101
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Shih O, Liao KF, Yeh YQ, Su CJ, Wang CA, Chang JW, Wu WR, Liang CC, Lin CY, Lee TH, Chang CH, Chiang LC, Chang CF, Liu DG, Lee MH, Liu CY, Hsu TW, Mansel B, Ho MC, Shu CY, Lee F, Yen E, Lin TC, Jeng U. Performance of the new biological small- and wide-angle X-ray scattering beamline 13A at the Taiwan Photon Source. J Appl Crystallogr 2022; 55:340-352. [PMID: 35497659 PMCID: PMC8985603 DOI: 10.1107/s1600576722001923] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/18/2022] [Indexed: 12/02/2022] Open
Abstract
A new endstation for biological small- and wide-angle X-ray scattering is detailed, which provides development opportunities for studying correlated local and global structures of biomolecules in solution. Recent developments in the instrumentation and data analysis of synchrotron small-angle X-ray scattering (SAXS) on biomolecules in solution have made biological SAXS (BioSAXS) a mature and popular tool in structural biology. This article reports on an advanced endstation developed at beamline 13A of the 3.0 GeV Taiwan Photon Source for biological small- and wide-angle X-ray scattering (SAXS–WAXS or SWAXS). The endstation features an in-vacuum SWAXS detection system comprising two mobile area detectors (Eiger X 9M/1M) and an online size-exclusion chromatography system incorporating several optical probes including a UV–Vis absorption spectrometer and refractometer. The instrumentation and automation allow simultaneous SAXS–WAXS data collection and data reduction for high-throughput biomolecular conformation and composition determinations. The performance of the endstation is illustrated with the SWAXS data collected for several model proteins in solution, covering a scattering vector magnitude q across three orders of magnitude. The crystal-model fittings to the data in the q range ∼0.005–2.0 Å−1 indicate high similarity of the solution structures of the proteins to their crystalline forms, except for some subtle hydration-dependent local details. These results open up new horizons of SWAXS in studying correlated local and global structures of biomolecules in solution.
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102
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Bourhis JM, Yabukarski F, Communie G, Schneider R, Volchkova VA, Frénéat M, Gérard F, Ducournau C, Mas C, Tarbouriech N, Ringkjøbing Jensen M, Volchkov VE, Blackledge M, Jamin M. Structural dynamics of the C-terminal X domain of Nipah and Hendra viruses controls the attachment to the C-terminal tail of the nucleocapsid protein. J Mol Biol 2022; 434:167551. [DOI: 10.1016/j.jmb.2022.167551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/01/2022] [Accepted: 03/14/2022] [Indexed: 10/18/2022]
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103
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He W, Henning-Knechtel A, Kirmizialtin S. Visualizing RNA Structures by SAXS-Driven MD Simulations. FRONTIERS IN BIOINFORMATICS 2022; 2:781949. [PMID: 36304317 PMCID: PMC9580860 DOI: 10.3389/fbinf.2022.781949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022] Open
Abstract
The biological role of biomolecules is intimately linked to their structural dynamics. Experimental or computational techniques alone are often insufficient to determine accurate structural ensembles in atomic detail. We use all-atom molecular dynamics (MD) simulations and couple it to small-angle X-ray scattering (SAXS) experiments to resolve the structural dynamics of RNA molecules. To accomplish this task, we utilize a set of re-weighting and biasing techniques tailored for RNA molecules. To showcase our approach, we study two RNA molecules: a riboswitch that shows structural variations upon ligand binding, and a two-way junction RNA that displays structural heterogeneity and sensitivity to salt conditions. Integration of MD simulations and experiments allows the accurate construction of conformational ensembles of RNA molecules. We observe a dynamic change of the SAM-I riboswitch conformations depending on its binding partners. The binding of SAM and Mg2+ cations stabilizes the compact state. The absence of Mg2+ or SAM leads to the loss of tertiary contacts, resulting in a dramatic expansion of the riboswitch conformations. The sensitivity of RNA structures to the ionic strength demonstrates itself in the helix junction helix (HJH). The HJH shows non-monotonic compaction as the ionic strength increases. The physics-based picture derived from the experimentally guided MD simulations allows biophysical characterization of RNA molecules. All in all, SAXS-guided MD simulations offer great prospects for studying RNA structural dynamics.
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Affiliation(s)
- Weiwei He
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Chemistry, New York University, New York, NY, United States
| | - Anja Henning-Knechtel
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- *Correspondence: Serdal Kirmizialtin,
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104
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Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins. Biochem Soc Trans 2022; 50:541-554. [PMID: 35129612 DOI: 10.1042/bst20210499] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic weights. Determining conformational ensembles usually involves the integration of biophysical experiments and computational models. In this review, we discuss current approaches to determine conformational ensembles of IDPs and multidomain proteins, including the choice of biophysical experiments, computational models used to sample protein conformations, models to calculate experimental observables from protein structure, and methods to refine ensembles against experimental data. We also provide examples of recent applications of integrative conformational ensemble determination to study IDPs and multidomain proteins and suggest future directions for research in the field.
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105
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A FRET-Based Biosensor for the Src N-Terminal Regulatory Element. BIOSENSORS 2022; 12:bios12020096. [PMID: 35200356 PMCID: PMC8870054 DOI: 10.3390/bios12020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/17/2022]
Abstract
In signaling proteins, intrinsically disordered regions often represent regulatory elements, which are sensitive to environmental effects, ligand binding, and post-translational modifications. The conformational space sampled by disordered regions can be affected by environmental stimuli and these changes trigger, vis a vis effector domain, downstream processes. The disordered nature of these regulatory elements enables signal integration and graded responses but prevents the application of classical approaches for drug screening based on the existence of a fixed three-dimensional structure. We have designed a genetically encodable biosensor for the N-terminal regulatory element of the c-Src kinase, the first discovered protooncogene and lead representative of the Src family of kinases. The biosensor is formed by two fluorescent proteins forming a FRET pair fused at the two extremes of a construct including the SH4, unique and SH3 domains of Src. An internal control is provided by an engineered proteolytic site allowing the generation of an identical mixture of the disconnected fluorophores. We show FRET variations induced by ligand binding. The biosensor has been used for a high-throughput screening of a library of 1669 compounds with seven hits confirmed by NMR.
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106
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Meijer DH, Frias CP, Beugelink JW, Deurloo YN, Janssen BJC. Teneurin4 dimer structures reveal a calcium‐stabilized compact conformation supporting homomeric trans‐interactions. EMBO J 2022; 41:e107505. [PMID: 35099835 PMCID: PMC9058538 DOI: 10.15252/embj.2020107505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/18/2022] Open
Abstract
Establishment of correct synaptic connections is a crucial step during neural circuitry formation. The Teneurin family of neuronal transmembrane proteins promotes cell–cell adhesion via homophilic and heterophilic interactions, and is required for synaptic partner matching in the visual and hippocampal systems in vertebrates. It remains unclear how individual Teneurins form macromolecular cis‐ and trans‐synaptic protein complexes. Here, we present a 2.7 Å cryo‐EM structure of the dimeric ectodomain of human Teneurin4. The structure reveals a compact conformation of the dimer, stabilized by interactions mediated by the C‐rich, YD‐shell, and ABD domains. A 1.5 Å crystal structure of the C‐rich domain shows three conserved calcium binding sites, and thermal unfolding assays and SAXS‐based rigid‐body modeling demonstrate that the compactness and stability of Teneurin4 dimers are calcium‐dependent. Teneurin4 dimers form a more extended conformation in conditions that lack calcium. Cellular assays reveal that the compact cis‐dimer is compatible with homomeric trans‐interactions. Together, these findings support a role for teneurins as a scaffold for macromolecular complex assembly and the establishment of cis‐ and trans‐synaptic interactions to construct functional neuronal circuits.
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Affiliation(s)
- Dimphna H Meijer
- Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Delft The Netherlands
- Department of Chemistry Faculty of Science Structural Biochemistry Bijvoet Center for Biomolecular Research Utrecht University Utrecht The Netherlands
| | - Cátia P Frias
- Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Delft The Netherlands
| | - J Wouter Beugelink
- Department of Chemistry Faculty of Science Structural Biochemistry Bijvoet Center for Biomolecular Research Utrecht University Utrecht The Netherlands
| | - Yanthi N Deurloo
- Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Delft The Netherlands
| | - Bert J C Janssen
- Department of Chemistry Faculty of Science Structural Biochemistry Bijvoet Center for Biomolecular Research Utrecht University Utrecht The Netherlands
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107
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Virk K, Yonezawa K, Choukate K, Singh L, Shimizu N, Chaudhuri B. K-edge anomalous SAXS for protein solution structure modeling. Acta Crystallogr D Struct Biol 2022; 78:204-211. [DOI: 10.1107/s205979832101247x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/23/2021] [Indexed: 11/10/2022] Open
Abstract
K-edge anomalous SAXS intensity was measured from a small, dimeric, partly unstructured protein segment of myosin X by using cupric ions bound to its C-terminal polyhistidine tags. Energy-dependent anomalous SAXS can provide key location-specific information about metal-labeled protein structures in solution that cannot be obtained from routine SAXS analysis. However, anomalous SAXS is seldom used for protein research due to practical difficulties, such as a lack of generic multivalent metal-binding tags and the challenges of measuring weak anomalous signal at the metal absorption edge. This pilot feasibility study suggests that weak K-edge anomalous SAXS signal can be obtained from transition metals bound to terminally located histidine tags of small proteins. The measured anomalous signal can provide information about the distribution of all metal–protein distances in the complex. Such an anomalous SAXS signal can assist in the modeling and validation of structured or unstructured proteins in solution and may potentially become a new addition to the repertoire of techniques in integrative structural biology.
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108
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Kjaergaard M. Estimation of Effective Concentrations Enforced by Complex Linker Architectures from Conformational Ensembles. Biochemistry 2022; 61:171-182. [DOI: 10.1021/acs.biochem.1c00737] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
- The Danish Research Institute for Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus 8000, Denmark
- Center for Proteins in Memory─PROMEMO, Danish National Research Foundation, Aarhus University, Aarhus 8000, Denmark
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109
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Hou XN, Tochio H. Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints. Biophys Rev 2022; 14:55-66. [PMID: 35340613 PMCID: PMC8921464 DOI: 10.1007/s12551-021-00916-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
It has been over two decades since paramagnetic NMR started to form part of the essential techniques for structural analysis of proteins under physiological conditions. Paramagnetic NMR has significantly expanded our understanding of the inherent flexibility of proteins, in particular, those that are formed by combinations of two or more domains. Here, we present a brief overview of techniques to characterize conformational ensembles of such multi-domain proteins using paramagnetic NMR restraints produced through anisotropic metals, with a focus on the basics of anisotropic paramagnetic effects, the general procedures of conformational ensemble reconstruction, and some representative reweighting approaches.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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110
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Czaplewski C, Gong Z, Lubecka EA, Xue K, Tang C, Liwo A. Recent Developments in Data-Assisted Modeling of Flexible Proteins. Front Mol Biosci 2022; 8:765562. [PMID: 35004845 PMCID: PMC8740120 DOI: 10.3389/fmolb.2021.765562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this article, we review the recent developments in the concept and methods for the determination of the dynamic structures of flexible peptides and proteins. In particular, we describe ways to extract information from nuclear magnetic resonance small-angle X-ray scattering (SAXS), and chemical cross-linking coupled with mass spectroscopy (XL-MS) measurements. All these techniques can be used to obtain ensemble-averaged restraints or to re-weight the simulated conformational ensembles.
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Affiliation(s)
| | - Zhou Gong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Emilia A Lubecka
- Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Gdańsk, Poland
| | - Kai Xue
- PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chun Tang
- PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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111
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Kodera N, Ando T. Visualization of intrinsically disordered proteins by high-speed atomic force microscopy. Curr Opin Struct Biol 2022; 72:260-266. [PMID: 34998124 DOI: 10.1016/j.sbi.2021.11.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/30/2022]
Abstract
High-speed atomic force microscopy (HS-AFM) is a powerful tool established 13 years ago. This methodology can capture individual protein molecules carrying out functional activities under near-physiological conditions, without chemical labeling, at 2-3 nm lateral and ∼0.1 nm vertical spatial resolution, and at sub-100 ms temporal resolution. Although most biological HS-AFM studies thus far target structured proteins, HS-AFM is also ideally suited to study the dynamics of intrinsically disordered proteins. Here we review some of the dynamic structures and processes of intrinsically disordered proteins that have been unveiled by HS-AFM imaging.
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Affiliation(s)
- Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
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112
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Krueger S. Planning, executing and assessing the validity of SANS contrast variation experiments. Methods Enzymol 2022; 677:127-155. [DOI: 10.1016/bs.mie.2022.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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113
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Biebl MM, Delhommel F, Faust O, Zak KM, Agam G, Guo X, Mühlhofer M, Dahiya V, Hillebrand D, Popowicz GM, Kampmann M, Lamb DC, Rosenzweig R, Sattler M, Buchner J. NudC guides client transfer between the Hsp40/70 and Hsp90 chaperone systems. Mol Cell 2022; 82:555-569.e7. [DOI: 10.1016/j.molcel.2021.12.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/03/2021] [Accepted: 12/21/2021] [Indexed: 12/21/2022]
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114
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Fang X, Gallego J, Wang YX. Deriving RNA topological structure from SAXS. Methods Enzymol 2022; 677:479-529. [DOI: 10.1016/bs.mie.2022.08.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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115
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Naudi-Fabra S, Blackledge M, Milles S. Synergies of Single Molecule Fluorescence and NMR for the Study of Intrinsically Disordered Proteins. Biomolecules 2021; 12:biom12010027. [PMID: 35053175 PMCID: PMC8773649 DOI: 10.3390/biom12010027] [Citation(s) in RCA: 5] [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: 11/19/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Single molecule fluorescence and nuclear magnetic resonance spectroscopy (NMR) are two very powerful techniques for the analysis of intrinsically disordered proteins (IDPs). Both techniques have individually made major contributions to deciphering the complex properties of IDPs and their interactions, and it has become evident that they can provide very complementary views on the distance-dynamics relationships of IDP systems. We now review the first approaches using both NMR and single molecule fluorescence to decipher the molecular properties of IDPs and their interactions. We shed light on how these two techniques were employed synergistically for multidomain proteins harboring intrinsically disordered linkers, for veritable IDPs, but also for liquid–liquid phase separated systems. Additionally, we provide insights into the first approaches to use single molecule Förster resonance energy transfer (FRET) and NMR for the description of multiconformational models of IDPs.
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116
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Lopez A, Dahiya V, Delhommel F, Freiburger L, Stehle R, Asami S, Rutz D, Blair L, Buchner J, Sattler M. Client binding shifts the populations of dynamic Hsp90 conformations through an allosteric network. SCIENCE ADVANCES 2021; 7:eabl7295. [PMID: 34919431 PMCID: PMC8682993 DOI: 10.1126/sciadv.abl7295] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 05/31/2023]
Abstract
Hsp90 is a molecular chaperone that interacts with a specific set of client proteins and assists their folding. The underlying molecular mechanisms, involving dynamic transitions between open and closed conformations, are still enigmatic. Combining nuclear magnetic resonance, small-angle x-ray scattering, and biochemical experiments, we have identified a key intermediate state of Hsp90 induced by adenosine triphosphate (ATP) binding, in which rotation of the Hsp90 N-terminal domain (NTD) yields a domain arrangement poised for closing. This ATP-stabilized NTD rotation is allosterically communicated across the full Hsp90 dimer, affecting distant client sites. By analyzing the interactions of four distinct clients, i.e., steroid hormone receptors (glucocorticoid receptor and mineralocorticoid receptor), p53, and Tau, we show that client-specific interactions with Hsp90 select and enhance the NTD-rotated state and promote closing of the full-length Hsp90 dimer. The p23 co-chaperone shifts the population of Hsp90 toward the closed state, thereby enhancing client interaction and processing.
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Affiliation(s)
- Abraham Lopez
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Vinay Dahiya
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Lee Freiburger
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Ralf Stehle
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Sam Asami
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Daniel Rutz
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
- Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Laura Blair
- USF Health Byrd Institute, Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL, USA
| | - Johannes Buchner
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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117
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Ecsédi P, Gógl G, Nyitray L. Studying the Structures of Relaxed and Fuzzy Interactions: The Diverse World of S100 Complexes. Front Mol Biosci 2021; 8:749052. [PMID: 34708078 PMCID: PMC8542695 DOI: 10.3389/fmolb.2021.749052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/06/2021] [Indexed: 01/04/2023] Open
Abstract
S100 proteins are small, dimeric, Ca2+-binding proteins of considerable interest due to their associations with cancer and rheumatic and neurodegenerative diseases. They control the functions of numerous proteins by forming protein–protein complexes with them. Several of these complexes were found to display “fuzzy” properties. Examining these highly flexible interactions, however, is a difficult task, especially from a structural biology point of view. Here, we summarize the available in vitro techniques that can be deployed to obtain structural information about these dynamic complexes. We also review the current state of knowledge about the structures of S100 complexes, focusing on their often-asymmetric nature.
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Affiliation(s)
- Péter Ecsédi
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Gergő Gógl
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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118
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Lyu C, Da Vela S, Al-Hilaly Y, Marshall KE, Thorogate R, Svergun D, Serpell LC, Pastore A, Hanger DP. The Disease Associated Tau35 Fragment has an Increased Propensity to Aggregate Compared to Full-Length Tau. Front Mol Biosci 2021; 8:779240. [PMID: 34778381 PMCID: PMC8581542 DOI: 10.3389/fmolb.2021.779240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Tau35 is a truncated form of tau found in human brain in a subset of tauopathies. Tau35 expression in mice recapitulates key features of human disease, including progressive increase in tau phosphorylation, along with cognitive and motor dysfunction. The appearance of aggregated tau suggests that Tau35 may have structural properties distinct from those of other tau species that could account for its pathological role in disease. To address this hypothesis, we performed a structural characterization of monomeric and aggregated Tau35 and compared the results to those of two longer isoforms, 2N3R and 2N4R tau. We used small angle X-ray scattering to show that Tau35, 2N3R and 2N4R tau all behave as disordered monomeric species but Tau35 exhibits higher rigidity. In the presence of the poly-anion heparin, Tau35 increases thioflavin T fluorescence significantly faster and to a greater extent than full-length tau, demonstrating a higher propensity to aggregate. By using atomic force microscopy, circular dichroism, transmission electron microscopy and X-ray fiber diffraction, we provide evidence that Tau35 aggregation is mechanistically and morphologically similar to previously reported tau fibrils but they are more densely packed. These data increase our understanding of the aggregation inducing properties of clinically relevant tau fragments and their potentially damaging role in the pathogenesis of human tauopathies.
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Affiliation(s)
- Chen Lyu
- Department of Basic and Clinical Neuroscience, King’s College London, London, United Kingdom
| | - Stefano Da Vela
- European Molecular Biology Laboratory, Hamburg Site, Hamburg, Germany
| | - Youssra Al-Hilaly
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Karen E. Marshall
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Richard Thorogate
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Site, Hamburg, Germany
| | - Louise C. Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Annalisa Pastore
- Department of Basic and Clinical Neuroscience, King’s College London, London, United Kingdom
| | - Diane P. Hanger
- Department of Basic and Clinical Neuroscience, King’s College London, London, United Kingdom
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119
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Fairman CW, Lever AML, Kenyon JC. Evaluating RNA Structural Flexibility: Viruses Lead the Way. Viruses 2021; 13:v13112130. [PMID: 34834937 PMCID: PMC8624864 DOI: 10.3390/v13112130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/12/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022] Open
Abstract
Our understanding of RNA structure has lagged behind that of proteins and most other biological polymers, largely because of its ability to adopt multiple, and often very different, functional conformations within a single molecule. Flexibility and multifunctionality appear to be its hallmarks. Conventional biochemical and biophysical techniques all have limitations in solving RNA structure and to address this in recent years we have seen the emergence of a wide diversity of techniques applied to RNA structural analysis and an accompanying appreciation of its ubiquity and versatility. Viral RNA is a particularly productive area to study in that this economy of function within a single molecule admirably suits the minimalist lifestyle of viruses. Here, we review the major techniques that are being used to elucidate RNA conformational flexibility and exemplify how the structure and function are, as in all biology, tightly linked.
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Affiliation(s)
| | - Andrew M. L. Lever
- Department of Medicine, Cambridge University, Level 5, Addenbrookes’ Hospital (Box 157), Cambridge CB2 0QQ, UK
- Correspondence: (A.M.L.L.); (J.C.K.); Tel.: +44-(0)-1223-747308 (A.M.L.L. & J.C.K.)
| | - Julia C. Kenyon
- Homerton College, University of Cambridge, Cambridge CB2 8PH, UK;
- Department of Medicine, Cambridge University, Level 5, Addenbrookes’ Hospital (Box 157), Cambridge CB2 0QQ, UK
- Correspondence: (A.M.L.L.); (J.C.K.); Tel.: +44-(0)-1223-747308 (A.M.L.L. & J.C.K.)
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120
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Varming AK, Rasmussen KK, Zong Z, Thulstrup PW, Kilstrup M, Lo Leggio L. Flexible linker modulates the binding affinity of the TP901-1 CI phage repressor to DNA. FEBS J 2021; 289:1135-1148. [PMID: 34665941 DOI: 10.1111/febs.16238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/16/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Temperate bacteriophages can switch between two life cycles following infection of a host bacterium: the lytic or lysogenic life cycle. The choice between these is controlled by a bistable genetic switch. We investigated the genetic switch of the lactococcal temperate bacteriophage, TP901-1, which is controlled by two regulatory proteins, the Clear 1 (CI) repressor and modulator of repression (MOR) antirepressor. CI consists of a DNA-binding N-terminal domain and a C-terminal domain responsible for oligomerization, connected by a flexible interdomain linker. Full-length CI is hexameric, whereas the truncated version CI with 58 C-terminal residues truncated (CIΔ58), missing the second C-terminal subdomain, is dimeric, but binds with the same affinity as full-length CI to the OL operator site, responsible for lytic genes transcription repression. Three variants of CIΔ58 with shorter, longer, and PP substituted linkers were produced and confirmed by circular dichroism spectroscopy and nanodifferential scanning fluorimetry to be well folded. With small-angle X-ray scattering, we delineated the conformational space sampled by the variants and wild-type in solution and found that shortening and lengthening the linker decrease and increase this, respectively, as also substantiated by molecular dynamics and as intended. Isoelectric focusing electrophoresis confirmed that all variants are able to bind to the MOR antirepressor. However, using electrophoretic mobility shift assays, we showed that shortening and lengthening the linker lead to a 94 and 17 times decrease in affinity to OL , respectively. Thus, an appropriate linker length appears to be crucial for appropriate DNA-binding and subsequent TP901-1 genetic switch function.
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Affiliation(s)
| | | | - Zhiyou Zong
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | | | - Mogens Kilstrup
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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121
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Structural Insights into the Unique Modes of Relaxin-Binding and Tethered-Agonist Mediated Activation of RXFP1 and RXFP2. J Mol Biol 2021; 433:167217. [PMID: 34454945 DOI: 10.1016/j.jmb.2021.167217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/09/2021] [Accepted: 08/19/2021] [Indexed: 01/01/2023]
Abstract
Our poor understanding of the mechanism by which the peptide-hormone H2 relaxin activates its G protein coupled receptor, RXFP1 and the related receptor RXFP2, has hindered progress in its therapeutic development. Both receptors possess large ectodomains, which bind H2 relaxin, and contain an N-terminal LDLa module that is essential for receptor signaling and postulated to be a tethered agonist. Here, we show that a conserved motif (GDxxGWxxxF), C-terminal to the LDLa module, is critical for receptor activity. Importantly, this motif adopts different structures in RXFP1 and RXFP2, suggesting distinct activation mechanisms. For RXFP1, the motif is flexible, weakly associates with the LDLa module, and requires H2 relaxin binding to stabilize an active conformation. Conversely, the GDxxGWxxxF motif in RXFP2 is more closely associated with the LDLa module, forming an essential binding interface for H2 relaxin. These differences in the activation mechanism will aid drug development targeting these receptors.
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122
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Sallaberry CA, Voss BJ, Majewski J, Biernat J, Mandelkow E, Chi EY, Vander Zanden CM. Tau and Membranes: Interactions That Promote Folding and Condensation. Front Cell Dev Biol 2021; 9:725241. [PMID: 34621743 PMCID: PMC8491580 DOI: 10.3389/fcell.2021.725241] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/31/2021] [Indexed: 12/15/2022] Open
Abstract
Tau misfolding and assembly is linked to a number of neurodegenerative diseases collectively described as tauopathies, including Alzheimer’s disease (AD) and Parkinson’s disease. Anionic cellular membranes, such as the cytosolic leaflet of the plasma membrane, are sites that concentrate and neutralize tau, primarily due to electrostatic interactions with tau’s microtubule binding repeat domain (RD). In addition to electrostatic interactions with lipids, tau also has interactions with membrane proteins, which are important for tau’s cellular functions. Tau also interacts with lipid tails to facilitate direct translocation across the membrane and can form stable protein-lipid complexes involved in cell-to-cell transport. Concentrated tau monomers at the membrane surface can form reversible condensates, change secondary structures, and induce oligomers, which may eventually undergo irreversible crosslinking and fibril formation. These β-sheet rich tau structures are capable of disrupting membrane organization and are toxic in cell-based assays. Given the evidence for relevant membrane-based tau assembly, we review the emerging hypothesis that polyanionic membranes may serve as a site for phase-separated tau condensation. Membrane-mediated phase separation may have important implications for regulating tau folding/misfolding, and may be a powerful mechanism to spatially direct tau for native membrane-mediated functions.
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Affiliation(s)
- Chad A Sallaberry
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Barbie J Voss
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Jaroslaw Majewski
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA, United States.,Department of Chemical & Biological Engineering, Center for Biomedical Engineering, The University of New Mexico, Albuquerque, NM, United States.,Theoretical Biology and Biophysics Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Jacek Biernat
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Center of Advanced European Studies and Research (CAESAR) Center, Bonn, Germany.,Department of Neurodegenerative Disease and Geriatric Psychiatry, Medical School, University of Bonn, Bonn, Germany
| | - Eva Y Chi
- Department of Chemical & Biological Engineering, Center for Biomedical Engineering, The University of New Mexico, Albuquerque, NM, United States
| | - Crystal M Vander Zanden
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, United States
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123
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Prieto VA, Namitz KEW, Showalter SA. Transient Electrostatic Interactions between Fcp1 and Rap74 Bias the Conformational Ensemble of the Complex with Minimal Impact on Binding Affinity. J Phys Chem B 2021; 125:10917-10927. [PMID: 34550709 DOI: 10.1021/acs.jpcb.1c05131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intrinsically disordered protein (IDP) sequences often contain a high proportion of charged residues in conjunction with their high degree of hydrophilicity and solvation. For high net charge IDPs, long-range electrostatic interactions are thought to play a role in modulating the strength or kinetics of protein-protein interactions. In this work, we examined intramolecular interactions mediated by charged regions of a model IDP, the C-terminal tail of the phosphatase Fcp1. Specifically, this work focuses on intermolecular interactions between acidic and basic patches in the primary structure of Fcp1 and their contributions to binding its predominantly basic partner, the winged helix domain of Rap74. We observe both intramolecular and intermolecular interactions through paramagnetic relaxation enhancement (PRE) consistent with oppositely charged regions associating with one another, both in unbound Fcp1 and in the Fcp1-Rap74 complex. Formation of this complex is strongly driven by hydrophobic interactions in the minimal binding motif. Here, we test the hypothesis that charged residues in Fcp1 that flank the binding helix also contribute to the strength of binding. Charge inversion mutations in Fcp1 generally support this hypothesis, while PRE data suggest substitution of observed transient interactions in the unbound ensemble for similarly transient interactions with Rap74 in the complex.
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Affiliation(s)
- Victor A Prieto
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kevin E W Namitz
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Scott A Showalter
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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124
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Silva NSM, Rodrigues LFDC, Dores-Silva PR, Montanari CA, Ramos CHI, Barbosa LRS, Borges JC. Structural, thermodynamic and functional studies of human 71 kDa heat shock cognate protein (HSPA8/hHsc70). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140719. [PMID: 34571256 DOI: 10.1016/j.bbapap.2021.140719] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/29/2021] [Accepted: 09/21/2021] [Indexed: 01/14/2023]
Abstract
Human 71 kDa heat shock cognate protein (HSPA8, also known as Hsc70, Hsp70-8, Hsc71, Hsp71 or Hsp73) is a constitutively expressed chaperone that is critical for cell proteostasis. In the cytosol, HSPA8 plays a pivotal role in folding and refolding, facilitates protein trafficking across membranes and targets proteins for degradation, among other functions. Here, we report an in solution study of recombinant HSPA8 (rHSPA8) using a variety of biophysical and biochemical approaches. rHSPA8 shares several structural and functional similarities with others human Hsp70s. It has two domains with different stabilities and interacts with adenosine nucleotides with dissociation constants in the low micromolar range, which were higher in the presence of Mg2+. rHSPA8 showed lower ATPase activity than its homolog HSPA5/hGrp78/hBiP, but it was 4-fold greater than that of recombinant HSPA1A/hHsp70-1A, with which it is 86% identical. Small angle X-ray scattering indicated that rHSPA8 behaved as an elongated monomeric protein in solution with dimensions similar to those observed for HSPA1A. In addition, rHSPA8 showed structural flexibility between its compacted and extended conformations. The data also indicated that HSPA8 has capacity in preventing the aggregation of model client proteins. The present study expands the understanding of the structure and activity of this chaperone and aligns with the idea that human homologous Hsp70s have divergent functions.
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Affiliation(s)
| | | | - Paulo Roberto Dores-Silva
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, Brazil; Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | | | | | - Leandro Ramos Souza Barbosa
- Institute of Physics, University of São Paulo, São Paulo, SP, Brazil; Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Júlio César Borges
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, Brazil.
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125
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Affiliation(s)
- Brian A. Collins
- Physics and Astronomy Washington State University Pullman Washington USA
| | - Eliot Gann
- Material Measurement Laboratory National Institute of Standards and Technology Gaithersburg Maryland USA
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126
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Gomes T, Martin-Malpartida P, Ruiz L, Aragón E, Cordeiro TN, Macias MJ. Conformational landscape of multidomain SMAD proteins. Comput Struct Biotechnol J 2021; 19:5210-5224. [PMID: 34630939 PMCID: PMC8479633 DOI: 10.1016/j.csbj.2021.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/21/2022] Open
Abstract
SMAD transcription factors, the main effectors of the TGFβ (transforming growth factor β) network, have a mixed architecture of globular domains and flexible linkers. Such a complicated architecture precluded the description of their full-length (FL) structure for many years. In this study, we unravel the structures of SMAD4 and SMAD2 proteins through an integrative approach combining Small-angle X-ray scattering, Nuclear Magnetic Resonance spectroscopy, X-ray, and computational modeling. We show that both proteins populate ensembles of conformations, with the globular domains tethered by disordered and flexible linkers, which defines a new dimension of regulation. The flexibility of the linkers facilitates DNA and protein binding and modulates the protein structure. Yet, SMAD4FL is monomeric, whereas SMAD2FL is in different monomer-dimer-trimer states, driven by interactions of the MH2 domains. Dimers are present regardless of the SMAD2FL activation state and concentration. Finally, we propose that SMAD2FL dimers are key building blocks for the quaternary structures of SMAD complexes.
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Affiliation(s)
- Tiago Gomes
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Pau Martin-Malpartida
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Lidia Ruiz
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Eric Aragón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Tiago N. Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria J. Macias
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
- ICREA, Passeig Lluís Companys 23, Barcelona 08010, Spain
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127
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Rengifo-Gonzalez JC, El Hage K, Clément MJ, Steiner E, Joshi V, Craveur P, Durand D, Pastré D, Bouhss A. The cooperative binding of TDP-43 to GU-rich RNA repeats antagonizes TDP-43 aggregation. eLife 2021; 10:67605. [PMID: 34490845 PMCID: PMC8523171 DOI: 10.7554/elife.67605] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
TDP-43 is a nuclear RNA-binding protein that forms neuronal cytoplasmic inclusions in two major neurodegenerative diseases, ALS and FTLD. While the self-assembly of TDP-43 by its structured N-terminal and intrinsically disordered C-terminal domains has been widely studied, the mechanism by which mRNA preserves TDP-43 solubility in the nucleus has not been addressed. Here, we demonstrate that tandem RNA recognition motifs of TDP-43 bind to long GU-repeats in a cooperative manner through intermolecular interactions. Moreover, using mutants whose cooperativity is impaired, we found that the cooperative binding of TDP-43 to mRNA may be critical to maintain the solubility of TDP-43 in the nucleus and the miscibility of TDP-43 in cytoplasmic stress granules. We anticipate that the knowledge of a higher order assembly of TDP-43 on mRNA may clarify its role in intron processing and provide a means of interfering with the cytoplasmic aggregation of TDP-43.
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Affiliation(s)
- Juan Carlos Rengifo-Gonzalez
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Krystel El Hage
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Marie-Jeanne Clément
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Emilie Steiner
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Vandana Joshi
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | | | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - David Pastré
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Ahmed Bouhss
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
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128
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Anandan A, Dunstan NW, Ryan TM, Mertens HDT, Lim KYL, Evans GL, Kahler CM, Vrielink A. Conformational flexibility of EptA driven by an interdomain helix provides insights for enzyme-substrate recognition. IUCRJ 2021; 8:732-746. [PMID: 34584735 PMCID: PMC8420757 DOI: 10.1107/s2052252521005613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Many pathogenic gram-negative bacteria have developed mechanisms to increase resistance to cationic antimicrobial peptides by modifying the lipid A moiety. One modification is the addition of phospho-ethano-lamine to lipid A by the enzyme phospho-ethano-lamine transferase (EptA). Previously we reported the structure of EptA from Neisseria, revealing a two-domain architecture consisting of a periplasmic facing soluble domain and a transmembrane domain, linked together by a bridging helix. Here, the conformational flexibility of EptA in different detergent environments is probed by solution scattering and intrinsic fluorescence-quenching studies. The solution scattering studies reveal the enzyme in a more compact state with the two domains positioned close together in an n-do-decyl-β-d-maltoside micelle environment and an open extended structure in an n-do-decyl-phospho-choline micelle environment. Intrinsic fluorescence quenching studies localize the domain movements to the bridging helix. These results provide important insights into substrate binding and the molecular mechanism of endotoxin modification by EptA.
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Affiliation(s)
- Anandhi Anandan
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Nicholas W. Dunstan
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Timothy M. Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Unit, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Katherine Y. L. Lim
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Genevieve L. Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Charlene M. Kahler
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
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129
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Dendooven T, Paris G, Shkumatov AV, Islam MS, Burt A, Kubańska MA, Yang TY, Hardwick SW, Luisi BF. Multi-scale ensemble properties of the Escherichia coli RNA degradosome. Mol Microbiol 2021; 117:102-120. [PMID: 34415624 PMCID: PMC7613265 DOI: 10.1111/mmi.14800] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022]
Abstract
In organisms from all domains of life, multi-enzyme assemblies play central roles in defining transcript lifetimes and facilitating RNA-mediated regulation of gene expression. An assembly dedicated to such roles, known as the RNA degradosome, is found amongst bacteria from highly diverse lineages. About a fifth of the assembly mass of the degradosome of Escherichia coli and related species is predicted to be intrinsically disordered - a property that has been sustained for over a billion years of bacterial molecular history and stands in marked contrast to the high degree of sequence variation of that same region. Here, we characterize the conformational dynamics of the degradosome using a hybrid structural biology approach that combines solution scattering with ad hoc ensemble modelling, cryo-electron microscopy, and other biophysical methods. The E. coli degradosome can form punctate bodies in vivo that may facilitate its functional activities, and based on our results, we propose an electrostatic switch model to account for the propensity of the degradosome to undergo programmable puncta formation.
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Affiliation(s)
- Tom Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giulia Paris
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Alexander V Shkumatov
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Md Saiful Islam
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Alister Burt
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Marta A Kubańska
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tai Yuchen Yang
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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130
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Lee SJ, Kim Y, Kim TW, Yang C, Thamilselvan K, Jeong H, Hyun J, Ihee H. Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100512. [PMID: 35509376 PMCID: PMC9062587 DOI: 10.1016/j.xcrp.2021.100512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Molecular switches alterable between two stable states by environmental stimuli, such as light and temperature, offer the potential for controlling biological functions. Here, we report a circular photoswitchable protein complex made of multiple protein molecules that can rapidly and reversibly switch with significant conformational changes. The structural and photochromic properties of photoactive yellow protein (PYP) are harnessed to construct circular oligomer PYPs (coPYPs) of desired sizes. Considering the light-induced N-terminal protrusion of monomer PYP, we expected coPYPs would expand upon irradiation, but time-resolved X-ray scattering data reveal that the late intermediate has a pronounced light-induced contraction motion. This work not only provides an approach to engineering a novel protein-based molecular switch based on circular oligomers of well-known protein units but also demonstrates the importance of characterizing the structural dynamics of designed molecular switches.
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Affiliation(s)
- Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Youngmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kamatchi Thamilselvan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hyeongseop Jeong
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
| | - Jaekyung Hyun
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology (OIST), Okinawa 904-0495, Japan
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Lead contact
- Correspondence:
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131
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Chen Z, Qian Y, Song Y, Xu X, Tao L, Mussa N, Ghose S, Li ZJ. Design of next-generation therapeutic IgG4 with improved manufacturability and bioanalytical characteristics. MAbs 2021; 12:1829338. [PMID: 33044887 PMCID: PMC7577236 DOI: 10.1080/19420862.2020.1829338] [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] [Indexed: 12/19/2022] Open
Abstract
Manufacturability of immunoglobulin G4 (IgG4) antibodies from the Chemistry, Manufacture, and Controls (CMC) perspective has received little attention during early drug discovery. Despite the success of protein engineering in improving antibody biophysical properties, a clear gap still exists between rational design of IgG4 candidates and their manufacturing suitability. Here, we illustrate that undesirable two-peak elution profiles in cation-exchange chromatography are attributed to the S228P mutation (in IgG4 core-hinge region) intentionally designed to prevent Fab-arm exchange. A new scaffolding platform for engineering IgG4 antibodies amenable to bioprocessing and bioanalysis is proposed by introducing an “IgG1-like” single-point mutation in the hinge or CH1 region of IgG4S228P. This work offers insight into the design, discovery, and development of innovative therapeutic antibodies that are well suited for robust biomanufacturing and quality control.
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Affiliation(s)
- Zhiqiang Chen
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb Company , Devens, MA, USA
| | - Yueming Qian
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb Company , Devens, MA, USA
| | - Yuanli Song
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb Company , Devens, MA, USA
| | - Xuankuo Xu
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb Company , Devens, MA, USA
| | - Li Tao
- Biophysical Characterization, Global Product Development and Supply, Bristol Myers Squibb Company , New Brunswick, NJ, USA
| | - Nesredin Mussa
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb Company , Devens, MA, USA
| | - Sanchayita Ghose
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb Company , Devens, MA, USA
| | - Zheng Jian Li
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb Company , Devens, MA, USA
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132
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Lindorff-Larsen K, Kragelund BB. On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins. J Mol Biol 2021; 433:167196. [PMID: 34390736 DOI: 10.1016/j.jmb.2021.167196] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as having no persistent tertiary structure; instead they interconvert between a large number of different and often expanded structures. IDPs and IDRs are involved in an enormously wide range of biological functions and reveal novel mechanisms of interactions, and while they defy the common structure-function paradigm of folded proteins, their structural preferences and dynamics are important for their function. We here discuss open questions in the field of IDPs and IDRs, focusing on areas where machine learning and other computational methods play a role. We discuss computational methods aimed to predict transiently formed local and long-range structure, including methods for integrative structural biology. We discuss the many different ways in which IDPs and IDRs can bind to other molecules, both via short linear motifs, as well as in the formation of larger dynamic complexes such as biomolecular condensates. We discuss how experiments are providing insight into such complexes and may enable more accurate predictions. Finally, we discuss the role of IDPs in disease and how new methods are needed to interpret the mechanistic effects of genomic variants in IDPs.
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Affiliation(s)
- 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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133
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Thapa C, Roivas P, Haataja T, Permi P, Pentikäinen U. Interaction mechanism of endogenous PP2A inhibitor protein ENSA with PP2A. FEBS J 2021; 289:519-534. [PMID: 34346186 DOI: 10.1111/febs.16150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 01/09/2023]
Abstract
The vast diversity of protein phosphatase 2A (PP2A) holoenzyme composition ensures its multifaceted role in the regulation of cellular growth and signal transduction. In several pathological conditions, such as cancer, PP2A is inhibited by endogenous inhibitor proteins. Several PP2A inhibitor proteins have been identified, one of which is α-endosulfine (ENSA). ENSA inhibits PP2A activity when it is phosphorylated at Ser67 by Greatwall (Gwl) kinase. The role of ENSA in PP2A inhibition is rather well characterized, but knowledge of the mechanism of inhibition is scarce. In this study, we have performed comprehensive structural characterization of ENSA, and its interaction with PP2A A- and various B56-subunit isoforms by combining NMR spectroscopy, small-angle X-ray scattering (SAXS) and interaction assays. The results clearly indicate that ENSA is an intrinsically disordered protein containing three transient α-helical structures. ENSA was observed to interact PP2A mainly via A-subunit, as the affinity with the A-subunit is significantly stronger than with any of the B56 subunits. Based on our results, it seems that ENSA follows the dock-and-coalesce mechanism in associating with PP2A A-subunit. Taken together, our results provide an essential structural and molecular framework to understanding molecular bases of ENSA-mediated PP2A inhibition, which is crucial for the development of new therapies for diseases linked to PP2A inhibition.
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Affiliation(s)
- Chandan Thapa
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Finland.,Turku BioScience, University of Turku, Finland
| | - Pekka Roivas
- Institute of Biomedicine, University of Turku, Finland.,Turku BioScience, University of Turku, Finland
| | - Tatu Haataja
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Finland.,Department of Chemistry and Nanoscience Center, University of Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Institute of Biomedicine, University of Turku, Finland.,Turku BioScience, University of Turku, Finland
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134
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Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J. Structure and dynamics of the quaternary hunchback mRNA translation repression complex. Nucleic Acids Res 2021; 49:8866-8885. [PMID: 34329466 PMCID: PMC8421216 DOI: 10.1093/nar/gkab635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/05/2021] [Accepted: 07/27/2021] [Indexed: 01/02/2023] Open
Abstract
A key regulatory process during Drosophila development is the localized suppression of the hunchback mRNA translation at the posterior, which gives rise to a hunchback gradient governing the formation of the anterior-posterior body axis. This suppression is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for proper Drosophila development. The RNA contacts have been elucidated for the proteins individually in several atomic-resolution structures. However, the interplay of all three proteins during RNA suppression remains a long-standing open question. Here, we characterize the quaternary complex of the RNA-binding domains of Brat, Pum and Nanos with hunchback mRNA by combining NMR spectroscopy, SANS/SAXS, XL/MS with MD simulations and ITC assays. The quaternary hunchback mRNA suppression complex comprising the RNA binding domains is flexible with unoccupied nucleotides functioning as a flexible linker between the Brat and Pum-Nanos moieties of the complex. Moreover, the presence of the Pum-HD/Nanos-ZnF complex has no effect on the equilibrium RNA binding affinity of the Brat RNA binding domain. This is in accordance with previous studies, which showed that Brat can suppress mRNA independently and is distributed uniformly throughout the embryo.
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Affiliation(s)
- Jakub Macošek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Sophie L Winter
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jaelle Foot
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Kathryn Perez
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Miloš T Ivanović
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Inga Loedige
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Frank Gabel
- Institut Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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135
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Molecular insights on CALX-CBD12 interdomain dynamics from MD simulations, RDCs, and SAXS. Biophys J 2021; 120:3664-3675. [PMID: 34310942 DOI: 10.1016/j.bpj.2021.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/25/2021] [Accepted: 07/20/2021] [Indexed: 11/23/2022] Open
Abstract
Na+/Ca2+ exchangers (NCXs) are secondary active transporters that couple the translocation of Na+ with the transport of Ca2+ in the opposite direction. The exchanger is an essential Ca2+ extrusion mechanism in excitable cells. It consists of a transmembrane domain and a large intracellular loop that contains two Ca2+-binding domains, CBD1 and CBD2. The two CBDs are adjacent to each other and form a two-domain Ca2+ sensor called CBD12. Binding of intracellular Ca2+ to CBD12 activates the NCX but inhibits the NCX of Drosophila, CALX. NMR spectroscopy and SAXS studies showed that CALX and NCX CBD12 constructs display significant interdomain flexibility in the apo state but assume rigid interdomain arrangements in the Ca2+-bound state. However, detailed structure information on CBD12 in the apo state is missing. Structural characterization of proteins formed by two or more domains connected by flexible linkers is notoriously challenging and requires the combination of orthogonal information from multiple sources. As an attempt to characterize the conformational ensemble of CALX-CBD12 in the apo state, we applied molecular dynamics (MD) simulations, NMR (1H-15N residual dipolar couplings), and small-angle x-ray scattering (SAXS) data in a combined strategy to select an ensemble of conformations in agreement with the experimental data. This joint approach demonstrated that CALX-CBD12 preferentially samples closed conformations, whereas the wide-open interdomain arrangement characteristic of the Ca2+-bound state is less frequently sampled. These results are consistent with the view that Ca2+ binding shifts the CBD12 conformational ensemble toward extended conformers, which could be a key step in the NCXs' allosteric regulation mechanism. This strategy, combining MD with NMR and SAXS, provides a powerful approach to select ensembles of conformations that could be applied to other flexible multidomain systems.
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136
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Chen EHL, Lin KM, Sang JC, Ho MR, Lee CH, Shih O, Su CJ, Yeh YQ, Jeng US, Chen RPY. Condition-dependent structural collapse in the intrinsically disordered N-terminal domain of prion protein. IUBMB Life 2021; 74:780-793. [PMID: 34288372 DOI: 10.1002/iub.2528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/06/2022]
Abstract
Prion protein is composed of a structure-unsolved N-terminal domain and a globular C-terminal domain. Under limited trypsin digestion, mouse recombinant prion protein can be cleaved into two parts at residue Lys105. Here, we termed these two fragments as the N-domain (sequence 23-105) and the C-domain (sequence 106-230). In this study, the structural properties of the N-domain, the C-domain, and the full-length protein were explored using small-angle X-ray scattering, analytical ultracentrifugation, circular dichroism spectroscopy, and the 8-anilino-1-naphthalenesulfonic acid binding assay. The conformation and size of the prion protein were found to change sensitively under the solvent conditions. The positive residues in the sequence 23-99 of the N-domain were found to be responsible for the enhanced flexibility with the salt concentration reduced below 5 mM. The C-domain containing a hydrophobic patch tends to unfold and aggregate during a salt-induced structural collapse. The N-domain collapsed together with the C-domain at pH 5.2, whereas it collapsed independently at pH 4.2. The positively charged cluster (sequence 100-105) in the N-domain contributed to protecting the exposed hydrophobic surface of the C-domain.
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Affiliation(s)
- Eric H-L Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuei-Ming Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Jason C Sang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chih-Hsuan Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan.,Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Rita P-Y Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.,Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan
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137
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Kursula P. Small-angle X-ray scattering for the proteomics community: current overview and future potential. Expert Rev Proteomics 2021; 18:415-422. [PMID: 34210208 DOI: 10.1080/14789450.2021.1951242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Proteins are biological nanoparticles. For structural proteomics and hybrid structural biology, complementary methods are required that allow both high throughput and accurate automated data analysis. Small-angle X-ray scattering (SAXS) is a method for observing the size and shape of particles, such as proteins and complexes, in solution. SAXS data can be used to model both the structure, oligomeric state, conformational changes, and flexibility of biomolecular samples.Areas covered: The key principles of SAXS, its sample requirements, and its current and future applications for structural proteomics are briefly reviewed. Recent technical developments in SAXS experiments are discussed, and future potential of the method in structural proteomics is evaluated.Expert opinion: SAXS is a method suitable for several aspects of integrative structural proteomics, with current technical developments allowing for higher throughput and time-resolved studies, as well as the analysis of complex samples, such as membrane proteins. Increasing automation and streamlined data analysis are expected to equip SAXS for structure-based screening workflows. Originally, structural genomics had a heavy focus on folded, crystallizable proteins and complexes - SAXS is a method allowing an expansion of this focus to flexible and disordered systems.
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Affiliation(s)
- Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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138
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Hawley KL, Montezuma-Rusca JM, Delgado KN, Singh N, Uversky VN, Caimano MJ, Radolf JD, Luthra A. Structural Modeling of the Treponema pallidum Outer Membrane Protein Repertoire: a Road Map for Deconvolution of Syphilis Pathogenesis and Development of a Syphilis Vaccine. J Bacteriol 2021; 203:e0008221. [PMID: 33972353 PMCID: PMC8407342 DOI: 10.1128/jb.00082-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/27/2021] [Indexed: 01/11/2023] Open
Abstract
Treponema pallidum, an obligate human pathogen, has an outer membrane (OM) whose physical properties, ultrastructure, and composition differ markedly from those of phylogenetically distant Gram-negative bacteria. We developed structural models for the outer membrane protein (OMP) repertoire (OMPeome) of T. pallidum Nichols using solved Gram-negative structures, computational tools, and small-angle X-ray scattering (SAXS) of selected recombinant periplasmic domains. The T. pallidum "OMPeome" harbors two "stand-alone" proteins (BamA and LptD) involved in OM biogenesis and four paralogous families involved in the influx/efflux of small molecules: 8-stranded β-barrels, long-chain-fatty-acid transporters (FadLs), OM factors (OMFs) for efflux pumps, and T. pallidum repeat proteins (Tprs). BamA (TP0326), the central component of a β-barrel assembly machine (BAM)/translocation and assembly module (TAM) hybrid, possesses a highly flexible polypeptide-transport-associated (POTRA) 1-5 arm predicted to interact with TamB (TP0325). TP0515, an LptD ortholog, contains a novel, unstructured C-terminal domain that models inside the β-barrel. T. pallidum has four 8-stranded β-barrels, each containing positively charged extracellular loops that could contribute to pathogenesis. Three of five FadL-like orthologs have a novel α-helical, presumptively periplasmic C-terminal extension. SAXS and structural modeling further supported the bipartite membrane topology and tridomain architecture of full-length members of the Tpr family. T. pallidum's two efflux pumps presumably extrude noxious small molecules via four coexpressed OMFs with variably charged tunnels. For BamA, LptD, and OMFs, we modeled the molecular machines that deliver their substrates into the OM or external milieu. The spirochete's extended families of OM transporters collectively confer a broad capacity for nutrient uptake. The models also furnish a structural road map for vaccine development. IMPORTANCE The unusual outer membrane (OM) of T. pallidum, the syphilis spirochete, is the ultrastructural basis for its well-recognized capacity for invasiveness, immune evasion, and persistence. In recent years, we have made considerable progress in identifying T. pallidum's repertoire of OMPs. Here, we developed three-dimensional (3D) models for the T. pallidum Nichols OMPeome using structural modeling, bioinformatics, and solution scattering. The OM contains three families of OMP transporters, an OMP family involved in the extrusion of noxious molecules, and two "stand-alone" proteins involved in OM biogenesis. This work represents a major advance toward elucidating host-pathogen interactions during syphilis; understanding how T. pallidum, an extreme auxotroph, obtains a wide array of biomolecules from its obligate human host; and developing a vaccine with global efficacy.
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Affiliation(s)
- Kelly L. Hawley
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases and Immunology, Connecticut Children’s, Hartford, Connecticut, USA
| | - Jairo M. Montezuma-Rusca
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases, UConn Health, Farmington, Connecticut, USA
| | | | - Navreeta Singh
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Melissa J. Caimano
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Justin D. Radolf
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
| | - Amit Luthra
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
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139
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Bourgeois B, Gui T, Hoogeboom D, Hocking HG, Richter G, Spreitzer E, Viertler M, Richter K, Madl T, Burgering BMT. Multiple regulatory intrinsically disordered motifs control FOXO4 transcription factor binding and function. Cell Rep 2021; 36:109446. [PMID: 34320339 DOI: 10.1016/j.celrep.2021.109446] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 04/15/2021] [Accepted: 07/02/2021] [Indexed: 12/11/2022] Open
Abstract
Transcription factors harbor defined regulatory intrinsically disordered regions (IDRs), which raises the question of how they mediate binding to structured co-regulators and modulate their activity. Here, we present a detailed molecular regulatory mechanism of Forkhead box O4 (FOXO4) by the structured transcriptional co-regulator β-catenin. We find that the disordered FOXO4 C-terminal region, which contains its transactivation domain, binds β-catenin through two defined interaction sites, and this is regulated by combined PKB/AKT- and CK1-mediated phosphorylation. Binding of β-catenin competes with the autoinhibitory interaction of the FOXO4 disordered region with its DNA-binding Forkhead domain, and thereby enhances FOXO4 transcriptional activity. Furthermore, we show that binding of the β-catenin inhibitor protein ICAT is compatible with FOXO4 binding to β-catenin, suggesting that ICAT acts as a molecular switch between anti-proliferative FOXO and pro-proliferative Wnt/TCF/LEF signaling. These data illustrate how the interplay of IDRs, post-translational modifications, and co-factor binding contribute to transcription factor function.
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Affiliation(s)
- Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Tianshu Gui
- Oncode Institute and Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Diana Hoogeboom
- Oncode Institute and Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Henry G Hocking
- Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Gesa Richter
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Martin Viertler
- Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Klaus Richter
- Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
| | - Boudewijn M T Burgering
- Oncode Institute and Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands.
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140
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Clerc I, Sagar A, Barducci A, Sibille N, Bernadó P, Cortés J. The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective. Comput Struct Biotechnol J 2021; 19:3817-3828. [PMID: 34285781 PMCID: PMC8273358 DOI: 10.1016/j.csbj.2021.06.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 01/15/2023] Open
Abstract
Intrinsically Disordered Proteins and Regions (IDPs/IDRs) are key components of a multitude of biological processes. Conformational malleability enables IDPs/IDRs to perform very specialized functions that cannot be accomplished by globular proteins. The functional role for most of these proteins is related to the recognition of other biomolecules to regulate biological processes or as a part of signaling pathways. Depending on the extent of disorder, the number of interacting sites and the type of partner, very different architectures for the resulting assemblies are possible. More recently, molecular condensates with liquid-like properties composed of multiple copies of IDPs and nucleic acids have been proven to regulate key processes in eukaryotic cells. The structural and kinetic details of disordered biomolecular complexes are difficult to unveil experimentally due to their inherent conformational heterogeneity. Computational approaches, alone or in combination with experimental data, have emerged as unavoidable tools to understand the functional mechanisms of this elusive type of assemblies. The level of description used, all-atom or coarse-grained, strongly depends on the size of the molecular systems and on the timescale of the investigated mechanism. In this mini-review, we describe the most relevant architectures found for molecular interactions involving IDPs/IDRs and the computational strategies applied for their investigation.
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Affiliation(s)
- Ilinka Clerc
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Amin Sagar
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Alessandro Barducci
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Nathalie Sibille
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
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141
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Shapiro DM, Ney M, Eghtesadi SA, Chilkoti A. Protein Phase Separation Arising from Intrinsic Disorder: First-Principles to Bespoke Applications. J Phys Chem B 2021; 125:6740-6759. [PMID: 34143622 DOI: 10.1021/acs.jpcb.1c01146] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The phase separation of biomolecules has become the focus of intense research in the past decade, with a growing body of research implicating this phenomenon in essentially all biological functions, including but not limited to homeostasis, stress responses, gene regulation, cell differentiation, and disease. Excellent reviews have been published previously on the underlying physical basis of liquid-liquid phase separation (LLPS) of biological molecules (Nat. Phys. 2015, 11, 899-904) and LLPS as it occurs natively in physiology and disease (Science 2017, 357, eaaf4382; Biochemistry 2018, 57, 2479-2487; Chem. Rev. 2014, 114, 6844-6879). Here, we review how the theoretical physical basis of LLPS has been used to better understand the behavior of biomolecules that undergo LLPS in natural systems and how this understanding has also led to the development of novel synthetic systems that exhibit biomolecular phase separation, and technologies that exploit these phenomena. In part 1 of this Review, we explore the theory behind the phase separation of biomolecules and synthetic macromolecules and introduce a few notable phase-separating biomolecules. In part 2, we cover experimental and computational methods used to study phase-separating proteins and how these techniques have uncovered the mechanisms underlying phase separation in physiology and disease. Finally, in part 3, we cover the development and applications of engineered phase-separating polypeptides, ranging from control of their self-assembly to create defined supramolecular architectures to reprogramming biological processes using engineered IDPs that exhibit LLPS.
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Affiliation(s)
- Daniel Mark Shapiro
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Max Ney
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Seyed Ali Eghtesadi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
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142
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Ben-Bassat A, Giladi M, Haitin Y. Structure of KCNH2 cyclic nucleotide-binding homology domain reveals a functionally vital salt-bridge. J Gen Physiol 2021; 152:151568. [PMID: 32191791 PMCID: PMC7141593 DOI: 10.1085/jgp.201912505] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/24/2020] [Accepted: 02/12/2020] [Indexed: 01/04/2023] Open
Abstract
Human KCNH2 channels (hKCNH2, ether-à-go-go [EAG]–related gene, hERG) are best known for their contribution to cardiac action potential repolarization and have key roles in various pathologies. Like other KCNH family members, hKCNH2 channels contain a unique intracellular complex, consisting of an N-terminal eag domain and a C-terminal cyclic nucleotide-binding homology domain (CNBHD), which is crucial for channel function. Previous studies demonstrated that the CNBHD is occupied by an intrinsic ligand motif, in a self-liganded conformation, providing a structural mechanism for the lack of KCNH channel regulation by cyclic nucleotides. While there have been significant advancements in the structural and functional characterization of the CNBHD of KCNH channels, a high-resolution structure of the hKCNH2 intracellular complex has been missing. Here, we report the 1.5 Å resolution structure of the hKCNH2 channel CNBHD. The structure reveals the canonical fold shared by other KCNH family members, where the spatial organization of the intrinsic ligand is preserved within the β-roll region. Moreover, measurements of small-angle x-ray scattering profile in solution, as well as comparison with a recent NMR analysis of hKCNH2, revealed high agreement with the crystallographic structure, indicating an overall low flexibility in solution. Importantly, we identified a novel salt-bridge (E807-R863) which was not previously resolved in the NMR and cryo-EM structures. Electrophysiological analysis of charge-reversal mutations revealed the bridge’s crucial role in hKCNH2 function. Moreover, comparison with other KCNH members revealed the structural conservation of this salt-bridge, consistent with its functional significance. Together with the available structure of the mouse KCNH1 intracellular complex and previous electrophysiological and spectroscopic studies of KCNH family members, we propose that this salt-bridge serves as a strategically positioned linchpin to support both the spatial organization of the intrinsic ligand and the maintenance of the intracellular complex interface.
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Affiliation(s)
- Ariel Ben-Bassat
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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143
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Hammel M, Tainer JA. X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology. Protein Sci 2021; 30:1735-1756. [PMID: 34056803 PMCID: PMC8376411 DOI: 10.1002/pro.4133] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022]
Abstract
Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIVBRCT–Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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144
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Matsuo T. Viewing SARS-CoV-2 Nucleocapsid Protein in Terms of Molecular Flexibility. BIOLOGY 2021; 10:454. [PMID: 34064163 PMCID: PMC8224284 DOI: 10.3390/biology10060454] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022]
Abstract
The latest coronavirus SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19) pneumonia leading to the pandemic, contains 29 proteins. Among them, nucleocapsid protein (NCoV2) is one of the abundant proteins and shows multiple functions including packaging the RNA genome during the infection cycle. It has also emerged as a potential drug target. In this review, the current status of the research of NCoV2 is described in terms of molecular structure and dynamics. NCoV2 consists of two domains, i.e., the N-terminal domain (NTD) and the C-terminal domain (CTD) with a disordered region between them. Recent simulation studies have identified several potential drugs that can bind to NTD or CTD with high affinity. Moreover, it was shown that the degree of flexibility in the disordered region has a large effect on drug binding rate, suggesting the importance of molecular flexibility for the NCoV2 function. Molecular flexibility has also been shown to be integral to the formation of droplets, where NCoV2, RNA and/or other viral proteins gather through liquid-liquid phase separation and considered important for viral replication. Finally, as one of the future research directions, a strategy for obtaining the structural and dynamical information on the proteins contained in droplets is presented.
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Affiliation(s)
- Tatsuhito Matsuo
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1106, Japan;
- Laboratoire Interdisciplinaire de Physique (LiPhy), Grenoble-Alpes University, 140 Rue de la Physique, 38402 Saint Martin d’Hères, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, CEDEX 9, 38042 Grenoble, France
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145
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Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin. Nat Commun 2021; 12:2953. [PMID: 34012049 PMCID: PMC8134635 DOI: 10.1038/s41467-021-23268-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 04/16/2021] [Indexed: 12/28/2022] Open
Abstract
Recent cryo-EM structures show the highly dynamic nature of the MLL1-NCP (nucleosome core particle) interaction. Functional implication and regulation of such dynamics remain unclear. Here we show that DPY30 and the intrinsically disordered regions (IDRs) of ASH2L work together in restricting the rotational dynamics of the MLL1 complex on the NCP. We show that DPY30 binding to ASH2L leads to stabilization and integration of ASH2L IDRs into the MLL1 complex and establishes new ASH2L-NCP contacts. The significance of ASH2L-DPY30 interactions is demonstrated by requirement of both ASH2L IDRs and DPY30 for dramatic increase of processivity and activity of the MLL1 complex. This DPY30 and ASH2L-IDR dependent regulation is NCP-specific and applies to all members of the MLL/SET1 family of enzymes. We further show that DPY30 is causal for de novo establishment of H3K4me3 in ESCs. Our study provides a paradigm of how H3K4me3 is regulated on chromatin and how H3K4me3 heterogeneity can be modulated by ASH2L IDR interacting proteins. Regulation of the MLL family of histone H3K4 methyltransferases on the nucleosome core particle (NCP) remains largely unknown. Here the authors show that intrinsically disordered regions of ASH2L and DPY30 restrict the rotational dynamics of MLL1 on the NCP, allowing more efficient enzyme-substrate engagement and higher H3K4 trimethylation activity.
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146
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Higasi PMR, Velasco JA, Pellegrini VOA, de Araújo EA, França BA, Keller MB, Labate CA, Blossom BM, Segato F, Polikarpov I. Light-stimulated T. thermophilus two-domain LPMO9H: Low-resolution SAXS model and synergy with cellulases. Carbohydr Polym 2021; 260:117814. [PMID: 33712158 DOI: 10.1016/j.carbpol.2021.117814] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/06/2021] [Accepted: 02/10/2021] [Indexed: 12/19/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs), monocopper enzymes that oxidatively cleave recalcitrant polysaccharides, have important biotechnological applications. Thermothelomyces thermophilus is a rich source of biomass-active enzymes, including many members from auxiliary activities family 9 LPMOs. Here, we report biochemical and structural characterization of recombinant TtLPMO9H which oxidizes cellulose at the C1 and C4 positions and shows enhanced activity in light-driven catalysis assays. TtLPMO9H also shows activity against xyloglucan. The addition of TtLPMO9H to endoglucanases from four different glucoside hydrolase families (GH5, GH12, GH45 and GH7) revealed that the product formation was remarkably increased when TtLPMO9H was combined with GH7 endoglucanase. Finally, we determind the first low resolution small-angle X-ray scattering model of the two-domain TtLPMO9H in solution that shows relative positions of its two functional domains and a conformation of the linker peptide, which can be relevant for the catalytic oxidation of cellulose and xyloglucan.
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Affiliation(s)
- Paula M R Higasi
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense 400, São Carlos, São Paulo, Brazil
| | - Josman A Velasco
- Lorena School of Engineering, University of São Paulo, Estrada Municipal do Campinho s/n, Lorena, São Paulo, Brazil
| | - Vanessa O A Pellegrini
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense 400, São Carlos, São Paulo, Brazil
| | - Evandro A de Araújo
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense 400, São Carlos, São Paulo, Brazil
| | - Bruno Alves França
- Lorena School of Engineering, University of São Paulo, Estrada Municipal do Campinho s/n, Lorena, São Paulo, Brazil
| | - Malene B Keller
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Carlos A Labate
- Luiz de Queiroz College of Agriculture, University of São Paulo, Av. Pádua Dias 11, Piracicaba, São Paulo, Brazil
| | - Benedikt M Blossom
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Fernando Segato
- Lorena School of Engineering, University of São Paulo, Estrada Municipal do Campinho s/n, Lorena, São Paulo, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense 400, São Carlos, São Paulo, Brazil.
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147
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Covaceuszach S, Peche L, Konarev P, Lamba D. A combined evolutionary and structural approach to disclose the primary structural determinants essential for proneurotrophins biological functions. Comput Struct Biotechnol J 2021; 19:2891-2904. [PMID: 34094000 PMCID: PMC8144349 DOI: 10.1016/j.csbj.2021.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 05/03/2021] [Indexed: 12/24/2022] Open
Abstract
The neurotrophins, i.e., Nerve Growth Factor (NGF), Brain-Derived Neurotrophic Factor (BDNF), Neurotrophin 3 (NT3) and Neurotrophin 4 (NT4), are known to play a range of crucial functions in the developing and adult peripheral and central nervous systems. Initially synthesized as precursors, i.e., proneurotrophins (proNTs), that are cleaved to release C-terminal mature forms, they act through two types of receptors, the specific Trk receptors (Tropomyosin-related kinases) and the pan-neurotrophin receptor p75NTR, to initiate survival and differentiative responses. Recently, all the proNTs but proNT4 have been demonstrated to be not just inactive precursors, but signaling ligands that mediate opposing actions in fundamental aspects of the nervous system with respect to the mature counterparts through dual-receptor complexes formation with a member of the VPS10 family and p75NTR. Despite the functional relevance, the molecular determinants underpinning the interactions between the pro-domains and their receptors are still elusive probably due to their intrinsically disordered nature. Here we present an evolutionary approach coupled to an experimental study aiming to uncover the structural and dynamical basis of the biological function displayed by proNGF, proBDNF and proNT3 but missing in proNT4. A bioinformatic analysis allowed to elucidate the functional adaptability of the proNTs family in vertebrates, identifying conserved key structural features. The combined biochemical and SAXS experiments shed lights on the structure and dynamic behavior of the human proNTs in solution, giving insights on the evolutionary conserved structural motifs, essential for the multifaceted roles of proNTs in physiological as well as in pathological contexts.
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Affiliation(s)
- S. Covaceuszach
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy
| | - L.Y. Peche
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy
| | - P.V. Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
| | - D. Lamba
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy
- Interuniversity Consortium “Biostructures and Biosystems National Institute”, Roma, Italy
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148
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Solovyova AS, Peters DT, Dura G, Waller H, Lakey JH, Fulton DA. Probing the oligomeric re-assembling of bacterial fimbriae in vitro: a small-angle X-ray scattering and analytical ultracentrifugation study. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:597-611. [PMID: 33948690 PMCID: PMC8190007 DOI: 10.1007/s00249-021-01543-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 04/14/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023]
Abstract
Capsular antigen fragment 1 (Caf1) is an oligomeric protein consisting of 15 kDa monomeric subunits that are non-covalently linked through exceptionally strong and kinetically inert interactions into a linear polymer chain. It has been shown that after its thermal depolymerisation into unfolded monomeric subunits, Caf1 is able to efficiently repolymerise in vitro to reform its polymeric structure. However, little is known about the nature of the repolymerisation process. An improved understanding of this process will lead to the development of methods to better control the lengths of the repolymerised species, and ultimately, to better design of the properties of Caf1-based materials. Here we utilize small-angle X-ray scattering to estimate the size of Caf1 polymers during the first 24 h of the re-polymerisation process. Analytical ultracentrifugation measurements were also used to investigate the process post-24 h, where the rate of repolymerisation becomes considerably slower. Results show that in vitro polymerisation proceeds in a linear manner with no evidence observed for the formation of a lateral polymer network or uncontrolled aggregates. The rate of Caf1 in vitro repolymerisation was found to be concentration-dependent. Importantly, the rate of polymer growth was found to be relatively fast over the first few hours, before continuing at a dramatically slower rate. This observation is not consistent with the previously proposed step-growth mechanism of in vitro polymerisation of Caf1, where a linear increase in polymer length would be expected with time. We speculate how our observations may support the idea that the polymerisation process may be occurring at the ends of the chains with monomers adding sequentially. Our findings will contribute towards the development of new biomaterials for 3D cell culture and bio-printing.
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Affiliation(s)
- Alexandra S Solovyova
- Proteome and Protein Analysis, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, UK.
| | - Daniel T Peters
- Biosciences Institute, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Gema Dura
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Departamento de Química Inorgánica, Orgánica y Bioquímica, Universidad de Castilla-La Mancha, Facultad de Ciencias yTecnologías Químicas-IRICA, Avda. C. J. Cela, 10, 13071, Ciudad Real, Spain
| | - Helen Waller
- Biosciences Institute, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Jeremy H Lakey
- Biosciences Institute, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, UK
| | - David A Fulton
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.
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149
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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.
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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
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150
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Ferrari ML, Charova SN, Sansonetti PJ, Mylonas E, Gazi AD. Structural Insights of Shigella Translocator IpaB and Its Chaperone IpgC in Solution. Front Cell Infect Microbiol 2021; 11:673122. [PMID: 33996640 PMCID: PMC8117225 DOI: 10.3389/fcimb.2021.673122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/12/2021] [Indexed: 12/18/2022] Open
Abstract
Bacterial Type III Secretion Systems (T3SSs) are specialized multicomponent nanomachines that mediate the transport of proteins either to extracellular locations or deliver Type III Secretion effectors directly into eukaryotic host cell cytoplasm. Shigella, the causing agent of bacillary dysentery or shigellosis, bears a set of T3SS proteins termed translocators that form a pore in the host cell membrane. IpaB, the major translocator of the system, is a key factor in promoting Shigella pathogenicity. Prior to secretion, IpaB is maintained inside the bacterial cytoplasm in a secretion competent folding state thanks to its cognate chaperone IpgC. IpgC couples T3SS activation to transcription of effector genes through its binding to MxiE, probably after the delivery of IpaB to the secretion export gate. Small Angle X-ray Scattering experiments and modeling reveal that IpgC is found in different oligomeric states in solution, as it forms a stable heterodimer with full-length IpaB in contrast to an aggregation-prone homodimer in the absence of the translocator. These results support a stoichiometry of interaction 1:1 in the IpgC/IpaB complex and the multi-functional nature of IpgC under different T3SS states.
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Affiliation(s)
- Mariana L. Ferrari
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
- INSERM U1202, Paris, France
| | - Spyridoula N. Charova
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas (IMBB-FORTH), Heraklion, Crete, Greece
| | - Philippe J. Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
- INSERM U1202, Paris, France
- Collège de France, Paris, France
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas (IMBB-FORTH), Heraklion, Crete, Greece
| | - Anastasia D. Gazi
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
- INSERM U1202, Paris, France
- UtechS Ultrastructural Bio-Imaging (UBI), Institut Pasteur, Paris, France
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