). To better understand the misfolding mechanism caused by CF-causing point mutations in the NBD1, which is poorly understood, differential scanning fluorimetry (DSF) and hydrogen deuterium exchange coupled with mass spectrometry (HDX-MS) are the choice of techniques. These established methods can measure the conformational dynamics of the NBD1 globally and at peptide resolution level by monitoring backbone amide HDX, respectively, and will be instrumental to evaluate the mechanism of action of CF mutations and folding correctors that rescue CFTR folding defects via stabilizing the mutant NBD1.
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Gaglione R, Smaldone G, Di Girolamo R, Piccoli R, Pedone E, Arciello A. Cell milieu significantly affects the fate of AApoAI amyloidogenic variants: predestination or serendipity? Biochim Biophys Acta Gen Subj 2017; 1862:377-384. [PMID: 29174954 DOI: 10.1016/j.bbagen.2017.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/17/2017] [Accepted: 11/21/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Specific apolipoprotein A-I variants are associated to severe hereditary amyloidoses. The organ distribution of AApoAI amyloidosis seems to depend on the position of the mutation, since mutations in residues from 1 to 75 are mainly associated to hepatic and renal amyloidosis, while mutations in residues from 173 to 178 are mostly responsible for cardiac, laryngeal, and cutaneous amyloidosis. Molecular bases of this tissue specificity are still poorly understood, but it is increasingly emerging that protein destabilization induced by amyloidogenic mutations is neither necessary nor sufficient for amyloidosis development. METHODS By using a multidisciplinary approach, including circular dichroism, dynamic light scattering, spectrofluorometric and atomic force microscopy analyses, the effect of target cells on the conformation and fibrillogenic pathway of the two AApoAI amyloidogenic variants AApoAIL75P and AApoAIL174S has been monitored. RESULTS Our data show that specific cell milieus selectively affect conformation, aggregation propensity and fibrillogenesis of the two AApoAI amyloidogenic variants. CONCLUSIONS An intriguing picture emerged indicating that defined cell contexts selectively induce fibrillogenesis of specific AApoAI variants. GENERAL SIGNIFICANCE An innovative methodological approach, based on the use of whole intact cells to monitor the effects of cell context on AApoAI variants fibrillogenic pathway, has been set up.
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Affiliation(s)
- Rosa Gaglione
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | | | - Rocco Di Girolamo
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Renata Piccoli
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; Istituto Nazionale di Biostrutture e Biosistemi (INBB), Italy
| | - Emilia Pedone
- Istituto di Biostrutture e Bioimmagini, CNR, Naples, Italy; Research Centre on Bioactive Peptides (CIRPeB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy.
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; Istituto Nazionale di Biostrutture e Biosistemi (INBB), Italy.
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Pallarès I, Ventura S. Understanding and predicting protein misfolding and aggregation: Insights from proteomics. Proteomics 2016; 16:2570-2581. [PMID: 27479752 DOI: 10.1002/pmic.201500529] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/08/2016] [Accepted: 07/25/2016] [Indexed: 11/09/2022]
Abstract
Protein misfolding and aggregation are being found to be associated with an increasing number of human diseases and premature aging, either because they promote a loss of protein function or, more frequently, because the aggregated species gain a toxic activity. Despite potentially harmful, aggregation seems to be a generic property of polypeptide chains and aggregation-prone protein sequences seem to be ubiquitous, which, counterintuitively, suggests that they serve evolutionary conserved functions. The in vitro study of individual aggregation reactions of a large number of proteins has provided important insights on the structural and sequential determinants of this process. However, it is clear that understanding the role played by protein aggregation and its regulation in health and disease at the cellular, developmental, and evolutionary levels require more global approaches. The use of model organisms and their proteomic analysis hold the power to provide answers to such issues. In the present review, we address how, initially, computational large-scale analysis and, more recently, experimental proteomics are helping us to rationalize how, why and when proteins aggregate, as well as to decipher the strategies organisms have developed to control proteins aggregation propensities.
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Affiliation(s)
- Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain. .,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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