1
|
Bonnecaze L, Jumel K, Vial A, Khemtemourian L, Feuillie C, Molinari M, Lecomte S, Mathelié-Guinlet M. N-Formylation modifies membrane damage associated with PSMα3 interfacial fibrillation. NANOSCALE HORIZONS 2024. [PMID: 38689531 DOI: 10.1039/d4nh00088a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The virulence of Staphylococcus aureus, a multi-drug resistant pathogen, notably depends on the expression of the phenol soluble modulins α3 (PSMα3) peptides, able to self-assemble into amyloid-like cross-α fibrils. Despite remarkable advances evidencing the crucial, yet insufficient, role of fibrils in PSMα3 cytotoxic activities towards host cells, the relationship between its molecular structures, assembly propensities, and modes of action remains an open intriguing problem. In this study, combining atomic force microscopy (AFM) imaging and infrared spectroscopy, we first demonstrated in vitro that the charge provided by the N-terminal capping of PSMα3 alters its interactions with model membranes of controlled lipid composition without compromising its fibrillation kinetics or morphology. N-formylation eventually dictates PSMα3-membrane binding via electrostatic interactions with the lipid head groups. Furthermore, PSMα3 insertion within the lipid bilayer is favoured by hydrophobic interactions with the lipid acyl chains only in the fluid phase of membranes and not in the gel-like ordered domains. Strikingly, our real-time AFM imaging emphasizes how intermediate protofibrillar entities, formed along PSMα3 self-assembly and promoted at the membrane interface, likely disrupt membrane integrity via peptide accumulation and subsequent membrane thinning in a peptide concentration and lipid-dependent manner. Overall, our multiscale and multimodal approach sheds new light on the key roles of N-formylation and intermediate self-assembling entities, rather than mature fibrils, in dictating deleterious interactions of PSMα3 with membrane lipids, likely underscoring its ultimate cellular toxicity in vivo, and in turn S. aureus pathogenesis.
Collapse
Affiliation(s)
- Laura Bonnecaze
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.
| | - Katlyn Jumel
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.
| | - Anthony Vial
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.
| | | | - Cécile Feuillie
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.
| | - Michael Molinari
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.
| | - Sophie Lecomte
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.
| | | |
Collapse
|
2
|
Tolstova AP, Makarov AA, Adzhubei AA. Structure Comparison of Beta Amyloid Peptide Aβ 1-42 Isoforms. Molecular Dynamics Modeling. J Chem Inf Model 2024; 64:918-932. [PMID: 38241093 DOI: 10.1021/acs.jcim.3c01624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Beta amyloid peptide Aβ 1-42 (Aβ42) has a unique dual role in the human organism, as both the peptide with an important physiological function and one of the most toxic biological compounds provoking Alzheimer's disease (AD). There are several known Aβ42 isoforms that we discuss here that are highly neurotoxic and lead to the early onset of AD. Aβ42 is an intrinsically disordered protein with no experimentally solved structure under physiological conditions. The objective of this research was to establish the appropriate molecular dynamics (MD) methodology and model a uniform set of structures for the Aβ42 isoforms that form the core of this study. For that purpose, force field selection and verification including convergence testing for MD simulations was made. Replica exchange MD and conventional MD modeling of several Aβ42 and Aβ16 isoforms that have neurotoxic and amyloidogenic effects impacting the severity of Alzheimer's disease were carried out with the optimal force field and solvent parameters. A standardized ensemble of structures for the Aβ42 and Aβ16 isoforms covering 30-50% of the conformational ensembles extracted from the free energy minima was calculated from MD trajectories. The resulting data set of modeled structures includes Aβ42 wild type, isoD7, pS8, D7H, and H6R-Aβ42 and Aβ16 wild type, isoD7, pS8, D7H, and H6R-Aβ16. The representative structures are given in the Supporting Information; they are open for public access. In the study, we also evaluated the differences between the structures of Aβ42 isoforms and speculate on their possible relevance to the known functions. Utilizing several representative structures for a single disordered protein for docking, with their subsequent averaging by conformations, would markedly increase the reliability of docking results.
Collapse
Affiliation(s)
- Anna P Tolstova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexei A Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Washington University School of Medicine and Health Sciences, Washington 20052, D.C., United States
| |
Collapse
|
3
|
Rando C, Grasso G, Sarkar D, Sciacca MFM, Cucci LM, Cosentino A, Forte G, Pannuzzo M, Satriano C, Bhunia A, La Rosa C. GxxxG Motif Stabilize Ion-Channel like Pores through C α-H···O Interaction in Aβ (1-40). Int J Mol Sci 2023; 24:ijms24032192. [PMID: 36768518 PMCID: PMC9917128 DOI: 10.3390/ijms24032192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Aβ (1-40) can transfer from the aqueous phase to the bilayer and thus form stable ion-channel-like pores where the protein has alpha-helical conformation. The stability of the pores is due to the presence of the GXXXG motif. It has been reported that these ion-channel-like pores are stabilized by a Cα-H···O hydrogen bond that is established between a glycine of the GXXXG sequence of an alpha-helix and another amino acid of a vicinal alpha-helix. However, conflicting data are reported in the literature. Some authors have suggested that hydrogen bonding does not have a stabilizing function. Here we synthesized pentapeptides having a GXXXG motif to explore its role in pore stability. We used molecular dynamics simulations, quantum mechanics, and experimental biophysical techniques to determine whether hydrogen bonding was formed and had a stabilizing function in ion-channel-like structures. Starting from our previous molecular dynamics data, molecular quantum mechanics simulations, and ATR data showed that a stable ion-channel-like pore formed and a band centered at 2910 cm-1 was attributed to the interaction between Gly 7 of an alpha-helix and Asp 23 of a vicinal alpha-helix.
Collapse
Affiliation(s)
- Carola Rando
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Giuseppe Grasso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Dibakar Sarkar
- Department of Biophysics Bose Institute, Unified Academic Campus, Bidhan Nagar, EN 80, Kolkata 700091, India
| | | | - Lorena Maria Cucci
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Alessia Cosentino
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Giuseppe Forte
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Martina Pannuzzo
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Cristina Satriano
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Anirban Bhunia
- Department of Biophysics Bose Institute, Unified Academic Campus, Bidhan Nagar, EN 80, Kolkata 700091, India
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy
- Correspondence:
| |
Collapse
|
4
|
Cross interactions between Apolipoprotein E and amyloid proteins in neurodegenerative diseases. Comput Struct Biotechnol J 2023; 21:1189-1204. [PMID: 36817952 PMCID: PMC9932299 DOI: 10.1016/j.csbj.2023.01.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
Three common Apolipoprotein E isoforms, ApoE2, ApoE3, and ApoE4, are key regulators of lipid homeostasis, among other functions. Apolipoprotein E can interact with amyloid proteins. The isoforms differ by one or two residues at positions 112 and 158, and possess distinct structural conformations and functions, leading to isoform-specific roles in amyloid-based neurodegenerative diseases. Over 30 different amyloid proteins have been found to share similar characteristics of structure and toxicity, suggesting a common interactome. The molecular and genetic interactions of ApoE with amyloid proteins have been extensively studied in neurodegenerative diseases, but have not yet been well connected and clarified. Here we summarize essential features of the interactions between ApoE and different amyloid proteins, identify gaps in the understanding of the interactome and propose the general interaction mechanism between ApoE isoforms and amyloid proteins. Perhaps more importantly, this review outlines what we can learn from the interactome of ApoE and amyloid proteins; that is the need to see both ApoE and amyloid proteins as a basis to understand neurodegenerative diseases.
Collapse
|
5
|
Membrane cholesterol modulates the dynamics and depth of penetration of κ-casein. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
6
|
The Association of Lipids with Amyloid Fibrils. J Biol Chem 2022; 298:102108. [PMID: 35688209 PMCID: PMC9293637 DOI: 10.1016/j.jbc.2022.102108] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 01/02/2023] Open
Abstract
Amyloid formation continues to be a widely studied area because of its association with numerous diseases, such as Alzheimer’s and Parkinson’s diseases. Despite a large body of work on protein aggregation and fibril formation, there are still significant gaps in our understanding of the factors that differentiate toxic amyloid formation in vivo from alternative misfolding pathways. In addition to proteins, amyloid fibrils are often associated in their cellular context with several types of molecule, including carbohydrates, polyanions, and lipids. This review focuses in particular on evidence for the presence of lipids in amyloid fibrils and the routes by which those lipids may become incorporated. Chemical analyses of fibril composition, combined with studies to probe the lipid distribution around fibrils, provide evidence that in some cases, lipids have a strong association with fibrils. In addition, amyloid fibrils formed in the presence of lipids have distinct morphologies and material properties. It is argued that lipids are an integral part of many amyloid deposits in vivo, where their presence has the potential to influence the nucleation, morphology, and mechanical properties of fibrils. The role of lipids in these structures is therefore worthy of further study.
Collapse
|
7
|
Sevcuka A, White K, Terry C. Factors That Contribute to hIAPP Amyloidosis in Type 2 Diabetes Mellitus. Life (Basel) 2022; 12:life12040583. [PMID: 35455074 PMCID: PMC9025880 DOI: 10.3390/life12040583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 12/24/2022] Open
Abstract
Cases of Type 2 Diabetes Mellitus (T2DM) are increasing at an alarming rate due to the rise in obesity, sedentary lifestyles, glucose-rich diets and other factors. Numerous studies have increasingly illustrated the pivotal role that human islet amyloid polypeptide (hIAPP) plays in the pathology of T2DM through damage and subsequent loss of pancreatic β-cell mass. HIAPP can misfold and form amyloid fibrils which are preceded by pre-fibrillar oligomers and monomers, all of which have been linked, to a certain extent, to β-cell cytotoxicity through a range of proposed mechanisms. This review provides an up-to-date summary of recent progress in the field, highlighting factors that contribute to hIAPP misfolding and aggregation such as hIAPP protein concentration, cell stress, molecular chaperones, the immune system response and cross-seeding with other amyloidogenic proteins. Understanding the structure of hIAPP and how these factors affect amyloid formation will help us better understand how hIAPP misfolds and aggregates and, importantly, help identify potential therapeutic targets for inhibiting amyloidosis so alternate and more effective treatments for T2DM can be developed.
Collapse
|
8
|
Tempra C, Scollo F, Pannuzzo M, Lolicato F, La Rosa C. A unifying framework for amyloid-mediated membrane damage: The lipid-chaperone hypothesis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140767. [PMID: 35144022 DOI: 10.1016/j.bbapap.2022.140767] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Over the past thirty years, researchers have highlighted the role played by a class of proteins or polypeptides that forms pathogenic amyloid aggregates in vivo, including i) the amyloid Aβ peptide, which is known to form senile plaques in Alzheimer's disease; ii) α-synuclein, responsible for Lewy body formation in Parkinson's disease and iii) IAPP, which is the protein component of type 2 diabetes-associated islet amyloids. These proteins, known as intrinsically disordered proteins (IDPs), are present as highly dynamic conformational ensembles. IDPs can partially (mis) fold into (dys) functional conformations and accumulate as amyloid aggregates upon interaction with other cytosolic partners such as proteins or lipid membranes. In addition, an increasing number of reports link the toxicity of amyloid proteins to their harmful effects on membrane integrity. Still, the molecular mechanism underlying the amyloidogenic proteins transfer from the aqueous environment to the hydrocarbon core of the membrane is poorly understood. This review starts with a historical overview of the toxicity models of amyloidogenic proteins to contextualize the more recent lipid-chaperone hypothesis. Then, we report the early molecular-level events in the aggregation and ion-channel pore formation of Aβ, IAPP, and α-synuclein interacting with model membranes, emphasizing the complexity of these processes due to their different spatial-temporal resolutions. Next, we underline the need for a combined experimental and computational approach, focusing on the strengths and weaknesses of the most commonly used techniques. Finally, the last two chapters highlight the crucial role of lipid-protein complexes as molecular switches among ion-channel-like formation, detergent-like, and fibril formation mechanisms and their implication in fighting amyloidogenic diseases.
Collapse
Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
| | - Federica Scollo
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Pannuzzo
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy.
| |
Collapse
|
9
|
Al Adem K, Shanti A, Srivastava A, Homouz D, Thomas SA, Khair M, Stefanini C, Chan V, Kim TY, Lee S. Linking Alzheimer’s Disease and Type 2 Diabetes: Characterization and Inhibition of Cytotoxic Aβ and IAPP Hetero-Aggregates. Front Mol Biosci 2022; 9:842582. [PMID: 35372522 PMCID: PMC8968156 DOI: 10.3389/fmolb.2022.842582] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/07/2022] [Indexed: 12/18/2022] Open
Abstract
The cytotoxic self-aggregation of β-amyloid (Aβ) peptide and islet amyloid polypeptide (IAPP) is implicated in the pathogenesis of Alzheimer’s disease (AD) and Type 2 diabetes (T2D), respectively. Increasing evidence, particularly the co-deposition of Aβ and IAPP in both brain and pancreatic tissues, suggests that Aβ and IAPP cross-interaction may be responsible for a pathological link between AD and T2D. Here, we examined the nature of IAPP-Aβ40 co-aggregation and its inhibition by small molecules. In specific, we characterized the kinetic profiles, morphologies, secondary structures and toxicities of IAPP-Aβ40 hetero-assemblies and compared them to those formed by their homo-assemblies. We demonstrated that monomeric IAPP and Aβ40 form stable hetero-dimers and hetero-assemblies that further aggregate into β-sheet-rich hetero-aggregates that are toxic (cell viability <50%) to both PC-12 cells, a neuronal cell model, and RIN-m5F cells, a pancreatic cell model for β-cells. We then selected polyphenolic candidates to inhibit IAPP or Aβ40 self-aggregation and examined the inhibitory effect of the most potent candidate on IAPP-Aβ40 co-aggregation. We demonstrated that epigallocatechin gallate (EGCG) form inter-molecular hydrogen bonds with each of IAPP and Aβ40. We also showed that EGCG reduced hetero-aggregate formation and resulted in lower β-sheets content and higher unordered structures in IAPP-Aβ40-EGCG samples. Importantly, we showed that EGCG is highly effective in reducing the toxicity of IAPP-Aβ40 hetero-aggregates on both cell models, specifically at concentrations that are equivalent to or are 2.5-fold higher than the mixed peptide concentrations. To the best of our knowledge, this is the first study to report the inhibition of IAPP-Aβ40 co-aggregation by small molecules. We conclude that EGCG is a promising candidate to prevent co-aggregation and cytotoxicity of IAPP-Aβ40, which in turn, contribute to the pathological link between AD and T2D.
Collapse
Affiliation(s)
- Kenana Al Adem
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Aya Shanti
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Amit Srivastava
- Department of Physics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Dirar Homouz
- Department of Physics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Physics, University of Houston, Houston, TX, United States
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Sneha Ann Thomas
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Mostafa Khair
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Cesare Stefanini
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Vincent Chan
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Tae-Yeon Kim
- Department of Civil Infrastructure and Environmental Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Sungmun Lee
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Khalifa University’s Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- *Correspondence: Sungmun Lee,
| |
Collapse
|
10
|
Mrdenovic D, Pieta IS, Nowakowski R, Kutner W, Lipkowski J, Pieta P. Amyloid β interaction with model cell membranes – What are the toxicity-defining properties of amyloid β? Int J Biol Macromol 2022; 200:520-531. [DOI: 10.1016/j.ijbiomac.2022.01.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 01/26/2023]
|
11
|
Schwarze B, Korn A, Höfling C, Zeitschel U, Krueger M, Roßner S, Huster D. Peptide backbone modifications of amyloid β (1-40) impact fibrillation behavior and neuronal toxicity. Sci Rep 2021; 11:23767. [PMID: 34887476 PMCID: PMC8660793 DOI: 10.1038/s41598-021-03091-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022] Open
Abstract
Fibril formation of amyloid β (Aβ) peptides is one of the key molecular events connected to Alzheimer's disease. The pathway of formation and mechanism of action of Aβ aggregates in biological systems is still object of very active research. To this end, systematic modifications of the Phe19-Leu34 hydrophobic contact, which has been reported in almost all structural studies of Aβ40 fibrils, helps understanding Aβ folding pathways and the underlying free energy landscape of the amyloid formation process. In our approach, a series of Aβ40 peptide variants with two types of backbone modifications, namely incorporation of (i) a methylene or an ethylene spacer group and (ii) a N-methylation at the amide functional group, of the amino acids at positions 19 or 34 was applied. These mutations are expected to challenge the inter-β-strand side chain contacts as well as intermolecular backbone β-sheet hydrogen bridges. Using a multitude of biophysical methods, it is shown that these backbone modifications lead, in most of the cases, to alterations in the fibril formation kinetics, a higher local structural heterogeneity, and a somewhat modified fibril morphology without generally impairing the fibril formation capacity of the peptides. The toxicological profile found for the variants depend on the type and extent of the modification.
Collapse
Affiliation(s)
- Benedikt Schwarze
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Alexander Korn
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Corinna Höfling
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Ulrike Zeitschel
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Martin Krueger
- Institute of Anatomy, Leipzig University, Liebigstr. 13, 04103, Leipzig, Germany
| | - Steffen Roßner
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstr. 19, 04103, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16/18, 04107, Leipzig, Germany.
| |
Collapse
|
12
|
Fatafta H, Kav B, Bundschuh BF, Loschwitz J, Strodel B. Disorder-to-order transition of the amyloid-β peptide upon lipid binding. Biophys Chem 2021; 280:106700. [PMID: 34784548 DOI: 10.1016/j.bpc.2021.106700] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 12/18/2022]
Abstract
There is mounting evidence that Alzheimer's disease progression and severity are linked to neuronal membrane damage caused by aggregates of the amyloid-β (Aβ) peptide. However, the detailed mechanism behind the membrane damage is not well understood yet. Recently, the lipid-chaperone hypothesis has been put forward, based on which the formation of complexes between Aβ and free lipids enables an easy insertion of Aβ into membranes. In order to test this hypothesis, we performed numerous all-atom molecular dynamics simulations. We studied the complex formation between individual lipids, considering both POPC and DPPC, and Aβ and examined whether the resulting complexes would be able to insert into lipid membranes. Complex formation at a one-to-one ratio was readily observed, yet with minimal effects on Aβ's characteristics. Most importantly, the peptide remains largely disordered in 1:1 complexes, and the complex does not insert into the membrane; instead, it is adsorbed to the membrane surface. The results change considerably once Aβ forms a complex with a POPC cluster composed of three lipid molecules. The hydrophobic interactions between Aβ and the lipid tails cause the peptide to fold into either a helical or a β-sheet structure. These observations provide atomic insight into the disorder-to-order transition that is needed for membrane insertion or amyloid aggregation to proceed.
Collapse
Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Bastian F Bundschuh
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany
| | - Jennifer Loschwitz
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany.
| |
Collapse
|
13
|
Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
Collapse
Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
| |
Collapse
|
14
|
Lesma J, Bizet F, Berardet C, Tonali N, Pellegrino S, Taverna M, Khemtemourian L, Soulier JL, van Heijenoort C, Halgand F, Ha-Duong T, Kaffy J, Ongeri S. β-Hairpin Peptide Mimics Decrease Human Islet Amyloid Polypeptide (hIAPP) Aggregation. Front Cell Dev Biol 2021; 9:729001. [PMID: 34604227 PMCID: PMC8481668 DOI: 10.3389/fcell.2021.729001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Amyloid diseases are degenerative pathologies, highly prevalent today because they are closely related to aging, that have in common the erroneous folding of intrinsically disordered proteins (IDPs) which aggregate and lead to cell death. Type 2 Diabetes involves a peptide called human islet amyloid polypeptide (hIAPP), which undergoes a conformational change, triggering the aggregation process leading to amyloid aggregates and fibers rich in β-sheets mainly found in the pancreas of all diabetic patients. Inhibiting the aggregation of amyloid proteins has emerged as a relevant therapeutic approach and we have recently developed the design of acyclic flexible hairpins based on peptidic recognition sequences of the amyloid β peptide (Aβ1–42) as a successful strategy to inhibit its aggregation involved in Alzheimer’s disease. The present work reports the extension of our strategy to hIAPP aggregation inhibitors. The design, synthesis, conformational analyses, and biophysical evaluations of dynamic β-hairpin like structures built on a piperidine-pyrrolidine β-turn inducer are described. By linking to this β-turn inducer three different arms (i) pentapeptide, (ii) tripeptide, and (iii) α/aza/aza/pseudotripeptide, we demonstrate that the careful selection of the peptide-based arms from the sequence of hIAPP allowed to selectively modulate its aggregation, while the peptide character can be decreased. Biophysical assays combining, Thioflavin-T fluorescence, transmission electronic microscopy, capillary electrophoresis, and mass spectrometry showed that the designed compounds inhibit both the oligomerization and the fibrillization of hIAPP. They are also capable to decrease the aggregation process in the presence of membrane models and to strongly delay the membrane-leakage induced by hIAPP. More generally, this work provides the proof of concept that our rational design is a versatile and relevant strategy for developing efficient and selective inhibitors of aggregation of amyloidogenic proteins.
Collapse
Affiliation(s)
- Jacopo Lesma
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Faustine Bizet
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Corentin Berardet
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France.,Institute Galien Paris-Saclay, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Nicolo Tonali
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Sara Pellegrino
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini," Università degli Studi di Milano, Milan, Italy
| | - Myriam Taverna
- Institute Galien Paris-Saclay, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Lucie Khemtemourian
- Institute of Chemistry and Biology of Membranes and Nanoobjects, Institut Polytechnique Bordeaux, CNRS UMR 5248, Université de Bordeaux, Pessac, France
| | | | - Carine van Heijenoort
- ICSN, Equipe Biologie et Chimie Structurales, Département de Chimie et Biologie Structurales et Analytiques, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Frédéric Halgand
- Institut de Chimie Physique, Equipe Chimie Analytique Physicochimie Réactivité des Ions, CNRS, Université Paris-Saclay, Orsay, France
| | - Tâp Ha-Duong
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Julia Kaffy
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Sandrine Ongeri
- BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| |
Collapse
|
15
|
Yahi N, Di Scala C, Chahinian H, Fantini J. Innovative treatment targeting gangliosides aimed at blocking the formation of neurotoxic α-synuclein oligomers in Parkinson's disease. Glycoconj J 2021; 39:1-11. [PMID: 34328594 DOI: 10.1007/s10719-021-10012-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022]
Abstract
Parkinson's disease (PD) is a major neurodegenerative disorder which exhibits many of the characteristics of a pandemic. Current therapeutic strategies are centered on the dopaminergic system, with limited efficacy, so that a treatment that has a direct impact on the underlying disease pathogenesis is urgently needed. Although α-synuclein is a privileged target for such therapies, this protein has been in the past wrongly considered as exclusively intracellular, so that the impact of paracrine neurotoxicity mechanisms in PD have been largely ignored. In this article we review the data showing that lipid rafts act as plasma membrane machineries for the formation of α-synuclein pore-like oligomers which trigger an increase of intracellular Ca2+. This Ca2+ influx is responsible for a self-sustained cascade of neurotoxic events, including mitochondrial oxidative stress, tau phosphorylation, Ca2+ release from the endoplasmic reticulum, Lewy body formation, and extracellular release of α-synuclein in exosomes. The first step of this cascade is the binding of α-synuclein to lipid raft gangliosides, suggesting that PD should be considered as both a proteinopathy and a ganglioside membrane disorder lipidopathy. Accordingly, blocking α-synuclein-ganglioside interactions should annihilate the whole neurotoxic cascade and stop disease progression. A pipeline of anti-oligomer molecules is under development, among which an in-silico designed synthetic peptide AmyP53 which is the first drug targeting gangliosides and thus able to prevent the formation of α-synuclein oligomers and all downstream neurotoxicity. These new therapeutic avenues challenge the current symptomatic approaches by finally targeting the root cause of PD through a long-awaited paradigm shift.
Collapse
Affiliation(s)
- Nouara Yahi
- INSERM UMR_S 1072, Aix-Marseille Université, 13015, Marseille, France
| | - Coralie Di Scala
- Neuroscience Center-HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Henri Chahinian
- INSERM UMR_S 1072, Aix-Marseille Université, 13015, Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, 13015, Marseille, France.
| |
Collapse
|
16
|
Divakara MB, Ashwini R, Santosh MS, Priyanka M, Ravikumar CR, Viswanatha R, Murthy HCA. Early-stage culprit in protein misfolding diseases investigated using electrochemical parameters: New insights over peptide-membrane interactions. Biomed Pharmacother 2021; 142:111964. [PMID: 34329823 DOI: 10.1016/j.biopha.2021.111964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
The dysfunctioning of β-cells caused by the unspecific misfolding of the human islet amyloid polypeptide (hIAPP) at the membrane results in type 2 diabetes mellitus. Here, we report for the first time, the early-stage interaction of hIAPP oligomers on the DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) lipid membrane using electrochemical parameters. Electrochemical techniques are better than other techniques to detect hIAPP at significantly lower concentrations. The surface level interactions between the peptide (hIAPP) and lipid membrane (DMPC) were investigated using atomic force microscopy (AFM), confocal microscopy (CM) and electrochemical techniques such as Tafel polarization, cyclic voltammetry (CV), differential pulse voltammetry (DPV), linear sweep voltammetry (LSV) and electrochemical impedance spectroscopy (EIS). Inserting IAPP into the fluid domains results in breaking the lipid-to-lipid interaction, leading to restriction of membrane mobility. The SLateral values of the liposome and IAPP co-solubilized liposome indicates the cooperative insertion of IAPP. Further, a new method of immobilizing a membrane to the gold surface has been employed, resulting in an electrical contact with the buffer, preventing the direct utilization of a steady-state voltage across the bilayer. The electrochemical studies revealed that the charge transfer resistance decreased for 3-mercaptopropanoic acid modified gold (MPA-Au) electrode coated with the liposome and after the addition of IAPP, followed by an increase in the capacitance. The present study has opened up new dimensions to the understanding of peptide-membrane interactions and shows different experimental approaches for the future researchers in this domain.
Collapse
Affiliation(s)
- M B Divakara
- Centre for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology (Affiliated to Visvesvaraya Technological University (VTU), Belgaum), Thataguni, Off Kanakapura Road, Bengaluru 560082, Karnataka, India
| | - R Ashwini
- Centre for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology (Affiliated to Visvesvaraya Technological University (VTU), Belgaum), Thataguni, Off Kanakapura Road, Bengaluru 560082, Karnataka, India
| | - M S Santosh
- Centre for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology (Affiliated to Visvesvaraya Technological University (VTU), Belgaum), Thataguni, Off Kanakapura Road, Bengaluru 560082, Karnataka, India.
| | - M Priyanka
- East Point college of Medical Sciences and Research Centre (affiliated to RGUHS), Jnana Prabha, Virgonagar Post, Bidrahalli, Bengaluru 560049, Karnataka, India
| | - C R Ravikumar
- Research Centre, Department of Science, East West Institute of Technology, Bengaluru 560091, India
| | - R Viswanatha
- Centre for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology (Affiliated to Visvesvaraya Technological University (VTU), Belgaum), Thataguni, Off Kanakapura Road, Bengaluru 560082, Karnataka, India
| | - H C Ananda Murthy
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, P O Box 1888, Adama, Ethiopia.
| |
Collapse
|
17
|
Odularu AT, Ajibade PA. Challenge of diabetes mellitus and researchers’ contributions to its control. OPEN CHEM 2021. [DOI: 10.1515/chem-2020-0153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The aim of this review study was to assess the past significant events on diabetes mellitus, transformations that took place over the years in the medical records of treatment, countries involved, and the researchers who brought about the revolutions. This study used the content analysis to report the existence of diabetes mellitus and the treatments provided by researchers to control it. The focus was mainly on three main types of diabetes (type 1, type 2, and type 3 diabetes). Ethical consideration has also helped to boost diabetic studies globally. The research has a history path from pharmaceuticals of organic-based drugs to metal-based drugs with their nanoparticles in addition to the impacts of nanomedicine, biosensors, and telemedicine. Ongoing and future studies in alternative medicine such as vanadium nanoparticles (metal nanoparticles) are promising.
Collapse
Affiliation(s)
- Ayodele T. Odularu
- Department of Chemistry, University of Fort Hare , Private Bag X1314 , Alice 5700 , Eastern Cape , South Africa
| | - Peter A. Ajibade
- Department of Chemistry, University of KwaZulu-Natal , Pietermaritzburg Campus , Scottsville 3209 , South Africa
| |
Collapse
|
18
|
Gonzalez-Garcia M, Fusco G, De Simone A. Membrane Interactions and Toxicity by Misfolded Protein Oligomers. Front Cell Dev Biol 2021; 9:642623. [PMID: 33791300 PMCID: PMC8006268 DOI: 10.3389/fcell.2021.642623] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/08/2021] [Indexed: 01/13/2023] Open
Abstract
The conversion of otherwise soluble proteins into insoluble amyloid aggregates is associated with a range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases, as well as non-neuropathic conditions such as type II diabetes and systemic amyloidoses. It is increasingly evident that the most pernicious species among those forming during protein aggregation are small prefibrillar oligomers. In this review, we describe the recent progress in the characterization of the cellular and molecular interactions by toxic misfolded protein oligomers. A fundamental interaction by these aggregates involves biological membranes, resulting in two major model mechanisms at the onset of the cellular toxicity. These include the membrane disruption model, resulting in calcium imbalance, mitochondrial dysfunction and intracellular reactive oxygen species, and the direct interaction with membrane proteins, leading to the alteration of their native function. A key challenge remains in the characterization of transient interactions involving heterogeneous protein aggregates. Solving this task is crucial in the quest of identifying suitable therapeutic approaches to suppress the cellular toxicity in protein misfolding diseases.
Collapse
Affiliation(s)
- Mario Gonzalez-Garcia
- Department of Life Sciences, Imperial College London, South Kensington, United Kingdom
| | - Giuliana Fusco
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, United Kingdom.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
| |
Collapse
|
19
|
Bokor M, Tantos Á. Secondary Structures of Proteins: A Comparison of Models and Experimental Results. J Proteome Res 2021; 20:1802-1808. [PMID: 33620224 PMCID: PMC8028322 DOI: 10.1021/acs.jproteome.0c00986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Secondary structure predictions of proteins were compared to experimental results by wide-line 1H NMR. IUPred2A was used to generate predictions of disordered protein or binding regions. Thymosin-β4 and the stabilin-2 cytoplasmic domain were found to be mainly disordered, in agreement with the experimental results. α-Synuclein variants were predicted to be disordered, as in the experiments, but the A53T mutant showed less predicted disorder, in contrast with the wide-line 1H NMR result. A disordered binding site was found for thymosin-β4, whereas the stabilin-2 cytoplasmic domain was indicated as such in its entire length. The last third of the α-synuclein variant's sequence was a disordered binding site. Thymosin-β4 and the stabilin-2 cytoplasmic domain contained only coils and helices according to five secondary structure prediction methods (SPIDER3-SPOT-1D, PSRSM, MUFold-SSW, Porter 5, and RaptorX). β-Sheets are present in α-synucleins, and they extend to more amino acid residues in the A53T mutant according to the predictions. The latter is verified by experiments. The comparison of the predictions with the experiments suggests that helical parts are buried.
Collapse
Affiliation(s)
- Mónika Bokor
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Konkoly-Thege út 29-33, 1121 Budapest, Hungary
| | - Ágnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary
| |
Collapse
|
20
|
Tempra C, La Rosa C, Lolicato F. The role of alpha-helix on the structure-targeting drug design of amyloidogenic proteins. Chem Phys Lipids 2021; 236:105061. [PMID: 33610597 DOI: 10.1016/j.chemphyslip.2021.105061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/26/2021] [Accepted: 02/12/2021] [Indexed: 12/17/2022]
Abstract
The most accredited hypothesis links the toxicity of amyloid proteins to their harmful effects on membrane integrity through the formation of prefibrillar-transient oligomers able to disrupt cell membranes. However, damage mechanisms necessarily assume a first step in which the amyloidogenic protein transfers from the aqueous phase to the membrane hydrophobic core. This determinant step is still poorly understood. However, according to our lipid-chaperon hypothesis, free lipids in solution play a crucial role in facilitating this footfall. Free phospholipid concentration in the aqueous phase acts as a switch between ion channel-like pore and fibril formation, so that high free lipid concentration in solution promotes pore and repress fibril formation. Conversely, low free lipids in the solution favor fibril and repress pore formation. This behavior is due to the formation of stable lipid-protein complexes. Here, we hypothesize that the helix propensity is a fundamental requirement to fulfill the lipid-chaperon model. The alpha-helix region seems to be responsible for the binding with amphiphilic molecules fostering the proposed mechanism. Indeed, our results show the dependency of protein-lipid binding from the helical structure presence. When the helix content is substantially lower than the wild type, the contact probability decreases. Instead, if the helix is broadening, the contact probability increases. Our findings open a new perspective for in silico screening of secondary structure-targeting drugs of amyloidogenic proteins.
Collapse
Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
| | | | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
21
|
Fusco G, Gianni S. Function, Regulation, and Dysfunction of Intrinsically Disordered Proteins. Life (Basel) 2021; 11:life11020140. [PMID: 33673214 PMCID: PMC7917908 DOI: 10.3390/life11020140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/07/2021] [Indexed: 12/16/2022] Open
Abstract
The discovery that a considerable fraction of the eukaryotic proteins lacks a well-defined three-dimensional structure in their native state has revolutionised our general understanding of proteins [...].
Collapse
Affiliation(s)
- Giuliana Fusco
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Correspondence: (G.F.); (S.G.)
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli,” Sapienza Università di Roma, 00185 Rome, Italy
- Correspondence: (G.F.); (S.G.)
| |
Collapse
|
22
|
Gallo G, Caignard G, Badonnel K, Chevreux G, Terrier S, Szemiel A, Roman-Sosa G, Binder F, Gu Q, Da Silva Filipe A, Ulrich RG, Kohl A, Vitour D, Tordo N, Ermonval M. Interactions of Viral Proteins from Pathogenic and Low or Non-Pathogenic Orthohantaviruses with Human Type I Interferon Signaling. Viruses 2021; 13:140. [PMID: 33478127 PMCID: PMC7835746 DOI: 10.3390/v13010140] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/12/2021] [Accepted: 01/16/2021] [Indexed: 12/13/2022] Open
Abstract
Rodent-borne orthohantaviruses are asymptomatic in their natural reservoir, but they can cause severe diseases in humans. Although an exacerbated immune response relates to hantaviral pathologies, orthohantaviruses have to antagonize the antiviral interferon (IFN) response to successfully propagate in infected cells. We studied interactions of structural and nonstructural (NSs) proteins of pathogenic Puumala (PUUV), low-pathogenic Tula (TULV), and non-pathogenic Prospect Hill (PHV) viruses, with human type I and III IFN (IFN-I and IFN-III) pathways. The NSs proteins of all three viruses inhibited the RIG-I-activated IFNβ promoter, while only the glycoprotein precursor (GPC) of PUUV, or its cleavage product Gn/Gc, and the nucleocapsid (N) of TULV inhibited it. Moreover, the GPC of both PUUV and TULV antagonized the promoter of IFN-stimulated responsive elements (ISRE). Different viral proteins could thus contribute to inhibition of IFNβ response in a viral context. While PUUV and TULV strains replicated similarly, whether expressing entire or truncated NSs proteins, only PUUV encoding a wild type NSs protein led to late IFN expression and activation of IFN-stimulated genes (ISG). This, together with the identification of particular domains of NSs proteins and different biological processes that are associated with cellular proteins in complex with NSs proteins, suggested that the activation of IFN-I is probably not the only antiviral pathway to be counteracted by orthohantaviruses and that NSs proteins could have multiple inhibitory functions.
Collapse
Affiliation(s)
- Giulia Gallo
- Unité des Stratégies Antivirales, Institut Pasteur, 75015 Paris, France; (G.G.); (N.T.)
- Ecole Doctorale Complexité du Vivant, Sorbonne Université, 75006 Paris, France
| | - Grégory Caignard
- UMR 1161 Virologie, Anses-INRAE-EnvA, 94700 Maisons-Alfort, France; (G.C.); (D.V.)
| | - Karine Badonnel
- BREED, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Guillaume Chevreux
- Institut Jacques Monod, CNRS UMR 7592, ProteoSeine Mass Spectrometry Plateform, Université de Paris, 75013 Paris, France; (G.C.); (S.T.)
| | - Samuel Terrier
- Institut Jacques Monod, CNRS UMR 7592, ProteoSeine Mass Spectrometry Plateform, Université de Paris, 75013 Paris, France; (G.C.); (S.T.)
| | - Agnieszka Szemiel
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (A.S.); (Q.G.); (A.D.S.F.); (A.K.)
| | | | - Florian Binder
- Friedrich-Loeffler-Institut, Institute of Novel and Emerging Infectious Diseases, 17493 Greifswald-Insel Riems, Germany; (F.B.); (R.G.U.)
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (A.S.); (Q.G.); (A.D.S.F.); (A.K.)
| | - Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (A.S.); (Q.G.); (A.D.S.F.); (A.K.)
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Institute of Novel and Emerging Infectious Diseases, 17493 Greifswald-Insel Riems, Germany; (F.B.); (R.G.U.)
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (A.S.); (Q.G.); (A.D.S.F.); (A.K.)
| | - Damien Vitour
- UMR 1161 Virologie, Anses-INRAE-EnvA, 94700 Maisons-Alfort, France; (G.C.); (D.V.)
| | - Noël Tordo
- Unité des Stratégies Antivirales, Institut Pasteur, 75015 Paris, France; (G.G.); (N.T.)
- Institut Pasteur de Guinée, BP 4416 Conakry, Guinea
| | - Myriam Ermonval
- Unité des Stratégies Antivirales, Institut Pasteur, 75015 Paris, France; (G.G.); (N.T.)
| |
Collapse
|
23
|
Milardi D, Gazit E, Radford SE, Xu Y, Gallardo RU, Caflisch A, Westermark GT, Westermark P, Rosa CL, Ramamoorthy A. Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chem Rev 2021; 121:1845-1893. [PMID: 33427465 DOI: 10.1021/acs.chemrev.0c00981] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The possible link between hIAPP accumulation and β-cell death in diabetic patients has inspired numerous studies focusing on amyloid structures and aggregation pathways of this hormone. Recent studies have reported on the importance of early oligomeric intermediates, the many roles of their interactions with lipid membrane, pH, insulin, and zinc on the mechanism of aggregation of hIAPP. The challenges posed by the transient nature of amyloid oligomers, their structural heterogeneity, and the complex nature of their interaction with lipid membranes have resulted in the development of a wide range of biophysical and chemical approaches to characterize the aggregation process. While the cellular processes and factors activating hIAPP-mediated cytotoxicity are still not clear, it has recently been suggested that its impaired turnover and cellular processing by proteasome and autophagy may contribute significantly toward toxic hIAPP accumulation and, eventually, β-cell death. Therefore, studies focusing on the restoration of hIAPP proteostasis may represent a promising arena for the design of effective therapies. In this review we discuss the current knowledge of the structures and pathology associated with hIAPP self-assembly and point out the opportunities for therapy that a detailed biochemical, biophysical, and cellular understanding of its aggregation may unveil.
Collapse
Affiliation(s)
- Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via P. Gaifami 18, 95126 Catania, Italy
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Gunilla T Westermark
- Department of Medical Cell Biology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 41809-1055, United States
| |
Collapse
|
24
|
Sciacca MF, Lolicato F, Tempra C, Scollo F, Sahoo BR, Watson MD, García-Viñuales S, Milardi D, Raudino A, Lee JC, Ramamoorthy A, La Rosa C. Lipid-Chaperone Hypothesis: A Common Molecular Mechanism of Membrane Disruption by Intrinsically Disordered Proteins. ACS Chem Neurosci 2020; 11:4336-4350. [PMID: 33269918 DOI: 10.1021/acschemneuro.0c00588] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
An increasing number of human diseases has been shown to be linked to aggregation and amyloid formation by intrinsically disordered proteins (IDPs). Amylin, amyloid-β, and α-synuclein are, indeed, involved in type-II diabetes, Alzheimer's, and Parkinson's, respectively. Despite the correlation of the toxicity of these proteins at early aggregation stages with membrane damage, the molecular events underlying the process is quite complex to understand. In this study, we demonstrate the crucial role of free lipids in the formation of lipid-protein complex, which enables an easy membrane insertion for amylin, amyloid-β, and α-synuclein. Experimental results from a variety of biophysical methods and molecular dynamics results reveal that this common molecular pathway in membrane poration is shared by amyloidogenic (amylin, amyloid-β, and α-synuclein) and nonamyloidogenic (rat IAPP, β-synuclein) proteins. Based on these results, we propose a "lipid-chaperone" hypothesis as a unifying framework for protein-membrane poration.
Collapse
Affiliation(s)
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg 69120, Germany
- Department of Physics, University of Helsinki, P.O. Box 64, Helsinki FI-00014, Finland
| | - Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Prague 160 00, Czech Republic
- Department of Chemical Sciences, University of Catania, Catania 95124, Italy
| | - Federica Scollo
- Department of Chemical Sciences, University of Catania, Catania 95124, Italy
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 117 20, Czech Republic
| | - Bikash R. Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Matthew D. Watson
- National Institutes of Health, Bethesda, Maryland 20892-0001, United States
| | | | | | - Antonio Raudino
- Department of Chemical Sciences, University of Catania, Catania 95124, Italy
| | - Jennifer C. Lee
- National Institutes of Health, Bethesda, Maryland 20892-0001, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Carmelo La Rosa
- Department of Chemical Sciences, University of Catania, Catania 95124, Italy
| |
Collapse
|
25
|
Kosolapova AO, Antonets KS, Belousov MV, Nizhnikov AA. Biological Functions of Prokaryotic Amyloids in Interspecies Interactions: Facts and Assumptions. Int J Mol Sci 2020; 21:E7240. [PMID: 33008049 PMCID: PMC7582709 DOI: 10.3390/ijms21197240] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023] Open
Abstract
Amyloids are fibrillar protein aggregates with an ordered spatial structure called "cross-β". While some amyloids are associated with development of approximately 50 incurable diseases of humans and animals, the others perform various crucial physiological functions. The greatest diversity of amyloids functions is identified within prokaryotic species where they, being the components of the biofilm matrix, function as adhesins, regulate the activity of toxins and virulence factors, and compose extracellular protein layers. Amyloid state is widely used by different pathogenic bacterial species in their interactions with eukaryotic organisms. These amyloids, being functional for bacteria that produce them, are associated with various bacterial infections in humans and animals. Thus, the repertoire of the disease-associated amyloids includes not only dozens of pathological amyloids of mammalian origin but also numerous microbial amyloids. Although the ability of symbiotic microorganisms to produce amyloids has recently been demonstrated, functional roles of prokaryotic amyloids in host-symbiont interactions as well as in the interspecies interactions within the prokaryotic communities remain poorly studied. Here, we summarize the current findings in the field of prokaryotic amyloids, classify different interspecies interactions where these amyloids are involved, and hypothesize about their real occurrence in nature as well as their roles in pathogenesis and symbiosis.
Collapse
Affiliation(s)
- Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| |
Collapse
|