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Usher ET, Fossat MJ, Holehouse AS. Phosphorylation of disordered proteins tunes local and global intramolecular interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598315. [PMID: 38915510 PMCID: PMC11195077 DOI: 10.1101/2024.06.10.598315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Protein post-translational modifications, such as phosphorylation, are important regulatory signals for diverse cellular functions. In particular, intrinsically disordered protein regions (IDRs) are subject to phosphorylation as a means to modulate their interactions and functions. Toward understanding the relationship between phosphorylation in IDRs and specific functional outcomes, we must consider how phosphorylation affects the IDR conformational ensemble. Various experimental techniques are suited to interrogate the features of IDR ensembles; molecular simulations can provide complementary insights and even illuminate ensemble features that may be experimentally inaccessible. Therefore, we sought to expand the tools available to study phosphorylated IDRs by all-atom Monte Carlo simulations. To this end, we implemented parameters for phosphoserine (pSer) and phosphothreonine (pThr) into the OPLS version of the continuum solvent model, ABSINTH, and assessed their performance in all-atom simulations compared to published findings. We simulated short (< 20 residues) and long (> 80 residues) phospho-IDRs that, collectively, survey both local and global phosphorylation-induced changes to the ensemble. Our simulations of four well-studied phospho-IDRs show near-quantitative agreement with published findings for these systems via metrics including changes to radius of gyration, transient helicity, and persistence length. We also leveraged the inherent advantage of sequence control in molecular simulations to explore the conformational effects of diverse combinations of phospho-sites in two multi-phosphorylated IDRs. Our results support and expand on prior observations that connect phosphorylation to changes in the IDR conformational ensemble. Herein, we describe phosphorylation as a means to alter sequence chemistry, net charge and charge patterning, and intramolecular interactions, which can collectively modulate the local and global IDR ensemble features.
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Affiliation(s)
- Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Martin J. Fossat
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
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2
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Ghosh C, Nagpal S, Muñoz V. Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins. Curr Opin Struct Biol 2024; 84:102756. [PMID: 38118365 PMCID: PMC11242915 DOI: 10.1016/j.sbi.2023.102756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023]
Abstract
Intrinsically disordered proteins (IDPs) exploit their plasticity to deploy a rich panoply of soft interactions and binding phenomena. Advances in tailoring molecular simulations for IDPs combined with experimental cross-validation offer an atomistic view of the mechanisms that control IDP binding, function, and dysfunction. The emerging theme is that unbound IDPs autonomously form transient local structures and self-interactions that determine their binding behavior. Recent results have shed light on whether and how IDPs fold, stay disordered or drive condensation upon binding; how they achieve binding specificity and select among competing partners. The disorder-binding paradigm is now being proactively used by researchers to target IDPs for rational drug design and engineer molecular responsive elements for biosensing applications.
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Affiliation(s)
- Catherine Ghosh
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 CA, USA; Department of Bioengineering, University of California at Merced, Merced, 95343 CA, USA. https://twitter.com/cat_ghosh
| | - Suhani Nagpal
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 CA, USA; Department of Bioengineering, University of California at Merced, Merced, 95343 CA, USA; OpenEye, Cadence Molecular Sciences, Boston, 02114 MA, USA
| | - Victor Muñoz
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 CA, USA; Department of Bioengineering, University of California at Merced, Merced, 95343 CA, USA.
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3
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Payliss BJ, Wyatt HDM. Protocol for in vitro phosphorylation of the MUS81-binding region of SLX4 using CDK1-cyclin B. STAR Protoc 2023; 4:102152. [PMID: 36917604 PMCID: PMC10025271 DOI: 10.1016/j.xpro.2023.102152] [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: 12/23/2022] [Revised: 01/23/2023] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
Phosphorylation is a post-translational modification that can alter protein structure and regulate protein-protein interactions. Here, we present a procedure for in vitro phosphorylation of the MUS81-binding region of SLX4 (SLX4MBR) using cyclin-dependent kinase 1-cyclin B. We describe steps for the dialysis and phosphorylation of target proteins followed by purification using size-exclusion chromatography. Finally, we detail a system to monitor phosphorylation effectiveness and identify phosphorylated residues. We anticipate this protocol to be readily adapted for other protein targets or kinases. For complete details on the use and execution of this protocol, please refer to Payliss et al. (2022).1.
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Affiliation(s)
- Brandon J Payliss
- Department of Biochemistry, University of Toronto, Toronto, ON M56 1A8, Canada.
| | - Haley D M Wyatt
- Department of Biochemistry, University of Toronto, Toronto, ON M56 1A8, Canada; Canada Research Chairs Program, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
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4
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Payliss BJ, Tse YWE, Reichheld SE, Lemak A, Yun HY, Houliston S, Patel A, Arrowsmith CH, Sharpe S, Wyatt HD. Phosphorylation of the DNA repair scaffold SLX4 drives folding of the SAP domain and activation of the MUS81-EME1 endonuclease. Cell Rep 2022; 41:111537. [DOI: 10.1016/j.celrep.2022.111537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 11/03/2022] Open
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5
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Korneev A, Begun A, Liubimov S, Kachlishvili K, Molochkov A, Niemi AJ, Maisuradze GG. Exploring Structural Flexibility and Stability of α-Synuclein by the Landau-Ginzburg-Wilson Approach. J Phys Chem B 2022; 126:6878-6890. [PMID: 36053833 PMCID: PMC9482328 DOI: 10.1021/acs.jpcb.2c04651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
α-Synuclein (αS) is the principal protein component of the Lewy body and Lewy neurite deposits that are found in the brains of the victims of one of the most prevalent neurodegenerative disorders, Parkinson's disease. αS can be qualified as a chameleon protein because of the large number of different conformations that it is able to adopt: it is disordered under physiological conditions in solution, in equilibrium with a minor α-helical tetrameric form in the cytoplasm, and is α-helical when bound to a cell membrane. Also, in vitro, αS forms polymorphic amyloid fibrils with unique arrangements of cross-β-sheet motifs. Therefore, it is of interest to elucidate the origins of the structural flexibility of αS and what makes αS stable in different conformations. We address these questions here by analyzing the experimental structures of the micelle-bound, tetrameric, and fibrillar αS in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. It is illustrated that without molecular dynamics simulations the kinks are capable of identifying the key residues causing structural flexibility of αS. Also, the stability of the experimental structures of αS is investigated by simulating heating/cooling trajectories using the Glauber algorithm. The findings are consistent with experiments.
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Affiliation(s)
- Anatolii Korneev
- Pacific Quantum Center, Far Eastern Federal University, 690922, Vladivostok, Russia
| | - Alexander Begun
- Pacific Quantum Center, Far Eastern Federal University, 690922, Vladivostok, Russia
| | - Sergei Liubimov
- Pacific Quantum Center, Far Eastern Federal University, 690922, Vladivostok, Russia
| | - Khatuna Kachlishvili
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, U. S. A
| | - Alexander Molochkov
- Pacific Quantum Center, Far Eastern Federal University, 690922, Vladivostok, Russia
| | - Antti J. Niemi
- Pacific Quantum Center, Far Eastern Federal University, 690922, Vladivostok, Russia
- Nordita, Stockholm University and Uppsala University, SE-106 91 Stockholm, Sweden
- Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, F37200, Tours, France
- School of Physics, Beijing Institute of Technology, Beijing 100081, P.R. China
| | - Gia G. Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, U. S. A
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6
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Guzzo A, Delarue P, Rojas A, Nicolaï A, Maisuradze GG, Senet P. Wild-Type α-Synuclein and Variants Occur in Different Disordered Dimers and Pre-Fibrillar Conformations in Early Stage of Aggregation. Front Mol Biosci 2022; 9:910104. [PMID: 35836937 PMCID: PMC9273784 DOI: 10.3389/fmolb.2022.910104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/16/2022] [Indexed: 12/15/2022] Open
Abstract
α-Synuclein is a 140 amino-acid intrinsically disordered protein mainly found in the brain. Toxic α-synuclein aggregates are the molecular hallmarks of Parkinson’s disease. In vitro studies showed that α-synuclein aggregates in oligomeric structures of several 10th of monomers and into cylindrical structures (fibrils), comprising hundred to thousands of proteins, with polymorphic cross-β-sheet conformations. Oligomeric species, formed at the early stage of aggregation remain, however, poorly understood and are hypothezised to be the most toxic aggregates. Here, we studied the formation of wild-type (WT) and mutant (A30P, A53T, and E46K) dimers of α-synuclein using coarse-grained molecular dynamics. We identified two principal segments of the sequence with a higher propensity to aggregate in the early stage of dimerization: residues 36–55 and residues 66–95. The transient α-helices (residues 53–65 and 73–82) of α-synuclein monomers are destabilized by A53T and E46K mutations, which favors the formation of fibril native contacts in the N-terminal region, whereas the helix 53–65 prevents the propagation of fibril native contacts along the sequence for the WT in the early stages of dimerization. The present results indicate that dimers do not adopt the Greek key motif of the monomer fold in fibrils but form a majority of disordered aggregates and a minority (9–15%) of pre-fibrillar dimers both with intra-molecular and intermolecular β-sheets. The percentage of residues in parallel β-sheets is by increasing order monomer < disordered dimers < pre-fibrillar dimers. Native fibril contacts between the two monomers are present in the NAC domain for WT, A30P, and A53T and in the N-domain for A53T and E46K. Structural properties of pre-fibrillar dimers agree with rupture-force atomic force microscopy and single-molecule Förster resonance energy transfer available data. This suggests that the pre-fibrillar dimers might correspond to the smallest type B toxic oligomers. The probability density of the dimer gyration radius is multi-peaks with an average radius that is 10 Å larger than the one of the monomers for all proteins. The present results indicate that even the elementary α-synuclein aggregation step, the dimerization, is a complicated phenomenon that does not only involve the NAC region.
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Affiliation(s)
- Adrien Guzzo
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, Dijon, France
| | - Patrice Delarue
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, Dijon, France
| | - Ana Rojas
- Schrödinger, Inc., New York, NY, United States
| | - Adrien Nicolaï
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, Dijon, France
| | - Gia G. Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Patrick Senet
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, Dijon, France
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
- *Correspondence: Patrick Senet,
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7
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Roterman I, Sieradzan A, Stapor K, Fabian P, Wesołowski P, Konieczny L. On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field. J Mol Graph Model 2022; 114:108166. [PMID: 35325843 DOI: 10.1016/j.jmgm.2022.108166] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
During the protein folding process in computer simulations involving the use of a United RESidue (UNRES) force field, an additional module was introduced to represent directly the presence of a polar solvent in water form. This module implements the fuzzy oil drop model (FOD) where the 3D Gauss function expresses the presence of a polar environment which directs the polypeptide chain folding process towards the generation of a centric hydrophobic core. Sample test polypeptide chains of 8 proteins with chain lengths ranging from 37 to 75 aa were simulated in silico using the UNRES (U) package with an implicit solvent model and a built-in module expressing the FOD model (UNRES-FOD-UNRES (U + F) interleaved simulation). The protein structure obtained by both *** simulation schemes, i.e., accordingly***U and U + F, for all the analyzed protein models shows the presence of a hydrophobic core including where it is absent in the native structure. The proposed FOD-M model (M-modified) explaining the source of this phenomenon reveals the need to modify the external field expressing the role of a folding environment. The modification takes into account the influence of other than polar factors present in the folding environment.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College Medyczna 7, 30-688, Kraków, Poland.
| | - Adam Sieradzan
- Faculty of Chemistry, Gdansk University, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Katarzyna Stapor
- Faculty of Automatic, Electronics and Computer Science, Department of Applied Informatics, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
| | - Piotr Fabian
- Faculty of Automatic, Electronics and Computer Science, Department of Algorithmics and Software, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
| | - Patryk Wesołowski
- Faculty of Chemistry, Gdansk University, Wita Stwosza 63, 80-308, Gdańsk, Poland; Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307, Gdańsk, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry - Jagiellonian University - Medical College, Kopernika 7, 31-034, Kraków, Poland.
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8
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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9
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Salem A, Wilson CJ, Rutledge BS, Dilliott A, Farhan S, Choy WY, Duennwald ML. Matrin3: Disorder and ALS Pathogenesis. Front Mol Biosci 2022; 8:794646. [PMID: 35083279 PMCID: PMC8784776 DOI: 10.3389/fmolb.2021.794646] [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: 10/13/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the degeneration of both upper and lower motor neurons in the brain and spinal cord. ALS is associated with protein misfolding and inclusion formation involving RNA-binding proteins, including TAR DNA-binding protein (TDP-43) and fused in sarcoma (FUS). The 125-kDa Matrin3 is a highly conserved nuclear DNA/RNA-binding protein that is implicated in many cellular processes, including binding and stabilizing mRNA, regulating mRNA nuclear export, modulating alternative splicing, and managing chromosomal distribution. Mutations in MATR3, the gene encoding Matrin3, have been identified as causal in familial ALS (fALS). Matrin3 lacks a prion-like domain that characterizes many other ALS-associated RNA-binding proteins, including TDP-43 and FUS, however, our bioinformatics analyses and preliminary studies document that Matrin3 contains long intrinsically disordered regions that may facilitate promiscuous interactions with many proteins and may contribute to its misfolding. In addition, these disordered regions in Matrin3 undergo numerous post-translational modifications, including phosphorylation, ubiquitination and acetylation that modulate the function and misfolding of the protein. Here we discuss the disordered nature of Matrin3 and review the factors that may promote its misfolding and aggregation, two elements that might explain its role in ALS pathogenesis.
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Affiliation(s)
- Ahmed Salem
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Carter J. Wilson
- Department of Applied Mathematics, Western University, London, ON, Canada
| | - Benjamin S. Rutledge
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Allison Dilliott
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
| | - Sali Farhan
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
- Department of Human Genetics, McGill Universty, Montreal, QC, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Martin L. Duennwald
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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10
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Guzzo A, Delarue P, Rojas A, Nicolaï A, Maisuradze GG, Senet P. Missense Mutations Modify the Conformational Ensemble of the α-Synuclein Monomer Which Exhibits a Two-Phase Characteristic. Front Mol Biosci 2021; 8:786123. [PMID: 34912851 PMCID: PMC8667727 DOI: 10.3389/fmolb.2021.786123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
α-Synuclein is an intrinsically disordered protein occurring in different conformations and prone to aggregate in β-sheet structures, which are the hallmark of the Parkinson disease. Missense mutations are associated with familial forms of this neuropathy. How these single amino-acid substitutions modify the conformations of wild-type α-synuclein is unclear. Here, using coarse-grained molecular dynamics simulations, we sampled the conformational space of the wild type and mutants (A30P, A53P, and E46K) of α-synuclein monomers for an effective time scale of 29.7 ms. To characterize the structures, we developed an algorithm, CUTABI (CUrvature and Torsion based of Alpha-helix and Beta-sheet Identification), to identify residues in the α-helix and β-sheet from Cα-coordinates. CUTABI was built from the results of the analysis of 14,652 selected protein structures using the Dictionary of Secondary Structure of Proteins (DSSP) algorithm. DSSP results are reproduced with 93% of success for 10 times lower computational cost. A two-dimensional probability density map of α-synuclein as a function of the number of residues in the α-helix and β-sheet is computed for wild-type and mutated proteins from molecular dynamics trajectories. The density of conformational states reveals a two-phase characteristic with a homogeneous phase (state B, β-sheets) and a heterogeneous phase (state HB, mixture of α-helices and β-sheets). The B state represents 40% of the conformations for the wild-type, A30P, and E46K and only 25% for A53T. The density of conformational states of the B state for A53T and A30P mutants differs from the wild-type one. In addition, the mutant A53T has a larger propensity to form helices than the others. These findings indicate that the equilibrium between the different conformations of the α-synuclein monomer is modified by the missense mutations in a subtle way. The α-helix and β-sheet contents are promising order parameters for intrinsically disordered proteins, whereas other structural properties such as average gyration radius, Rg, or probability distribution of Rg cannot discriminate significantly the conformational ensembles of the wild type and mutants. When separated in states B and HB, the distributions of Rg are more significantly different, indicating that global structural parameters alone are insufficient to characterize the conformational ensembles of the α-synuclein monomer.
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Affiliation(s)
- Adrien Guzzo
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, Dijon, France
| | - Patrice Delarue
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, Dijon, France
| | - Ana Rojas
- Schrödinger, Inc., New York, NY, United States
| | - Adrien Nicolaï
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, Dijon, France
| | - Gia G Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Patrick Senet
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, Dijon, France.,Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
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11
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Rieloff E, Skepö M. Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison. Int J Mol Sci 2021; 22:10174. [PMID: 34576338 PMCID: PMC8470740 DOI: 10.3390/ijms221810174] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/21/2022] Open
Abstract
Phosphorylation is a common post-translational modification among intrinsically disordered proteins and regions, which helps regulate function by changing the protein conformations, dynamics, and interactions with binding partners. To fully comprehend the effects of phosphorylation, computer simulations are a helpful tool, although they are dependent on the accuracy of the force field used. Here, we compared the conformational ensembles produced by Amber ff99SB-ILDN+TIP4P-D and CHARMM36m, for four phosphorylated disordered peptides ranging in length from 14-43 residues. CHARMM36m consistently produced more compact conformations with a higher content of bends, mainly due to more stable salt bridges. Based on comparisons with experimental size estimates for the shortest and longest peptide, CHARMM36m appeared to overestimate the compactness. The difference between the force fields was largest for the peptide showing the greatest separation between positively charged and phosphorylated residues, in line with the importance of charge distribution. For this peptide, the conformational ensemble did not change significantly upon increasing the ionic strength from 0 mM to 150 mM, despite a reduction of the salt-bridging probability in the CHARMM36m simulations, implying that salt concentration has negligible effects in this study.
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Affiliation(s)
- Ellen Rieloff
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden;
| | - Marie Skepö
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden;
- LINXS—Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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