1
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Stief T, Vormann K, Lakomek NA. Sensitivity-enhanced NMR 15N R 1 and R 1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields. Methods 2024; 223:1-15. [PMID: 38242384 DOI: 10.1016/j.ymeth.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/21/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024] Open
Abstract
NMR relaxation experiments provide residue-specific insights into the structural dynamics of proteins. Here, we present an optimized set of sensitivity-enhanced 15N R1 and R1ρ relaxation experiments applicable to fully protonated proteins. The NMR pulse sequences are conceptually similar to the set of TROSY-based sequences and their HSQC counterpart (Lakomek et al., J. Biomol. NMR 2012). Instead of the TROSY read-out scheme, a sensitivity-enhanced HSQC read-out scheme is used, with improved and easier optimized water suppression. The presented pulse sequences are applied on the cytoplasmic domain of the SNARE protein Synpatobrevin-2 (Syb-2), which is intrinsically disordered in its monomeric pre-fusion state. A two-fold increase in the obtained signal-to-noise ratio is observed for this intrinsically disordered protein, therefore offering a four-fold reduction of measurement time compared to the TROSY-detected version. The inter-scan recovery delay can be shortened to two seconds. Pulse sequences were tested at 600 MHz and 1200 MHz 1H Larmor frequency, thus applicable over a wide magnetic field range. A comparison between protonated and deuterated protein samples reveals high agreement, indicating that reliable 15N R1 and R1ρ rate constants can be extracted for fully protonated and deuterated samples. The presented pulse sequences will benefit not only for IDPs but also for an entire range of low and medium-sized proteins.
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Affiliation(s)
- Tobias Stief
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, Jülich, Germany; Institute of Physical Biology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Katharina Vormann
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, Jülich, Germany; Institute of Physical Biology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nils-Alexander Lakomek
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, Jülich, Germany; Institute of Physical Biology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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2
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Chaves-Arquero B, Martínez-Lumbreras S, Sibille N, Camero S, Bernadó P, Jiménez MÁ, Zorrilla S, Pérez-Cañadillas JM. eIF4G1 N-terminal intrinsically disordered domain is a multi-docking station for RNA, Pab1, Pub1, and self-assembly. Front Mol Biosci 2022; 9:986121. [PMID: 36213119 PMCID: PMC9537944 DOI: 10.3389/fmolb.2022.986121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Yeast eIF4G1 interacts with RNA binding proteins (RBPs) like Pab1 and Pub1 affecting its function in translation initiation and stress granules formation. We present an NMR and SAXS study of the N-terminal intrinsically disordered region of eIF4G1 (residues 1-249) and its interactions with Pub1, Pab1 and RNA. The conformational ensemble of eIF4G11-249 shows an α-helix within the BOX3 conserved element and a dynamic network of fuzzy π-π and π-cation interactions involving arginine and aromatic residues. The Pab1 RRM2 domain interacts with eIF4G1 BOX3, the canonical interaction site, but also with BOX2, a conserved element of unknown function to date. The RNA1 region interacts with RNA through a new RNA interaction motif and with the Pub1 RRM3 domain. This later also interacts with eIF4G1 BOX1 modulating its intrinsic self-assembly properties. The description of the biomolecular interactions involving eIF4G1 to the residue detail increases our knowledge about biological processes involving this key translation initiation factor.
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Affiliation(s)
- Belén Chaves-Arquero
- Department of Biological Physical Chemistry, Institute of Physical-Chemistry “Rocasolano”, CSIC, Madrid, Spain
| | - Santiago Martínez-Lumbreras
- Department of Biological Physical Chemistry, Institute of Physical-Chemistry “Rocasolano”, CSIC, Madrid, Spain
| | - Nathalie Sibille
- Centre de Biochimie Structurale (CBS), CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Sergio Camero
- Department of Biological Physical Chemistry, Institute of Physical-Chemistry “Rocasolano”, CSIC, Madrid, Spain
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - M. Ángeles Jiménez
- Department of Biological Physical Chemistry, Institute of Physical-Chemistry “Rocasolano”, CSIC, Madrid, Spain
| | - Silvia Zorrilla
- Department of Cellular and Molecular Biology, Biological Research Center, CSIC, Madrid, Spain
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3
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Abstract
Thanks to recent improvements in NMR spectrometer hardware and pulse sequence design, modern 13C NMR has become a useful tool for biomolecular applications. The complete assignment of a protein can be accomplished by using 13C detected multinuclear experiments and it can provide unique information relevant for the study of a variety of different biomolecules including paramagnetic proteins and intrinsically disordered proteins. A wide range of NMR observables can be measured, concurring to the structural and dynamic characterization of a protein in isolation, as part of a larger complex, or even inside a living cell. We present the different properties of 13C with respect to 1H, which provide the rationale for the experiments developed and their application, the technical aspects that need to be faced, and the many experimental variants designed to address different cases. Application areas where these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C. Felli
- Department of Chemistry “Ugo
Schiff” and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo
Schiff” and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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4
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Abyzov A, Blackledge M, Zweckstetter M. Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry. Chem Rev 2022; 122:6719-6748. [PMID: 35179885 PMCID: PMC8949871 DOI: 10.1021/acs.chemrev.1c00774] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Motions in biomolecules
are critical for biochemical reactions.
In cells, many biochemical reactions are executed inside of biomolecular
condensates formed by ultradynamic intrinsically disordered proteins.
A deep understanding of the conformational dynamics of intrinsically
disordered proteins in biomolecular condensates is therefore of utmost
importance but is complicated by diverse obstacles. Here we review
emerging data on the motions of intrinsically disordered proteins
inside of liquidlike condensates. We discuss how liquid–liquid
phase separation modulates internal motions across a wide range of
time and length scales. We further highlight the importance of intermolecular
interactions that not only drive liquid–liquid phase separation
but appear as key determinants for changes in biomolecular motions
and the aging of condensates in human diseases. The review provides
a framework for future studies to reveal the conformational dynamics
of intrinsically disordered proteins in the regulation of biomolecular
condensate chemistry.
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Affiliation(s)
- Anton Abyzov
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Martin Blackledge
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 38044 Grenoble, France.,CEA, DSV, IBS, 38044 Grenoble, France.,CNRS, IBS, 38044 Grenoble, France
| | - Markus Zweckstetter
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany.,Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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5
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Saikia N, Yanez-Orozco IS, Qiu R, Hao P, Milikisiyants S, Ou E, Hamilton GL, Weninger KR, Smirnova TI, Sanabria H, Ding F. Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100616. [PMID: 34888535 PMCID: PMC8654206 DOI: 10.1016/j.xcrp.2021.100616] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
SNAP-25 (synaptosomal-associated protein of 25 kDa) is a prototypical intrinsically disordered protein (IDP) that is unstructured by itself but forms coiled-coil helices in the SNARE complex. With high conformational heterogeneity, detailed structural dynamics of unbound SNAP-25 remain elusive. Here, we report an integrative method to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics (rxDMD) simulations and label-based experiments at ensemble and single-molecule levels. The rxDMD simulations systematically characterize the coil-to-molten globular transition and reconstruct structural ensemble consistent with prior ensemble experiments. Label-based experiments using Förster resonance energy transfer and double electron-electron resonance further probe the conformational dynamics of SNAP-25. Agreements between simulations and experiments under both ensemble and single-molecule conditions allow us to assign specific helix-coil transitions in SNAP-25 that occur in submillisecond timescales and potentially play a vital role in forming the SNARE complex. We expect that this integrative approach may help further our understanding of IDPs.
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Affiliation(s)
- Nabanita Saikia
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Department of Chemistry, Navajo Technical University, Chinle, AZ 86503, USA
| | | | - Ruoyi Qiu
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Pengyu Hao
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Erkang Ou
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - George L. Hamilton
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Keith R. Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Tatyana I. Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Lead contact
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6
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Chen YW, Rahman SK. Fatal Attraction: The Case of Toxic Soluble Dimers of Truncated PQBP-1 Mutants in X-Linked Intellectual Disability. Int J Mol Sci 2021; 22:ijms22052240. [PMID: 33668121 PMCID: PMC7956452 DOI: 10.3390/ijms22052240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/20/2021] [Accepted: 02/20/2021] [Indexed: 11/16/2022] Open
Abstract
The frameshift mutants K192Sfs*7 and R153Sfs*41, of the polyglutamine tract-binding protein 1 (PQBP-1), are stable intrinsically disordered proteins (IDPs). They are each associated with the severe cognitive disorder known as the Renpenning syndrome, a form of X-linked intellectual disability (XLID). Relative to the monomeric wild-type protein, these mutants are dimeric, contain more folded contents, and have higher thermal stabilities. Comparisons can be drawn to the toxic oligomerisation in the “conformational diseases”, which collectively describe medical conditions involving a substantial protein structural transition in the pathogenic mechanism. At the molecular level, the end state of these diseases is often cytotoxic protein aggregation. The conformational disease proteins contain varying extents of intrinsic disorder, and the consensus pathogenesis includes an early oligomer formation. We reviewed the experimental characterisation of the toxic oligomers in representative cases. PQBP-1 mutant dimerisation was then compared to the oligomerisation of the conformational disease proteins. The PQBP-1 mutants are unique in behaving as stable soluble dimers, which do not further develop into higher oligomers or aggregates. The toxicity of the PQBP-1 mutant dimers lies in the native functions (in transcription regulation and possibly, RNA splicing) being compromised, rather than proceeding to aggregation. Other examples of stable IDP dimers were discussed and we speculated on the roles of IDP dimerisation in protein evolution.
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Affiliation(s)
- Yu Wai Chen
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom 999077, Hong Kong
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hunghom 999077, Hong Kong
- Correspondence:
| | - Shah Kamranur Rahman
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK;
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7
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Kawasaki R, Tate SI. Impact of the Hereditary P301L Mutation on the Correlated Conformational Dynamics of Human Tau Protein Revealed by the Paramagnetic Relaxation Enhancement NMR Experiments. Int J Mol Sci 2020; 21:ijms21113920. [PMID: 32486218 PMCID: PMC7313075 DOI: 10.3390/ijms21113920] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/23/2022] Open
Abstract
Tau forms intracellular insoluble aggregates as a neuropathological hallmark of Alzheimer’s disease. Tau is largely unstructured, which complicates the characterization of the tau aggregation process. Recent studies have demonstrated that tau samples two distinct conformational ensembles, each of which contains the soluble and aggregation-prone states of tau. A shift to populate the aggregation-prone ensemble may promote tau fibrillization. However, the mechanism of this ensemble transition remains elusive. In this study, we explored the conformational dynamics of a tau fragment by using paramagnetic relaxation enhancement (PRE) and interference (PRI) NMR experiments. The PRE correlation map showed that tau is composed of segments consisting of residues in correlated motions. Intriguingly, residues forming the β-structures in the heparin-induced tau filament coincide with residues in these segments, suggesting that each segment behaves as a structural unit in fibrillization. PRI data demonstrated that the P301L mutation exclusively alters the transiently formed tau structures by changing the short- and long-range correlated motions among residues. The transient conformations of P301L tau expose the amyloid motif PHF6 to promote tau self-aggregation. We propose the correlated motions among residues within tau determine the population sizes of the conformational ensembles, and perturbing the correlated motions populates the aggregation-prone form.
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Affiliation(s)
- Ryosuke Kawasaki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
| | - Shin-ichi Tate
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
- Department of Mathematical and Life Sciences, Graduate School of the Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Correspondence: ; Tel.: +81-82-424-7387
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8
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Probing Surfaces in Dynamic Protein Interactions. J Mol Biol 2020; 432:2949-2972. [DOI: 10.1016/j.jmb.2020.02.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 01/09/2023]
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9
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Mendes LFS, Batista MRB, Judge PJ, Watts A, Redfield C, Costa-Filho AJ. Conformational flexibility of GRASPs and their constituent PDZ subdomains reveals structural basis of their promiscuous interactome. FEBS J 2020; 287:3255-3272. [PMID: 31920006 DOI: 10.1111/febs.15206] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/19/2019] [Accepted: 01/08/2020] [Indexed: 01/04/2023]
Abstract
The Golgi complex is a central component of the secretory pathway, responsible for several critical cellular functions in eukaryotes. The complex is organized by the Golgi matrix that includes the Golgi reassembly and stacking protein (GRASP), which was shown to be involved in cisternae stacking and lateral linkage in metazoan. GRASPs also have critical roles in other processes, with an unusual ability to interact with several different binding partners. The conserved N terminus of the GRASP family includes two PSD-95, DLG, and ZO-1 (PDZ) domains. Previous crystallographic studies of orthologues suggest that PDZ1 and PDZ2 have similar conformations and secondary structure content. However, PDZ1 alone mediates nearly all interactions between GRASPs and their partners. In this work, NMR, synchrotron radiation CD, and molecular dynamics (MD) were used to examine the structure, flexibility, and stability of the two constituent PDZ domains. GRASP PDZs are structured in an unusual β3 α1 β4 β5 α2 β6 β1 β2 secondary structural arrangement and NMR data indicate that the PDZ1 binding pocket is formed by a stable β2 -strand and a more flexible and unstable α2 -helix, suggesting an explanation for the higher PDZ1 promiscuity. The conformational free energy profiles of the two PDZ domains were calculated using MD simulations. The data suggest that, after binding, the protein partner significantly reduces the conformational space that GRASPs can access by stabilizing one particular conformation, in a partner-dependent fashion. The structural flexibility of PDZ1, modulated by PDZ2, and the coupled, coordinated movement between the two PDZs enable GRASPs to interact with multiple partners, allowing them to function as promiscuous, multitasking proteins.
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Affiliation(s)
- Luis Felipe S Mendes
- Molecular Biophysics Laboratory, Ribeirão Preto School of Philosophy, Sciences and Literature, Physics Department, University of São Paulo, Ribeirão Preto, Brazil.,Department of Biochemistry, University of Oxford, UK
| | - Mariana R B Batista
- Molecular Biophysics Laboratory, Ribeirão Preto School of Philosophy, Sciences and Literature, Physics Department, University of São Paulo, Ribeirão Preto, Brazil
| | - Peter J Judge
- Department of Biochemistry, University of Oxford, UK
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, UK
| | | | - Antonio J Costa-Filho
- Molecular Biophysics Laboratory, Ribeirão Preto School of Philosophy, Sciences and Literature, Physics Department, University of São Paulo, Ribeirão Preto, Brazil
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10
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Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit. Int J Mol Sci 2019; 20:ijms20174186. [PMID: 31461845 PMCID: PMC6747279 DOI: 10.3390/ijms20174186] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/22/2022] Open
Abstract
Traditionally, X-ray crystallography and NMR spectroscopy represent major workhorses of structural biologists, with the lion share of protein structures reported in protein data bank (PDB) being generated by these powerful techniques. Despite their wide utilization in protein structure determination, these two techniques have logical limitations, with X-ray crystallography being unsuitable for the analysis of highly dynamic structures and with NMR spectroscopy being restricted to the analysis of relatively small proteins. In recent years, we have witnessed an explosive development of the techniques based on Cryo-electron microscopy (Cryo-EM) for structural characterization of biological molecules. In fact, single-particle Cryo-EM is a special niche as it is a technique of choice for the structural analysis of large, structurally heterogeneous, and dynamic complexes. Here, sub-nanometer atomic resolution can be achieved (i.e., resolution below 10 Å) via single-particle imaging of non-crystalline specimens, with accurate 3D reconstruction being generated based on the computational averaging of multiple 2D projection images of the same particle that was frozen rapidly in solution. We provide here a brief overview of single-particle Cryo-EM and show how Cryo-EM has revolutionized structural investigations of membrane proteins. We also show that the presence of intrinsically disordered or flexible regions in a target protein represents one of the major limitations of this promising technique.
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11
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Uluca B, Viennet T, Petrović D, Shaykhalishahi H, Weirich F, Gönülalan A, Strodel B, Etzkorn M, Hoyer W, Heise H. DNP-Enhanced MAS NMR: A Tool to Snapshot Conformational Ensembles of α-Synuclein in Different States. Biophys J 2019; 114:1614-1623. [PMID: 29642031 PMCID: PMC5954275 DOI: 10.1016/j.bpj.2018.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/04/2018] [Accepted: 02/07/2018] [Indexed: 11/06/2022] Open
Abstract
Intrinsically disordered proteins dynamically sample a wide conformational space and therefore do not adopt a stable and defined three-dimensional conformation. The structural heterogeneity is related to their proper functioning in physiological processes. Knowledge of the conformational ensemble is crucial for a complete comprehension of this kind of proteins. We here present an approach that utilizes dynamic nuclear polarization-enhanced solid-state NMR spectroscopy of sparsely isotope-labeled proteins in frozen solution to take snapshots of the complete structural ensembles by exploiting the inhomogeneously broadened line-shapes. We investigated the intrinsically disordered protein α-synuclein (α-syn), which plays a key role in the etiology of Parkinson’s disease, in three different physiologically relevant states. For the free monomer in frozen solution we could see that the so-called “random coil conformation” consists of α-helical and β-sheet-like conformations, and that secondary chemical shifts of neighboring amino acids tend to be correlated, indicative of frequent formation of secondary structure elements. Based on these results, we could estimate the number of disordered regions in fibrillar α-syn as well as in α-syn bound to membranes in different protein-to-lipid ratios. Our approach thus provides quantitative information on the propensity to sample transient secondary structures in different functional states. Molecular dynamics simulations rationalize the results.
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Affiliation(s)
- Boran Uluca
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Thibault Viennet
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Dušan Petrović
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Hamed Shaykhalishahi
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Franziska Weirich
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Ayşenur Gönülalan
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Manuel Etzkorn
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Henrike Heise
- Institute of Complex Systems, Structural Biochemistry, Research Center Jülich, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
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12
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Chan-Yao-Chong M, Durand D, Ha-Duong T. Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles. J Chem Inf Model 2019; 59:1743-1758. [PMID: 30840442 DOI: 10.1021/acs.jcim.8b00928] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The concept of intrinsically disordered proteins (IDPs) has emerged relatively slowly, but over the past 20 years, it has become an intense research area in structural biology. Indeed, because of their considerable flexibility and structural heterogeneity, the determination of IDP conformational ensemble is particularly challenging and often requires a combination of experimental measurements and computational approaches. With the improved accuracy of all-atom force fields and the increasing computing performances, molecular dynamics (MD) simulations have become more and more reliable to generate realistic conformational ensembles. And the combination of MD simulations with experimental approaches, such as nuclear magnetic resonance (NMR) and/or small-angle X-ray scattering (SAXS) allows one to converge toward a more accurate and exhaustive description of IDP structures. In this Review, we discuss the state of the art of MD simulations of IDP conformational ensembles, with a special focus on studies that back-calculated and directly compared theoretical and experimental NMR or SAXS observables, such as chemical shifts (CS), 3J-couplings (3Jc), residual dipolar couplings (RDC), or SAXS intensities. We organize the review in three parts. In the first section, we discuss the studies which used NMR and/or SAXS data to test and validate the development of force fields or enhanced sampling techniques. In the second part, we explore different methods for the refinement of MD-derived structural ensembles, such as NMR or SAXS data-restrained MD simulations or ensemble reweighting to better fit experiments. Finally, we survey some recent studies combining MD simulations with NMR and/or SAXS measurements to investigate the relationship between IDP conformational ensemble and biological activity, as well as their implication in human diseases. From this review, we noticed that quite a few studies compared MD-generated conformational ensembles with both NMR and SAXS measurements to validate IDP structures at both local and global levels. Yet, beside the IDP propensity to form local secondary structures, their dynamic extension or compactness also appears important for their activity. Thus, we believe that a close synergy between MD simulations, NMR, and SAXS experiments would be greatly appropriate to address the challenges of characterizing the disordered structures of proteins and their complexes, relative to their biological functions.
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Affiliation(s)
- Maud Chan-Yao-Chong
- BioCIS, Université Paris-Sud, CNRS , Université Paris-Saclay , 92290 Châtenay-Malabry , France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex, France
| | - Tâp Ha-Duong
- BioCIS, Université Paris-Sud, CNRS , Université Paris-Saclay , 92290 Châtenay-Malabry , France
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13
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Kumari P, Frey L, Sobol A, Lakomek NA, Riek R. 15N transverse relaxation measurements for the characterization of µs-ms dynamics are deteriorated by the deuterium isotope effect on 15N resulting from solvent exchange. JOURNAL OF BIOMOLECULAR NMR 2018; 72:125-137. [PMID: 30306288 DOI: 10.1007/s10858-018-0211-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
Abstract
15N R2 relaxation measurements are key for the elucidation of the dynamics of both folded and intrinsically disordered proteins (IDPs). Here we show, on the example of the intrinsically disordered protein α-synuclein and the folded domain PDZ2, that at physiological pH and near physiological temperatures amide-water exchange can severely skew Hahn-echo based 15N R2 relaxation measurements as well as low frequency data points in CPMG relaxation dispersion experiments. The nature thereof is the solvent exchange with deuterium in the sample buffer, which modulates the 15N chemical shift tensor via the deuterium isotope effect, adding to the apparent relaxation decay which leads to systematic errors in the relaxation data. This results in an artificial increase of the measured apparent 15N R2 rate constants-which should not be mistaken with protein inherent chemical exchange contributions, Rex, to 15N R2. For measurements of 15N R2 rate constants of IDPs and folded proteins at physiological temperatures and pH, we recommend therefore the use of a very low D2O molar fraction in the sample buffer, as low as 1%, or the use of an external D2O reference along with a modified 15N R2 Hahn-echo based experiment. This combination allows for the measurement of Rex contributions to 15N R2 originating from conformational exchange in a time window from µs to ms.
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Affiliation(s)
- Pratibha Kumari
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Alexander Sobol
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Nils-Alexander Lakomek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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14
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LeBlanc SJ, Kulkarni P, Weninger KR. Single Molecule FRET: A Powerful Tool to Study Intrinsically Disordered Proteins. Biomolecules 2018; 8:biom8040140. [PMID: 30413085 PMCID: PMC6315554 DOI: 10.3390/biom8040140] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are often modeled using ideas from polymer physics that suggest they smoothly explore all corners of configuration space. Experimental verification of this random, dynamic behavior is difficult as random fluctuations of IDPs cannot be synchronized across an ensemble. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) is one of the few approaches that are sensitive to transient populations of sub-states within molecular ensembles. In some implementations, smFRET has sufficient time resolution to resolve transitions in IDP behaviors. Here we present experimental issues to consider when applying smFRET to study IDP configuration. We illustrate the power of applying smFRET to IDPs by discussing two cases in the literature of protein systems for which smFRET has successfully reported phosphorylation-induced modification (but not elimination) of the disordered properties that have been connected to impacts on the related biological function. The examples we discuss, PAGE4 and a disordered segment of the GluN2B subunit of the NMDA receptor, illustrate the great potential of smFRET to inform how IDP function can be regulated by controlling the detailed ensemble of disordered states within biological networks.
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Affiliation(s)
- Sharonda J LeBlanc
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA.
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
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15
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Snead D, Eliezer D. Spectroscopic Characterization of Structure-Function Relationships in the Intrinsically Disordered Protein Complexin. Methods Enzymol 2018; 611:227-286. [PMID: 30471689 DOI: 10.1016/bs.mie.2018.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Complexins play a critical role in the regulation of neurotransmission by regulating SNARE-mediated exocytosis of synaptic vesicles. Complexins can exert either a facilitatory or an inhibitory effect on neurotransmitter release, depending on the context, and different complexin domains contribute differently to these opposing roles. Structural characterization of the central helix domain of complexin bound to the assembled SNARE bundle provided key insights into the functional mechanism of this domain of complexin, which is critical for both complexin activities, but many questions remain, particularly regarding the roles and mechanisms of other complexin domains. Recent progress has clarified the structural properties of these additional domains, and has led to various proposals regarding how they contribute to complexin function. This chapter describes spectroscopic approaches used in our laboratory and others, primarily involving circular dichroism and solution-state NMR spectroscopy, to characterize structure within complexins when isolated or when bound to interaction partners. The ability to characterize complexin structure enables structure/function studies employing in vitro or in vivo assays of complexin function. More generally, these types of approaches can be used to study the binding of other intrinsically disordered proteins or protein regions to membrane surfaces or for that matter to other large physiological binding partners.
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Affiliation(s)
- David Snead
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, United States
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, United States.
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16
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Beier A, Schwarz TC, Kurzbach D, Platzer G, Tribuzio F, Konrat R. Modulation of Correlated Segment Fluctuations in IDPs upon Complex Formation as an Allosteric Regulatory Mechanism. J Mol Biol 2018; 430:2439-2452. [PMID: 29733855 DOI: 10.1016/j.jmb.2018.04.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/13/2018] [Accepted: 04/26/2018] [Indexed: 12/29/2022]
Abstract
Molecular recognition of and by intrinsically disordered proteins (IDPs) is an intriguing and still largely elusive phenomenon. Typically, protein recognition involving IDPs requires either folding upon binding or, alternatively, the formation of "fuzzy complexes." Here we show via correlation analyses of paramagnetic relaxation enhancement data unprecedented and striking alterations of the concerted fluctuations within the conformational ensemble of IDPs upon ligand binding. We study the binding of α-synuclein to calmodulin, a ubiquitous calcium-binding protein, and the binding of the extracellular matrix IDP osteopontin to heparin, a mimic of the extracellular matrix ligand hyaluronic acid. In both cases, binding leads to reduction of correlated long-range motions in these two IDPs and thus indicates a loosening of structural compaction upon binding. Most importantly, however, the simultaneous presence of correlated and anti-correlated fluctuations in IDPs suggests the prevalence of "energetic frustration" and provides an explanation for the puzzling observation of disordered allostery in IDPs.
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Affiliation(s)
- Andreas Beier
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Thomas C Schwarz
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Dennis Kurzbach
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Francesca Tribuzio
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, A-1030 Vienna, Austria; Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
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17
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Nußbaumer F, Juen MA, Gasser C, Kremser J, Müller T, Tollinger M, Kreutz C. Synthesis and incorporation of 13C-labeled DNA building blocks to probe structural dynamics of DNA by NMR. Nucleic Acids Res 2017; 45:9178-9192. [PMID: 28911104 PMCID: PMC5587810 DOI: 10.1093/nar/gkx592] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/23/2017] [Accepted: 06/29/2017] [Indexed: 11/30/2022] Open
Abstract
We report the synthesis of atom-specifically 13C-modified building blocks that can be incorporated into DNA via solid phase synthesis to facilitate investigations on structural and dynamic features via NMR spectroscopy. In detail, 6-13C-modified pyrimidine and 8-13C purine DNA phosphoramidites were synthesized and incorporated into a polypurine tract DNA/RNA hybrid duplex to showcase the facile resonance assignment using site-specific labeling. We also addressed micro- to millisecond dynamics in the mini-cTAR DNA. This DNA is involved in the HIV replication cycle and our data points toward an exchange process in the lower stem of the hairpin that is up-regulated in the presence of the HIV-1 nucleocapsid protein 7. As another example, we picked a G-quadruplex that was earlier shown to exist in two folds. Using site-specific 8-13C-2'deoxyguanosine labeling we were able to verify the slow exchange between the two forms on the chemical shift time scale. In a real-time NMR experiment the re-equilibration of the fold distribution after a T-jump could be monitored yielding a rate of 0.012 min-1. Finally, we used 13C-ZZ-exchange spectroscopy to characterize the kinetics between two stacked X-conformers of a Holliday junction mimic. At 25°C, the refolding process was found to occur at a forward rate constant of 3.1 s-1 and with a backward rate constant of 10.6 s-1.
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Affiliation(s)
- Felix Nußbaumer
- Institute of Organic Chemistry, Leopold-Franzens-University of Innsbruck, and Center for Molecular Biosciences Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Michael Andreas Juen
- Institute of Organic Chemistry, Leopold-Franzens-University of Innsbruck, and Center for Molecular Biosciences Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Catherina Gasser
- Institute of Organic Chemistry, Leopold-Franzens-University of Innsbruck, and Center for Molecular Biosciences Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Johannes Kremser
- Institute of Organic Chemistry, Leopold-Franzens-University of Innsbruck, and Center for Molecular Biosciences Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Thomas Müller
- Institute of Organic Chemistry, Leopold-Franzens-University of Innsbruck, and Center for Molecular Biosciences Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry, Leopold-Franzens-University of Innsbruck, and Center for Molecular Biosciences Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Leopold-Franzens-University of Innsbruck, and Center for Molecular Biosciences Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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18
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Eukaryotic transcription factors: paradigms of protein intrinsic disorder. Biochem J 2017; 474:2509-2532. [DOI: 10.1042/bcj20160631] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/19/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022]
Abstract
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from ‘negative noodles’ to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions. It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms and structural analysis of ID in the context of full-length TFs and suggests future directions for research in TF ID.
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