51
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Aneskievich BJ, Shamilov R, Vinogradova O. Intrinsic disorder in integral membrane proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:101-134. [PMID: 34656327 DOI: 10.1016/bs.pmbts.2021.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The well-defined roles and specific protein-protein interactions of many integral membrane proteins (IMPs), such as those functioning as receptors for extracellular matrix proteins and soluble growth factors, easily align with considering IMP structure as a classical "lock-and-key" concept. Nevertheless, continued advances in understanding protein conformation, such as those which established the widespread existence of intrinsically disordered proteins (IDPs) and especially intrinsically disordered regions (IDRs) in otherwise three-dimensionally organized proteins, call for ongoing reevaluation of transmembrane proteins. Here, we present basic traits of IDPs and IDRs, and, for some select single-span IMPs, consider the potential functional advantages intrinsic disorder might provide and the possible conformational impact of disease-associated mutations. For transmembrane proteins in general, we highlight several investigational approaches, such as biophysical and computational methods, stressing the importance of integrating them to produce a more-complete mechanistic model of disorder-containing IMPs. These procedures, when synergized with in-cell assessments, will likely be key in translating in silico and in vitro results to improved understanding of IMP conformational flexibility in normal cell physiology as well as disease, and will help to extend their potential as therapeutic targets.
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Affiliation(s)
- Brian J Aneskievich
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
| | - Rambon Shamilov
- Graduate Program in Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States.
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52
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Saad D, Paissoni C, Chaves-Sanjuan A, Nardini M, Mantovani R, Gnesutta N, Camilloni C. High Conformational Flexibility of the E2F1/DP1/DNA Complex. J Mol Biol 2021; 433:167119. [PMID: 34181981 DOI: 10.1016/j.jmb.2021.167119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 10/21/2022]
Abstract
The E2F1 transcription factor is a master regulator of cell-cycle progression whose uncontrolled activation contributes to tumor cells growth. E2F1 binds DNA as a heterodimer with DP partners, resulting in a multi-domain quaternary-structure complex composed of DNA binding domains, a coiled coil domain and a marked box domain separated by short linkers. Building on the 3D knowledge of the single domains of E2F and DPs, we characterized the structure and dynamics of the complete E2F1/DP1/DNA complex by a combination of small-angle X-ray scattering and molecular dynamics simulations. It shows an asymmetric contribution of the dynamics of the two proteins. Namely, the coiled-coil domain leans toward the DP1 side of the complex; the DP1 loop between α2 and α3 of the DBD partially populates a helical structure leaning far from the DNA and in the same direction of the coiled-coil domain; and the N-terminal disordered region of DP1, rich in basic residues, contributes to DNA binding stabilization. Intriguingly, tumor mutations in the flexible regions of the complex suggest that perturbation of protein dynamics could affect protein function in a context-dependent way. Our data suggest fundamental contributions of DP proteins in distinct aspects of E2F biology.
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Affiliation(s)
- Dana Saad
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Cristina Paissoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Antonio Chaves-Sanjuan
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Marco Nardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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53
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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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54
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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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55
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Nasir I, Bentley EP, Deniz AA. Ratiometric Single-Molecule FRET Measurements to Probe Conformational Subpopulations of Intrinsically Disordered Proteins. ACTA ACUST UNITED AC 2021; 12:e80. [PMID: 32159932 PMCID: PMC7508418 DOI: 10.1002/cpch.80] [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: 11/09/2022]
Abstract
Over the past few decades, numerous examples have demonstrated that intrinsic disorder in proteins lies at the heart of many vital processes, including transcriptional regulation, stress response, cellular signaling, and most recently protein liquid-liquid phase separation. The so-called intrinsically disordered proteins (IDPs) involved in these processes have presented a challenge to the classic protein "structure-function paradigm," as their functions do not necessarily involve well-defined structures. Understanding the mechanisms of IDP function is likewise challenging because traditional structure determination methods often fail with such proteins or provide little information about the diverse array of structures that can be related to different functions of a single IDP. Single-molecule fluorescence methods can overcome this ensemble-average masking, allowing the resolution of subpopulations and dynamics and thus providing invaluable insights into IDPs and their function. In this protocol, we describe a ratiometric single-molecule Förster resonance energy transfer (smFRET) routine that permits the investigation of IDP conformational subpopulations and dynamics. We note that this is a basic protocol, and we provide brief information and references for more complex analysis schemes available for in-depth characterization. This protocol covers optical setup preparation and protein handling and provides insights into experimental design and outcomes, together with background information about theory and a brief discussion of troubleshooting. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Ratiometric smFRET detection and analysis of IDPs Support Protocol 1: Fluorophore labeling of a protein through maleimide chemistry Support Protocol 2: Sample chamber preparation Support Protocol 3: Determination of direct excitation of acceptor by donor excitation and leakage of donor emission to acceptor emission channel.
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Affiliation(s)
- Irem Nasir
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.,Department of Biology and Biological Engineering, Division of Chemical Biology, Chalmers Institute of Technology, Gothenburg, Sweden
| | - Emily P Bentley
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
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56
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Ahmed MC, Skaanning LK, Jussupow A, Newcombe EA, Kragelund BB, Camilloni C, Langkilde AE, Lindorff-Larsen K. Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods. Front Mol Biosci 2021; 8:654333. [PMID: 33968988 PMCID: PMC8100456 DOI: 10.3389/fmolb.2021.654333] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/12/2021] [Indexed: 12/22/2022] Open
Abstract
The inherent flexibility of intrinsically disordered proteins (IDPs) makes it difficult to interpret experimental data using structural models. On the other hand, molecular dynamics simulations of IDPs often suffer from force-field inaccuracies, and long simulation times or enhanced sampling methods are needed to obtain converged ensembles. Here, we apply metainference and Bayesian/Maximum Entropy reweighting approaches to integrate prior knowledge of the system with experimental data, while also dealing with various sources of errors and the inherent conformational heterogeneity of IDPs. We have measured new SAXS data on the protein α-synuclein, and integrate this with simulations performed using different force fields. We find that if the force field gives rise to ensembles that are much more compact than what is implied by the SAXS data it is difficult to recover a reasonable ensemble. On the other hand, we show that when the simulated ensemble is reasonable, we can obtain an ensemble that is consistent with the SAXS data, but also with NMR diffusion and paramagnetic relaxation enhancement data.
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Affiliation(s)
- Mustapha Carab Ahmed
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Line K Skaanning
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Jussupow
- Department of Chemistry, Institute for Advanced Study, Technical University of Munich, Munich, Germany
| | - Estella A Newcombe
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark.,Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Carlo Camilloni
- Department of Chemistry, Institute for Advanced Study, Technical University of Munich, Munich, Germany.,Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Annette E Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
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57
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Ding C, Wang S, Zhang Z. Integrating an Enhanced Sampling Method and Small-Angle X-Ray Scattering to Study Intrinsically Disordered Proteins. Front Mol Biosci 2021; 8:621128. [PMID: 34150843 PMCID: PMC8213455 DOI: 10.3389/fmolb.2021.621128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/08/2021] [Indexed: 11/23/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) have been paid more and more attention over the past decades because they are involved in a multitude of crucial biological functions. Despite their functional importance, IDPs are generally difficult to investigate because they are very flexible and lack stable structures. Computer simulation may serve as a useful tool in studying IDPs. With the development of computer software and hardware, computational methods, such as molecular dynamics (MD) simulations, are popularly used. However, there is a sampling problem in MD simulations. In this work, this issue is investigated using an IDP called unique long region 11 (UL11), which is the conserved outer tegument component from herpes simplex virus 1. After choosing a proper force field and water model that is suitable for simulating IDPs, integrative modeling by combining an enhanced sampling method and experimental data like small-angle X-ray scattering (SAXS) is utilized to efficiently sample the conformations of UL11. The simulation results are in good agreement with experimental data. This work may provide a general protocol to study structural ensembles of IDPs.
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Affiliation(s)
- Chengtao Ding
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, National Science Center for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | | | - Zhiyong Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, National Science Center for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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58
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Sagar A, Jeffries CM, Petoukhov MV, Svergun DI, Bernadó P. Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method. J Chem Theory Comput 2021; 17:2014-2021. [PMID: 33725442 DOI: 10.1021/acs.jctc.1c00014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Ensemble Optimization Method (EOM) is a popular approach to describe small-angle X-ray scattering (SAXS) data from highly disordered proteins. The EOM algorithm selects subensembles of coexisting states from large pools of randomized conformations to fit the SAXS data. Based on the unphysical bimodal radius of gyration (Rg) distribution of conformations resulting from the EOM analysis, a recent article (Fagerberg et al. J. Chem. Theory Comput. 2019, 15 (12), 6968-6983) concluded that this approach inadequately described the SAXS data measured for human Histatin 5 (Hst5), a peptide with antifungal properties. Using extensive experimental and synthetic data, we explored the origin of this observation. We found that the one-bead-per-residue coarse-grained representation with averaged scattering form factors (provided in the EOM as an add-on to represent disordered missing loops or domains) may not be appropriate for EOM analyses of scattering data from short (below 50 residues) proteins/peptides. The method of choice for these proteins is to employ atomistic models (e.g., from molecular dynamics simulations) to sample the protein conformational landscape. As a convenient alternative, we have also improved the coarse-grained approach by introducing amino acid specific form factors in the calculations. We also found that, for small proteins, the search for relatively large subensembles of 20-50 conformers (as implemented in the original EOM version) more adequately describes the conformational space sampled in solution than the procedures optimizing the ensemble size. Our observations have been added as recommendations into the information for EOM users to promote the proper utilization of the program for ensemble-based modeling of SAXS data for all types of disordered systems.
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Affiliation(s)
- Amin Sagar
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maxim V Petoukhov
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, 119333 Moscow, Russia
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
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59
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Sagar A, Herranz-Trillo F, Langkilde AE, Vestergaard B, Bernadó P. Structure and thermodynamics of transient protein-protein complexes by chemometric decomposition of SAXS datasets. Structure 2021; 29:1074-1090.e4. [PMID: 33862013 DOI: 10.1016/j.str.2021.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/17/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Transient biomolecular interactions play crucial roles in many cellular signaling and regulation processes. However, deciphering the structure of these assemblies is challenging owing to the difficulties in isolating complexes from the individual partners. The additive nature of small-angle X-ray scattering (SAXS) data allows for probing the species present in these mixtures, but decomposition into structural and thermodynamic information is difficult. We present a chemometric approach enabling the decomposition of titration SAXS data into species-specific information. Using extensive synthetic SAXS data, we demonstrate that robust decomposition can be achieved for titrations with a maximum fraction of complex of 0.5 that can be extended to 0.3 when two orthogonal titrations are simultaneously analyzed. The effect of the structural features, titration points, relative concentrations, and noise are thoroughly analyzed. The validation of the strategy with experimental data highlights the power of the approach to provide unique insights into this family of biomolecular assemblies.
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Affiliation(s)
- Amin Sagar
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
| | - Fátima Herranz-Trillo
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Annette Eva Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
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60
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Argudo PG, Giner-Casares JJ. Folding and self-assembly of short intrinsically disordered peptides and protein regions. NANOSCALE ADVANCES 2021; 3:1789-1812. [PMID: 36133101 PMCID: PMC9417027 DOI: 10.1039/d0na00941e] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/17/2021] [Indexed: 05/15/2023]
Abstract
Proteins and peptide fragments are highly relevant building blocks in self-assembly for nanostructures with plenty of applications. Intrinsically disordered proteins (IDPs) and protein regions (IDRs) are defined by the absence of a well-defined secondary structure, yet IDPs/IDRs show a significant biological activity. Experimental techniques and computational modelling procedures for the characterization of IDPs/IDRs are discussed. Directed self-assembly of IDPs/IDRs allows reaching a large variety of nanostructures. Hybrid materials based on the derivatives of IDPs/IDRs show a promising performance as alternative biocides and nanodrugs. Cell mimicking, in vivo compartmentalization, and bone regeneration are demonstrated for IDPs/IDRs in biotechnological applications. The exciting possibilities of IDPs/IDRs in nanotechnology with relevant biological applications are shown.
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Affiliation(s)
- Pablo G Argudo
- Université de Bordeaux, CNRS, Bordeaux INP, LCPO 16 Avenue Pey-Berland 33600 Pessac France
| | - Juan J Giner-Casares
- Departamento de Química Física y T. Aplicada, Instituto Universitario de Nanoquímica IUNAN, Facultad de Ciencias, Universidad de Córdoba (UCO) Campus de Rabanales, Ed. Marie Curie E-14071 Córdoba Spain
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61
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Levengood JD, Peterson J, Tolbert BS, Roche J. Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR. Proteins 2021; 89:781-791. [PMID: 33550645 DOI: 10.1002/prot.26058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/21/2020] [Accepted: 01/31/2021] [Indexed: 11/09/2022]
Abstract
We have investigated the pressure- and temperature-induced conformational changes associated with the low complexity domain of hnRNP A1, an RNA-binding protein able to phase separate in response to cellular stress. Solution NMR spectra of the hnRNP A1 low-complexity domain fused with protein-G B1 domain were collected from 1 to 2500 bar and from 268 to 290 K. While the GB1 domain shows the typical pressure-induced and cold temperature-induced unfolding expected for small globular domains, the low-complexity domain of hnRNP A1 exhibits unusual pressure and temperature dependences. We observed that the low-complexity domain is pressure sensitive, undergoing a major conformational transition within the prescribed pressure range. Remarkably, this transition has the inverse temperature dependence of a typical folding-unfolding transition. Our results suggest the presence of a low-lying extended and fully solvated state(s) of the low-complexity domain that may play a role in phase separation. This study highlights the exquisite sensitivity of solution NMR spectroscopy to observe subtle conformational changes and illustrates how pressure perturbation can be used to determine the properties of metastable conformational ensembles.
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Affiliation(s)
- Jeffrey D Levengood
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jake Peterson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
| | - Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
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62
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Smith NC, Wilkinson-White LE, Kwan AHY, Trewhella J, Matthews JM. Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification. JOURNAL OF STRUCTURAL BIOLOGY-X 2021; 5:100043. [PMID: 33458649 PMCID: PMC7797366 DOI: 10.1016/j.yjsbx.2020.100043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 11/29/2022]
Abstract
The mechanisms by which ISL1 and LHX3 specify neuronal cell identity are unknown. EMSA/SPR data show ISL1 and LHX3 have markedly different DNA-binding behaviours. SAXS shows ISL1/LHX3:DNA complexes are flexible in nature. ISL1 binds DNA poorly but appears to modulate the DNA-binding specificity of LHX3.
The roles of ISL1 and LHX3 in the development of spinal motor neurons have been well established. Whereas LHX3 triggers differentiation into interneurons, the additional expression of ISL1 in developing neuronal cells is sufficient to redirect their developmental trajectory towards spinal motor neurons. However, the underlying mechanism of this action by these transcription factors is less well understood. Here, we used electrophoretic mobility shift assays (EMSAs) and surface plasmon resonance (SPR) to probe the different DNA-binding behaviours of these two proteins, both alone and in complexes mimicking those found in developing neurons, and found that ISL1 shows markedly different binding properties to LHX3. We used small angle X-ray scattering (SAXS) to structurally characterise DNA-bound species containing ISL1 and LHX3. Taken together, these results have allowed us to develop a model of how these two DNA-binding modules coordinate to regulate gene expression and direct development of spinal motor neurons.
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Affiliation(s)
- Ngaio C Smith
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | | | - Ann H Y Kwan
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, University of Sydney, NSW 2006, Australia
| | - Jill Trewhella
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
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63
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Blazquez-Martín A, Verde-Sesto E, Moreno AJ, Arbe A, Colmenero J, Pomposo JA. Advances in the Multi-Orthogonal Folding of Single Polymer Chains into Single-Chain Nanoparticles. Polymers (Basel) 2021; 13:293. [PMID: 33477597 PMCID: PMC7831314 DOI: 10.3390/polym13020293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 11/16/2022] Open
Abstract
The folding of certain proteins (e.g., enzymes) into perfectly defined 3D conformations via multi-orthogonal interactions is critical to their function. Concerning synthetic polymers chains, the "folding" of individual polymer chains at high dilution via intra-chain interactions leads to so-called single-chain nanoparticles (SCNPs). This review article describes the advances carried out in recent years in the folding of single polymer chains into discrete SCNPs via multi-orthogonal interactions using different reactive chemical species where intra-chain bonding only occurs between groups of the same species. First, we summarize results from computer simulations of multi-orthogonally folded SCNPs. Next, we comprehensively review multi-orthogonally folded SCNPs synthesized via either non-covalent bonds or covalent interactions. Finally, we conclude by summarizing recent research about multi-orthogonally folded SCNPs prepared through both reversible (dynamic) and permanent bonds.
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Affiliation(s)
- Agustín Blazquez-Martín
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
| | - Ester Verde-Sesto
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
| | - Angel J. Moreno
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
| | - Juan Colmenero
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
- Departamento de Polímeros y Materiales Avanzados: Física, Química y Tecnología, University of the Basque Country (UPV/EHU), PO Box 1072, E-20800 San Sebastián, Spain
| | - José A. Pomposo
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (A.B.-M.); (E.V.-S.); (A.J.M.); (A.A.); (J.C.)
- Departamento de Polímeros y Materiales Avanzados: Física, Química y Tecnología, University of the Basque Country (UPV/EHU), PO Box 1072, E-20800 San Sebastián, Spain
- IKERBASQUE—Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
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64
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Kinetic and structural characterization of whey protein aggregation in a millifluidic continuous process. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106137] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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65
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Ruan H, Kiselar J, Zhang W, Li S, Xiong R, Liu Y, Yang S, Lai L. Integrative structural modeling of a multidomain polo-like kinase. Phys Chem Chem Phys 2020; 22:27581-27589. [PMID: 33236741 DOI: 10.1039/d0cp05030j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polo-like kinase 1 (PLK1) is a key regulator and coordinator for mitotic signaling that contains two major functional units of a kinase domain (KD) and a polo-box domain (PBD). While individual domain structures of the KD and the PBD are known, how they interact and assemble into a functional complex remains an open question. The structural model from the KD-PBD-Map205PBM heterotrimeric crystal structure of zebrafish PLK1 represents a major step in understanding the KD and the PBD interactions. However, how these two domains interact when connected by a linker in the full length PLK1 needs further investigation. By integrating different sources of structural data from small-angle X-ray scattering, hydroxyl radical protein footprinting, and computational sampling, here we report an overall architecture for PLK1 multidomain assembly between the KD and the PBD. Our model revealed that the KD uses its C-lobe to interact with the PBD via the site near the phosphopeptide binding site in its auto-inhibitory state in solution. Disruption of this auto-inhibition via site-directed mutagenesis at the KD-PBD interface increases its kinase activity, supporting the functional role of KD-PBD interactions predicted for regulating the PLK1 kinase function. Our results indicate that the full length human PLK1 takes dynamic structures with a variety of domain-domain interfaces in solution.
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Affiliation(s)
- Hao Ruan
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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66
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Dynamics of proteins with different molecular structures under solution condition. Sci Rep 2020; 10:21678. [PMID: 33303822 PMCID: PMC7728768 DOI: 10.1038/s41598-020-78311-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/20/2020] [Indexed: 11/08/2022] Open
Abstract
Incoherent quasielastic neutron scattering (iQENS) is a fascinating technique for investigating the internal dynamics of protein. However, low flux of neutron beam, low signal to noise ratio of QENS spectrometers and unavailability of well-established analyzing method have been obstacles for studying internal dynamics under physiological condition (in solution). The recent progress of neutron source and spectrometer provide the fine iQENS profile with high statistics and as well the progress of computational technique enable us to quantitatively reveal the internal dynamic from the obtained iQENS profile. The internal dynamics of two proteins, globular domain protein (GDP) and intrinsically disordered protein (IDP) in solution, were measured with the state-of-the art QENS spectrometer and then revealed with the newly developed analyzing method. It was clarified that the average relaxation rate of IDP was larger than that of GDP and the fraction of mobile H atoms of IDP was also much higher than that of GDP. Combined with the structural analysis and the calculation of solvent accessible surface area of amino acid residue, it was concluded that the internal dynamics were related to the highly solvent exposed amino acid residues depending upon protein's structure.
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67
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Lombardo D, Calandra P, Kiselev MA. Structural Characterization of Biomaterials by Means of Small Angle X-rays and Neutron Scattering (SAXS and SANS), and Light Scattering Experiments. Molecules 2020; 25:E5624. [PMID: 33260426 PMCID: PMC7730346 DOI: 10.3390/molecules25235624] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Scattering techniques represent non-invasive experimental approaches and powerful tools for the investigation of structure and conformation of biomaterial systems in a wide range of distances, ranging from the nanometric to micrometric scale. More specifically, small-angle X-rays and neutron scattering and light scattering techniques represent well-established experimental techniques for the investigation of the structural properties of biomaterials and, through the use of suitable models, they allow to study and mimic various biological systems under physiologically relevant conditions. They provide the ensemble averaged (and then statistically relevant) information under in situ and operando conditions, and represent useful tools complementary to the various traditional imaging techniques that, on the contrary, reveal more local structural information. Together with the classical structure characterization approaches, we introduce the basic concepts that make it possible to examine inter-particles interactions, and to study the growth processes and conformational changes in nanostructures, which have become increasingly relevant for an accurate understanding and prediction of various mechanisms in the fields of biotechnology and nanotechnology. The upgrade of the various scattering techniques, such as the contrast variation or time resolved experiments, offers unique opportunities to study the nano- and mesoscopic structure and their evolution with time in a way not accessible by other techniques. For this reason, highly performant instruments are installed at most of the facility research centers worldwide. These new insights allow to largely ameliorate the control of (chemico-physical and biologic) processes of complex (bio-)materials at the molecular length scales, and open a full potential for the development and engineering of a variety of nano-scale biomaterials for advanced applications.
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Affiliation(s)
- Domenico Lombardo
- CNR-IPCF, Consiglio Nazionale delle Ricerche, Istituto per i Processi Chimico-Fisici, 98158 Messina, Italy
| | - Pietro Calandra
- CNR-ISMN, Consiglio Nazionale delle Ricerche, Istituto Studio Materiali Nanostrutturati, 00015 Roma, Italy;
| | - Mikhail A. Kiselev
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980 Moscow, Russia;
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68
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O'Carroll IP, Fan L, Kroupa T, McShane EK, Theodore C, Yates EA, Kondrup B, Ding J, Martin TS, Rein A, Wang YX. Structural Mimicry Drives HIV-1 Rev-Mediated HERV-K Expression. J Mol Biol 2020; 432:166711. [PMID: 33197463 DOI: 10.1016/j.jmb.2020.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 10/23/2022]
Abstract
Expression of the Human Endogenous Retrovirus Type K (HERV-K), the youngest and most active HERV, has been associated with various cancers and neurodegenerative diseases. As in all retroviruses, a fraction of HERV-K transcripts is exported from the nucleus in unspliced or incompletely spliced forms to serve as templates for translation of viral proteins. In a fraction of HERV-K loci (Type 2 proviruses), nuclear export of the unspliced HERV-K mRNA appears to be mediated by a cis-acting signal on the mRNA, the RcRE, and the protein Rec-these are analogous to the RRE-Rev system in HIV-1. Interestingly, the HIV-1 Rev protein is able to mediate the nuclear export of the HERV-K RcRE, contributing to elevated HERV-K expression in HIV-infected patients. We aimed to understand the structural basis for HIV Rev-HERV-K RcRE recognition. We examined the conformation of the RcRE RNA in solution using small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM). We found that the 433-nt long RcRE can assume folded or extended conformations as observed by AFM. SAXS analysis of a truncated RcRE variant revealed an "A"-shaped topological structure similar to the one previously reported for the HIV-1 RRE. The effect of the overall topology was examined using several deletion variants. SAXS and biochemical analyses demonstrated that the "A" shape is necessary for efficient Rev-RcRE complex formation in vitro and nuclear export activity in cell culture. The findings provide insight into the mechanism of HERV-K expression and a structural explanation for HIV-1 Rev-mediated expression of HERV-K in HIV-infected patients. IMPORTANCE: Expression of the human endogenous retrovirus type K (HERV-K) has been associated with various cancers and autoimmune diseases. Nuclear export of both HIV-1 and HERV-K mRNAs is dependent on the interaction between a small viral protein (Rev in HIV-1 and Rec in HERV-K) and a region on the mRNA (RRE in HIV-1 and RcRE in HERV-K). HIV-1 Rev is able to mediate the nuclear export of RcRE-containing HERV-K mRNAs, which contributes to elevated production of HERV-K proteins in HIV-infected patients. We report the solution conformation of the RcRE RNA-the first three-dimensional topological structure for a HERV molecule-and find that the RcRE resembles the HIV-1 nuclear export signal, RRE. The finding reveals the structural basis for the increased HERV-K expression observed in HIV-infected patients. Elevated HERV expression, mediated by HIV infection or other stressors, can have various HERV-related biological consequences. The findings provide structural insight for regulation of HERV-K expression.
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Affiliation(s)
- Ina P O'Carroll
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA.
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of the National Cancer Institute, Frederick, MD 21702, USA
| | - Tomáš Kroupa
- HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Erin K McShane
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA
| | - Christophe Theodore
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA
| | - Elizabeth A Yates
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA
| | - Benjamin Kondrup
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA
| | - Jienyu Ding
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Tyler S Martin
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA
| | - Alan Rein
- HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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69
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Lee M, Ghosh U, Thurber KR, Kato M, Tycko R. Molecular structure and interactions within amyloid-like fibrils formed by a low-complexity protein sequence from FUS. Nat Commun 2020; 11:5735. [PMID: 33184287 PMCID: PMC7665218 DOI: 10.1038/s41467-020-19512-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Protein domains without the usual distribution of amino acids, called low complexity (LC) domains, can be prone to self-assembly into amyloid-like fibrils. Self-assembly of LC domains that are nearly devoid of hydrophobic residues, such as the 214-residue LC domain of the RNA-binding protein FUS, is particularly intriguing from the biophysical perspective and is biomedically relevant due to its occurrence within neurons in amyotrophic lateral sclerosis, frontotemporal dementia, and other neurodegenerative diseases. We report a high-resolution molecular structural model for fibrils formed by the C-terminal half of the FUS LC domain (FUS-LC-C, residues 111-214), based on a density map with 2.62 Å resolution from cryo-electron microscopy (cryo-EM). In the FUS-LC-C fibril core, residues 112-150 adopt U-shaped conformations and form two subunits with in-register, parallel cross-β structures, arranged with quasi-21 symmetry. All-atom molecular dynamics simulations indicate that the FUS-LC-C fibril core is stabilized by a plethora of hydrogen bonds involving sidechains of Gln, Asn, Ser, and Tyr residues, both along and transverse to the fibril growth direction, including diverse sidechain-to-backbone, sidechain-to-sidechain, and sidechain-to-water interactions. Nuclear magnetic resonance measurements additionally show that portions of disordered residues 151-214 remain highly dynamic in FUS-LC-C fibrils and that fibrils formed by the N-terminal half of the FUS LC domain (FUS-LC-N, residues 2-108) have the same core structure as fibrils formed by the full-length LC domain. These results contribute to our understanding of the molecular structural basis for amyloid formation by FUS and by LC domains in general.
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Affiliation(s)
- Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA
| | - Ujjayini Ghosh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA
| | - Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75390-9152, USA
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba, 263-8555, Japan
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA.
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70
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Schiavina M, Salladini E, Murrali MG, Tria G, Felli IC, Pierattelli R, Longhi S. Ensemble description of the intrinsically disordered N-terminal domain of the Nipah virus P/V protein from combined NMR and SAXS. Sci Rep 2020; 10:19574. [PMID: 33177626 PMCID: PMC7658984 DOI: 10.1038/s41598-020-76522-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
Using SAXS and NMR spectroscopy, we herein provide a high-resolution description of the intrinsically disordered N-terminal domain (PNT, aa 1-406) shared by the Nipah virus (NiV) phosphoprotein (P) and V protein, two key players in viral genome replication and in evasion of the host innate immune response, respectively. The use of multidimensional NMR spectroscopy allowed us to assign as much as 91% of the residues of this intrinsically disordered domain whose size constitutes a technical challenge for NMR studies. Chemical shifts and nuclear relaxation measurements provide the picture of a highly flexible protein. The combination of SAXS and NMR information enabled the description of the conformational ensemble of the protein in solution. The present results, beyond providing an overall description of the conformational behavior of this intrinsically disordered region, also constitute an asset for obtaining atomistic information in future interaction studies with viral and/or cellular partners. The present study can thus be regarded as the starting point towards the design of inhibitors that by targeting crucial protein-protein interactions involving PNT might be instrumental to combat this deadly virus.
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Affiliation(s)
- Marco Schiavina
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Edoardo Salladini
- Lab. Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille University and CNRS, 163 Avenue de Luminy, Case 932, Marseille, France
| | - Maria Grazia Murrali
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Giancarlo Tria
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
- Florence Center for Electron Nanoscopy (FloCEN), University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Isabella C Felli
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy.
| | - Sonia Longhi
- Lab. Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille University and CNRS, 163 Avenue de Luminy, Case 932, Marseille, France.
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71
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Kolonko M, Bystranowska D, Taube M, Kozak M, Bostock M, Popowicz G, Ożyhar A, Greb-Markiewicz B. The intrinsically disordered region of GCE protein adopts a more fixed structure by interacting with the LBD of the nuclear receptor FTZ-F1. Cell Commun Signal 2020; 18:180. [PMID: 33153474 PMCID: PMC7643343 DOI: 10.1186/s12964-020-00662-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022] Open
Abstract
The Drosophila melanogaster Germ cell-expressed protein (GCE) is a paralog of the juvenile hormone (JH) receptor - Methoprene tolerant protein (MET). Both proteins mediate JH function, preventing precocious differentiation during D. melanogaster development. Despite that GCE and MET are often referred to as equivalent JH receptors, their functions are not fully redundant and show tissue specificity. Both proteins belong to the family of bHLH-PAS transcription factors. The similarity of their primary structure is limited to defined bHLH and PAS domains, while their long C-terminal fragments (GCEC, METC) show significant differences and are expected to determine differences in GCE and MET protein activities. In this paper we present the structural characterization of GCEC as a coil-like intrinsically disordered protein (IDP) with highly elongated and asymmetric conformation. In comparison to previously characterized METC, GCEC is less compacted, contains more molecular recognition elements (MoREs) and exhibits a higher propensity for induced folding. The NMR shifts perturbation experiment and pull-down assay clearly demonstrated that the GCEC fragment is sufficient to form an interaction interface with the ligand binding domain (LBD) of the nuclear receptor Fushi Tarazu factor-1 (FTZ-F1). Significantly, these interactions can force GCEC to adopt more fixed structure that can modulate the activity, structure and functions of the full-length receptor. The discussed relation of protein functionality with the structural data of inherently disordered GCEC fragment is a novel look at this protein and contributes to a better understanding of the molecular basis of the functions of the C-terminal fragments of the bHLH-PAS family. Video abstract.
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Affiliation(s)
- Marta Kolonko
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Dominika Bystranowska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Michał Taube
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland.,National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Czerwone Maki 98, 30-392, Krakow, Poland
| | - Mark Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Oberschleißheim, Germany
| | - Grzegorz Popowicz
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Oberschleißheim, Germany
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
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72
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González-Burgos M, Asenjo-Sanz I, Pomposo JA, Radulescu A, Ivanova O, Pasini S, Arbe A, Colmenero J. Structure and Dynamics of Irreversible Single-Chain Nanoparticles in Dilute Solution. A Neutron Scattering Investigation. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marina González-Burgos
- Centro de Fı́sica de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - Isabel Asenjo-Sanz
- Centro de Fı́sica de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - José A. Pomposo
- Centro de Fı́sica de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Departamento de Fı́sica de Materiales (UPV/EHU), Apartado 1072, E-20018 San Sebastián, Spain
| | - Aurel Radulescu
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Oxana Ivanova
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Stefano Pasini
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Arantxa Arbe
- Centro de Fı́sica de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - Juan Colmenero
- Centro de Fı́sica de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Departamento de Fı́sica de Materiales (UPV/EHU), Apartado 1072, E-20018 San Sebastián, Spain
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
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73
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Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae. Sci Rep 2020; 10:13775. [PMID: 32792608 PMCID: PMC7426924 DOI: 10.1038/s41598-020-70749-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/22/2020] [Indexed: 12/17/2022] Open
Abstract
Chitin is one of the most abundant renewable organic materials found on earth. The chitin utilization locus in Flavobacterium johnsoniae, which encodes necessary proteins for complete enzymatic depolymerization of crystalline chitin, has recently been characterized but no detailed structural information on the enzymes was provided. Here we present protein structures of the F. johnsoniae chitobiase (FjGH20) and chitinase B (FjChiB). FjGH20 is a multi-domain enzyme with a helical domain not before observed in other chitobiases and a domain organization reminiscent of GH84 (β-N-acetylglucosaminidase) family members. The structure of FjChiB reveals that the protein lacks loops and regions associated with exo-acting activity in other chitinases and instead has a more solvent accessible substrate binding cleft, which is consistent with its endo-chitinase activity. Additionally, small angle X-ray scattering data were collected for the internal 70 kDa region that connects the N- and C-terminal chitinase domains of the unique 158 kDa multi-domain chitinase A (FjChiA). The resulting model of the molecular envelope supports bioinformatic predictions of the region comprising six domains, each with similarities to either Fn3-like or Ig-like domains. Taken together, the results provide insights into chitin utilization by F. johnsoniae and reveal structural diversity in bacterial chitin metabolism.
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74
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Baul U, Bley M, Dzubiella J. Thermal Compaction of Disordered and Elastin-like Polypeptides: A Temperature-Dependent, Sequence-Specific Coarse-Grained Simulation Model. Biomacromolecules 2020; 21:3523-3538. [DOI: 10.1021/acs.biomac.0c00546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Upayan Baul
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| | - Michael Bley
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| | - Joachim Dzubiella
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
- Cluster of Excellence livMatS@FIT—Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
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75
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Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering. Proc Natl Acad Sci U S A 2020; 117:14996-15005. [PMID: 32541047 PMCID: PMC7334511 DOI: 10.1073/pnas.1913442117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.
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76
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Lazar T, Guharoy M, Vranken W, Rauscher S, Wodak SJ, Tompa P. Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins. Biophys J 2020; 118:2952-2965. [PMID: 32502383 DOI: 10.1016/j.bpj.2020.05.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/24/2020] [Accepted: 05/04/2020] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered proteins are proteins whose native functional states represent ensembles of highly diverse conformations. Such ensembles are a challenge for quantitative structure comparisons because their conformational diversity precludes optimal superimposition of the atomic coordinates necessary for deriving common similarity measures such as the root mean-square deviation of these coordinates. Here, we introduce superimposition-free metrics that are based on computing matrices of the Cα-Cα distance distributions within ensembles and comparing these matrices between ensembles. Differences between two matrices yield information on the similarity between specific regions of the polypeptide, whereas the global structural similarity is captured by the root mean-square difference between the medians of the Cα-Cα distance distributions of two ensembles. Together, our metrics enable rigorous investigations of structure-function relationships in conformational ensembles of intrinsically disordered proteins derived using experimental restraints or by molecular simulations and for proteins containing both structured and disordered regions.
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Affiliation(s)
- Tamas Lazar
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Mainak Guharoy
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Wim Vranken
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
| | - Sarah Rauscher
- Department of Physics & Department of Chemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Shoshana J Wodak
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie, Brussels, Belgium.
| | - Peter Tompa
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.
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77
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Jensen MR, Yabukarski F, Communie G, Condamine E, Mas C, Volchkova V, Tarbouriech N, Bourhis JM, Volchkov V, Blackledge M, Jamin M. Structural Description of the Nipah Virus Phosphoprotein and Its Interaction with STAT1. Biophys J 2020; 118:2470-2488. [PMID: 32348724 PMCID: PMC7231922 DOI: 10.1016/j.bpj.2020.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 12/25/2022] Open
Abstract
The structural characterization of modular proteins containing long intrinsically disordered regions intercalated with folded domains is complicated by their conformational diversity and flexibility and requires the integration of multiple experimental approaches. Nipah virus (NiV) phosphoprotein, an essential component of the viral RNA transcription/replication machine and a component of the viral arsenal that hijacks cellular components and counteracts host immune responses, is a prototypical model for such modular proteins. Curiously, the phosphoprotein of NiV is significantly longer than the corresponding protein of other paramyxoviruses. Here, we combine multiple biophysical methods, including x-ray crystallography, NMR spectroscopy, and small angle x-ray scattering, to characterize the structure of this protein and provide an atomistic representation of the full-length protein in the form of a conformational ensemble. We show that full-length NiV phosphoprotein is tetrameric, and we solve the crystal structure of its tetramerization domain. Using NMR spectroscopy and small angle x-ray scattering, we show that the long N-terminal intrinsically disordered region and the linker connecting the tetramerization domain to the C-terminal X domain exchange between multiple conformations while containing short regions of residual secondary structure. Some of these transient helices are known to interact with partners, whereas others represent putative binding sites for yet unidentified proteins. Finally, using NMR spectroscopy and isothermal titration calorimetry, we map a region of the phosphoprotein, comprising residues between 110 and 140 and common to the V and W proteins, that binds with weak affinity to STAT1 and confirm the involvement of key amino acids of the viral protein in this interaction. This provides new, to our knowledge, insights into how the phosphoprotein and the nonstructural V and W proteins of NiV perform their multiple functions.
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Affiliation(s)
| | - Filip Yabukarski
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Guillaume Communie
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Eric Condamine
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Caroline Mas
- Integrated Structural Biology Grenoble CNRS, CEA, University Grenoble Alpes, EMBL, Grenoble, France
| | - Valentina Volchkova
- Molecular Basis of Viral Pathogenicity, Centre International de Recherche en Infectiologie, INSERMU1111-CNRS UMR5308, Université Claude Bernard Lyon 1, ENS de Lyon, Lyon, France
| | - Nicolas Tarbouriech
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Jean-Marie Bourhis
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Viktor Volchkov
- Molecular Basis of Viral Pathogenicity, Centre International de Recherche en Infectiologie, INSERMU1111-CNRS UMR5308, Université Claude Bernard Lyon 1, ENS de Lyon, Lyon, France
| | - Martin Blackledge
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Marc Jamin
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France.
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78
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Zheng W, Dignon G, Brown M, Kim YC, Mittal J. Hydropathy Patterning Complements Charge Patterning to Describe Conformational Preferences of Disordered Proteins. J Phys Chem Lett 2020; 11:3408-3415. [PMID: 32227994 PMCID: PMC7450210 DOI: 10.1021/acs.jpclett.0c00288] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Understanding the conformational ensemble of an intrinsically disordered protein (IDP) is of great interest due to its relevance to critical intracellular functions and diseases. It is now well established that the polymer scaling behavior can provide a great deal of information about the conformational properties as well as liquid-liquid phase separation of an IDP. It is, therefore, extremely desirable to be able to predict an IDP's scaling behavior from the protein sequence itself. The work in this direction so far has focused on highly charged proteins and how charge patterning can perturb their structural properties. As naturally occurring IDPs are composed of a significant fraction of uncharged amino acids, the rules based on charge content and patterning are only partially helpful in solving the problem. Here, we propose a new order parameter, sequence hydropathy decoration, which can provide a near-quantitative understanding of scaling and structural properties of IDPs devoid of charged residues. We combine this with a charge patterning parameter, sequence charge decoration, to obtain a general equation, parametrized from extensive coarse-grained simulation data, for predicting protein dimensions from the sequence. We finally test this equation against available experimental data and find a semiquantitative match in predicting the scaling behavior. We also provide guidance on how to extend this approach to experimental data, which should be feasible in the near future.
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Affiliation(s)
- Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
| | - Gregory Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Matthew Brown
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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79
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Yan Y, Tao H, He J, Huang SY. The HDOCK server for integrated protein–protein docking. Nat Protoc 2020; 15:1829-1852. [DOI: 10.1038/s41596-020-0312-x] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/03/2020] [Indexed: 12/27/2022]
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80
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Nazir R, Parida D, Guex AG, Rentsch D, Zarei A, Gooneie A, Salmeia KA, Yar KM, Alihosseini F, Sadeghpour A, Gaan S. Structurally Tunable pH-responsive Phosphine Oxide Based Gels by Facile Synthesis Strategy. ACS APPLIED MATERIALS & INTERFACES 2020; 12:7639-7649. [PMID: 31972075 DOI: 10.1021/acsami.9b22808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Design and synthesis of nanostructured responsive gels have attracted increasing attention, particularly in the biomedical domain. Polymer chain configurations and nanodomain sizes within the network can be used to steer their functions as drug carriers. Here, a catalyst-free facile one-step synthesis strategy is reported for the design of pH-responsive gels and controlled structures in nanoscale. Transparent and impurity free gels were directly synthesized from trivinylphosphine oxide (TVPO) and cyclic secondary diamine monomers via Michael addition polymerization under mild conditions. NMR analysis confirmed the consumption of all TVPO and the absence of side products, thereby eliminating post purification steps. The small-angle X-ray scattering (SAXS) elucidates the nanoscale structural features in gels, that is, it demonstrates the presence of collapsed nanodomains within gel networks and it was possible to tune the size of these domains by varying the amine monomers and the nature of the solvent. The fabricated gels demonstrate structure tunability via solvent-polymer interactions and pH specific drug release behavior. Three different anionic dyes (acid blue 80, acid blue 90, and fluorescein) of varying size and chemistry were incorporated into the hydrogel as model drugs and their release behavior was studied. Compared to acidic pH, a higher and faster release of acid blue 80 and fluorescein was observed at pH 10, possibly because of their increased solubility in alkaline pH. In addition, their release in phosphate buffered saline (PBS) and simulated body fluid (SBF) matrix was positively influenced by the ionic interaction with positively charged metal ions. In the case of hydrogel containing acid blue 90 a very low drug release (<1%) was observed, which is due to the reaction of its accessible free amino group with the vinyl groups of the TVPO. In vitro evaluation of the prepared hydrogel using human dermal fibroblasts indicates no cytotoxic effects, warranting further research for biomedical applications. Our strategy of such gel synthesis lays the basis for the design of other gel-based functional materials.
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Affiliation(s)
- Rashid Nazir
- Laboratory of Advanced Fibers , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Dambarudhar Parida
- Laboratory of Advanced Fibers , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Anne Géraldine Guex
- Laboratory for Biointerfaces and Laboratory for Biomimetic Membranes and Textiles , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Daniel Rentsch
- Laboratory for Functional Polymers , Empa, Swiss Federal Laboratories for Materials Science and Technology , Überlandstrasse 129 , 8600 Dübendorf , Switzerland
| | - Afsaneh Zarei
- Department of Textile Engineering , Isfahan University of Technology , Isfahan , 84156-83111 , Iran
| | - Ali Gooneie
- Laboratory of Advanced Fibers , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Khalifah A Salmeia
- Laboratory of Advanced Fibers , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Kevin M Yar
- Laboratory of Advanced Fibers , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Farzaneh Alihosseini
- Department of Textile Engineering , Isfahan University of Technology , Isfahan , 84156-83111 , Iran
| | - Amin Sadeghpour
- Center for X-Ray Analytics , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
| | - Sabyasachi Gaan
- Laboratory of Advanced Fibers , Empa, Swiss Federal Laboratories for Materials Science and Technology , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
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81
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Ronnebaum TA, Gupta K, Christianson DW. Higher-order oligomerization of a chimeric αβγ bifunctional diterpene synthase with prenyltransferase and class II cyclase activities is concentration-dependent. J Struct Biol 2020; 210:107463. [PMID: 31978464 DOI: 10.1016/j.jsb.2020.107463] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/03/2020] [Accepted: 01/15/2020] [Indexed: 12/11/2022]
Abstract
The unusual diterpene (C20) synthase copalyl diphosphate synthase from Penicillium verruculosum (PvCPS) is the first bifunctional terpene synthase identified with both prenyltransferase and class II cyclase activities in a single polypeptide chain with αβγ domain architecture. The C-terminal prenyltransferase α domain generates geranylgeranyl diphosphate which is then cyclized to form copalyl diphosphate at the N-terminal βγ domain interface. We now demonstrate that PvCPS exists as a hexamer at high concentrations - a unique quaternary structure for known αβγ terpene synthases. Hexamer assembly is corroborated by a 2.41 Å-resolution crystal structure of the α domain prenyltransferase obtained from limited proteolysis of full-length PvCPS, as well as the ab initio model of full-length PvCPS derived from small-angle X-ray scattering data. Hexamerization of the prenyltransferase α domain appears to drive the hexamerization of full-length PvCPS. The PvCPS hexamer dissociates into lower-order species at lower concentrations, as evidenced by size-exclusion chromatography in-line with multiangle light scattering, sedimentation velocity analytical ultracentrifugation, and native polyacrylamide gel electrophoresis experiments, suggesting that oligomerization is concentration dependent. Even so, PvCPS oligomer assembly does not affect prenyltransferase activity in vitro.
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Affiliation(s)
- Trey A Ronnebaum
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.
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82
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Guillien M, le Maire A, Mouhand A, Bernadó P, Bourguet W, Banères JL, Sibille N. IDPs and their complexes in GPCR and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:105-155. [DOI: 10.1016/bs.pmbts.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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83
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White MA, Tsalkova T, Mei FC, Cheng X. Conformational States of Exchange Protein Directly Activated by cAMP (EPAC1) Revealed by Ensemble Modeling and Integrative Structural Biology. Cells 2019; 9:cells9010035. [PMID: 31877746 PMCID: PMC7016869 DOI: 10.3390/cells9010035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 02/08/2023] Open
Abstract
Exchange proteins directly activated by cAMP (EPAC1 and EPAC2) are important allosteric regulators of cAMP-mediated signal transduction pathways. To understand the molecular mechanism of EPAC activation, we performed detailed Small-Angle X-ray Scattering (SAXS) analysis of EPAC1 in its apo (inactive), cAMP-bound, and effector (Rap1b)-bound states. Our study demonstrates that we can model the solution structures of EPAC1 in each state using ensemble analysis and homology models derived from the crystal structures of EPAC2. The N-terminal domain of EPAC1, which is not conserved between EPAC1 and EPAC2, appears folded and interacts specifically with another component of EPAC1 in each state. The apo-EPAC1 state is a dynamic mixture of a compact (Rg = 32.9 Å, 86%) and a more extended (Rg = 38.5 Å, 13%) conformation. The cAMP-bound form of EPAC1 in the absence of Rap1 forms a dimer in solution; but its molecular structure is still compatible with the active EPAC1 conformation of the ternary complex model with cAMP and Rap1. Herein, we show that SAXS can elucidate the conformational states of EPAC1 activation as it proceeds from the compact, inactive apo conformation through a previously unknown intermediate-state, to the extended cAMP-bound form, and then binds to its effector (Rap1b) in a ternary complex.
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Affiliation(s)
- Mark Andrew White
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Correspondence: (M.A.W.); (X.C.); Tel.: +409-747-4747 (M.A.W.); +713-500-7487 (X.C.)
| | - Tamara Tsalkova
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Fang C. Mei
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA;
- Texas Therapeutics Institute, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA;
- Texas Therapeutics Institute, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Correspondence: (M.A.W.); (X.C.); Tel.: +409-747-4747 (M.A.W.); +713-500-7487 (X.C.)
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84
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Linker Dependence of Avidity in Multivalent Interactions Between Disordered Proteins. J Mol Biol 2019; 431:4784-4795. [DOI: 10.1016/j.jmb.2019.09.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/13/2019] [Accepted: 09/04/2019] [Indexed: 11/21/2022]
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85
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Sørensen CS, Kjaergaard M. Effective concentrations enforced by intrinsically disordered linkers are governed by polymer physics. Proc Natl Acad Sci U S A 2019; 116:23124-23131. [PMID: 31659043 PMCID: PMC6859346 DOI: 10.1073/pnas.1904813116] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many multidomain proteins contain disordered linkers that regulate interdomain contacts, and thus the effective concentrations that govern intramolecular reactions. Effective concentrations are rarely measured experimentally, and therefore little is known about how they relate to linker architecture. We have directly measured the effective concentrations enforced by disordered protein linkers using a fluorescent biosensor. We show that effective concentrations follow simple geometric models based on polymer physics, offering an indirect method to probe the structural properties of the linker. The compaction of the disordered linker depends not only on net charge, but also on the type of charged residues. In contrast to theoretical predictions, we found that polyampholyte linkers can contract to similar dimensions as globular proteins. Hydrophobicity has little effect in itself, but aromatic residues lead to strong compaction, likely through π-interactions. Finally, we find that the individual contributors to chain compaction are not additive. We thus demonstrate that direct measurement of effective concentrations can be used in systematic studies of the relationship between sequence and structure of intrinsically disordered proteins. A quantitative understanding of the relationship between effective concentration and linker sequence will be crucial for understanding disorder-based allosteric regulation in multidomain proteins.
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Affiliation(s)
- Charlotte S Sørensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark, DK-8000
- The Danish Research Institute for Translational Neuroscience (DANDRITE), Aarhus University, Aarhus, Denmark, DK-8000
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark, DK-8000;
- The Danish Research Institute for Translational Neuroscience (DANDRITE), Aarhus University, Aarhus, Denmark, DK-8000
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark, DK-8000
- Center for Proteins in Memory - PROMEMO, Danish National Research Foundation, Aarhus, Denmark, DK-8000
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86
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Shou K, Bremer A, Rindfleisch T, Knox-Brown P, Hirai M, Rekas A, Garvey CJ, Hincha DK, Stadler AM, Thalhammer A. Conformational selection of the intrinsically disordered plant stress protein COR15A in response to solution osmolarity - an X-ray and light scattering study. Phys Chem Chem Phys 2019; 21:18727-18740. [PMID: 31424463 DOI: 10.1039/c9cp01768b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The plant stress protein COR15A stabilizes chloroplast membranes during freezing. COR15A is an intrinsically disordered protein (IDP) in aqueous solution, but acquires an α-helical structure during dehydration or the increase of solution osmolarity. We have used small- and wide-angle X-ray scattering (SAXS/WAXS) combined with static and dynamic light scattering (SLS/DLS) to investigate the structural and hydrodynamic properties of COR15A in response to increasing solution osmolarity. Coarse-grained ensemble modelling allowed a structure-based interpretation of the SAXS data. Our results demonstrate that COR15A behaves as a biomacromolecule with polymer-like properties which strongly depend on solution osmolarity. Biomacromolecular self-assembly occurring at high solvent osmolarity is initiated by the occurrence of two specific structural subpopulations of the COR15A monomer. The osmolarity dependent structural selection mechanism is an elegant way for conformational regulation and assembly of COR15A. It highlights the importance of the polymer-like properties of IDPs for their associated biological function.
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Affiliation(s)
- Keyun Shou
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
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87
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Manalastas KG, Svergun DI. Molecular Dissection of the Intrinsically Disordered Estrogen Receptor Alpha-NTD. Structure 2019; 27:207-208. [PMID: 30726752 DOI: 10.1016/j.str.2019.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this issue of Structure, Peng et al. (2019) use a combination of computational modeling and solution-based experimental methods to characterize the intrinsically disordered N-terminal transactivation domain of estrogen receptor alpha. A long-range contact (I33-S118) was identified and was demonstrated to affect the protein conformation and coactivator binding.
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Affiliation(s)
- Karen G Manalastas
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany.
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88
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An ensemble of flexible conformations underlies mechanotransduction by the cadherin-catenin adhesion complex. Proc Natl Acad Sci U S A 2019; 116:21545-21555. [PMID: 31591245 PMCID: PMC6815173 DOI: 10.1073/pnas.1911489116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Adherens junctions are specialized cell–cell adhesion complexes found in epithelial, endothelial, and neuronal tissues of multicellular organism. The cadherin–catenin complex is the core component of the adherens junction and transmits mechanical stress from cell to cell. This study reveals that the cadherin–catenin complex displays a wide spectrum of flexible structures, which suggests a dynamic mechanism for this complex in mechanotransduction for cell–cell adhesion. The cadherin–catenin adhesion complex is the central component of the cell–cell adhesion adherens junctions that transmit mechanical stress from cell to cell. We have determined the nanoscale structure of the adherens junction complex formed by the α-catenin•β-catenin•epithelial cadherin cytoplasmic domain (ABE) using negative stain electron microscopy, small-angle X-ray scattering, and selective deuteration/small-angle neutron scattering. The ABE complex is highly pliable and displays a wide spectrum of flexible structures that are facilitated by protein-domain motions in α- and β-catenin. Moreover, the 107-residue intrinsically disordered N-terminal segment of β-catenin forms a flexible “tongue” that is inserted into α-catenin and participates in the assembly of the ABE complex. The unanticipated ensemble of flexible conformations of the ABE complex suggests a dynamic mechanism for sensitivity and reversibility when transducing mechanical signals, in addition to the catch/slip bond behavior displayed by the ABE complex under mechanical tension. Our results provide mechanistic insight into the structural dynamics for the cadherin–catenin adhesion complex in mechanotransduction.
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89
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Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proc Natl Acad Sci U S A 2019; 116:20446-20452. [PMID: 31548393 DOI: 10.1073/pnas.1907251116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.
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90
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Demerdash O, Shrestha UR, Petridis L, Smith JC, Mitchell JC, Ramanathan A. Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins. Front Mol Biosci 2019; 6:64. [PMID: 31475155 PMCID: PMC6705226 DOI: 10.3389/fmolb.2019.00064] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/16/2019] [Indexed: 12/26/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) play important roles in many aspects of normal cell physiology, such as signal transduction and transcription, as well as pathological states, including Alzheimer's, Parkinson's, and Huntington's disease. Unlike their globular counterparts that are defined by a few structures and free energy minima, IDP/IDR comprise a large ensemble of rapidly interconverting structures and a corresponding free energy landscape characterized by multiple minima. This aspect has precluded the use of structural biological techniques, such as X-ray crystallography and nuclear magnetic resonance (NMR) for resolving their structures. Instead, low-resolution techniques, such as small-angle X-ray or neutron scattering (SAXS/SANS), have become a mainstay in characterizing coarse features of the ensemble of structures. These are typically complemented with NMR data if possible or computational techniques, such as atomistic molecular dynamics, to further resolve the underlying ensemble of structures. However, over the past 10–15 years, it has become evident that the classical, pairwise-additive force fields that have enjoyed a high degree of success for globular proteins have been somewhat limited in modeling IDP/IDR structures that agree with experiment. There has thus been a significant effort to rehabilitate these models to obtain better agreement with experiment, typically done by optimizing parameters in a piecewise fashion. In this work, we take a different approach by optimizing a set of force field parameters simultaneously, using machine learning to adapt force field parameters to experimental SAXS scattering profiles. We demonstrate our approach in modeling three biologically IDP ensembles based on experimental SAXS profiles and show that our optimization approach significantly improve force field parameters that generate ensembles in better agreement with experiment.
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Affiliation(s)
- Omar Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Utsab R Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Loukas Petridis
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Arvind Ramanathan
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, United States
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91
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Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD. The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 2019; 46:4978-4990. [PMID: 29850894 PMCID: PMC6007315 DOI: 10.1093/nar/gky206] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/16/2018] [Indexed: 01/21/2023] Open
Abstract
Chromatin remodelers are ATP-dependent motors that reorganize DNA packaging by disrupting canonical histone–DNA contacts within the nucleosome. Here, we show that the Chd1 chromatin remodeler stimulates DNA unwrapping from the edge of the nucleosome in a nucleotide-dependent and DNA sequence-sensitive fashion. Nucleosome binding, monitored by stopped flow, was complex and sensitive to nucleotide, with AMP–PNP promoting faster binding than ADP·BeF3–. Nucleosome unwrapping by Chd1, examined by bulk FRET, occurred in the presence and absence of nucleotide and did not require the Chd1 DNA-binding domain. In AMP–PNP conditions, Chd1 unwrapped one side of the Widom 601 DNA more easily than the other, consistent with previous observations of 601 asymmetry and indicating that Chd1 amplifies intrinsic sequence properties of nucleosomal DNA. Using small angle X-ray scattering (SAXS) with contrast variation, we found distinct DNA conformations depending on the nucleotide analog bound to Chd1: with AMP–PNP, DNA primarily unwrapped in-plane with the nucleosomal disk, whereas with ADP·BeF3–, a significant fraction showed distinctive out-of-plane unwrapping as well. Taken together, our findings show tight coupling between entry/exit DNA of the nucleosome and the Chd1 ATPase motor, suggesting that dynamic nucleosome unwrapping is coupled to nucleosome binding and remodeling by Chd1.
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Affiliation(s)
- Joshua M Tokuda
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Ren Ren
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Rebecca J Tay
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Ming Yan
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
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92
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Cordeiro TN, Sibille N, Germain P, Barthe P, Boulahtouf A, Allemand F, Bailly R, Vivat V, Ebel C, Barducci A, Bourguet W, le Maire A, Bernadó P. Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression. Structure 2019; 27:1270-1285.e6. [DOI: 10.1016/j.str.2019.05.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/30/2019] [Accepted: 05/04/2019] [Indexed: 11/30/2022]
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93
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Schramm A, Bignon C, Brocca S, Grandori R, Santambrogio C, Longhi S. An arsenal of methods for the experimental characterization of intrinsically disordered proteins - How to choose and combine them? Arch Biochem Biophys 2019; 676:108055. [PMID: 31356778 DOI: 10.1016/j.abb.2019.07.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
In this review, we detail the most common experimental approaches to assess and characterize protein intrinsic structural disorder, with the notable exception of NMR and EPR spectroscopy, two ideally suited approaches that will be described in depth in two other reviews within this special issue. We discuss the advantages, the limitations, as well as the caveats of the various methods. We also describe less common and more demanding approaches that enable achieving further insights into the conformational properties of IDPs. Finally, we present recent developments that have enabled assessment of structural disorder in living cells, and discuss the currently available methods to model IDPs as conformational ensembles.
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Affiliation(s)
- Antoine Schramm
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
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94
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Tajielyato N, Alexov E. Modeling pKas of unfolded proteins to probe structural models of unfolded state. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Modeling unfolded states of proteins has implications for protein folding and stability. Since in unfolded state proteins adopt multiple conformations, any experimentally measured quantity is ensemble averaged, therefore the computed quantity should be ensemble averaged as well. Here, we investigate the possibility that one can model an unfolded state ensemble with the coil model approach, algorithm such as “flexible-meccano” [Ozenne V et al., Flexible-meccano: A tool for the generation of explicit ensemle descriptions of intrinsically disordered proteins and their associated experimental observables, Bioinformatics 28:1463–1470, 2012], developed to generate structures for intrinsically disordered proteins. We probe such a possibility by using generated structures to calculate pKas of titratable groups and compare with experimental data. It is demonstrated that even with a small number of representative structures of unfolded state, the average calculated pKas are in very good agreement with experimentally measured pKas. Also, predictions are made for titratable groups for which there is no experimental data available. This suggests that the coil model approach is suitable for generating 3D structures of unfolded state of proteins. To make the approach suitable for large-scale modeling, which requires limited number of structures, we ranked the structures according to their solvent accessible surface area (SASA). It is shown that in the majority of cases, the top structures with smallest SASA are enough to represent unfolded state.
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Affiliation(s)
- Nayere Tajielyato
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29630, USA
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29630, USA
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95
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Gielnik M, Pietralik Z, Zhukov I, Szymańska A, Kwiatek WM, Kozak M. PrP (58-93) peptide from unstructured N-terminal domain of human prion protein forms amyloid-like fibrillar structures in the presence of Zn 2+ ions. RSC Adv 2019; 9:22211-22219. [PMID: 35519468 PMCID: PMC9066832 DOI: 10.1039/c9ra01510h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/07/2019] [Indexed: 12/12/2022] Open
Abstract
Many transition metal ions modulate the aggregation of different amyloid peptides. Substoichiometric zinc concentrations can inhibit aggregation, while an excess of zinc can accelerate the formation of cytotoxic fibrils. In this study, we report the fibrillization of the octarepeat domain to amyloid-like structures. Interestingly, this self-assembling process occurred only in the presence of Zn(ii) ions. The formed peptide aggregates are able to bind amyloid specific dyes thioflavin T and Congo red. Atomic force microscopy and transmission electron microscopy revealed the formation of long, fibrillar structures. X-ray diffraction and Fourier transform infrared spectroscopy studies of the formed assemblies confirmed the presence of cross-β structure. Two-component analysis of synchrotron radiation SAXS data provided the evidence for a direct decrease in monomeric peptide species content and an increase in the fraction of aggregates as a function of Zn(ii) concentration. These results could shed light on Zn(ii) as a toxic agent and on the metal ion induced protein misfolding in prion diseases.
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Affiliation(s)
- Maciej Gielnik
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University Uniwersytetu Poznańskiego 2 PL 61-614 Poznań Poland
| | - Zuzanna Pietralik
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University Uniwersytetu Poznańskiego 2 PL 61-614 Poznań Poland
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences PL 02-106 Warszawa Poland
- NanoBioMedical Centre, Adam Mickiewicz University PL 61-614 Poznań Poland
| | - Aneta Szymańska
- Department of Biomedical Chemistry, Faculty of Chemistry, Gdańsk University PL 80-308 Gdańsk Poland
| | - Wojciech M Kwiatek
- Institute of Nuclear Physics Polish Academy of Sciences PL 31-342 Krakow Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University Uniwersytetu Poznańskiego 2 PL 61-614 Poznań Poland
- Joint Laboratory for SAXS Studies, Faculty of Physics, Adam Mickiewicz University PL 61-614 Poznań Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University PL 30-392 Kraków Poland
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96
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Pyles H, Zhang S, De Yoreo JJ, Baker D. Controlling protein assembly on inorganic crystals through designed protein interfaces. Nature 2019; 571:251-256. [PMID: 31292559 PMCID: PMC6948101 DOI: 10.1038/s41586-019-1361-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/10/2019] [Indexed: 11/09/2022]
Abstract
The ability of proteins and other macromolecules to interact with inorganic surfaces is critical to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains1-5, but the structures of most protein-inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein-mineral interfaces guided by the example of ice-binding proteins, which present arrays of threonine residues matched to the ice lattice that order clathrate waters into an ice-like structure6. We designed proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the K+ sublattice on muscovite mica (001). At low [K+] individual molecules bind independently to mica in the designed orientations, while at high [K+], the designs form 2D liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimeters. Incorporation of designed protein-protein interactions preserving the match between the proteins and the K+ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micron long single protein-diameter wires, and a designed trimeric interface yielded extensive honeycomb arrays. The nearest neighbor distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nm with 2.1 nm selectivity by changing the number of repeat units in the monomer. These results demonstrate that protein-inorganic lattice interactions can be systematically programmed and set the stage for designing protein-inorganic hybrid materials.
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Affiliation(s)
- Harley Pyles
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Shuai Zhang
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.,Department of Materials Science and Engineering, University of Washington, Seattle, WA, USA
| | - James J De Yoreo
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA. .,Department of Materials Science and Engineering, University of Washington, Seattle, WA, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA. .,Institute for Protein Design, University of Washington, Seattle, WA, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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97
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Chen PC, Shevchuk R, Strnad FM, Lorenz C, Karge L, Gilles R, Stadler AM, Hennig J, Hub JS. Combined Small-Angle X-ray and Neutron Scattering Restraints in Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:4687-4698. [DOI: 10.1021/acs.jctc.9b00292] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Po-chia Chen
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Roman Shevchuk
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Felix M. Strnad
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Charlotte Lorenz
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems ICS (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Lukas Karge
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Ralph Gilles
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems ICS (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
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98
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Ge J, Remesh SG, Hammel M, Pan S, Mahan AD, Wang S, Wang X. Functional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling. Structure 2019; 27:1296-1307.e5. [PMID: 31257107 DOI: 10.1016/j.str.2019.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/09/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
The interleukin 1 (IL-1) receptor family, whose members contain three immunoglobulin-like domains (D1-D3) in the extracellular region, is responsible for transmitting pleiotropic signals of IL-1 cytokines. The inter-domain flexibility of IL-1 receptors and its functional roles have not been fully elucidated. In this study, we used small-angle X-ray scattering to show that ligand-binding primary receptors and co-receptors in the family all have inherent inter-domain flexibility due to the D2/D3 linker. Variants of the IL-1RAcP and IL-18Rβ co-receptors with mutated D2/D3 linkers cannot form a cytokine-receptor complex and mediate signaling. Our analysis further revealed that these mutated co-receptors exhibited a changed conformational ensemble, suggesting that loss of function is due to the alteration of receptor dynamics. Taken together, our results demonstrate that the D2/D3 linker is a critical functional determinant of IL-1 receptor and underscore the important roles of the inter-domain flexibility in cytokine/receptor binding and signaling.
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Affiliation(s)
- Jiwan Ge
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Soumya G Remesh
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Si Pan
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Andrew D Mahan
- Janssen Bio Therapeutics, Janssen R&D, LLC, Spring House, PA 19477, USA
| | - Shuying Wang
- Department of Microbiology and Immunology, National Cheng Kung University Medical College, Tainan 701, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan.
| | - Xinquan Wang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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99
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Wei Y, Hu L, Yao J, Shao Z, Chen X. Facile Dissolution of Zein Using a Common Solvent Dimethyl Sulfoxide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:6640-6649. [PMID: 31041860 DOI: 10.1021/acs.langmuir.9b00670] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The conformation and stability of zein in solution are closely associated with its solvation process and influence the mechanical properties of the related zein-based materials. In this work, a common solvent dimethyl sulfoxide (DMSO) was used to dissolve zein, rather than solvents frequently used such as aqueous ethanol and acetic acid. It was found that DMSO could dissolve zein readily and the solution was stable for at least 2 weeks. Rheological analysis and small-angle X-ray scattering (SAXS) were employed to characterize the zein DMSO solution. Results of rheological analysis suggested a Huggins coefficient of 0.24, indicating DMSO to be a good solvent for zein. SAXS results revealed that zein adopted an elongated conformation and had dimensions of 2.8 nm × 2.8 nm × 14.8 nm in DMSO solution. Moreover, robust zein films were fabricated from zein DMSO solutions. The content of residual DMSO in the films was determined to be approximately 15 wt % by thermogravimetric analysis, in consistence with the value obtained by other two methods. The film showed a large breaking strain of 320.6% with a considerable breaking stress of 1.9 MPa, yielding a breaking energy of 376.2 MJ/m3. Therefore, the ease of dissolution and good mechanical performance of the final zein-based material make DMSO a potential solvent for fabrication of zein materials, thereby improving the scope of practical applications of zein.
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Affiliation(s)
- Yanxia Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials , Fudan University , 220 Handan Road , Shanghai 200433 , People's Republic of China
| | - Linli Hu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials , Fudan University , 220 Handan Road , Shanghai 200433 , People's Republic of China
| | - Jinrong Yao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials , Fudan University , 220 Handan Road , Shanghai 200433 , People's Republic of China
| | - Zhengzhong Shao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials , Fudan University , 220 Handan Road , Shanghai 200433 , People's Republic of China
| | - Xin Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials , Fudan University , 220 Handan Road , Shanghai 200433 , People's Republic of China
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100
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Zerze GH, Zheng W, Best RB, Mittal J. Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties. J Phys Chem Lett 2019; 10:2227-2234. [PMID: 30990694 PMCID: PMC7507668 DOI: 10.1021/acs.jpclett.9b00850] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Experimental studies on intrinsically disordered and unfolded proteins have shown that in isolation they typically have low populations of secondary structure and exhibit distance scalings suggesting that they are at near-theta-solvent conditions. Until recently, however, all-atom force fields failed to reproduce these fundamental properties of intrinsically disordered proteins (IDPs). Recent improvements by refining against ensemble-averaged experimental observables for polypeptides in aqueous solution have addressed deficiencies including secondary structure bias, global conformational properties, and thermodynamic parameters of biophysical reactions such as folding and collapse. To date, studies utilizing these improved all-atom force fields have mostly been limited to a small set of unfolded or disordered proteins. Here, we present data generated for a diverse library of unfolded or disordered proteins using three progressively improved generations of Amber03 force fields, and we explore how global and local properties are affected by each successive change in the force field. We find that the most recent force field refinements significantly improve the agreement of the global properties such as radii of gyration and end-to-end distances with experimental estimates. However, these global properties are largely independent of the local secondary structure propensity. This result stresses the need to validate force fields with reference to a combination of experimental data providing information about both local and global structure formation.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biomolecular Engineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Wenwei Zheng
- College of Integrative Sciences and Arts , Arizona State University , Mesa , Arizona 85212 , United States
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
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