1
|
Dyson HJ. Vital for Viruses: Intrinsically Disordered Proteins. J Mol Biol 2023; 435:167860. [PMID: 37330280 PMCID: PMC10656058 DOI: 10.1016/j.jmb.2022.167860] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/19/2023]
Abstract
Viruses infect all kingdoms of life; their genomes vary from DNA to RNA and in size from 2kB to 1 MB or more. Viruses frequently employ disordered proteins, that is, protein products of virus genes that do not themselves fold into independent three-dimensional structures, but rather, constitute a versatile molecular toolkit to accomplish a range of functions necessary for viral infection, assembly, and proliferation. Interestingly, disordered proteins have been discovered in almost all viruses so far studied, whether the viral genome consists of DNA or RNA, and whatever the configuration of the viral capsid or other outer covering. In this review, I present a wide-ranging set of stories illustrating the range of functions of IDPs in viruses. The field is rapidly expanding, and I have not tried to include everything. What is included is meant to be a survey of the variety of tasks that viruses accomplish using disordered proteins.
Collapse
Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
2
|
Bignon C, Longhi S. In Vivo Protein-Protein Binding Competition Assay Based on Split-GFP Reassembly: Proof of Concept. Biomolecules 2023; 13:biom13020354. [PMID: 36830723 PMCID: PMC9952896 DOI: 10.3390/biom13020354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The split-green fluorescent protein (GFP) reassembly assay is a well-established approach to study protein-protein interactions (PPIs). In this assay, when two interacting proteins X and Y, respectively fused to residues 1-157 and to residues 158-237 of GFP, are co-expressed in E. coli, the two GFP halves are brought to sufficient proximity to reassociate and fold to recreate the functional GFP. At constant protein expression level, the intensity of fluorescence produced by the bacteria is proportional to the binding affinity of X to Y. We hypothesized that adding a third partner (Z) endowed with an affinity for either X or Y would lead to an in vivo competition assay. We report here the different steps of the set-up of this competition assay, and define the experimental conditions required to obtained reliable results. Results show that this competition assay is a potentially interesting tool for screening libraries of binding inhibitors, Z being either a protein or a chemical reagent.
Collapse
|
3
|
Functional benefit of structural disorder for the replication of measles, Nipah and Hendra viruses. Essays Biochem 2022; 66:915-934. [PMID: 36148633 DOI: 10.1042/ebc20220045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022]
Abstract
Measles, Nipah and Hendra viruses are severe human pathogens within the Paramyxoviridae family. Their non-segmented, single-stranded, negative-sense RNA genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that is the substrate used by the viral RNA-dependent-RNA-polymerase (RpRd) for transcription and replication. The RpRd is a complex made of the large protein (L) and of the phosphoprotein (P), the latter serving as an obligate polymerase cofactor and as a chaperon for N. Both the N and P proteins are enriched in intrinsically disordered regions (IDRs), i.e. regions devoid of stable secondary and tertiary structure. N possesses a C-terminal IDR (NTAIL), while P consists of a large, intrinsically disordered N-terminal domain (NTD) and a C-terminal domain (CTD) encompassing alternating disordered and ordered regions. The V and W proteins, two non-structural proteins that are encoded by the P gene via a mechanism of co-transcriptional edition of the P mRNA, are prevalently disordered too, sharing with P the disordered NTD. They are key players in the evasion of the host antiviral response and were shown to phase separate and to form amyloid-like fibrils in vitro. In this review, we summarize the available information on IDRs within the N, P, V and W proteins from these three model paramyxoviruses and describe their molecular partnership. We discuss the functional benefit of disorder to virus replication in light of the critical role of IDRs in affording promiscuity, multifunctionality, fine regulation of interaction strength, scaffolding functions and in promoting liquid-liquid phase separation and fibrillation.
Collapse
|
4
|
Sponga A, Arolas JL, Schwarz TC, Jeffries CM, Rodriguez Chamorro A, Kostan J, Ghisleni A, Drepper F, Polyansky A, De Almeida Ribeiro E, Pedron M, Zawadzka-Kazimierczuk A, Mlynek G, Peterbauer T, Doto P, Schreiner C, Hollerl E, Mateos B, Geist L, Faulkner G, Kozminski W, Svergun DI, Warscheid B, Zagrovic B, Gautel M, Konrat R, Djinović-Carugo K. Order from disorder in the sarcomere: FATZ forms a fuzzy but tight complex and phase-separated condensates with α-actinin. SCIENCE ADVANCES 2021; 7:eabg7653. [PMID: 34049882 PMCID: PMC8163081 DOI: 10.1126/sciadv.abg7653] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/13/2021] [Indexed: 05/03/2023]
Abstract
In sarcomeres, α-actinin cross-links actin filaments and anchors them to the Z-disk. FATZ (filamin-, α-actinin-, and telethonin-binding protein of the Z-disk) proteins interact with α-actinin and other core Z-disk proteins, contributing to myofibril assembly and maintenance. Here, we report the first structure and its cellular validation of α-actinin-2 in complex with a Z-disk partner, FATZ-1, which is best described as a conformational ensemble. We show that FATZ-1 forms a tight fuzzy complex with α-actinin-2 and propose an interaction mechanism via main molecular recognition elements and secondary binding sites. The obtained integrative model reveals a polar architecture of the complex which, in combination with FATZ-1 multivalent scaffold function, might organize interaction partners and stabilize α-actinin-2 preferential orientation in Z-disk. Last, we uncover FATZ-1 ability to phase-separate and form biomolecular condensates with α-actinin-2, raising the question whether FATZ proteins can create an interaction hub for Z-disk proteins through membraneless compartmentalization during myofibrillogenesis.
Collapse
Affiliation(s)
- Antonio Sponga
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Joan L Arolas
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Thomas C Schwarz
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany
| | - Ariadna Rodriguez Chamorro
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Julius Kostan
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Andrea Ghisleni
- King's College London BHF Centre for Research Excellence, Randall Centre for Cell and Molecular Biophysics, London SE1 1UL, UK
| | - Friedel Drepper
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
- National Research University Higher School of Economics, Moscow 101000, Russia
| | - Euripedes De Almeida Ribeiro
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Miriam Pedron
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Anna Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Georg Mlynek
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Thomas Peterbauer
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Dr. BohrGasse 9, A-1030 Vienna, Austria
| | - Pierantonio Doto
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Claudia Schreiner
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Eneda Hollerl
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Leonhard Geist
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | | | - Wiktor Kozminski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Dmitri I Svergun
- King's College London BHF Centre for Research Excellence, Randall Centre for Cell and Molecular Biophysics, London SE1 1UL, UK
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Mathias Gautel
- King's College London BHF Centre for Research Excellence, Randall Centre for Cell and Molecular Biophysics, London SE1 1UL, UK
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
5
|
Goretzki B, Guhl C, Tebbe F, Harder JM, Hellmich UA. Unstructural Biology of TRP Ion Channels: The Role of Intrinsically Disordered Regions in Channel Function and Regulation. J Mol Biol 2021; 433:166931. [PMID: 33741410 DOI: 10.1016/j.jmb.2021.166931] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 12/13/2022]
Abstract
The first genuine high-resolution single particle cryo-electron microscopy structure of a membrane protein determined was a transient receptor potential (TRP) ion channel, TRPV1, in 2013. This methodical breakthrough opened up a whole new world for structural biology and ion channel aficionados alike. TRP channels capture the imagination due to the sheer endless number of tasks they carry out in all aspects of animal physiology. To date, structures of at least one representative member of each of the six mammalian TRP channel subfamilies as well as of a few non-mammalian families have been determined. These structures were instrumental for a better understanding of TRP channel function and regulation. However, all of the TRP channel structures solved so far are incomplete since they miss important information about highly flexible regions found mostly in the channel N- and C-termini. These intrinsically disordered regions (IDRs) can represent between a quarter to almost half of the entire protein sequence and act as important recruitment hubs for lipids and regulatory proteins. Here, we analyze the currently available TRP channel structures with regard to the extent of these "missing" regions and compare these findings to disorder predictions. We discuss select examples of intra- and intermolecular crosstalk of TRP channel IDRs with proteins and lipids as well as the effect of splicing and post-translational modifications, to illuminate their importance for channel function and to complement the prevalently discussed structural biology of these versatile and fascinating proteins with their equally relevant 'unstructural' biology.
Collapse
Affiliation(s)
- Benedikt Goretzki
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Charlotte Guhl
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany; TransMED - Mainz Research School of Translational Medicine, Johannes Gutenberg-University, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Frederike Tebbe
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Jean-Martin Harder
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany
| | - Ute A Hellmich
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany; TransMED - Mainz Research School of Translational Medicine, Johannes Gutenberg-University, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany; Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, 07743 Jena, Germany.
| |
Collapse
|
6
|
Tira R, De Cecco E, Rigamonti V, Santambrogio C, Barracchia CG, Munari F, Romeo A, Legname G, Prosperi D, Grandori R, Assfalg M. Dynamic molecular exchange and conformational transitions of alpha-synuclein at the nano-bio interface. Int J Biol Macromol 2020; 154:206-216. [DOI: 10.1016/j.ijbiomac.2020.03.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 10/24/2022]
|
7
|
Sequence-Based Prediction of Fuzzy Protein Interactions. J Mol Biol 2020; 432:2289-2303. [DOI: 10.1016/j.jmb.2020.02.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/24/2020] [Accepted: 02/14/2020] [Indexed: 12/31/2022]
|
8
|
Gao M, Yang J, Liu S, Su Z, Huang Y. Intrinsically Disordered Transactivation Domains Bind to TAZ1 Domain of CBP via Diverse Mechanisms. Biophys J 2019; 117:1301-1310. [PMID: 31521329 DOI: 10.1016/j.bpj.2019.08.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 02/06/2023] Open
Abstract
CREB-binding protein is a multidomain transcriptional coactivator whose transcriptional adaptor zinc-binding 1 (TAZ1) domain mediates interactions with a number of intrinsically disordered transactivation domains (TADs), including the CREB-binding protein/p300-interacting transactivator with ED-rich tail, the hypoxia inducible factor 1α, p53, the signal transducer and activator of transcription 2, and the NF-κB p65 subunit. These five disordered TADs undergo partial disorder-to-order transitions upon binding TAZ1, forming fuzzy complexes with helical segments. Interestingly, they wrap around TAZ1 with different orientations and occupy the binding sites with various orders. To elucidate the microscopic molecular details of the binding processes of TADs with TAZ1, in this work, we carried out extensive molecular dynamics simulations using a coarse-grained topology-based model. After careful calibration of the models to reproduce the residual helical contents and binding affinities, our simulations were able to recapitulate the experimentally observed flexibility profiles. Although great differences exist in the complex structures, we found similarities between hypoxia inducible factor 1α and signal transducer and activator of transcription 2 as well as between CREB-binding protein/p300-interacting transactivator with ED-rich tail and NF-κB p65 subunit in the binding kinetics and binding thermodynamics. Although the origins of similarities and differences in the binding mechanisms remain unclear, our results provide some clues that indicate that binding of TADs to TAZ1 could be templated by the target as well as encoded by the TADs.
Collapse
Affiliation(s)
- Meng Gao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China; Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Jing Yang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China; Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Sen Liu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China; Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Zhengding Su
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China; Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Yongqi Huang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China; Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China.
| |
Collapse
|
9
|
Schramm A, Bignon C, Brocca S, Grandori R, Santambrogio C, Longhi S. An arsenal of methods for the experimental characterization of intrinsically disordered proteins - How to choose and combine them? Arch Biochem Biophys 2019; 676:108055. [PMID: 31356778 DOI: 10.1016/j.abb.2019.07.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
In this review, we detail the most common experimental approaches to assess and characterize protein intrinsic structural disorder, with the notable exception of NMR and EPR spectroscopy, two ideally suited approaches that will be described in depth in two other reviews within this special issue. We discuss the advantages, the limitations, as well as the caveats of the various methods. We also describe less common and more demanding approaches that enable achieving further insights into the conformational properties of IDPs. Finally, we present recent developments that have enabled assessment of structural disorder in living cells, and discuss the currently available methods to model IDPs as conformational ensembles.
Collapse
Affiliation(s)
- Antoine Schramm
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
| |
Collapse
|
10
|
Bignon C, Troilo F, Gianni S, Longhi S. Modulation of Measles Virus N TAIL Interactions through Fuzziness and Sequence Features of Disordered Binding Sites. Biomolecules 2018; 9:biom9010008. [PMID: 30591682 PMCID: PMC6359293 DOI: 10.3390/biom9010008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 12/27/2022] Open
Abstract
In this paper we review our recent findings on the different interaction mechanisms of the C-terminal domain of the nucleoprotein (N) of measles virus (MeV) NTAIL, a model viral intrinsically disordered protein (IDP), with two of its known binding partners, i.e., the C-terminal X domain of the phosphoprotein of MeV XD (a globular viral protein) and the heat-shock protein 70 hsp70 (a globular cellular protein). The NTAIL binds both XD and hsp70 via a molecular recognition element (MoRE) that is flanked by two fuzzy regions. The long (85 residues) N-terminal fuzzy region is a natural dampener of the interaction with both XD and hsp70. In the case of binding to XD, the N-terminal fuzzy appendage of NTAIL reduces the rate of α-helical folding of the MoRE. The dampening effect of the fuzzy appendage on XD and hsp70 binding depends on the length and fuzziness of the N-terminal region. Despite this similarity, NTAIL binding to XD and hsp70 appears to rely on completely different requirements. Almost any mutation within the MoRE decreases XD binding, whereas many of them increase the binding to hsp70. In addition, XD binding is very sensitive to the α-helical state of the MoRE, whereas hsp70 is not. Thus, contrary to hsp70, XD binding appears to be strictly dependent on the wild-type primary and secondary structure of the MoRE.
Collapse
Affiliation(s)
- Christophe Bignon
- CNRS and Aix-Marseille Univ Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257 Marseille, France.
| | - Francesca Troilo
- CNRS and Aix-Marseille Univ Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257 Marseille, France.
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli' and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli' and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257 Marseille, France.
| |
Collapse
|
11
|
Xiong J, Gao M, Zhou J, Liu S, Su Z, Liu Z, Huang Y. The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding-binding process during target recognition. Proteins 2018; 87:265-275. [PMID: 30520528 DOI: 10.1002/prot.25646] [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] [Received: 05/12/2018] [Revised: 09/28/2018] [Accepted: 11/29/2018] [Indexed: 11/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) are extensively involved in dynamic signaling processes which require a high association rate and a high dissociation rate for rapid binding/unbinding events and at the same time a sufficient high affinity for specific recognition. Although the coupled folding-binding processes of IDPs have been extensively studied, it is still impossible to predict whether an unfolded protein is suitable for molecular signaling via coupled folding-binding. In this work, we studied the interplay between intrinsic folding mechanisms and coupled folding-binding process for unfolded proteins through molecular dynamics simulations. We first studied the folding process of three representative IDPs with different folded structures, that is, c-Myb, AF9, and E3 rRNase. We found the folding free energy landscapes of IDPs are downhill or show low barriers. To further study the influence of intrinsic folding mechanism on the binding process, we modulated the folding mechanism of barnase via circular permutation and simulated the coupled folding-binding process between unfolded barnase permutant and folded barstar. Although folding of barnase was coupled to target binding, the binding kinetics was significantly affected by the intrinsic folding free energy barrier, where reducing the folding free energy barrier enhances binding rate up to two orders of magnitude. This accelerating effect is different from previous results which reflect the effect of structure flexibility on binding kinetics. Our results suggest that coupling the folding of an unfolded protein with no/low folding free energy barrier with its target binding may provide a way to achieve high specificity and rapid binding/unbinding kinetics simultaneously.
Collapse
Affiliation(s)
- Junwen Xiong
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Meng Gao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Jingjing Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Sen Liu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Zhengding Su
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, China
| | - Yongqi Huang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| |
Collapse
|
12
|
Fuxreiter M. Fold or not to fold upon binding - does it really matter? Curr Opin Struct Biol 2018; 54:19-25. [PMID: 30340123 DOI: 10.1016/j.sbi.2018.09.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022]
Abstract
Protein interactions are usually determined by well-defined contact patterns. In this scenario, structuring of the interface is a prerequisite, which takes place prior or coupled to binding. Recent data, however, indicate plasticity of the templated folding pathway as well as considerable variations: polymorphism or dynamics in the bound-state. Conformational fluctuations in both cases are modulated by non-native, transient contacts, which complement suboptimal binding motifs to improve affinity. Here I discuss both templated folding and fuzzy binding mechanisms and propose a uniform scheme.
Collapse
Affiliation(s)
- Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary.
| |
Collapse
|
13
|
Chen J, Kriwacki RW. Intrinsically Disordered Proteins: Structure, Function and Therapeutics. J Mol Biol 2018; 430:2275-2277. [PMID: 29906412 DOI: 10.1016/j.jmb.2018.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, Amherst, MA 01003, United States; Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, United States.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, United States; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN 38105, United States.
| |
Collapse
|
14
|
Troilo F, Bignon C, Gianni S, Fuxreiter M, Longhi S. Experimental Characterization of Fuzzy Protein Assemblies: Interactions of Paramyxoviral NTAIL Domains With Their Functional Partners. Methods Enzymol 2018; 611:137-192. [DOI: 10.1016/bs.mie.2018.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
15
|
InSiDDe: A Server for Designing Artificial Disordered Proteins. Int J Mol Sci 2017; 19:ijms19010091. [PMID: 29286306 PMCID: PMC5796041 DOI: 10.3390/ijms19010091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/16/2022] Open
Abstract
InSiDDe (In Silico Disorder Design) is a program for the in silico design of intrinsically disordered proteins of desired length and disorder probability. The latter is assessed using IUPred and spans values ranging from 0.55 to 0.95 with 0.05 increments. One to ten artificial sequences per query, each made of 50 to 200 residues, can be generated by InSiDDe. We describe the rationale used to set up InSiDDe and show that an artificial sequence of 100 residues with an IUPred score of 0.6 designed by InSiDDe could be recombinantly expressed in E. coli at high levels without degradation when fused to a natural molecular recognition element (MoRE). In addition, the artificial fusion protein exhibited the expected behavior in terms of binding modulation of the specific partner recognized by the MoRE. To the best of our knowledge, InSiDDe is the first publicly available software for the design of intrinsically disordered protein (IDP) sequences. InSiDDE is publicly available online.
Collapse
|