1
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Pandey AK, Ganguly HK, Sinha SK, Daniels KE, Yap GPA, Patel S, Zondlo NJ. An Inherent Difference between Serine and Threonine Phosphorylation: Phosphothreonine Strongly Prefers a Highly Ordered, Compact, Cyclic Conformation. ACS Chem Biol 2023; 18:1938-1958. [PMID: 37595155 DOI: 10.1021/acschembio.3c00068] [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: 08/20/2023]
Abstract
Phosphorylation and dephosphorylation of proteins by kinases and phosphatases are central to cellular responses and function. The structural effects of serine and threonine phosphorylation were examined in peptides and in proteins, by circular dichroism, NMR spectroscopy, bioinformatics analysis of the PDB, small-molecule X-ray crystallography, and computational investigations. Phosphorylation of both serine and threonine residues induces substantial conformational restriction in their physiologically more important dianionic forms. Threonine exhibits a particularly strong disorder-to-order transition upon phosphorylation, with dianionic phosphothreonine preferentially adopting a cyclic conformation with restricted ϕ (ϕ ∼ -60°) stabilized by three noncovalent interactions: a strong intraresidue phosphate-amide hydrogen bond, an n → π* interaction between consecutive carbonyls, and an n → σ* interaction between the phosphate Oγ lone pair and the antibonding orbital of C-Hβ that restricts the χ2 side-chain conformation. Proline is unique among the canonical amino acids for its covalent cyclization on the backbone. Phosphothreonine can mimic proline's backbone cyclization via noncovalent interactions. The preferred torsions of dianionic phosphothreonine are ϕ,ψ = polyproline II helix > α-helix (ϕ ∼ -60°); χ1 = g-; χ2 ∼ +115° (eclipsed C-H/O-P bonds). This structural signature is observed in diverse proteins, including in the activation loops of protein kinases and in protein-protein interactions. In total, these results suggest a structural basis for the differential use and evolution of threonine versus serine phosphorylation sites in proteins, with serine phosphorylation typically inducing smaller, rheostat-like changes, versus threonine phosphorylation promoting larger, step function-like switches, in proteins.
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Affiliation(s)
- Anil K Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Himal K Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Sudipta Kumar Sinha
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Chemistry, Indian Institute of Technology Ropar, Nangal Road, Rupnagar 140001, India
| | - Kelly E Daniels
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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2
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Vesely CH, Reardon PN, Yu Z, Barbar E, Mehl RA, Cooley RB. Accessing isotopically labeled proteins containing genetically encoded phosphoserine for NMR with optimized expression conditions. J Biol Chem 2022; 298:102613. [PMID: 36265582 PMCID: PMC9678770 DOI: 10.1016/j.jbc.2022.102613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Phosphoserine (pSer) sites are primarily located within disordered protein regions, making it difficult to experimentally ascertain their effects on protein structure and function. Therefore, the production of 15N- (and 13C)-labeled proteins with site-specifically encoded pSer for NMR studies is essential to uncover molecular mechanisms of protein regulation by phosphorylation. While genetic code expansion technologies for the translational installation of pSer in Escherichia coli are well established and offer a powerful strategy to produce site-specifically phosphorylated proteins, methodologies to adapt them to minimal or isotope-enriched media have not been described. This shortcoming exists because pSer genetic code expansion expression hosts require the genomic ΔserB mutation, which increases pSer bioavailability but also imposes serine auxotrophy, preventing growth in minimal media used for isotopic labeling of recombinant proteins. Here, by testing different media supplements, we restored normal BL21(DE3) ΔserB growth in labeling media but subsequently observed an increase of phosphatase activity and mis-incorporation not typically seen in standard rich media. After rounds of optimization and adaption of a high-density culture protocol, we were able to obtain ≥10 mg/L homogenously labeled, phosphorylated superfolder GFP. To demonstrate the utility of this method, we also produced the intrinsically disordered serine/arginine-rich region of the SARS-CoV-2 Nucleocapsid protein labeled with 15N and pSer at the key site S188 and observed the resulting peak shift due to phosphorylation by 2D and 3D heteronuclear single quantum correlation analyses. We propose this cost-effective methodology will pave the way for more routine access to pSer-enriched proteins for 2D and 3D NMR analyses.
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Affiliation(s)
- Cat Hoang Vesely
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Patrick N. Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, Oregon, USA
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Ryan A. Mehl
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Richard B. Cooley
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA,For correspondence: Richard B. Cooley
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3
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Luo YY, Wu JJ, Li YM. Regulation of liquid-liquid phase separation with focus on post-translational modifications. Chem Commun (Camb) 2021; 57:13275-13287. [PMID: 34816836 DOI: 10.1039/d1cc05266g] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid-liquid phase separation (LLPS), a type of phase transition that is important in organisms, is a unique means of forming biomolecular condensates. LLPS plays a significant role in transcription, genome organisation, immune response and cell signaling, and its dysregulation may cause neurodegenerative diseases and cancers. Exploring the regulatory mechanism of LLPS contributes to the understanding of the pathogenic mechanism of abnormal phase transition and enables potential therapeutic targets to be proposed. Many factors have been found to regulate LLPS, of which post-translational modification (PTM) is among the most important. PTMs can change the structure, charge, hydrophobicity and other properties of the proteins involved in phase separation and thereby affect the phase transition behaviour. In this review, we discuss LLPS and the regulatory effects of PTMs, RNA and molecular chaperones in a phase separation system. We introduce several common PTMs (including phosphorylation, arginine methylation, arginine citrullination, acetylation, ubiquitination and poly(ADP-ribosyl)ation), highlight recent advances regarding their roles in LLPS and describe the regulatory mechanisms behind these features. This review provides a detailed overview of the field that will help further the understanding of and interventions in LLPS.
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Affiliation(s)
- Yun-Yi Luo
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
| | - Jun-Jun Wu
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China. .,Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, P. R. China
| | - Yan-Mei Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China. .,Beijing Institute for Brain Disorders, Beijing 100069, P. R. China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, P. R. China
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4
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Hu W, Bagramyan K, Bhatticharya S, Hong T, Tapia A, Wong P, Kalkum M, Shively JE. Phosphorylation of human CEACAM1-LF by PKA and GSK3β promotes its interaction with β-catenin. J Biol Chem 2021; 297:101305. [PMID: 34656562 PMCID: PMC8564729 DOI: 10.1016/j.jbc.2021.101305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 12/26/2022] Open
Abstract
CEACAM1-LF, a homotypic cell adhesion adhesion molecule, transduces intracellular signals via a 72 amino acid cytoplasmic domain that contains two immunoreceptor tyrosine-based inhibitory motifs (ITIMs) and a binding site for β-catenin. Phosphorylation of Ser503 by PKC in rodent CEACAM1 was shown to affect bile acid transport or hepatosteatosis via the level of ITIM phosphorylation, but the phosphorylation of the equivalent residue in human CEACAM1 (Ser508) was unclear. Here we studied this analogous phosphorylation by NMR analysis of the 15N labeled cytoplasmic domain peptide. Incubation with a variety of Ser/Thr kinases revealed phosphorylation of Ser508 by GSK3bβ but not by PKC. The lack of phosphorylation by PKC is likely due to evolutionary sequence changes between the rodent and human genes. Phosphorylation site assignment by mass spectrometry and NMR revealed phosphorylation of Ser472, Ser461 and Ser512 by PKA, of which Ser512 is part of a conserved consensus site for GSK3β binding. We showed here that only after phosphorylation of Ser512 by PKA was GSK3β able to phosphorylate Ser508. Phosphorylation of Ser512 by PKA promoted a tight association with the armadillo repeat domain of β-catenin at an extended region spanning the ITIMs of CEACAM1. The kinetics of phosphorylation of the ITIMs by Src, as well dephosphorylation by SHP2, were affected by the presence of Ser508/512 phosphorylation, suggesting that PKA and GSK3β may regulate the signal transduction activity of human CEACAM1-LF. The interaction of CEACAM1-LF with β-catenin promoted by PKA is suggestive of a tight association between the two ITIMs of CEACAM1-LF.
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Affiliation(s)
- Weidong Hu
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Karine Bagramyan
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Supriyo Bhatticharya
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Teresa Hong
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Alonso Tapia
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Patty Wong
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - John E Shively
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, California, USA.
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5
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He PY, Chen H, Hu HG, Hu JJ, Lim YJ, Li YM. Late-stage peptide and protein modifications through phospha-Michael addition reaction. Chem Commun (Camb) 2020; 56:12632-12635. [PMID: 32960198 DOI: 10.1039/d0cc04969g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We developed a late-stage modification strategy by a phospha-Michael addition reaction between various functional phosphines and unprotected dehydroalanine (Dha) peptides and proteins under mild conditions. This strategy was applied to generate a staple peptide to enhance its cell membrane penetrability, and it was also able to regulate α-synuclein aggregation properties and morphological characteristics with the addition of different charges.
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Affiliation(s)
- Pei-Yang He
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
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6
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Li H, Chao J, Hasan J, Tian G, Jin Y, Zhang Z, Qin C. Synthesis of Tri(4-formylphenyl) Phosphonate Derivatives as Recyclable Triple-Equivalent Supports of Peptide Synthesis. J Org Chem 2020; 85:6271-6280. [PMID: 32320241 DOI: 10.1021/acs.joc.9b03023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To seek the novel application of organophosphorus compounds, the designed tri(4-formylphenyl) phosphonate (TFP) derivatives were successfully synthesized herein, which were used as C-terminal protecting groups of amino acid or greener triple-equivalent supports in liquid-phase peptide synthesis (LPPS). Through the support-aided precipitation effect of TFP derivatives, the peptide intermediates during peptide synthesis were separated and collected via rapid precipitation and facile filtration without chromatographic purification. Furthermore, the TFP derivative support can be directly recycled for reuse without further regeneration after being sheared from the target peptide.
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Affiliation(s)
- Haidi Li
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710129, P. R. China
| | - Jie Chao
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710129, P. R. China
| | - Jaafar Hasan
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710129, P. R. China
| | - Guang Tian
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710129, P. R. China
| | - Yatao Jin
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710129, P. R. China
| | - Zixin Zhang
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710129, P. R. China
| | - Chuanguang Qin
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710129, P. R. China
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7
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Li H, Chao J, Tian G, Hasan J, Jin Y, Zhang Z, Qin C. Resin-free peptide synthesis mediated by tri(4-benzoylphenyl) phosphate (TBP) derivatives as small-molecule supports. Org Chem Front 2020. [DOI: 10.1039/c9qo01480b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A series of novel tri(4-benzoylphenyl) phosphate (TBP) derivatives with unique precipitation-inducing properties were synthesized and used as C-terminal protecting groups of amino acids and recyclable supports in peptide synthesis.
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Affiliation(s)
- Haidi Li
- Shaanxi Key Laboratory of Polymer Science & Technology
- OME Key Laboratory of Supernormal Material Physics & Chemistry
- School of Chemistry and Chemical Engineering
- Northwestern Polytechnical University
- Xi'an
| | - Jie Chao
- Shaanxi Key Laboratory of Polymer Science & Technology
- OME Key Laboratory of Supernormal Material Physics & Chemistry
- School of Chemistry and Chemical Engineering
- Northwestern Polytechnical University
- Xi'an
| | - Guang Tian
- Shaanxi Key Laboratory of Polymer Science & Technology
- OME Key Laboratory of Supernormal Material Physics & Chemistry
- School of Chemistry and Chemical Engineering
- Northwestern Polytechnical University
- Xi'an
| | - Jaafar Hasan
- Shaanxi Key Laboratory of Polymer Science & Technology
- OME Key Laboratory of Supernormal Material Physics & Chemistry
- School of Chemistry and Chemical Engineering
- Northwestern Polytechnical University
- Xi'an
| | - Yatao Jin
- Shaanxi Key Laboratory of Polymer Science & Technology
- OME Key Laboratory of Supernormal Material Physics & Chemistry
- School of Chemistry and Chemical Engineering
- Northwestern Polytechnical University
- Xi'an
| | - Zixin Zhang
- Shaanxi Key Laboratory of Polymer Science & Technology
- OME Key Laboratory of Supernormal Material Physics & Chemistry
- School of Chemistry and Chemical Engineering
- Northwestern Polytechnical University
- Xi'an
| | - Chuanguang Qin
- Shaanxi Key Laboratory of Polymer Science & Technology
- OME Key Laboratory of Supernormal Material Physics & Chemistry
- School of Chemistry and Chemical Engineering
- Northwestern Polytechnical University
- Xi'an
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8
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Hendus-Altenburger R, Fernandes CB, Bugge K, Kunze MBA, Boomsma W, Kragelund BB. Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range. JOURNAL OF BIOMOLECULAR NMR 2019; 73:713-725. [PMID: 31598803 PMCID: PMC6875518 DOI: 10.1007/s10858-019-00283-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/30/2019] [Indexed: 05/26/2023]
Abstract
Phosphorylation is one of the main regulators of cellular signaling typically occurring in flexible parts of folded proteins and in intrinsically disordered regions. It can have distinct effects on the chemical environment as well as on the structural properties near the modification site. Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins (IDPs) and the reliability of the analysis depends on an appropriate choice of random coil model. Random coil chemical shifts and sequence correction factors were previously determined for an Ac-QQXQQ-NH2-peptide series with X being any of the 20 common amino acids. However, a matching dataset on the phosphorylated states has so far only been incompletely determined or determined only at a single pH value. Here we extend the database by the addition of the random coil chemical shifts of the phosphorylated states of serine, threonine and tyrosine measured over a range of pH values covering the pKas of the phosphates and at several temperatures (www.bio.ku.dk/sbinlab/randomcoil). The combined results allow for accurate random coil chemical shift determination of phosphorylated regions at any pH and temperature, minimizing systematic biases of the secondary chemical shifts. Comparison of chemical shifts using random coil sets with and without inclusion of the phosphoryl group, revealed under/over estimations of helicity of up to 33%. The expanded set of random coil values will improve the reliability in detection and quantification of transient secondary structure in phosphorylation-modified IDPs.
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Affiliation(s)
- Ruth Hendus-Altenburger
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Catarina B Fernandes
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Micha B A Kunze
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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Kumar A, Narayanan V, Sekhar A. Characterizing Post-Translational Modifications and Their Effects on Protein Conformation Using NMR Spectroscopy. Biochemistry 2019; 59:57-73. [PMID: 31682116 DOI: 10.1021/acs.biochem.9b00827] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diversity of the cellular proteome substantially exceeds the number of genes coded by the DNA of an organism because one or more residues in a majority of eukaryotic proteins are post-translationally modified (PTM) by the covalent conjugation of specific chemical groups. We now know that PTMs alter protein conformation and function in ways that are not entirely understood at the molecular level. NMR spectroscopy has been particularly successful as an analytical tool in elucidating the themes underlying the structural role of PTMs. In this Perspective, we focus on the NMR-based characterization of three abundant PTMs: phosphorylation, acetylation, and glycosylation. We detail NMR methods that have found success in detecting these modifications at a site-specific level. We also highlight NMR studies that have mapped the conformational changes ensuing from these PTMs as well as evaluated their relation to function. The NMR toolbox is expanding rapidly with experiments available to probe not only the average structure of biomolecules but also how this structure changes with time on time scales ranging from picoseconds to seconds. The atomic resolution insights into the biomolecular structure, dynamics, and mechanism accessible from NMR spectroscopy ensure that NMR will continue to be at the forefront of research in the structural biology of PTMs.
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Affiliation(s)
- Ajith Kumar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
| | - Vaishali Narayanan
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
| | - Ashok Sekhar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
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10
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Conibear AC, Rosengren KJ, Becker CFW, Kaehlig H. Random coil shifts of posttranslationally modified amino acids. JOURNAL OF BIOMOLECULAR NMR 2019; 73:587-599. [PMID: 31317299 PMCID: PMC6859290 DOI: 10.1007/s10858-019-00270-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/09/2019] [Indexed: 05/14/2023]
Abstract
Most eukaryotic proteins are modified during and/or after translation, regulating their structure, function and localisation. The role of posttranslational modifications (PTMs) in both normal cellular processes and in diseases is already well recognised and methods for detection of PTMs and generation of specifically modified proteins have developed rapidly over the last decade. However, structural consequences of PTMs and their specific effects on protein dynamics and function are not well understood. Furthermore, while random coil NMR chemical shifts of the 20 standard amino acids are available and widely used for residue assignment, dihedral angle predictions and identification of structural elements or propensity, they are not available for most posttranslationally modified amino acids. Here, we synthesised a set of random coil peptides containing common naturally occurring PTMs and determined their random coil NMR chemical shifts under standardised conditions. We highlight unique NMR signatures of posttranslationally modified residues and their effects on neighbouring residues. This comprehensive dataset complements established random coil shift datasets of the 20 standard amino acids and will facilitate identification and assignment of posttranslationally modified residues. The random coil shifts will also aid in determination of secondary structure elements and prediction of structural parameters of proteins and peptides containing PTMs.
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Affiliation(s)
- Anne C Conibear
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria.
- School of Biomedical Sciences, The University of Queensland, QLD, 4072, Brisbane, Australia.
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, QLD, 4072, Brisbane, Australia
| | - Christian F W Becker
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria
| | - Hanspeter Kaehlig
- Faculty of Chemistry, Institute of Organic Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria
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11
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Bailey LS, Alves M, Galy N, Patrick AL, Polfer NC. Mechanistic insights into intramolecular phosphate group transfer during collision induced dissociation of phosphopeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:449-458. [PMID: 30860300 DOI: 10.1002/jms.4351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/22/2019] [Accepted: 03/04/2019] [Indexed: 05/28/2023]
Abstract
We report on the rearrangement chemistry of model phosphorylated peptides during collision-induced dissociation (CID), where intramolecular phosphate group transfers are observed from donor to acceptor residues. Such "scrambling" could result in inaccurate modification localization, potentially leading to misidentifications. Systematic studies presented herein provide mechanistic insights for the unusually high phosphate group rearrangements presented some time ago by Reid and coworkers (Proteomics 2013, 13 [6], 964-973). It is postulated here that a basic residue like histidine can play a key role in mediating the phosphate group transfer by deprotonating the serine acceptor site. The proposed mechanism is consistent with the observation that fast collisional activation by collision-cell CID and higher-energy collisional dissociation (HCD) can shut down rearrangement chemistry. Additionally, the rearrangement chemistry is highly dependent on the charge state of the peptide, mirroring previous studies that less rearrangement is observed under mobile proton conditions.
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Affiliation(s)
- Laura S Bailey
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Mélanie Alves
- Département de chimie, UFR 926, Sorbonne Université, Paris, France
| | - Nicolas Galy
- Département de chimie, Université Paul Sabatier, Toulouse, France
| | - Amanda L Patrick
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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12
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Highly disordered histone H1-DNA model complexes and their condensates. Proc Natl Acad Sci U S A 2018; 115:11964-11969. [PMID: 30301810 DOI: 10.1073/pnas.1805943115] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Disordered proteins play an essential role in a wide variety of biological processes, and are often posttranslationally modified. One such protein is histone H1; its highly disordered C-terminal tail (CH1) condenses internucleosomal linker DNA in chromatin in a way that is still poorly understood. Moreover, CH1 is phosphorylated in a cell cycle-dependent manner that correlates with changes in the chromatin condensation level. Here we present a model system that recapitulates key aspects of the in vivo process, and also allows a detailed structural and biophysical analysis of the stages before and after condensation. CH1 remains disordered in the DNA-bound state, despite its nanomolar affinity. Phase-separated droplets (coacervates) form, containing higher-order assemblies of CH1/DNA complexes. Phosphorylation at three serine residues, spaced along the length of the tail, has little effect on the local properties of the condensate. However, it dramatically alters higher-order structure in the coacervate and reduces partitioning to the coacervate phase. These observations show that disordered proteins can bind tightly to DNA without a disorder-to-order transition. Importantly, they also provide mechanistic insights into how higher-order structures can be exquisitely sensitive to perturbation by posttranslational modifications, thus broadening the repertoire of mechanisms that might regulate chromatin and other macromolecular assemblies.
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13
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Li QQ, Chen PG, Hu ZW, Cao Y, Chen LX, Chen YX, Zhao YF, Li YM. Selective inhibition of cancer cells by enzyme-induced gain of function of phosphorylated melittin analogues. Chem Sci 2017; 8:7675-7681. [PMID: 29568430 PMCID: PMC5849211 DOI: 10.1039/c7sc03217j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/12/2017] [Indexed: 01/16/2023] Open
Abstract
The selective killing of cancer cells and the avoidance of drug resistance are still difficult challenges in cancer therapy. Here, we report a new strategy that uses enzyme-induced gain of function (EIGF) to regulate the structure and function of phosphorylated melittin analogues (MelAs). Original MelAs have the capacity to disrupt plasma membranes and induce cell death without selectivity. However, phosphorylation of Thr23 on one of the MelAs (MelA2-P) efficiently ameliorated the membrane lysis potency as well as the cytotoxicity for normal mammalian cells. After treatment with alkaline phosphatase (ALP), which is more active in cancer cells than normal cells, MelA2-P restored the pore-forming function around the cancer cells and induced cancer cell death selectively. This mechanism was independent of the receptor proteins and the cell uptake process, which may partially bypass the development of drug resistance in cancer cells.
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Affiliation(s)
- Qian-Qian Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China . ; ; Tel: +86-10-62796197
| | - Pu-Guang Chen
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China . ; ; Tel: +86-10-62796197
| | - Zhi-Wen Hu
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China . ; ; Tel: +86-10-62796197
| | - Yuan Cao
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China . ; ; Tel: +86-10-62796197
| | - Liang-Xiao Chen
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China . ; ; Tel: +86-10-62796197
| | - Yong-Xiang Chen
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China . ; ; Tel: +86-10-62796197
| | - Yu-Fen Zhao
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China . ; ; Tel: +86-10-62796197
| | - Yan-Mei Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China . ; ; Tel: +86-10-62796197
- Beijing Institute for Brain Disorders , Beijing 100069 , P. R. China
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14
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Hendus-Altenburger R, Lambrughi M, Terkelsen T, Pedersen SF, Papaleo E, Lindorff-Larsen K, Kragelund BB. A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1). Cell Signal 2017; 37:40-51. [PMID: 28554535 DOI: 10.1016/j.cellsig.2017.05.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 11/26/2022]
Abstract
Intrinsically disordered proteins (IDPs) are involved in many pivotal cellular processes including phosphorylation and signalling. The structural and functional effects of phosphorylation of IDPs remain poorly understood and difficult to predict. Thus, a need exists to identify motifs that confer phosphorylation-dependent perturbation of the local preferences for forming e.g. helical structures as well as motifs that do not. The disordered distal tail of the Na+/H+ exchanger 1 (NHE1) is six-times phosphorylated (S693, S723, S726, S771, T779, S785) by the mitogen activated protein kinase 2 (MAPK1, ERK2). Using NMR spectroscopy, we found that two out of those six phosphorylation sites had a stabilizing effect on transient helices. One of these was further investigated by circular dichroism and NMR spectroscopy as well as by molecular dynamic simulations, which confirmed the stabilizing effect and resulted in the identification of a short linear motif for helix stabilisation: [S/T]-P-{3}-[R/K] where [S/T] is the phosphorylation-site. By analysing IDP and phosphorylation site databases we found that the motif is significantly enriched around known phosphorylation sites, supporting a potential wider-spread role in phosphorylation-mediated regulation of intrinsically disordered proteins. The identification of such motifs is important for understanding the molecular mechanism of cellular signalling, and is crucial for the development of predictors for the structural effect of phosphorylation; a tool of relevance for understanding disease-promoting mutations that for example interfere with signalling for instance through constitutive active and often cancer-promoting signalling.
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Affiliation(s)
- Ruth Hendus-Altenburger
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Matteo Lambrughi
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Strandboulevarden 49, 2100 Copenhagen, Denmark.
| | - Thilde Terkelsen
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Strandboulevarden 49, 2100 Copenhagen, Denmark.
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark.
| | - Elena Papaleo
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Strandboulevarden 49, 2100 Copenhagen, Denmark.
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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15
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Hu ZW, Ma MR, Chen YX, Zhao YF, Qiang W, Li YM. Phosphorylation at Ser 8 as an Intrinsic Regulatory Switch to Regulate the Morphologies and Structures of Alzheimer's 40-residue β-Amyloid (Aβ40) Fibrils. J Biol Chem 2017; 292:2611-2623. [PMID: 28031462 PMCID: PMC5314160 DOI: 10.1074/jbc.m116.757179] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 12/05/2016] [Indexed: 01/23/2023] Open
Abstract
Polymorphism of amyloid-β (Aβ) fibrils, implying different fibril structures, may play important pathological roles in Alzheimer's disease (AD). Morphologies of Aβ fibrils were found to be sensitive to fibrillation conditions. Herein, the Ser8-phosphorylated Aβ (pAβ), which is assumed to specially associate with symptomatic AD, is reported to modify the morphology, biophysical properties, cellular toxicity, and structures of Aβ fibrils. Under the same fibrillation conditions, pAβ favors the formation of fibrils (Fpβ), which are different from the wild-type Aβ fibrils (Fβ). Both Fβ and Fpβ fibrils show single predominant morphologies. Compared with Fβ, Fpβ exhibits higher propagation efficiency and higher neuronal cell toxicity. The residue-specific structural differences between the Fβ- and Fpβ-seeded Aβ fibrils were identified using magic angle spin NMR. Our results suggest a potential regulatory mechanism of phosphorylation on Aβ fibril formation in AD and imply that the post-translationally modified Aβ, especially the phosphorylated Aβ, may be an important target for the diagnosis or treatment of AD at specific stages.
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Affiliation(s)
- Zhi-Wen Hu
- From the Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Meng-Rong Ma
- From the Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yong-Xiang Chen
- From the Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yu-Fen Zhao
- From the Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, and
| | - Yan-Mei Li
- From the Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China,
- Beijing Institute for Brain Disorders, Beijing 100069, China
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16
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Messner CB, Bonn GK, Hofer TS. QM/MM MD simulations of La(iii)–phosphopeptide complexes. MOLECULAR BIOSYSTEMS 2015; 11:232-8. [DOI: 10.1039/c4mb00424h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hybrid quantum mechanical/molecular mechanical simulations have been used to study the structural and dynamical properties of a La(iii)–phosphopeptide complex.
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Affiliation(s)
- Christoph B. Messner
- Institute of Analytical Chemistry and Radiochemistry
- Leopold-Franzens University
- 6020 Innsbruck
- Austria
| | - Günther K. Bonn
- Institute of Analytical Chemistry and Radiochemistry
- Leopold-Franzens University
- 6020 Innsbruck
- Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Leopold-Franzens University
- 6020 Innsbruck
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17
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Lopez J, Ahuja P, Landrieu I, Cantrelle FX, Huvent I, Lippens G. H/D exchange of a 15N labelled Tau fragment as measured by a simple Relax-EXSY experiment. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 249:32-37. [PMID: 25462944 DOI: 10.1016/j.jmr.2014.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 10/03/2014] [Accepted: 10/06/2014] [Indexed: 06/04/2023]
Abstract
We present an equilibrium H/D exchange experiment to measure the exchange rates of labile amide protons in intrinsically unfolded proteins. By measuring the contribution of the H/D exchange to the apparent T1 relaxation rates in solvents of different D2O content, we can easily derive the rates of exchange for rapidly exchanging amide protons. The method does not require double isotope labelling, is sensitive, and requires limited fitting of the data. We demonstrate it on a functional fragment of Tau, and provide evidence for the hydrogen bond formation of the phosphate moiety of Ser214 with its own amide proton in the same fragment phosphorylated by the PKA kinase.
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Affiliation(s)
- Juan Lopez
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille 1, 59655 Villeneuve d'Ascq Cedex, France
| | - Puneet Ahuja
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille 1, 59655 Villeneuve d'Ascq Cedex, France
| | - Isabelle Landrieu
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille 1, 59655 Villeneuve d'Ascq Cedex, France; CNRS USR 3078, Institut de Recherche Interdisciplinaire, Centre National de la Recherche Scientifique, 59655 Villeneuve d'Ascq, France
| | - François-Xavier Cantrelle
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille 1, 59655 Villeneuve d'Ascq Cedex, France
| | - Isabelle Huvent
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille 1, 59655 Villeneuve d'Ascq Cedex, France
| | - Guy Lippens
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille 1, 59655 Villeneuve d'Ascq Cedex, France.
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18
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Elbaum MB, Zondlo NJ. OGlcNAcylation and phosphorylation have similar structural effects in α-helices: post-translational modifications as inducible start and stop signals in α-helices, with greater structural effects on threonine modification. Biochemistry 2014; 53:2242-60. [PMID: 24641765 PMCID: PMC4004263 DOI: 10.1021/bi500117c] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
OGlcNAcylation
and phosphorylation are the major competing intracellular
post-translational modifications of serine and threonine residues.
The structural effects of both post-translational modifications on
serine and threonine were examined within Baldwin model α-helical
peptides (Ac-AKAAAAKAAAAKAAGY-NH2 or Ac-YGAKAAAAKAAAAKAA-NH2). At the N-terminus of an α-helix, both phosphorylation
and OGlcNAcylation stabilized the α-helix relative to the free
hydroxyls, with a larger induced structure for phosphorylation than
for OGlcNAcylation, for the dianionic phosphate than for the monoanionic
phosphate, and for modifications on threonine than for modifications
on serine. Both phosphoserine and phosphothreonine resulted in peptides
more α-helical than alanine at the N-terminus, with dianionic
phosphothreonine the most α-helix-stabilizing residue here.
In contrast, in the interior of the α-helix, both post-translational
modifications were destabilizing with respect to the α-helix,
with the greatest destabilization seen for threonine OGlcNAcylation
at residue 5 and threonine phosphorylation at residue 10, with peptides
containing either post-translational modification existing as random
coils. At the C-terminus, both OGlcNAcylation and phosphorylation
were destabilizing with respect to the α-helix, though the induced
structural changes were less than in the interior of the α-helix.
In general, the structural effects of modifications on threonine were
greater than the effects on serine, because of both the lower α-helical
propensity of Thr and the more defined induced structures upon modification
of threonine than serine, suggesting threonine residues are particularly
important loci for structural effects of post-translational modifications.
The effects of serine and threonine post-translational modifications
are analogous to the effects of proline on α-helices, with the
effects of phosphothreonine being greater than those of proline throughout
the α-helix. These results provide a basis for understanding
the context-dependent structural effects of these competing protein
post-translational modifications.
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Affiliation(s)
- Michael B Elbaum
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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19
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Brister M, Pandey AK, Bielska AA, Zondlo NJ. OGlcNAcylation and phosphorylation have opposing structural effects in tau: phosphothreonine induces particular conformational order. J Am Chem Soc 2014; 136:3803-16. [PMID: 24559475 PMCID: PMC4004249 DOI: 10.1021/ja407156m] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Indexed: 01/12/2023]
Abstract
Phosphorylation and OGlcNAcylation are dynamic intracellular protein post-translational modifications that frequently are alternatively observed on the same serine and threonine residues. Phosphorylation and OGlcNAcylation commonly occur in natively disordered regions of proteins, and often have opposing functional effects. In the microtubule-associated protein tau, hyperphosphorylation is associated with protein misfolding and aggregation as the neurofibrillary tangles of Alzheimer's disease, whereas OGlcNAcylation stabilizes the soluble form of tau. A series of peptides derived from the proline-rich domain (residues 174-251) of tau was synthesized, with free Ser/Thr hydroxyls, phosphorylated Ser/Thr (pSer/pThr), OGlcNAcylated Ser/Thr, and diethylphosphorylated Ser/Thr. Phosphorylation and OGlcNAcylation were found by CD and NMR to have opposing structural effects on polyproline helix (PPII) formation, with phosphorylation favoring PPII, OGlcNAcylation opposing PPII, and the free hydroxyls intermediate in structure, and with phosphorylation structural effects greater than OGlcNAcylation. For tau196-209, phosphorylation and OGlcNAcylation had similar structural effects, opposing a nascent α-helix. Phosphomimic Glu exhibited PPII-favoring structural effects. Structural changes due to Thr phosphorylation were greater than those of Ser phosphorylation or Glu, with particular conformational restriction as the dianion, with mean (3)JαN = 3.5 Hz (pThr) versus 5.4 Hz (pSer), compared to 7.2, 6.8, and 6.2 Hz for Thr, Ser, and Glu, respectively, values that correlate with the backbone torsion angle ϕ. Dianionic phosphothreonine induced strong phosphothreonine amide protection and downfield amide chemical shifts (δmean = 9.63 ppm), consistent with formation of a stable phosphate-amide hydrogen bond. These data suggest potentially greater structural importance of threonine phosphorylation than serine phosphorylation due to larger induced structural effects.
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Affiliation(s)
| | | | - Agata A. Bielska
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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20
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Amata I, Maffei M, Igea A, Gay M, Vilaseca M, Nebreda AR, Pons M. Multi-phosphorylation of the intrinsically disordered unique domain of c-Src studied by in-cell and real-time NMR spectroscopy. Chembiochem 2013; 14:1820-7. [PMID: 23744817 DOI: 10.1002/cbic.201300139] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Indexed: 12/28/2022]
Abstract
Intrinsically disordered regions (IDRs) are preferred sites for post-translational modifications essential for regulating protein function. The enhanced local mobility of IDRs facilitates their observation by NMR spectroscopy in vivo. Phosphorylation events can occur at multiple sites and respond dynamically to changes in kinase-phosphatase networks. Here we used real-time NMR spectroscopy to study the effect of kinases and phosphatases present in Xenopus oocytes and egg extracts on the phosphorylation state of the "unique domain" of c-Src. We followed the phosphorylation of S17 in oocytes, and of S17, S69, and S75 in egg extracts by NMR spectroscopy, MS, and western blotting. Addition of specific kinase inhibitors showed that S75 and S69 are phosphorylated by CDKs (cyclin-dependent kinases) differently from Cdk1. Moreover, although PKA (cAMP-dependent protein kinase) can phosphorylate S17 in vitro, this was not the major S17 kinase in egg extracts. Changes in PKA activity affected the phosphorylation levels of CDK-dependent sites, thus suggesting indirect effects of kinase-phosphatase networks. This study provides a proof-of-concept of the use of real-time in vivo NMR spectroscopy to characterize kinase/phosphatase effects on intrinsically disordered regulatory domains.
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Affiliation(s)
- Irene Amata
- Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona, Baldiri Reixac, 10-12, 08028 Barcelona (Spain); Signaling and Cell Cycle Laboratory, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona (Spain)
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21
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Smet-Nocca C, Launay H, Wieruszeski JM, Lippens G, Landrieu I. Unraveling a phosphorylation event in a folded protein by NMR spectroscopy: phosphorylation of the Pin1 WW domain by PKA. JOURNAL OF BIOMOLECULAR NMR 2013; 55:323-337. [PMID: 23456038 DOI: 10.1007/s10858-013-9716-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 02/15/2013] [Indexed: 06/01/2023]
Abstract
The Pin1 protein plays a critical role in the functional regulation of the hyperphosphorylated neuronal Tau protein in Alzheimer's disease and is by itself regulated by phosphorylation. We have used Nuclear Magnetic Resonance (NMR) spectroscopy to both identify the PKA phosphorylation site in the Pin1 WW domain and investigate the functional consequences of this phosphorylation. Detection and identification of phosphorylation on serine/threonine residues in a globular protein, while mostly occurring in solvent-exposed flexible loops, does not lead to chemical shift changes as obvious as in disordered proteins and hence does not necessarily shift the resonances outside the spectrum of the folded protein. Other complications were encountered to characterize the extent of the phosphorylation, as part of the (1)H,(15)N amide resonances around the phosphorylation site are specifically broadened in the unphosphorylated state. Despite these obstacles, NMR spectroscopy was an efficient tool to confirm phosphorylation on S16 of the WW domain and to quantify the level of phosphorylation. Based on this analytical characterization, we show that WW phosphorylation on S16 abolishes its binding capacity to a phosphorylated Tau peptide. A reduced conformational heterogeneity and flexibility of the phospho-binding loop upon S16 phosphorylation could account for part of the decreased affinity for its phosphorylated partner. Additionally, a structural model of the phospho-WW obtained by molecular dynamics simulation and energy minimization suggests that the phosphate moiety of phospho-S16 could compete with the phospho-substrate.
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Affiliation(s)
- Caroline Smet-Nocca
- Institut Fédératif de Recherches 147, CNRS UMR 8576, Université de Lille-Nord de France, Villeneuve d'Ascq, France.
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22
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Theillet FX, Smet-Nocca C, Liokatis S, Thongwichian R, Kosten J, Yoon MK, Kriwacki RW, Landrieu I, Lippens G, Selenko P. Cell signaling, post-translational protein modifications and NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2012; 54:217-36. [PMID: 23011410 PMCID: PMC4939263 DOI: 10.1007/s10858-012-9674-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/07/2012] [Indexed: 05/13/2023]
Abstract
Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy.
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Affiliation(s)
- Francois-Xavier Theillet
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Caroline Smet-Nocca
- CNRS UMR 8576, Universite Lille Nord de France, 59655 Villeneuve d’Ascq, France
| | - Stamatios Liokatis
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Rossukon Thongwichian
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Jonas Kosten
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Mi-Kyung Yoon
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Isabelle Landrieu
- CNRS UMR 8576, Universite Lille Nord de France, 59655 Villeneuve d’Ascq, France
| | - Guy Lippens
- CNRS UMR 8576, Universite Lille Nord de France, 59655 Villeneuve d’Ascq, France
| | - Philipp Selenko
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
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23
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Li C, Zhao F, Huang Y, Liu X, Liu Y, Qiao R, Zhao Y. Metal-Free DNA Linearized Nuclease Based on PASP–Polyamine Conjugates. Bioconjug Chem 2012; 23:1832-7. [DOI: 10.1021/bc300162g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chao Li
- State Key
Laboratory of Chemical
Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Fangfang Zhao
- State Key
Laboratory of Chemical
Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yunan Huang
- State Key
Laboratory of Chemical
Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xueyuan Liu
- State Key
Laboratory of Chemical
Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yan Liu
- Department of Chemistry,
College
of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Renzhong Qiao
- State Key
Laboratory of Chemical
Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
- State Key Laboratory of Natural
and Biomimetic Drugs School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, 100083,
China
| | - Yufen Zhao
- Department of Chemistry,
College
of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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24
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Hydrogen-Bonding Interactions Induced by Phosphorylation Influence the Local Conformation of Phosphopeptides. Int J Pept Res Ther 2010. [DOI: 10.1007/s10989-010-9207-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Xu W, Yang X, Yang L, Jia ZL, Wei L, Liu F, Lu GY. Synthesis and DNA cleavage activity of triazacrown-anthraquinone conjugates. NEW J CHEM 2010. [DOI: 10.1039/c0nj00347f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Li J, Zhang J, Lu QS, Yue Y, Huang Y, Zhang DW, Lin HH, Chen SY, Yu XQ. Hydrolytic cleavage of DNA by urea-bridged macrocyclic polyamines. Eur J Med Chem 2009; 44:5090-3. [DOI: 10.1016/j.ejmech.2009.06.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 06/22/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
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27
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Jezierska A, Panek JJ. Investigations of an O-H...S hydrogen bond via Car-Parrinello and path integral molecular dynamics. J Comput Chem 2009; 30:1241-50. [PMID: 18988272 DOI: 10.1002/jcc.21158] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The presence of intramolecular hydrogen bonds influences the binding energy, tautomeric equilibrium, and spectroscopic properties of various classes of organic molecules. This article discusses the O-H...S bridge, one of the less commonly investigated types of intramolecular interactions. 3-mercapto-1,3-diphenylprop-2-en-1-one was considered as the model structure. This compound exhibits photochromic properties. Car-Parrinello molecular dynamics (CPMD) was applied to investigate the spectroscopic and molecular properties of this compound in the gas phase and in the solid state. The second part of the study is devoted to the effects of the quantization of nuclear motions, with special attention to the O-H...S moiety. Path integral molecular dynamics (PIMD) of the molecular crystal of 3-mercapto-1,3-diphenylprop-2-en-1-one was carried out for this purpose. The employment of this fully quantum mechanical technique enables one to study, in a time-averaged sense, the zero-point motion important for flat potential energy surfaces. Finally, the potentials of mean force (Pmfs) were calculated from the CPMD and PIMD data obtained for the solid-state calculations. The effect of including quantum nuclear motion was investigated. In the studied compound, quantum effects shortened the H-bridge and provided a better description of the free energy minimum. The computational results place this uncommon intramolecular H-bonding among the class of strong hydrogen bonds with large red shifts of O-H stretching modes, which correspond well with previously presented experimental data in the literature concerning this structure.
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Affiliation(s)
- Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland.
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Shao Y, Ding Y, Jia ZL, Lu XM, Ke ZH, Xu WH, Lu GY. Synthesis and DNA cleavage activity of 2-hydrazinyl-1,4,5,6-tetrahydropyrimidine containing hydroxy group. Bioorg Med Chem 2009; 17:4274-9. [DOI: 10.1016/j.bmc.2009.05.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 05/15/2009] [Accepted: 05/16/2009] [Indexed: 11/17/2022]
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Zhang J, Shao Y, Wei L, Li Y, Sheng X, Liu F, Lu G. Design of artificial nucleases and studies of their interaction with DNA. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11426-009-0029-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Jiang N, Ma J. Theoretical study of proton encircling modes in proton sponges with tetraamido/diamino quaternized macrocycles: the role of π-conjugated and aliphatic bridges. Phys Chem Chem Phys 2009; 11:5100-9. [DOI: 10.1039/b821127b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lee KK, Kim E, Joo C, Song J, Han H, Cho M. Site-selective Intramolecular Hydrogen-Bonding Interactions in Phosphorylated Serine and Threonine Dipeptides. J Phys Chem B 2008; 112:16782-7. [DOI: 10.1021/jp803285x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyung-Koo Lee
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Eunmyung Kim
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Cheonik Joo
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Jaewook Song
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Hogyu Han
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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Hu J, Zhao YF, Li YM. The Effects of Reversible Phosphorylation on Peptide and Protein Local Structure. PHOSPHORUS SULFUR 2008. [DOI: 10.1080/10426500701734141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Jia Hu
- a Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry , Tsinghua University , Beijing, P. R. China
| | - Yu-Fen Zhao
- a Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry , Tsinghua University , Beijing, P. R. China
| | - Yan-Mei Li
- a Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry , Tsinghua University , Beijing, P. R. China
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Du JT, Yu CH, Zhou LX, Wu WH, Lei P, Li Y, Zhao YF, Nakanishi H, Li YM. Phosphorylation modulates the local conformation and self-aggregation ability of a peptide from the fourth tau microtubule-binding repeat. FEBS J 2007; 274:5012-20. [PMID: 17725643 DOI: 10.1111/j.1742-4658.2007.06018.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphorylation of tau protein modulates both its physiological role and its aggregation into paired helical fragments, as observed in Alzheimer's diseased neurons. It is of fundamental importance to study paired helical fragment formation and its modulation by phosphorylation. This study focused on the fourth microtubule-binding repeat of tau, encompassing an abnormal phosphorylation site, Ser356. The aggregation propensities of this repeat peptide and its corresponding phosphorylated form were investigated using turbidity, thioflavin T fluorescence and electron microscopy. There is evidence for a conformational change in the fourth microtubule-binding repeat of tau peptide upon phosphorylation, as well as changes in aggregation activity. Although both tau peptides have the ability to aggregate, this is weaker in the phosphorylated peptide. This study reveals that both tau peptides are capable of self-aggregation and that phosphorylation at Ser356 can modulate this process.
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Affiliation(s)
- Jin-Tang Du
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
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Chen YX, Du JT, Zhou LX, Liu XH, Zhao YF, Nakanishi H, Li YM. Alternative O-GlcNAcylation/O-phosphorylation of Ser16 induce different conformational disturbances to the N terminus of murine estrogen receptor beta. ACTA ACUST UNITED AC 2006; 13:937-44. [PMID: 16984883 DOI: 10.1016/j.chembiol.2006.06.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Revised: 06/16/2006] [Accepted: 06/26/2006] [Indexed: 01/09/2023]
Abstract
Serine and threonine residues in many proteins can be modified by either phosphorylation or GlcNAcylation. To investigate the mechanism of O-GlcNAc and O-phosphate's reciprocal roles in modulating the degradation and activity of murine estrogen receptor beta (mER-beta), the conformational changes induced by O-GlcNAcylation and O-phosphorylation of Ser(16) in 17-mer model peptides corresponding to the N-terminal intrinsically disordered (ID) region of mER-beta were studied by NMR techniques, circular dichroism (CD), and molecular dynamics simulations. Our results suggest that O-phosphorylation discourages the turn formation in the S(15)STG(18) fragment. In contrast, O-GlcNAcylation promotes turn formation in this region. Thus, we postulate that the different changes of the local structure in the N-terminal S(15)STG(18) fragment of mER-beta caused by O-phosphate or O-GlcNAc modification might lead to the disturbances to the dynamic ensembles of the ID region of mER-beta, which is related to its modulatory activity.
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Affiliation(s)
- Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
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Zhou LX, Zeng ZY, Du JT, Zhao YF, Li YM. The self-assembly ability of the first microtubule-binding repeat from tau and its modulation by phosphorylation. Biochem Biophys Res Commun 2006; 348:637-42. [PMID: 16889747 DOI: 10.1016/j.bbrc.2006.07.099] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 07/20/2006] [Indexed: 10/24/2022]
Abstract
Aggregation of abnormally phosphorylated tau in the form of tangs of paired helical filaments (PHFs) is one of the hallmarks of Alzheimer's disease (AD) and other tauopathies. It is of fundamental importance to study the mechanism of PHF formation and its modulation by phosphorylation. In this work, we have focused on the first microtubule-binding repeat of tau encompassing an abnormal phosphorylation site Ser262. The assembly propensities of this repeat and its corresponding phosphorylated form were investigated by turbidity and electron microscopy. Additionally, conformation of the two peptides is also analyzed through circular dichroism (CD) and NMR spectroscopy. Our results reveal that both of them are capable of self-assembly and phosphorylation at Ser262 could speed up the process of assembly. A possible mechanism of PHF formation is proposed and enhancing effect of phosphorylation on assembly provides an explanation to its toxicity in Alzheimer's disease.
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Affiliation(s)
- Lian-Xiu Zhou
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, PR China
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