1
|
Ng YK, Konermann L. Mechanism of Protein Aggregation Inhibition by Arginine: Blockage of Anionic Side Chains Favors Unproductive Encounter Complexes. J Am Chem Soc 2024; 146:8394-8406. [PMID: 38477601 DOI: 10.1021/jacs.3c14180] [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: 03/14/2024]
Abstract
Aggregation refers to the assembly of proteins into nonphysiological higher order structures. While amyloid has been studied extensively, much less is known about amorphous aggregation, a process that interferes with protein expression and storage. Free arginine (Arg+) is a widely used aggregation inhibitor, but its mechanism remains elusive. Focusing on myoglobin (Mb), we recently applied atomistic molecular dynamics (MD) simulations for gaining detailed insights into amorphous aggregation (Ng J. Phys. Chem. B 2021, 125, 13099). Building on that approach, the current work for the first time demonstrates that MD simulations can directly elucidate aggregation inhibition mechanisms. Comparative simulations with and without Arg+ reproduced the experimental finding that Arg+ significantly decreased the Mb aggregation propensity. Our data reveal that, without Arg+, protein-protein encounter complexes readily form salt bridges and hydrophobic contacts, culminating in firmly linked dimeric aggregation nuclei. Arg+ promotes the dissociation of encounter complexes. These "unproductive" encounter complexes are favored because Arg+ binding to D- and E- lowers the tendency of these anionic residues to form interprotein salt bridges. Side chain blockage is mediated largely by the guanidinium group of Arg+, which binds carboxylates through H-bond-reinforced ionic contacts. Our MD data revealed Arg+ self-association into a dynamic quasi-infinite network, but we found no evidence that this self-association is important for protein aggregation inhibition. Instead, aggregation inhibition by Arg+ is similar to that mediated by free guanidinium ions. The computational strategy used here should be suitable for the rational design of aggregation inhibitors with enhanced potency.
Collapse
Affiliation(s)
- Yuen Ki Ng
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
2
|
Pinzi L, Bisi N, Sorbi C, Franchini S, Tonali N, Rastelli G. Insights into the Structural Conformations of the Tau Protein in Different Aggregation Status. Molecules 2023; 28:molecules28114544. [PMID: 37299020 DOI: 10.3390/molecules28114544] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Tau is a protein characterized by large structural portions displaying extended conformational changes. Unfortunately, the accumulation of this protein into toxic aggregates in neuronal cells leads to a number of severe pathologies, collectively named tauopathies. In the last decade, significant research advancements were achieved, including a better understanding of Tau structures and their implication in different tauopathies. Interestingly, Tau is characterized by a high structural variability depending on the type of disease, the crystallization conditions, and the formation of pathologic aggregates obtained from in vitro versus ex vivo samples. In this review, we reported an up-to-date and comprehensive overview of Tau structures reported in the Protein Data Bank, with a special focus on discussing the connections between structural features, different tauopathies, different crystallization conditions, and the use of in vitro or ex vivo samples. The information reported in this article highlights very interesting links between all these aspects, which we believe may be of particular relevance for a more informed structure-based design of compounds able to modulate Tau aggregation.
Collapse
Affiliation(s)
- Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| | - Nicolò Bisi
- Centre National de la Recherche Scientifique (CNRS), Université de Paris-Saclay, BioCIS, Bat. Henri Moissan, 17 Av. des Sciences, 91400 Orsay, France
| | - Claudia Sorbi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| | - Silvia Franchini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| | - Nicolò Tonali
- Centre National de la Recherche Scientifique (CNRS), Université de Paris-Saclay, BioCIS, Bat. Henri Moissan, 17 Av. des Sciences, 91400 Orsay, France
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| |
Collapse
|
3
|
Anacleto J, Lento C, Sarpe V, Maqsood A, Mehrazma B, Schriemer D, Wilson DJ. Apparatus for Automated Continuous Hydrogen Deuterium Exchange Mass Spectrometry Measurements from Milliseconds to Hours. Anal Chem 2023; 95:4421-4428. [PMID: 36880265 PMCID: PMC9996604 DOI: 10.1021/acs.analchem.2c05003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a rapidly growing technique for protein characterization in industry and academia, complementing the "static" picture provided by classical structural biology with information about the dynamic structural changes that accompany biological function. Conventional hydrogen deuterium exchange experiments, carried out on commercially available systems, typically collect 4-5 exchange timepoints on a timescale ranging from tens of seconds to hours using a workflow that can require 24 h or more of continuous data collection for triplicate measurements. A small number of groups have developed setups for millisecond timescale HDX, allowing for the characterization of dynamic shifts in weakly structured or disordered regions of proteins. This capability is particularly important given the central role that weakly ordered protein regions often play in protein function and pathogenesis. In this work, we introduce a new continuous flow injection setup for time-resolved HDX-MS (CFI-TRESI-HDX) that allows automated, continuous or discrete labeling time measurements from milliseconds to hours. The device is composed almost entirely of "off-the-shelf" LC components and can acquire an essentially unlimited number of timepoints with substantially reduced runtimes compared to conventional systems.
Collapse
Affiliation(s)
- Joseph Anacleto
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology, Calgary, Alberta T2N 4N1, Canada
| | - Ayesha Maqsood
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Banafsheh Mehrazma
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - David Schriemer
- Department of Biochemistry and Molecular Biology, Calgary, Alberta T2N 4N1, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| |
Collapse
|
4
|
Mass spectrometric insights into protein aggregation. Essays Biochem 2023; 67:243-253. [PMID: 36636963 PMCID: PMC10070474 DOI: 10.1042/ebc20220103] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/11/2022] [Accepted: 12/14/2022] [Indexed: 01/14/2023]
Abstract
Protein aggregation is now recognized as a generic and significant component of the protein energy landscape. Occurring through a complex and dynamic pathway of structural interconversion, the assembly of misfolded proteins to form soluble oligomers and insoluble aggregates remains a challenging topic of study, both in vitro and in vivo. Since the etiology of numerous human diseases has been associated with protein aggregation, and it has become a field of increasing importance in the biopharmaceutical industry, the biophysical characterization of protein misfolded states and their aggregation mechanisms continues to receive increased attention. Mass spectrometry (MS) has firmly established itself as a powerful analytical tool capable of both detection and characterization of proteins at all levels of structure. Given inherent advantages of biological MS, including high sensitivity, rapid timescales of analysis, and the ability to distinguish individual components from complex mixtures with unrivalled specificity, it has found widespread use in the study of protein aggregation, importantly, where traditional structural biology approaches are often not amenable. The present review aims to provide a brief overview of selected MS-based approaches that can provide a range of biophysical descriptors associated with protein conformation and the aggregation pathway. Recent examples highlight where this technology has provided unique structural and mechanistic understanding of protein aggregation.
Collapse
|
5
|
Developments in rapid hydrogen-deuterium exchange methods. Essays Biochem 2023; 67:165-174. [PMID: 36636941 DOI: 10.1042/ebc20220174] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/14/2023]
Abstract
Biological macromolecules, such as proteins, nucleic acids, and carbohydrates, contain heteroatom-bonded hydrogens that undergo exchange with solvent hydrogens on timescales ranging from microseconds to hours. In hydrogen-deuterium exchange mass spectrometry (HDX-MS), this exchange process is used to extract information about biomolecular structure and dynamics. This minireview focuses on millisecond timescale HDX-MS measurements, which, while less common than 'conventional' timescale (seconds to hours) HDX-MS, provide a unique window into weakly structured species, weak (or fast cycling) binding interactions, and subtle shifts in conformational dynamics. This includes intrinsically disordered proteins and regions (IDPs/IDRs) that are associated with cancer and amyloidotic neurodegenerative disease. For nucleic acids and carbohydrates, structures such as isomers, stems, and loops, can be elucidated and overall structural rigidity can be assessed. We will provide a brief overview of technical developments in rapid HDX followed by highlights of various applications, emphasising the importance of broadening the HDX timescale to improve throughput and to capture a wider range of function-relevant dynamic and structural shifts.
Collapse
|
6
|
Tucs A, Tsuda K, Sljoka A. Probing Conformational Dynamics of Antibodies with Geometric Simulations. Methods Mol Biol 2023; 2552:125-139. [PMID: 36346589 DOI: 10.1007/978-1-0716-2609-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to molecular dynamics (MD) simulations that can rapidly explore flexible motions in protein structures. FRODAN is highly suited for conformational dynamics analysis of large proteins, complexes, intrinsically disordered proteins, and dynamics that occurs on longer biologically relevant time scales that are normally inaccessible to classical MD simulations. This approach predicts protein dynamics at an all-atom scale while retaining realistic covalent bonding, maintaining dihedral angles in energetically good conformations while avoiding steric clashes in addition to performing other geometric and stereochemical criteria checks. In this chapter, we apply FRODAN to showcase its applicability for probing functionally relevant dynamics of IgG2a, including large-amplitude domain-domain motions and motions of complementarity determining region (CDR) loops. As was suggested in previous experimental studies, our simulations show that antibodies can explore a large range of conformational space.
Collapse
Affiliation(s)
- Andrejs Tucs
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Koji Tsuda
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Research and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Adnan Sljoka
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan.
- Department of Chemistry, York University, Toronto, Canada.
| |
Collapse
|
7
|
Shin G, Lim SI. Unveiling the biological interface of protein complexes by mass spectrometry-coupled methods. Proteins 2022; 91:593-607. [PMID: 36573681 DOI: 10.1002/prot.26459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Most biomolecules become functional and bioactive by forming protein complexes through interaction with ligands that are diverse in size, shape, and physicochemical properties. In the complex biological milieu, the interaction is ligand-specific, driven by molecular sensing, and involves the recognition of a binding interface localized within a protein structure. Mapping interfaces of protein complexes is a highly sought area of research as it delivers fundamental insights into proteomes and pathology and hence strategies for therapeutics. While X-ray crystallography and electron microscopy remain the gold standard for structural elucidation of protein complexes, their artificial and static analytic nature often produces a non-native interface that otherwise might be negligible or non-existent in a biological environment. Recently, the mass spectrometry-coupled approaches, chemical crosslinking (CLMS) and hydrogen-deuterium exchange (HDMS) have become valuable analytic complements to the traditional techniques. These methods explicitly identify hot residues and motifs embedded in binding interfaces, especially when the interaction is predominantly dynamic, transient, and/or caused by an intrinsically disordered domain. Here, we review the principal role of CLMS and HDMS in protein structural biology with a particular emphasis on the contribution of recent examples to exploring biological interfaces. Additionally, we describe recent studies that utilized these methods to expand our understanding of protein complex formation and the related biological processes, to increase the probability of structure-based drug design.
Collapse
Affiliation(s)
- Goeun Shin
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
| |
Collapse
|
8
|
Tajoddin NN, Konermann L. Structural Dynamics of a Thermally Stressed Monoclonal Antibody Characterized by Temperature-Dependent H/D Exchange Mass Spectrometry. Anal Chem 2022; 94:15499-15509. [DOI: 10.1021/acs.analchem.2c03931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nastaran N. Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
9
|
Bondarchuk TV, Shalak VF, Lozhko DM, Fatalska A, Szczepanowski R, Liudkovska V, Tsuvariev O, Dadlez M, El'skaya A, Negrutskii B. Quaternary organization of the human eEF1B complex reveals unique multi-GEF domain assembly. Nucleic Acids Res 2022; 50:9490-9504. [PMID: 35971611 PMCID: PMC9458455 DOI: 10.1093/nar/gkac685] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/12/2022] [Accepted: 07/31/2022] [Indexed: 12/24/2022] Open
Abstract
Protein synthesis in eukaryotic cell is spatially and structurally compartmentalized that ensures high efficiency of this process. One of the distinctive features of higher eukaryotes is the existence of stable multi-protein complexes of aminoacyl-tRNA synthetases and translation elongation factors. Here, we report a quaternary organization of the human guanine-nucleotide exchange factor (GEF) complex, eEF1B, comprising α, β and γ subunits that specifically associate into a heterotrimeric form eEF1B(αβγ)3. As both the eEF1Bα and eEF1Bβ proteins have structurally conserved GEF domains, their total number within the complex is equal to six. Such, so far, unique structural assembly of the guanine-nucleotide exchange factors within a stable complex may be considered as a 'GEF hub' that ensures efficient maintenance of the translationally active GTP-bound conformation of eEF1A in higher eukaryotes.
Collapse
Affiliation(s)
- Tetiana V Bondarchuk
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Vyacheslav F Shalak
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Dmytro M Lozhko
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Agnieszka Fatalska
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego 5a, 02-109 Warsaw, Poland
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Roman H Szczepanowski
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Vladyslava Liudkovska
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Oleksandr Yu Tsuvariev
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Akademik Glushkov Ave. 4-g, 03022 Kyiv, Ukraine
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego 5a, 02-109 Warsaw, Poland
| | - Anna V El'skaya
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Boris S Negrutskii
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| |
Collapse
|
10
|
Protein Function Analysis through Machine Learning. Biomolecules 2022; 12:biom12091246. [PMID: 36139085 PMCID: PMC9496392 DOI: 10.3390/biom12091246] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Machine learning (ML) has been an important arsenal in computational biology used to elucidate protein function for decades. With the recent burgeoning of novel ML methods and applications, new ML approaches have been incorporated into many areas of computational biology dealing with protein function. We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function. The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein–ligand binding, including allosteric effects, protein–protein interactions and protein-centric drug discovery. To quantify the mechanisms underlying protein function, a holistic approach that takes structure, flexibility, stability, and dynamics into account is required, as these aspects become inseparable through their interdependence. Another key component of protein function is conformational dynamics, which often manifest as protein kinetics. Computational methods that use ML to generate representative conformational ensembles and quantify differences in conformational ensembles important for function are included in this review. Future opportunities are highlighted for each of these topics.
Collapse
|
11
|
Low pH structure of heliorhodopsin reveals chloride binding site and intramolecular signaling pathway. Sci Rep 2022; 12:13955. [PMID: 35977989 PMCID: PMC9385722 DOI: 10.1038/s41598-022-17716-9] [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] [Received: 04/27/2022] [Accepted: 07/29/2022] [Indexed: 11/11/2022] Open
Abstract
Within the microbial rhodopsin family, heliorhodopsins (HeRs) form a phylogenetically distinct group of light-harvesting retinal proteins with largely unknown functions. We have determined the 1.97 Å resolution X-ray crystal structure of Thermoplasmatales archaeon SG8-52-1 heliorhodopsin (TaHeR) in the presence of NaCl under acidic conditions (pH 4.5), which complements the known 2.4 Å TaHeR structure acquired at pH 8.0. The low pH structure revealed that the hydrophilic Schiff base cavity (SBC) accommodates a chloride anion to stabilize the protonated retinal Schiff base when its primary counterion (Glu-108) is neutralized. Comparison of the two structures at different pH revealed conformational changes connecting the SBC and the extracellular loop linking helices A–B. We corroborated this intramolecular signaling transduction pathway with computational studies, which revealed allosteric network changes propagating from the perturbed SBC to the intracellular and extracellular space, suggesting TaHeR may function as a sensory rhodopsin. This intramolecular signaling mechanism may be conserved among HeRs, as similar changes were observed for HeR 48C12 between its pH 8.8 and pH 4.3 structures. We additionally performed DEER experiments, which suggests that TaHeR forms possible dimer-of-dimer associations which may be integral to its putative functionality as a light sensor in binding a transducer protein.
Collapse
|
12
|
Tran MH, Schoeder CT, Schey KL, Meiler J. Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook. Front Immunol 2022; 13:859964. [PMID: 35720345 PMCID: PMC9204306 DOI: 10.3389/fimmu.2022.859964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022] Open
Abstract
Although computational structure prediction has had great successes in recent years, it regularly fails to predict the interactions of large protein complexes with residue-level accuracy, or even the correct orientation of the protein partners. The performance of computational docking can be notably enhanced by incorporating experimental data from structural biology techniques. A rapid method to probe protein-protein interactions is hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS has been increasingly used for epitope-mapping of antibodies (Abs) to their respective antigens (Ags) in the past few years. In this paper, we review the current state of HDX-MS in studying protein interactions, specifically Ab-Ag interactions, and how it has been used to inform computational structure prediction calculations. Particularly, we address the limitations of HDX-MS in epitope mapping and techniques and protocols applied to overcome these barriers. Furthermore, we explore computational methods that leverage HDX-MS to aid structure prediction, including the computational simulation of HDX-MS data and the combination of HDX-MS and protein docking. We point out challenges in interpreting and incorporating HDX-MS data into Ab-Ag complex docking and highlight the opportunities they provide to build towards a more optimized hybrid method, allowing for more reliable, high throughput epitope identification.
Collapse
Affiliation(s)
- Minh H. Tran
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, United States
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Clara T. Schoeder
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
| | - Kevin L. Schey
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Jens Meiler
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
| |
Collapse
|
13
|
Ye H, Han Y, Li P, Su Z, Huang Y. The Role of Post-Translational Modifications on the Structure and Function of Tau Protein. J Mol Neurosci 2022; 72:1557-1571. [PMID: 35325356 DOI: 10.1007/s12031-022-02002-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/14/2022] [Indexed: 12/14/2022]
Abstract
Involving addition of chemical groups or protein units to specific residues of the target protein, post-translational modifications (PTMs) alter the charge, hydrophobicity, and conformation of a protein, which in tune influences protein function, protein - protein interaction, and protein aggregation. While the occurrence of PTMs is dynamic and subject to regulations, conformational disorder of the target protein facilitates PTMs. The microtubule-associated protein tau is a typical intrinsically disordered protein that undergoes a variety of PTMs including phosphorylation, acetylation, ubiquitination, methylation, and oxidation. Accumulated evidence shows that these PTMs play a critical role in regulating tau-microtubule interaction, tau localization, tau degradation and aggregation, and reinforces the correlation between tau PTMs and pathogenesis of neurodegenerative disease. Here, we review tau PTMs with an emphasis on their influence on tau structure. With available biophysical characterization results, we describe how PTMs induce conformational changes in tau monomer and regulate tau aggregation. Compared to functional analysis of tau PTMs, biophysical characterization of tau PTMs is lagging. While it is challenging, characterizing the specific effects of PTMs on tau conformation and interaction is indispensable to unravel the tau PTM code.
Collapse
Affiliation(s)
- Haiqiong Ye
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, China.,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China.,Department of Biological Engineering, Hubei University of Technology, Wuhan, 430068, China
| | - Yue Han
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, China.,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China.,Department of Biological Engineering, Hubei University of Technology, Wuhan, 430068, China
| | - Ping Li
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, China.,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China.,Department of Biological Engineering, Hubei University of Technology, Wuhan, 430068, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, China.,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China.,Department of Biological Engineering, Hubei University of Technology, Wuhan, 430068, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, China. .,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068, China. .,Department of Biological Engineering, Hubei University of Technology, Wuhan, 430068, China.
| |
Collapse
|
14
|
Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex. Molecules 2022; 27:molecules27030799. [PMID: 35164065 PMCID: PMC8839245 DOI: 10.3390/molecules27030799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/02/2022] Open
Abstract
The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.
Collapse
|
15
|
Ng YK, Tajoddin NN, Scrosati PM, Konermann L. Mechanism of Thermal Protein Aggregation: Experiments and Molecular Dynamics Simulations on the High-Temperature Behavior of Myoglobin. J Phys Chem B 2021; 125:13099-13110. [PMID: 34808050 DOI: 10.1021/acs.jpcb.1c07210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Proteins that encounter unfavorable solvent conditions are prone to aggregation, a phenomenon that remains poorly understood. This work focuses on myoglobin (Mb) as a model protein. Upon heating, Mb produces amorphous aggregates. Thermal unfolding experiments at low concentration (where aggregation is negligible), along with centrifugation assays, imply that Mb aggregation proceeds via globally unfolded conformers. This contrasts studies on other proteins that emphasized the role of partially folded structures as aggregate precursors. Molecular dynamics (MD) simulations were performed to gain insights into the mechanism by which heat-unfolded Mb molecules associate with one another. A prerequisite for these simulations was the development of a method for generating monomeric starting structures. Periodic boundary condition artifacts necessitated the implementation of a partially immobilized water layer lining the walls of the simulation box. Aggregation simulations were performed at 370 K to track the assembly of monomeric Mb into pentameric species. Binding events were preceded by multiple unsuccessful encounters. Even after association, protein-protein contacts remained in flux. Binding was mediated by hydrophobic contacts, along with salt bridges that involved hydrophobically embedded Lys residues. Overall, this work illustrates that atomistic MD simulations are well suited for garnering insights into protein aggregation mechanisms.
Collapse
Affiliation(s)
- Yuen Ki Ng
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Nastaran N Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Pablo M Scrosati
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
16
|
James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
Collapse
Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
17
|
Gadhave K, Kumar D, Uversky VN, Giri R. A multitude of signaling pathways associated with Alzheimer's disease and their roles in AD pathogenesis and therapy. Med Res Rev 2021; 41:2689-2745. [PMID: 32783388 PMCID: PMC7876169 DOI: 10.1002/med.21719] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/13/2020] [Accepted: 07/29/2020] [Indexed: 02/06/2023]
Abstract
The exact molecular mechanisms associated with Alzheimer's disease (AD) pathology continue to represent a mystery. In the past decades, comprehensive data were generated on the involvement of different signaling pathways in the AD pathogenesis. However, the utilization of signaling pathways as potential targets for the development of drugs against AD is rather limited due to the immense complexity of the brain and intricate molecular links between these pathways. Therefore, finding a correlation and cross-talk between these signaling pathways and establishing different therapeutic targets within and between those pathways are needed for better understanding of the biological events responsible for the AD-related neurodegeneration. For example, autophagy is a conservative cellular process that shows link with many other AD-related pathways and is crucial for maintenance of the correct cellular balance by degrading AD-associated pathogenic proteins. Considering the central role of autophagy in AD and its interplay with many other pathways, the finest therapeutic strategy to fight against AD is the use of autophagy as a target. As an essential step in this direction, this comprehensive review represents recent findings on the individual AD-related signaling pathways, describes key features of these pathways and their cross-talk with autophagy, represents current drug development, and introduces some of the multitarget beneficial approaches and strategies for the therapeutic intervention of AD.
Collapse
Affiliation(s)
- Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Deepak Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| |
Collapse
|
18
|
Lento C, Wilson DJ. Subsecond Time-Resolved Mass Spectrometry in Dynamic Structural Biology. Chem Rev 2021; 122:7624-7646. [PMID: 34324314 DOI: 10.1021/acs.chemrev.1c00222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Life at the molecular level is a dynamic world, where the key players-proteins, oligonucleotides, lipids, and carbohydrates-are in a perpetual state of structural flux, shifting rapidly between local minima on their conformational free energy landscapes. The techniques of classical structural biology, X-ray crystallography, structural NMR, and cryo-electron microscopy (cryo-EM), while capable of extraordinary structural resolution, are innately ill-suited to characterize biomolecules in their dynamically active states. Subsecond time-resolved mass spectrometry (MS) provides a unique window into the dynamic world of biological macromolecules, offering the capacity to directly monitor biochemical processes and conformational shifts with a structural dimension provided by the electrospray charge-state distribution, ion mobility, covalent labeling, or hydrogen-deuterium exchange. Over the past two decades, this suite of techniques has provided important insights into the inherently dynamic processes that drive function and pathogenesis in biological macromolecules, including (mis)folding, complexation, aggregation, ligand binding, and enzyme catalysis, among others. This Review provides a comprehensive account of subsecond time-resolved MS and the advances it has enabled in dynamic structural biology, with an emphasis on insights into the dynamic drivers of protein function.
Collapse
Affiliation(s)
- Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| |
Collapse
|
19
|
Candelise N, Scaricamazza S, Salvatori I, Ferri A, Valle C, Manganelli V, Garofalo T, Sorice M, Misasi R. Protein Aggregation Landscape in Neurodegenerative Diseases: Clinical Relevance and Future Applications. Int J Mol Sci 2021; 22:ijms22116016. [PMID: 34199513 PMCID: PMC8199687 DOI: 10.3390/ijms22116016] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 12/13/2022] Open
Abstract
Intrinsic disorder is a natural feature of polypeptide chains, resulting in the lack of a defined three-dimensional structure. Conformational changes in intrinsically disordered regions of a protein lead to unstable β-sheet enriched intermediates, which are stabilized by intermolecular interactions with other β-sheet enriched molecules, producing stable proteinaceous aggregates. Upon misfolding, several pathways may be undertaken depending on the composition of the amino acidic string and the surrounding environment, leading to different structures. Accumulating evidence is suggesting that the conformational state of a protein may initiate signalling pathways involved both in pathology and physiology. In this review, we will summarize the heterogeneity of structures that are produced from intrinsically disordered protein domains and highlight the routes that lead to the formation of physiological liquid droplets as well as pathogenic aggregates. The most common proteins found in aggregates in neurodegenerative diseases and their structural variability will be addressed. We will further evaluate the clinical relevance and future applications of the study of the structural heterogeneity of protein aggregates, which may aid the understanding of the phenotypic diversity observed in neurodegenerative disorders.
Collapse
Affiliation(s)
- Niccolò Candelise
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
- Correspondence: ; Tel.: +39-338-891-2668
| | - Silvia Scaricamazza
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
| | - Illari Salvatori
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Alberto Ferri
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Cristiana Valle
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Valeria Manganelli
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Tina Garofalo
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Maurizio Sorice
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Roberta Misasi
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| |
Collapse
|
20
|
The Potential of Induced Pluripotent Stem Cells to Treat and Model Alzheimer's Disease. Stem Cells Int 2021; 2021:5511630. [PMID: 34122554 PMCID: PMC8172295 DOI: 10.1155/2021/5511630] [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: 03/02/2021] [Revised: 04/20/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022] Open
Abstract
An estimated 6.2 million Americans aged 65 or older are currently living with Alzheimer's disease (AD), a neurodegenerative disease that disrupts an individual's ability to function independently through the degeneration of key regions in the brain, including but not limited to the hippocampus, the prefrontal cortex, and the motor cortex. The cause of this degeneration is not known, but research has found two proteins that undergo posttranslational modifications: tau, a protein concentrated in the axons of neurons, and amyloid precursor protein (APP), a protein concentrated near the synapse. Through mechanisms that have yet to be elucidated, the accumulation of these two proteins in their abnormal aggregate forms leads to the neurodegeneration that is characteristic of AD. Until the invention of induced pluripotent stem cells (iPSCs) in 2006, the bulk of research was carried out using transgenic animal models that offered little promise in their ability to translate well from benchtop to bedside, creating a bottleneck in the development of therapeutics. However, with iPSC, patient-specific cell cultures can be utilized to create models based on human cells. These human cells have the potential to avoid issues in translatability that have plagued animal models by providing researchers with a model that closely resembles and mimics the neurons found in humans. By using human iPSC technology, researchers can create more accurate models of AD ex vivo while also focusing on regenerative medicine using iPSC in vivo. The following review focuses on the current uses of iPSC and how they have the potential to regenerate damaged neuronal tissue, in the hopes that these technologies can assist in getting through the bottleneck of AD therapeutic research.
Collapse
|
21
|
Oganesyan I, Lento C, Tandon A, Wilson DJ. Conformational Dynamics of α-Synuclein during the Interaction with Phospholipid Nanodiscs by Millisecond Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1169-1179. [PMID: 33784451 DOI: 10.1021/jasms.0c00463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Both normal and pathological functions of α-synuclein (αSN), an abundant protein in the central and peripheral nervous system, have been linked to its interaction with membrane lipid bilayers. The ability to characterize structural transitions of αSN upon membrane complexation will clarify molecular mechanisms associated with αSN-linked pathologies, including Parkinson's disease (PD), multiple systems atrophy, and other synucleinopathies. In this work, time-resolved electrospray ionization hydrogen/deuterium exchange mass spectrometry (TRESI-HDX-MS) was employed to acquire a detailed picture of αSN's conformational transitions as it undergoes complexation with nanodisc membrane mimics with different headgroup charges (zwitterionic DMPC and negative POPG). Using this approach, αSN interactions with DMPC nanodiscs were shown to be rapid exchanging and to have little impact on the αSN conformational ensemble. Interactions with nanodiscs containing lipids known to promote amyloidogenesis (e.g., POPG), on the other hand, were observed to induce substantial and specific changes in the αSN conformational ensemble. Ultimately, we identify a region corresponding residues 19-28 and 45-57 of the αSN sequence that is uniquely impacted by interactions with "amyloidogenic" lipid membranes, supporting the existing "broken-helix" model for α-synuclein/membrane interactions, but do not detect a "helical extension" that is also thought to play a role in αSN aggregation.
Collapse
Affiliation(s)
- Irina Oganesyan
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Anurag Tandon
- Department of Medicine, University of Toronto, Toronto M5S 1A1, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University, Toronto M3J 1P3, Canada
| |
Collapse
|
22
|
Prikas E, Ahel H, Stefanoska K, Asih PR, Volkerling A, Ittner LM, Ittner A. Interaction between the guanylate kinase domain of PSD-95 and the proline-rich region and microtubule binding repeats 2 and 3 of tau. Biochem Cell Biol 2021; 99:606-616. [PMID: 33794133 DOI: 10.1139/bcb-2020-0604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The microtubule-associated protein tau is a key factor in neurodegenerative proteinopathies and is predominantly found in the neuronal axon. However, somatodendritic localization of tau occurs for a subset of pathological and physiologic tau. Dendritic tau can localize to post-synapses where it interacts with proteins of the post-synaptic density (PSD) protein PSD-95, a membrane-associated guanylate kinase (MAGUK) scaffold factor for organization of protein complexes within the PSD, to mediate downstream signals. The sub-molecular details of this interaction, however, remain unclear. Here, we use interaction mapping in cultured cells to demonstrate that tau interacts with the guanylate kinase (GUK) domain in the C-terminal region of PSD-95. The PSD-95 GUK domain is required and sufficient for a complex with full-length human tau. Mapping the interaction of the MAGUK core on tau revealed the microtubule binding repeats 2 and 3 and the proline-rich region contribute to this interaction, while the N- and C-terminal regions of tau inhibit interaction. These results reveal intramolecular determinants of the protein complex of tau and PSD-95 and increase our understanding of tau interactions regulating neurotoxic signaling at the molecular level.
Collapse
Affiliation(s)
- Emmanuel Prikas
- Macquarie University, 7788, Sydney, New South Wales, Australia;
| | - Holly Ahel
- Macquarie University, 7788, Sydney, New South Wales, Australia;
| | | | | | | | - Lars M Ittner
- Macquarie University, 7788, Biomedical Sciences, Sydney, New South Wales, Australia;
| | - Arne Ittner
- Macquarie University, 7788, Biomedical Sciences, Sydney, New South Wales, Australia;
| |
Collapse
|
23
|
Dyakin VV, Wisniewski TM, Lajtha A. Racemization in Post-Translational Modifications Relevance to Protein Aging, Aggregation and Neurodegeneration: Tip of the Iceberg. Symmetry (Basel) 2021; 13:455. [PMID: 34350031 PMCID: PMC8330555 DOI: 10.3390/sym13030455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Homochirality of DNA and prevalent chirality of free and protein-bound amino acids in a living organism represents the challenge for modern biochemistry and neuroscience. The idea of an association between age-related disease, neurodegeneration, and racemization originated from the studies of fossils and cataract disease. Under the pressure of new results, this concept has a broader significance linking protein folding, aggregation, and disfunction to an organism's cognitive and behavioral functions. The integrity of cognitive function is provided by a delicate balance between the evolutionarily imposed molecular homo-chirality and the epigenetic/developmental impact of spontaneous and enzymatic racemization. The chirality of amino acids is the crucial player in the modulation the structure and function of proteins, lipids, and DNA. The collapse of homochirality by racemization is the result of the conformational phase transition. The racemization of protein-bound amino acids (spontaneous and enzymatic) occurs through thermal activation over the energy barrier or by the tunnel transfer effect under the energy barrier. The phase transition is achieved through the intermediate state, where the chirality of alpha carbon vanished. From a thermodynamic consideration, the system in the homo-chiral (single enantiomeric) state is characterized by a decreased level of entropy. The oscillating protein chirality is suggesting its distinct significance in the neurotransmission and flow of perceptual information, adaptive associative learning, and cognitive laterality. The common pathological hallmarks of neurodegenerative disorders include protein misfolding, aging, and the deposition of protease-resistant protein aggregates. Each of the landmarks is influenced by racemization. The brain region, cell type, and age-dependent racemization critically influence the functions of many intracellular, membrane-bound, and extracellular proteins including amyloid precursor protein (APP), TAU, PrP, Huntingtin, α-synuclein, myelin basic protein (MBP), and collagen. The amyloid cascade hypothesis in Alzheimer's disease (AD) coexists with the failure of amyloid beta (Aβ) targeting drug therapy. According to our view, racemization should be considered as a critical factor of protein conformation with the potential for inducing order, disorder, misfolding, aggregation, toxicity, and malfunctions.
Collapse
Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
| | - Thomas M. Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, New York University School of Medicine, New York, NY 10016, USA
| | - Abel Lajtha
- Center for Neurochemistry, The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
| |
Collapse
|
24
|
Zeng Y, Yang J, Zhang B, Gao M, Su Z, Huang Y. The structure and phase of tau: from monomer to amyloid filament. Cell Mol Life Sci 2021; 78:1873-1886. [PMID: 33078207 PMCID: PMC11073437 DOI: 10.1007/s00018-020-03681-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/20/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022]
Abstract
Tau is a microtubule-associated protein involved in regulation of assembly and spatial organization of microtubule in neurons. However, in pathological conditions, tau monomers assemble into amyloid filaments characterized by the cross-β structures in a number of neurodegenerative diseases known as tauopathies. In this review, we summarize recent progression on the characterization of structures of tau monomer and filament, as well as the dynamic liquid droplet assembly. Our aim is to reveal how post-translational modifications, amino acid mutations, and interacting molecules modulate the conformational ensemble of tau monomer, and how they accelerate or inhibit tau assembly into aggregates. Structure-based aggregation inhibitor design is also discussed in the context of dynamics and heterogeneity of tau structures.
Collapse
Affiliation(s)
- Yifan Zeng
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Jing Yang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Bailing Zhang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Meng Gao
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China.
| |
Collapse
|
25
|
Haas P, Muralidharan M, Krogan NJ, Kaake RM, Hüttenhain R. Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology. J Proteome Res 2021; 20:1133-1152. [PMID: 33464917 PMCID: PMC7839417 DOI: 10.1021/acs.jproteome.0c00764] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Indexed: 12/17/2022]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), was declared a pandemic infection in March 2020. As of December 2020, two COVID-19 vaccines have been authorized for emergency use by the U.S. Food and Drug Administration, but there are no effective drugs to treat COVID-19, and pandemic mitigation efforts like physical distancing have had acute social and economic consequences. In this perspective, we discuss how the proteomic research community can leverage technologies and expertise to address the pandemic by investigating four key areas of study in SARS-CoV-2 biology. Specifically, we discuss how (1) mass spectrometry-based structural techniques can overcome limitations and complement traditional structural approaches to inform the dynamic structure of SARS-CoV-2 proteins, complexes, and virions; (2) virus-host protein-protein interaction mapping can identify the cellular machinery required for SARS-CoV-2 replication; (3) global protein abundance and post-translational modification profiling can characterize signaling pathways that are rewired during infection; and (4) proteomic technologies can aid in biomarker identification, diagnostics, and drug development in order to monitor COVID-19 pathology and investigate treatment strategies. Systems-level high-throughput capabilities of proteomic technologies can yield important insights into SARS-CoV-2 biology that are urgently needed during the pandemic, and more broadly, can inform coronavirus virology and host biology.
Collapse
Affiliation(s)
- Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monita Muralidharan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nevan J. Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robyn M. Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
26
|
Sljoka A. Probing Allosteric Mechanism with Long-Range Rigidity Transmission Across Protein Networks. Methods Mol Biol 2021; 2253:61-75. [PMID: 33315218 DOI: 10.1007/978-1-0716-1154-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Allosteric transmission refers to regulation of protein function at a distance. "Allostery" involves regulation and/or signal transduction induced by a perturbation event. Allostery, which has been coined the "second secret of life," is a fundamental property of most dynamics proteins. Most of critical questions surrounding allostery are largely unresolved. One of the key puzzles is to describe the physical mechanism of distant coupled conformational change. Another hot research area surrounding allostery is detection of allosteric pathways or regions (residues) in the protein that are the most critical for transmission of allosteric information. Using techniques inspired by mathematical rigidity theory and mechanical linkages, we have previously proposed a mechanistic model and description of allosteric transmission and an accompanying computational method, the Rigidity Transmission Allostery (RTA) algorithm. The RTA algorithm and method are designed to predict if mechanical perturbation of rigidity, for example, due to ligand binding, at one site of the protein can transmit and propagate across a protein structure and in turn cause a change in available conformational degrees of freedom and a change in conformation at a second distant site, equivalently resulting in allosteric transmission. The RTA algorithm is computationally very fast and can rapidly scan many unknown sites for allosteric transmission, identifying potential novel allosteric sites and quantify their allosteric effect. In this chapter we will discuss the rigidity-based mechanistic model of allosteric communication. As a case illustrative study, we will demonstrate RTA analysis on a G protein coupled receptor (GPCR) human adenosine A2A receptor. Our method gives important implications and a novel prospective for general mechanistic description of allosteric communication.
Collapse
Affiliation(s)
- Adnan Sljoka
- Department of Informatics, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan.
- CREST, Japan Science and Technology Agency (JST), Tokyo, Japan.
- RIKEN, Center for Advanced Intelligence Project, Tokyo, Japan.
| |
Collapse
|
27
|
Merezhko M, Uronen RL, Huttunen HJ. The Cell Biology of Tau Secretion. Front Mol Neurosci 2020; 13:569818. [PMID: 33071756 PMCID: PMC7539664 DOI: 10.3389/fnmol.2020.569818] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/26/2020] [Indexed: 12/27/2022] Open
Abstract
The progressive accumulation and spread of misfolded tau protein in the nervous system is the hallmark of tauopathies, progressive neurodegenerative diseases with only symptomatic treatments available. A growing body of evidence suggests that spreading of tau pathology can occur via cell-to-cell transfer involving secretion and internalization of pathological forms of tau protein followed by templated misfolding of normal tau in recipient cells. Several studies have addressed the cell biological mechanisms of tau secretion. It now appears that instead of a single mechanism, cells can secrete tau via three coexisting pathways: (1) translocation through the plasma membrane; (2) membranous organelles-based secretion; and (3) ectosomal shedding. The relative importance of these pathways in the secretion of normal and pathological tau is still elusive, though. Moreover, glial cells contribute to tau propagation, and the involvement of different cell types, as well as different secretion pathways, complicates the understanding of prion-like propagation of tauopathy. One of the important regulators of tau secretion in neuronal activity, but its mechanistic connection to tau secretion remains unclear and may involve all three secretion pathways of tau. This review article summarizes recent advancements in the field of tau secretion with an emphasis on cell biological aspects of the secretion process and discusses the role of neuronal activity and glial cells in the spread of pathological forms of tau.
Collapse
Affiliation(s)
- Maria Merezhko
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - Henri J Huttunen
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
| |
Collapse
|
28
|
Mitra G. Emerging Role of Mass Spectrometry-Based Structural Proteomics in Elucidating Intrinsic Disorder in Proteins. Proteomics 2020; 21:e2000011. [PMID: 32959512 DOI: 10.1002/pmic.202000011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/30/2020] [Indexed: 12/14/2022]
Abstract
Inherent disorder is an integral part of all proteomes, represented as fully or partially unfolded proteins. The lack of order in intrinsically disordered proteins (IDPs) results in an incredibly flexible, floppy, and heterogeneous ensemble, contrary to the well-structured and unique organization of folded proteins. Despite such unusual demeanor, IDPs are crucial for numerous cellular processes and are increasingly being associated with disease-causing pathologies. These warrant more intensive investigation of this atypical class of protein. Traditional biophysical tools, however, fall short of analyzing IDPs, thus making their structure-function characterization challenging. Mass spectrometry (MS) in recent years has evolved as a valuable tool for elucidating the unusual conformational facets of IDPs. In this review, the features of advanced MS techniques such as Hydrogen-deuterium exchange (HDX)-MS, native MS, limited proteolysis (LiP)-MS, chemical cross-linking (XL)-MS, and Fast photochemical oxidation of proteins (FPOP)-MS are briefly discussed. Recent MS studies on IDPs and the unique advantages/shortfalls associated with the above methods while evaluating structural proteomics of IDPs, are illustrated. Eventually the future scope of the MS methods in further decoding the unexplored landscapes of IDPs is presented.
Collapse
Affiliation(s)
- Gopa Mitra
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St John's Medical College, St. John's National Academy of Health Sciences, 100 Feet Road, Koramangala, Bangalore, Karnataka, 560034, India
| |
Collapse
|
29
|
Shillcock JC, Brochut M, Chénais E, Ipsen JH. Phase behaviour and structure of a model biomolecular condensate. SOFT MATTER 2020; 16:6413-6423. [PMID: 32584357 DOI: 10.1039/d0sm00813c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phase separation of immiscible fluids is a common phenomenon in polymer chemistry, and is recognized as an important mechanism by which cells compartmentalize their biochemical reactions. Biomolecular condensates are condensed fluid droplets in cells that form by liquid-liquid phase separation of intrinsically-disordered proteins. They have a wide range of functions and are associated with chronic neurodegenerative diseases in which they become pathologically rigid. However, it remains unclear how their material properties depend on the molecular structure of the proteins. Here we explore the phase behaviour and structure of a model biomolecular condensate composed of semi-flexible polymers with attractive end-caps using coarse-grained simulations. The model contains the minimal molecular features that are sufficient to observe liquid-liquid phase separation of soluble polymers into a porous, three-dimensional network in which their end-caps reversibly bind at junctions. The distance between connected junctions scales with the polymer length as a self-avoiding random walk over a wide range of concentration with a weak affinity-dependent prefactor. By contrast, the average number of polymers that meet at the junctions depends on the end-cap affinity but only weakly on the polymer length. The structured porosity of the condensed phase suggests a mechanism for cells to regulate biomolecular condensates. Protein interaction sites may be turned on or off to modulate the condensate's porosity and therefore the diffusion and interaction of additional proteins.
Collapse
Affiliation(s)
- J C Shillcock
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | | | | | | |
Collapse
|
30
|
Wong CO. Endosomal-Lysosomal Processing of Neurodegeneration-Associated Proteins in Astrocytes. Int J Mol Sci 2020; 21:ijms21145149. [PMID: 32708198 PMCID: PMC7404029 DOI: 10.3390/ijms21145149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 12/15/2022] Open
Abstract
Most common neurodegenerative diseases (NDs) are characterized by deposition of protein aggregates that are resulted from misfolding, dysregulated trafficking, and compromised proteolytic degradation. These proteins exert cellular toxicity to a broad range of brain cells and are found in both neurons and glia. Extracellular monomeric and oligomeric ND-associated proteins are taken up by astrocytes, the most abundant glial cell in the brain. Internalization, intracellular trafficking, processing, and disposal of these proteins are executed by the endosomal-lysosomal system of astrocytes. Endosomal-lysosomal organelles thus mediate the cellular impact and metabolic fate of these toxic protein species. Given the indispensable role of astrocytes in brain metabolic homeostasis, the endosomal-lysosomal processing of these proteins plays a fundamental role in altering the trajectory of neurodegeneration. This review aims at summarizing the mounting evidence that has established the essential role of astrocytic endosomal-lysosomal organelles in the processing of amyloid precursor proteins, Apolipoprotein E (ApoE), tau, alpha synuclein, and huntingtin, which are associated with NDs such as Alzheimer’s, Parkinson’s, and Huntington diseases.
Collapse
Affiliation(s)
- Ching-On Wong
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| |
Collapse
|
31
|
Narang D, Lento C, J. Wilson D. HDX-MS: An Analytical Tool to Capture Protein Motion in Action. Biomedicines 2020; 8:biomedicines8070224. [PMID: 32709043 PMCID: PMC7399943 DOI: 10.3390/biomedicines8070224] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/07/2023] Open
Abstract
Virtually all protein functions in the cell, including pathogenic processes, require coordinated motion of atoms or domains, i.e., conformational dynamics. Understanding protein dynamics is therefore critical both for drug development and to learn about the underlying molecular causes of many diseases. Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) provides valuable information about protein dynamics, which is highly complementary to the static picture provided by conventional high-resolution structural tools (i.e., X-ray crystallography and structural NMR). The amount of protein required to carry out HDX-MS experiments is a fraction of the amount required by alternative biophysical techniques, which are also usually lower resolution. Use of HDX-MS is growing quickly both in industry and academia, and it has been successfully used in numerous drug and vaccine development efforts, with important roles in understanding allosteric effects and mapping binding sites.
Collapse
Affiliation(s)
- Dominic Narang
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
| | - Derek J. Wilson
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
- Centre for Research of Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University, Toronto, ON M3J 1P3, Canada
- Correspondence:
| |
Collapse
|
32
|
Tajoddin NN, Konermann L. Analysis of Temperature-Dependent H/D Exchange Mass Spectrometry Experiments. Anal Chem 2020; 92:10058-10067. [DOI: 10.1021/acs.analchem.0c01828] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nastaran N. Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
33
|
Kawasaki R, Tate SI. Impact of the Hereditary P301L Mutation on the Correlated Conformational Dynamics of Human Tau Protein Revealed by the Paramagnetic Relaxation Enhancement NMR Experiments. Int J Mol Sci 2020; 21:ijms21113920. [PMID: 32486218 PMCID: PMC7313075 DOI: 10.3390/ijms21113920] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/23/2022] Open
Abstract
Tau forms intracellular insoluble aggregates as a neuropathological hallmark of Alzheimer’s disease. Tau is largely unstructured, which complicates the characterization of the tau aggregation process. Recent studies have demonstrated that tau samples two distinct conformational ensembles, each of which contains the soluble and aggregation-prone states of tau. A shift to populate the aggregation-prone ensemble may promote tau fibrillization. However, the mechanism of this ensemble transition remains elusive. In this study, we explored the conformational dynamics of a tau fragment by using paramagnetic relaxation enhancement (PRE) and interference (PRI) NMR experiments. The PRE correlation map showed that tau is composed of segments consisting of residues in correlated motions. Intriguingly, residues forming the β-structures in the heparin-induced tau filament coincide with residues in these segments, suggesting that each segment behaves as a structural unit in fibrillization. PRI data demonstrated that the P301L mutation exclusively alters the transiently formed tau structures by changing the short- and long-range correlated motions among residues. The transient conformations of P301L tau expose the amyloid motif PHF6 to promote tau self-aggregation. We propose the correlated motions among residues within tau determine the population sizes of the conformational ensembles, and perturbing the correlated motions populates the aggregation-prone form.
Collapse
Affiliation(s)
- Ryosuke Kawasaki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
| | - Shin-ichi Tate
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
- Department of Mathematical and Life Sciences, Graduate School of the Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Correspondence: ; Tel.: +81-82-424-7387
| |
Collapse
|
34
|
The Order-Disorder Continuum: Linking Predictions of Protein Structure and Disorder through Molecular Simulation. Sci Rep 2020; 10:2068. [PMID: 32034199 PMCID: PMC7005769 DOI: 10.1038/s41598-020-58868-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/16/2019] [Indexed: 12/11/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions within proteins (IDRs) serve an increasingly expansive list of biological functions, including regulation of transcription and translation, protein phosphorylation, cellular signal transduction, as well as mechanical roles. The strong link between protein function and disorder motivates a deeper fundamental characterization of IDPs and IDRs for discovering new functions and relevant mechanisms. We review recent advances in experimental techniques that have improved identification of disordered regions in proteins. Yet, experimentally curated disorder information still does not currently scale to the level of experimentally determined structural information in folded protein databases, and disorder predictors rely on several different binary definitions of disorder. To link secondary structure prediction algorithms developed for folded proteins and protein disorder predictors, we conduct molecular dynamics simulations on representative proteins from the Protein Data Bank, comparing secondary structure and disorder predictions with simulation results. We find that structure predictor performance from neural networks can be leveraged for the identification of highly dynamic regions within molecules, linked to disorder. Low accuracy structure predictions suggest a lack of static structure for regions that disorder predictors fail to identify. While disorder databases continue to expand, secondary structure predictors and molecular simulations can improve disorder predictor performance, which aids discovery of novel functions of IDPs and IDRs. These observations provide a platform for the development of new, integrated structural databases and fusion of prediction tools toward protein disorder characterization in health and disease.
Collapse
|
35
|
Minde DP, Ramakrishna M, Lilley KS. Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions. Commun Biol 2020; 3:38. [PMID: 31969649 PMCID: PMC6976632 DOI: 10.1038/s42003-020-0758-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023] Open
Abstract
Intrinsically Disordered Regions (IDRs) are enriched in disease-linked proteins known to have multiple post-translational modifications, but there is limited in vivo information about how locally unfolded protein regions contribute to biological functions. We reasoned that IDRs should be more accessible to targeted in vivo biotinylation than ordered protein regions, if they retain their flexibility in human cells. Indeed, we observed increased biotinylation density in predicted IDRs in several cellular compartments >20,000 biotin sites from four proximity proteomics studies. We show that in a biotin ‘painting’ time course experiment, biotinylation events in Escherichia coli ribosomes progress from unfolded and exposed regions at 10 s, to structured and less accessible regions after five minutes. We conclude that biotin proximity tagging favours sites of local disorder in proteins and suggest the possibility of using biotin painting as a method to gain unique insights into in vivo condition-dependent subcellular plasticity of proteins. David-Paul Minde, Manasa Ramakrishna et al. look at intrinsically disordered regions of disease-linked proteins in vivo by biotinylation. They show that biotin “painting” could be used as a method to examine the condition-dependent plasticity of proteins in vivo.
Collapse
Affiliation(s)
- David-Paul Minde
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Manasa Ramakrishna
- Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Road, Leicester, LE1 9HN, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
| |
Collapse
|
36
|
Pyridine-2,3-dicarboxylate, quinolinic acid, induces 1N4R Tau amyloid aggregation in vitro: Another evidence for the detrimental effect of the inescapable endogenous neurotoxin. Chem Biol Interact 2019; 315:108884. [PMID: 31678113 DOI: 10.1016/j.cbi.2019.108884] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/18/2019] [Accepted: 10/26/2019] [Indexed: 01/19/2023]
Abstract
Quinolinic acid (QA) known as a neuro-active metabolite associated with the kynurenine pathway. At high concentrations, QA is often involved in the initiation and development of several human neurologic diseases, like Alzheimer's disease. Because of the QA action as the NMDA receptor, it is considered as a potent excitotoxin in vivo. Since it is probable that different mechanisms are employed by QA, activation of NMDA receptors cannot fully explain the revealed toxicity and it is even believed that there are multiple unknown mechanisms/targets leading to QA cytotoxicity. Herein we report accelerated amyloid oligomerization of 1N4R Tau under the effect of QA, in vitro, then the molecular structure, morphology and toxicity of the protein aggregate were documented by using various theoretical/experimental approaches. The possible mechanism of action of QA-induced Tau oligomerization has also been explored.
Collapse
|
37
|
Brown KA, Rajendran S, Dowd J, Wilson DJ. Rapid characterization of structural and functional similarity for a candidate bevacizumab (Avastin) biosimilar using a multipronged mass‐spectrometry‐based approach. Drug Test Anal 2019; 11:1207-1217. [DOI: 10.1002/dta.2609] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Kerene A. Brown
- Chemistry DepartmentYork University Toronto ON Canada
- The Centre for Research in Mass SpectrometryYork University Toronto ON Canada
| | | | - Jason Dowd
- Apobiologix (division of Apotex Inc.) Toronto ON Canada
| | - Derek J. Wilson
- Chemistry DepartmentYork University Toronto ON Canada
- The Centre for Research in Mass SpectrometryYork University Toronto ON Canada
| |
Collapse
|
38
|
Boyko S, Qi X, Chen TH, Surewicz K, Surewicz WK. Liquid-liquid phase separation of tau protein: The crucial role of electrostatic interactions. J Biol Chem 2019; 294:11054-11059. [PMID: 31097543 PMCID: PMC6643045 DOI: 10.1074/jbc.ac119.009198] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 05/14/2019] [Indexed: 12/14/2022] Open
Abstract
Recent studies have indicated that tau, a protein involved in Alzheimer's disease and other neurodegenerative disorders, has a propensity to undergo liquid–liquid phase separation (LLPS). However, the mechanism of this process remains unknown. Here, we demonstrate that tau LLPS is largely driven by intermolecular electrostatic interactions between the negatively charged N-terminal and positively charged middle/C-terminal regions, whereas hydrophobic interactions play a surprisingly small role. Furthermore, our results reveal that, in contrast to previous suggestions, phosphorylation is not required for tau LLPS. These findings provide a foundation for understanding the mechanism by which phosphorylation and other posttranslational modifications could modulate tau LLPS in the context of specific physiological functions as well as pathological interactions.
Collapse
Affiliation(s)
- Solomiia Boyko
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Xu Qi
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Tien-Hao Chen
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Krystyna Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| |
Collapse
|
39
|
Olzscha H. Posttranslational modifications and proteinopathies: how guardians of the proteome are defeated. Biol Chem 2019; 400:895-915. [DOI: 10.1515/hsz-2018-0458] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/13/2019] [Indexed: 01/15/2023]
Abstract
Abstract
Protein folding is one of the fundamental processes in life and therefore needs to be tightly regulated. Many cellular quality control systems are in place to ensure that proteostasis is optimally adjusted for a changing environment, facilitating protein folding, translocation and degradation. These systems include the molecular chaperones and the major protein degradation systems, namely the ubiquitin proteasome system and autophagy. However, the capacity of the quality control systems can be exhausted and protein misfolding and aggregation, including the formation of amyloids, can occur as a result of ageing, mutations or exogenous influences. There are many known diseases in which protein misfolding and aggregation can be the underlying cause of the pathological condition; these are referred to as proteinopathies. Over the last decade, it has become clear that posttranslational modifications can govern and modulate protein folding, and that aberrant posttranslational modifications can cause or contribute to proteinopathies. This review provides an overview of protein folding and misfolding and the role of the major protein quality control systems. It focusses on different posttranslational modifications and gives examples of how these posttranslational modifications can alter protein folding and cause or accompany proteinopathies.
Collapse
Affiliation(s)
- Heidi Olzscha
- Institut für Physiologische Chemie , Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg , Hollystr. 1 , D-06114 Halle/Saale , Germany
| |
Collapse
|
40
|
14-3-3/Tau Interaction and Tau Amyloidogenesis. J Mol Neurosci 2019; 68:620-630. [PMID: 31062171 DOI: 10.1007/s12031-019-01325-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 04/22/2019] [Indexed: 01/02/2023]
Abstract
The major function of microtubule-associated protein tau is to promote microtubule assembly in the central nervous system. However, aggregation of abnormally phosphorylated tau is a hallmark of tauopathies. Although the molecular mechanisms of conformational transitions and assembling of tau molecules into amyloid fibril remain largely unknown, several factors have been shown to promote tau aggregation, including mutations, polyanions, phosphorylation, and interactions with other proteins. 14-3-3 proteins are a family of highly conserved, multifunctional proteins that are mainly expressed in the central nervous system. Being a scaffolding protein, 14-3-3 proteins interact with tau and regulate tau phosphorylation by bridging tau with various protein kinases. 14-3-3 proteins also directly regulate tau aggregation via specific and non-specific interactions with tau. In this review, we summarize recent advances in characterization of tau conformation and tau/14-3-3 interaction. We discuss the connection between 14-3-3 binding and tau aggregation with a special emphasis on the regulatory role of 14-3-3 on tau conformation.
Collapse
|
41
|
Tang M, Harrison J, Deaton CA, Johnson GVW. Tau Clearance Mechanisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1184:57-68. [PMID: 32096028 DOI: 10.1007/978-981-32-9358-8_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Efficient quality control mechanisms are essential for a healthy, functional neuron. Recognition and degradation of misfolded, damaged, or potentially toxic proteins, is a crucial aspect of protein quality control. Tau is a protein that is highly expressed in neurons, and plays an important role in modulating a number of physiological processes. Maintaining appropriate levels of tau is key for neuronal health; hence perturbations in tau clearance mechanisms are likely significant contributors to neurodegenerative diseases such as Alzheimer's disease and frontotemporal lobar degeneration. In this chapter we will first briefly review the two primary degradative mechanisms that mediate tau clearance: the proteasome system and the autophagy-lysosome pathway. This will be followed by a discussion about what is known about the contribution of each of these pathways to tau clearance. We will also present recent findings on tau degradation through the endolysosomal system. Further, how deficits in these degradative systems may contribute to the accumulation of dysfunctional or toxic forms of tau in neurodegenerative conditions is considered.
Collapse
|
42
|
Sarnataro D. Attempt to Untangle the Prion-Like Misfolding Mechanism for Neurodegenerative Diseases. Int J Mol Sci 2018; 19:ijms19103081. [PMID: 30304819 PMCID: PMC6213118 DOI: 10.3390/ijms19103081] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/01/2018] [Accepted: 10/05/2018] [Indexed: 12/15/2022] Open
Abstract
The misfolding and aggregation of proteins is the neuropathological hallmark for numerous diseases including Alzheimer's disease, Parkinson's disease, and prion diseases. It is believed that misfolded and abnormal β-sheets forms of wild-type proteins are the vectors of these diseases by acting as seeds for the aggregation of endogenous proteins. Cellular prion protein (PrPC) is a glycosyl-phosphatidyl-inositol (GPI) anchored glycoprotein that is able to misfold to a pathogenic isoform PrPSc, the causative agent of prion diseases which present as sporadic, dominantly inherited and transmissible infectious disorders. Increasing evidence highlights the importance of prion-like seeding as a mechanism for pathological spread in Alzheimer's disease and Tauopathy, as well as other neurodegenerative disorders. Here, we report the latest findings on the mechanisms controlling protein folding, focusing on the ER (Endoplasmic Reticulum) quality control of GPI-anchored proteins and describe the "prion-like" properties of amyloid-β and tau assemblies. Furthermore, we highlight the importance of pathogenic assemblies interaction with protein and lipid membrane components and their implications in both prion and Alzheimer's diseases.
Collapse
Affiliation(s)
- Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, School of Medicine, Via S. Pansini 5, 80131 Naples, Italy.
| |
Collapse
|
43
|
Câmara AB, de Souza ID, Dalmolin RJS. Sunlight Incidence, Vitamin D Deficiency, and Alzheimer's Disease. J Med Food 2018; 21:841-848. [DOI: 10.1089/jmf.2017.0130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Alice Barros Câmara
- Bioinformatics Multidisciplinary Environment, IMD, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Iara Dantas de Souza
- Bioinformatics Multidisciplinary Environment, IMD, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Rodrigo Juliani Siqueira Dalmolin
- Bioinformatics Multidisciplinary Environment, IMD, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Biochemistry, CB, Federal University of Rio Grande do Norte, Natal, Brazil
| |
Collapse
|
44
|
Rao SS, Adlard PA. Untangling Tau and Iron: Exploring the Interaction Between Iron and Tau in Neurodegeneration. Front Mol Neurosci 2018; 11:276. [PMID: 30174587 PMCID: PMC6108061 DOI: 10.3389/fnmol.2018.00276] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/20/2018] [Indexed: 11/16/2022] Open
Abstract
There is an emerging link between the accumulation of iron in the brain and abnormal tau pathology in a number of neurodegenerative disorders, such as Alzheimer’s disease (AD). Studies have demonstrated that iron can regulate tau phosphorylation by inducing the activity of multiple kinases that promote tau hyperphosphorylation and potentially also by impacting protein phosphatase 2A activity. Iron is also reported to induce the aggregation of hyperphosphorylated tau, possibly through a direct interaction via a putative iron binding motif in the tau protein, facilitating the formation of neurofibrillary tangles (NFTs). Furthermore, in human studies high levels of iron have been reported to co-localize with tau in NFT-bearing neurons. These data, together with our own work showing that tau has a role in mediating cellular iron efflux, provide evidence supporting a critical tau:iron interaction that may impact both the symptomatic presentation and the progression of disease. Importantly, this may also have relevance for therapeutic directions, and indeed, the use of iron chelators such as deferiprone and deferoxamine have been reported to alleviate the phenotypes, reduce phosphorylated tau levels and stabilize iron regulation in various animal models. As these compounds are also moving towards clinical translation, then it is imperative that we understand the intersection between iron and tau in neurodegeneration. In this article, we provide an overview of the key pathological and biochemical interactions between tau and iron. We also review the role of iron and tau in disease pathology and the potential of metal-based therapies for tauopathies.
Collapse
Affiliation(s)
- Shalini S Rao
- Division of Mental Health, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Paul Anthony Adlard
- Division of Mental Health, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
45
|
Jebarupa B, Muralidharan M, Srinivasu BY, Mandal AK, Mitra G. Effect of altered solution conditions on tau conformational dynamics: Plausible implication on order propensity and aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:668-679. [DOI: 10.1016/j.bbapap.2018.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/23/2023]
|
46
|
Wegmann S, Eftekharzadeh B, Tepper K, Zoltowska KM, Bennett RE, Dujardin S, Laskowski PR, MacKenzie D, Kamath T, Commins C, Vanderburg C, Roe AD, Fan Z, Molliex AM, Hernandez-Vega A, Muller D, Hyman AA, Mandelkow E, Taylor JP, Hyman BT. Tau protein liquid-liquid phase separation can initiate tau aggregation. EMBO J 2018; 37:e98049. [PMID: 29472250 PMCID: PMC5881631 DOI: 10.15252/embj.201798049] [Citation(s) in RCA: 616] [Impact Index Per Article: 102.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/17/2018] [Accepted: 01/19/2018] [Indexed: 11/13/2022] Open
Abstract
The transition between soluble intrinsically disordered tau protein and aggregated tau in neurofibrillary tangles in Alzheimer's disease is unknown. Here, we propose that soluble tau species can undergo liquid-liquid phase separation (LLPS) under cellular conditions and that phase-separated tau droplets can serve as an intermediate toward tau aggregate formation. We demonstrate that phosphorylated or mutant aggregation prone recombinant tau undergoes LLPS, as does high molecular weight soluble phospho-tau isolated from human Alzheimer brain. Droplet-like tau can also be observed in neurons and other cells. We found that tau droplets become gel-like in minutes, and over days start to spontaneously form thioflavin-S-positive tau aggregates that are competent of seeding cellular tau aggregation. Since analogous LLPS observations have been made for FUS, hnRNPA1, and TDP43, which aggregate in the context of amyotrophic lateral sclerosis, we suggest that LLPS represents a biophysical process with a role in multiple different neurodegenerative diseases.
Collapse
Affiliation(s)
- Susanne Wegmann
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Bahareh Eftekharzadeh
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Katharina Tepper
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Katarzyna M Zoltowska
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Rachel E Bennett
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Simon Dujardin
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Pawel R Laskowski
- Department for Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Danny MacKenzie
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Tarun Kamath
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Caitlin Commins
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Charles Vanderburg
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Allyson D Roe
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Zhanyun Fan
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Amandine M Molliex
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Daniel Muller
- Department for Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Anthony A Hyman
- Department for Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Max-Planck Institute for Metabolism Research, Hamburg Outstation c/o DESY, Hamburg, Germany
- CAESAR Research Center, Bonn, Germany
| | - J Paul Taylor
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| |
Collapse
|
47
|
Pretorius E, Bester J, Kell DB. A Bacterial Component to Alzheimer's-Type Dementia Seen via a Systems Biology Approach that Links Iron Dysregulation and Inflammagen Shedding to Disease. J Alzheimers Dis 2018; 53:1237-56. [PMID: 27340854 PMCID: PMC5325058 DOI: 10.3233/jad-160318] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The progression of Alzheimer's disease (AD) is accompanied by a great many observable changes, both molecular and physiological. These include oxidative stress, neuroinflammation, and (more proximal to cognitive decline) the death of neuronal and other cells. A systems biology approach seeks to organize these observed variables into pathways that discriminate those that are highly involved (i.e., causative) from those that are more usefully recognized as bystander effects. We review the evidence that iron dysregulation is one of the central causative pathway elements here, as this can cause each of the above effects. In addition, we review the evidence that dormant, non-growing bacteria are a crucial feature of AD, that their growth in vivo is normally limited by a lack of free iron, and that it is this iron dysregulation that is an important factor in their resuscitation. Indeed, bacterial cells can be observed by ultrastructural microscopy in the blood of AD patients. A consequence of this is that the growing cells can shed highly inflammatory components such as lipopolysaccharides (LPS). These too are known to be able to induce (apoptotic and pyroptotic) neuronal cell death. There is also evidence that these systems interact with elements of vitamin D metabolism. This integrative systems approach has strong predictive power, indicating (as has indeed been shown) that both natural and pharmaceutical iron chelators might have useful protective roles in arresting cognitive decline, and that a further assessment of the role of microbes in AD development is more than highly warranted.
Collapse
Affiliation(s)
- Etheresia Pretorius
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia, South Africa
| | - Janette Bester
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia, South Africa
| | - Douglas B Kell
- School of Chemistry, The University of Manchester, Manchester, Lancs, UK.,The Manchester Institute of Biotechnology, The University of Manchester, Manchester, Lancs, UK.,Centre for Synthetic Biology of Fine and Speciality Chemicals, The University of Manchester, Manchester, Lancs, UK
| |
Collapse
|
48
|
Huang RYC, Iacob RE, Sankaranarayanan S, Yang L, Ahlijanian M, Tao L, Tymiak AA, Chen G. Probing Conformational Dynamics of Tau Protein by Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:174-182. [PMID: 28971440 DOI: 10.1007/s13361-017-1815-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 06/07/2023]
Abstract
Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization. HDX-MS studies including anti-tau antibody epitope mapping experiments provided molecular level details of the full-length tau's conformational dynamics and its regional solvent accessibility upon soluble aggregates formation. The results demonstrate that R3 region in the full-length tau's microtubule binding repeat region (MTBR) is stabilized in the aggregation process, leaving both N and C terminal regions to be solvent exposed in the soluble aggregates and fibrils. The findings also illustrate the practical utility of orthogonal analytical methodologies for the characterization of protein higher order structure. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Richard Y-C Huang
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Sethu Sankaranarayanan
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Ling Yang
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Michael Ahlijanian
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Li Tao
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Hopewell, NJ, USA
| | - Adrienne A Tymiak
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA.
| |
Collapse
|
49
|
Cieplak-Rotowska MK, Tarnowski K, Rubin M, Fabian MR, Sonenberg N, Dadlez M, Niedzwiecka A. Structural Dynamics of the GW182 Silencing Domain Including its RNA Recognition motif (RRM) Revealed by Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:158-173. [PMID: 29080206 PMCID: PMC5785596 DOI: 10.1007/s13361-017-1830-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/08/2017] [Accepted: 10/01/2017] [Indexed: 06/07/2023]
Abstract
The human GW182 protein plays an essential role in micro(mi)RNA-dependent gene silencing. miRNA silencing is mediated, in part, by a GW182 C-terminal region called the silencing domain, which interacts with the poly(A) binding protein and the CCR4-NOT deadenylase complex to repress protein synthesis. Structural studies of this GW182 fragment are challenging due to its predicted intrinsically disordered character, except for its RRM domain. However, detailed insights into the properties of proteins containing disordered regions can be provided by hydrogen-deuterium exchange mass spectrometry (HDX/MS). In this work, we applied HDX/MS to define the structural state of the GW182 silencing domain. HDX/MS analysis revealed that this domain is clearly divided into a natively unstructured part, including the CCR4-NOT interacting motif 1, and a distinct RRM domain. The GW182 RRM has a very dynamic structure, since water molecules can penetrate the whole domain in 2 h. The finding of this high structural dynamics sheds new light on the RRM structure. Though this domain is one of the most frequently occurring canonical protein domains in eukaryotes, these results are - to our knowledge - the first HDX/MS characteristics of an RRM. The HDX/MS studies show also that the α2 helix of the RRM can display EX1 behavior after a freezing-thawing cycle. This means that the RRM structure is sensitive to environmental conditions and can change its conformation, which suggests that the state of the RRM containing proteins should be checked by HDX/MS in regard of the conformational uniformity. Graphical Abstract.
Collapse
Affiliation(s)
- Maja K Cieplak-Rotowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland
| | - Krzysztof Tarnowski
- Laboratory of Mass Spectrometry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, PL-02106, Warsaw, Poland
| | - Marcin Rubin
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland
| | - Marc R Fabian
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Goodman Cancer Center, McGill University, Montréal, Québec, Canada
| | - Michal Dadlez
- Laboratory of Mass Spectrometry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, PL-02106, Warsaw, Poland
| | - Anna Niedzwiecka
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland.
| |
Collapse
|
50
|
Deng B, Zhu S, Macklin AM, Xu J, Lento C, Sljoka A, Wilson DJ. Suppressing allostery in epitope mapping experiments using millisecond hydrogen / deuterium exchange mass spectrometry. MAbs 2017; 9:1327-1336. [PMID: 28933661 PMCID: PMC5680795 DOI: 10.1080/19420862.2017.1379641] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Localization of the interface between the candidate antibody and its antigen target, commonly known as epitope mapping, is a critical component of the development of therapeutic monoclonal antibodies. With the recent availability of commercial automated systems, hydrogen / deuterium eXchange (HDX) is rapidly becoming the tool for mapping epitopes preferred by researchers in both industry and academia. However, this approach has a significant drawback in that it can be confounded by ‘allosteric’ structural and dynamic changes that result from the interaction, but occur far from the point(s) of contact. Here, we introduce a ‘kinetic’ millisecond HDX workflow that suppresses allosteric effects in epitope mapping experiments. The approach employs a previously introduced microfluidic apparatus that enables millisecond HDX labeling times with on-chip pepsin digestion and electrospray ionization. The ‘kinetic’ workflow also differs from conventional HDX-based epitope mapping in that the antibody is introduced to the antigen at the onset of HDX labeling. Using myoglobin / anti-myoglobin as a model system, we demonstrate that at short ‘kinetic’ workflow labeling times (i.e., 200 ms), the HDX signal is already fully developed at the ‘true’ epitope, but is still largely below the significance threshold at allosteric sites. Identification of the ‘true’ epitope is supported by computational docking predictions and allostery modeling using the rigidity transmission allostery algorithm.
Collapse
Affiliation(s)
- Bin Deng
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Shaolong Zhu
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Andrew M Macklin
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Jianrong Xu
- c Department of Pharmacology, Institute of Medical Sciences , Shanghai Jiao Tong University School of Medicine , Shanghai , P.R. China
| | - Cristina Lento
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| | - Adnan Sljoka
- d Department of Informatics , Kwansei Gakuin University , Nishinomiya , Hyogo , Japan
| | - Derek J Wilson
- a Chemistry Department , York University , 4700 Keele Street, Toronto , ON , Canada.,b The Centre for Research in Mass Spectrometry , York University , Toronto , ON , Canada
| |
Collapse
|