1
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Baade T, Michaelis M, Prestel A, Paone C, Klishin N, Herbinger M, Scheinost L, Nedielkov R, Hauck CR, Möller HM. A flexible loop in the paxillin LIM3 domain mediates its direct binding to integrin β subunits. PLoS Biol 2024; 22:e3002757. [PMID: 39231388 PMCID: PMC11374337 DOI: 10.1371/journal.pbio.3002757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 07/17/2024] [Indexed: 09/06/2024] Open
Abstract
Integrins are fundamental for cell adhesion and the formation of focal adhesions (FA). Accordingly, these receptors guide embryonic development, tissue maintenance, and haemostasis but are also involved in cancer invasion and metastasis. A detailed understanding of the molecular interactions that drive integrin activation, FA assembly, and downstream signalling cascades is critical. Here, we reveal a direct association of paxillin, a marker protein of FA sites, with the cytoplasmic tails of the integrin β1 and β3 subunits. The binding interface resides in paxillin's LIM3 domain, where based on the NMR structure and functional analyses, a flexible, 7-amino acid loop engages the unstructured part of the integrin cytoplasmic tail. Genetic manipulation of the involved residues in either paxillin or integrin β3 compromises cell adhesion and motility of murine fibroblasts. This direct interaction between paxillin and the integrin cytoplasmic domain identifies an alternative, kindlin-independent mode of integrin outside-in signalling particularly important for integrin β3 function.
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Affiliation(s)
- Timo Baade
- Lehrstuhl Zellbiologie, Universität Konstanz, Konstanz, Germany
- Konstanz Research School Chemical Biology, Universität Konstanz, Konstanz, Germany
| | - Marcus Michaelis
- Analytische Chemie, Universität Potsdam, Potsdam, Germany
- DFG Research Training Group 2473 "Bioactive Peptides"
| | | | - Christoph Paone
- Lehrstuhl Zellbiologie, Universität Konstanz, Konstanz, Germany
- Konstanz Research School Chemical Biology, Universität Konstanz, Konstanz, Germany
| | - Nikolai Klishin
- Analytische Chemie, Universität Potsdam, Potsdam, Germany
- DFG Research Training Group 2473 "Bioactive Peptides"
| | | | - Laura Scheinost
- Lehrstuhl Zellbiologie, Universität Konstanz, Konstanz, Germany
| | | | - Christof R Hauck
- Lehrstuhl Zellbiologie, Universität Konstanz, Konstanz, Germany
- Konstanz Research School Chemical Biology, Universität Konstanz, Konstanz, Germany
| | - Heiko M Möller
- Analytische Chemie, Universität Potsdam, Potsdam, Germany
- DFG Research Training Group 2473 "Bioactive Peptides"
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2
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Mendoza-Hoffmann F, Yang L, Buratto D, Brito-Sánchez J, Garduño-Javier G, Salinas-López E, Uribe-Álvarez C, Ortega R, Sotelo-Serrano O, Cevallos MÁ, Ramírez-Silva L, Uribe-Carvajal S, Pérez-Hernández G, Celis-Sandoval H, García-Trejo JJ. Inhibitory to non-inhibitory evolution of the ζ subunit of the F 1F O-ATPase of Paracoccus denitrificans and α-proteobacteria as related to mitochondrial endosymbiosis. Front Mol Biosci 2023; 10:1184200. [PMID: 37664184 PMCID: PMC10469736 DOI: 10.3389/fmolb.2023.1184200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction: The ζ subunit is a potent inhibitor of the F1FO-ATPase of Paracoccus denitrificans (PdF1FO-ATPase) and related α-proteobacteria different from the other two canonical inhibitors of bacterial (ε) and mitochondrial (IF1) F1FO-ATPases. ζ mimics mitochondrial IF1 in its inhibitory N-terminus, blocking the PdF1FO-ATPase activity as a unidirectional pawl-ratchet and allowing the PdF1FO-ATP synthase turnover. ζ is essential for the respiratory growth of P. denitrificans, as we showed by a Δζ knockout. Given the vital role of ζ in the physiology of P. denitrificans, here, we assessed the evolution of ζ across the α-proteobacteria class. Methods: Through bioinformatic, biochemical, molecular biology, functional, and structural analyses of several ζ subunits, we confirmed the conservation of the inhibitory N-terminus of ζ and its divergence toward its C-terminus. We reconstituted homologously or heterologously the recombinant ζ subunits from several α-proteobacteria into the respective F-ATPases, including free-living photosynthetic, facultative symbiont, and intracellular facultative or obligate parasitic α-proteobacteria. Results and discussion: The results show that ζ evolved, preserving its inhibitory function in free-living α-proteobacteria exposed to broad environmental changes that could compromise the cellular ATP pools. However, the ζ inhibitory function was diminished or lost in some symbiotic α-proteobacteria where ζ is non-essential given the possible exchange of nutrients and ATP from hosts. Accordingly, the ζ gene is absent in some strictly parasitic pathogenic Rickettsiales, which may obtain ATP from the parasitized hosts. We also resolved the NMR structure of the ζ subunit of Sinorhizobium meliloti (Sm-ζ) and compared it with its structure modeled in AlphaFold. We found a transition from a compact ordered non-inhibitory conformation into an extended α-helical inhibitory N-terminus conformation, thus explaining why the Sm-ζ cannot exert homologous inhibition. However, it is still able to inhibit the PdF1FO-ATPase heterologously. Together with the loss of the inhibitory function of α-proteobacterial ε, the data confirm that the primary inhibitory function of the α-proteobacterial F1FO-ATPase was transferred from ε to ζ and that ζ, ε, and IF1 evolved by convergent evolution. Some key evolutionary implications on the endosymbiotic origin of mitochondria, as most likely derived from α-proteobacteria, are also discussed.
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Affiliation(s)
- Francisco Mendoza-Hoffmann
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Lingyun Yang
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Damiano Buratto
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Jorge Brito-Sánchez
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Gilberto Garduño-Javier
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Emiliano Salinas-López
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Cristina Uribe-Álvarez
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Raquel Ortega
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Oliver Sotelo-Serrano
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Leticia Ramírez-Silva
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Salvador Uribe-Carvajal
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
| | - Heliodoro Celis-Sandoval
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - José J. García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
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3
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DMSO-Induced Unfolding of the Antifungal Disulfide Protein PAF and Its Inactive Variant: A Combined NMR and DSC Study. Int J Mol Sci 2023; 24:ijms24021208. [PMID: 36674720 PMCID: PMC9864379 DOI: 10.3390/ijms24021208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
PAF and related antifungal proteins are promising antimicrobial agents. They have highly stable folds around room temperature due to the presence of 3-4 disulfide bonds. However, unfolded states persist and contribute to the thermal equilibrium in aqueous solution, and low-populated states might influence their biological impact. To explore such equilibria during dimethyl sulfoxide (DMSO)-induced chemical unfolding, we studied PAF and its inactive variant PAFD19S using nuclear magnetic resonance (NMR) and differential scanning calorimetry (DSC). According to the NMR monitoring at 310 K, the folded structures disappear above 80 v/v% DMSO concentration, while the unfolding is completely reversible. Evaluation of a few resolved peaks from viscosity-compensated 15N-1H HSQC spectra of PAF yielded ∆G = 23 ± 7 kJ/M as the average value for NMR unfolding enthalpy. The NMR-based structures of PAF and the mutant in 50 v/v% DMSO/H2O mixtures were more similar in the mixed solvents then they were in water. The 15N NMR relaxation dynamics in the same mixtures verified the rigid backbones of the NMR-visible fractions of the proteins; still, enhanced dynamics around the termini and some loops were observed. DSC monitoring of the Tm melting point showed parabolic dependence on the DMSO molar fraction and suggested that PAF is more stable than the inactive PAFD19S. The DSC experiments were irreversible due to the applied broad temperature range, but still suggestive of the endothermic unfolding of PAF.
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4
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Šede M, Fridmanis J, Otikovs M, Johansson J, Rising A, Kronqvist N, Jaudzems K. Solution Structure of Tubuliform Spidroin N-Terminal Domain and Implications for pH Dependent Dimerization. Front Mol Biosci 2022; 9:936887. [PMID: 35775078 PMCID: PMC9237525 DOI: 10.3389/fmolb.2022.936887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
The spidroin N-terminal domain (NT) is responsible for high solubility and pH-dependent assembly of spider silk proteins during storage and fiber formation, respectively. It forms a monomeric five-helix bundle at neutral pH and dimerizes at lowered pH, thereby firmly interconnecting the spidroins. Mechanistic studies with the NTs from major ampullate, minor ampullate, and flagelliform spidroins (MaSp, MiSp, and FlSp) have shown that the pH dependency is conserved between different silk types, although the residues that mediate this process can differ. Here we study the tubuliform spidroin (TuSp) NT from Argiope argentata, which lacks several well conserved residues involved in the dimerization of other NTs. We solve its structure at low pH revealing an antiparallel dimer of two five-α-helix bundles, which contrasts with a previously determined Nephila antipodiana TuSp NT monomer structure. Further, we study a set of mutants and find that the residues participating in the protonation events during dimerization are different from MaSp and MiSp NT. Charge reversal of one of these residues (R117 in TuSp) results in significantly altered electrostatic interactions between monomer subunits. Altogether, the structure and mutant studies suggest that TuSp NT monomers assemble by elimination of intramolecular repulsive charge interactions, which could lead to slight tilting of α-helices.
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Affiliation(s)
- Megija Šede
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Jēkabs Fridmanis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Martins Otikovs
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Jan Johansson
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, Huddinge, Sweden
| | - Anna Rising
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, Huddinge, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nina Kronqvist
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, Huddinge, Sweden
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
- Faculty of Chemistry, University of Latvia, Riga, Latvia
- *Correspondence: Kristaps Jaudzems,
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5
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Structural and Functional Analysis of BBA03, Borrelia burgdorferi Competitive Advantage Promoting Outer Surface Lipoprotein. Pathogens 2020; 9:pathogens9100826. [PMID: 33050189 PMCID: PMC7650648 DOI: 10.3390/pathogens9100826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 11/17/2022] Open
Abstract
BBA03 is a Borrelia burgdorferi outer surface lipoprotein encoded on one of the most conserved plasmids in Borrelia genome, linear plasmid 54 (lp54). Although many of its genes have been identified as contributing or essential for spirochete fitness in vivo, the majority of the proteins encoded on this plasmid have no known function and lack homologs in other organisms. In this paper, we report the solution NMR structure of the B. burgdorferi outer surface lipoprotein BBA03, which is known to provide a competitive advantage to the bacteria during the transmission from tick vector to mammalian host. BBA03 shows structural homology to other outer surface lipoproteins reflecting their genetic and evolutionary relatedness. Analysis of the structure reveals a pore in BBA03, which could potentially bind lipids.
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6
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Fridmanis J, Otikovs M, Brangulis K, Tārs K, Jaudzems K. Solution NMR structure of Borrelia burgdorferi outer surface lipoprotein BBP28, a member of the mlp protein family. Proteins 2020; 89:588-594. [PMID: 32949018 DOI: 10.1002/prot.26011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 07/05/2020] [Accepted: 09/13/2020] [Indexed: 12/19/2022]
Abstract
Lyme disease is the most widespread vector-transmitted disease in North America and Europe, caused by infection with Borrelia burgdorferi sensu lato complex spirochetes. We report the solution NMR structure of the B. burgdorferi outer surface lipoprotein BBP28, a member of the multicopy lipoprotein (mlp) family. The structure comprises a tether peptide, five α-helices and an extended C-terminal loop. The fold is similar to that of Borrelia turicatae outer surface protein BTA121, which is known to bind lipids. These results contribute to the understanding of Lyme disease pathogenesis by revealing the molecular structure of a protein from the widely found mlp family.
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Affiliation(s)
| | | | - Kalvis Brangulis
- Latvian Biomedical Research and Study Centre, Riga, Latvia.,Department of Human Physiology and Biochemistry, Riga Stradins University, Riga, Latvia
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Riga, Latvia.,Department of Molecular Biology, University of Latvia, Riga, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Riga, Latvia.,Department of Organic Chemistry, University of Latvia, Riga, Latvia
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7
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Structural and DNA binding properties of mycobacterial integration host factor mIHF. J Struct Biol 2020; 209:107434. [PMID: 31846718 DOI: 10.1016/j.jsb.2019.107434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 01/08/2023]
Abstract
In bacteria, nucleoid associated proteins (NAPs) take part in active chromosome organization by supercoil management, three-dimensional DNA looping and direct transcriptional control. Mycobacterial integration host factor (mIHF, rv1388) is a NAP restricted to Actinobacteria and essential for survival of the human pathogen Mycobacterium tuberculosis. We show in vitro that DNA binding by mIHF strongly stabilizes the protein and increases its melting temperature. The structure obtained by Nuclear Magnetic Resonance (NMR) spectroscopy characterizes mIHF as a globular protein with a protruding alpha helix and a disordered N-terminus, similar to Streptomyces coelicolor IHF (sIHF). NMR revealed no residues of high flexibility, suggesting that mIHF is a rigid protein overall that does not undergo structural rearrangements. We show that mIHF only binds to double stranded DNA in solution, through two DNA binding sites (DBSs) similar to those identified in the X-ray structure of sIHF. According to Atomic Force Microscopy, mIHF is able to introduce left-handed loops of ca. 100 nm size (~300 bp) in supercoiled cosmids, thereby unwinding and relaxing the DNA.
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8
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Kooijman L, Ansorge P, Schuster M, Baumann C, Löhr F, Jurt S, Güntert P, Zerbe O. Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs. JOURNAL OF BIOMOLECULAR NMR 2020; 74:45-60. [PMID: 31754899 PMCID: PMC7015963 DOI: 10.1007/s10858-019-00289-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/11/2019] [Indexed: 05/21/2023]
Abstract
Resonance assignments are challenging for membrane proteins due to the size of the lipid/detergent-protein complex and the presence of line-broadening from conformational exchange. As a consequence, many correlations are missing in the triple-resonance NMR experiments typically used for assignments. Herein, we present an approach in which correlations from these solution-state NMR experiments are supplemented by data from 13C unlabeling, single-amino acid type labeling, 4D NOESY data and proximity of moieties to lipids or water in combination with a structure of the protein. These additional data are used to edit the expected peaklists for the automated assignment protocol FLYA, a module of the program package CYANA. We demonstrate application of the protocol to the 262-residue proton pump from archaeal bacteriorhodopsin (bR) in lipid nanodiscs. The lipid-protein assembly is characterized by an overall correlation time of 44 ns. The protocol yielded assignments for 62% of all backbone (H, N, Cα, Cβ, C') resonances of bR, corresponding to 74% of all observed backbone spin systems, and 60% of the Ala, Met, Ile (δ1), Leu and Val methyl groups, thus enabling to assign a large fraction of the protein without mutagenesis data. Most missing resonances stem from the extracellular half, likely due intermediate exchange line-broadening. Further analysis revealed that missing information of the amino acid type of the preceding residue is the largest problem, and that 4D NOESY experiments are particularly helpful to compensate for that information loss.
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Affiliation(s)
- Laurens Kooijman
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Philipp Ansorge
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Matthias Schuster
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christian Baumann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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Structure of the PUB Domain from Ubiquitin Regulatory X Domain Protein 1 (UBXD1) and Its Interaction with the p97 AAA+ ATPase. Biomolecules 2019; 9:biom9120876. [PMID: 31847414 PMCID: PMC6995525 DOI: 10.3390/biom9120876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 01/19/2023] Open
Abstract
AAA+ ATPase p97/valosin-containing protein (VCP)/Cdc48 is a key player in various cellular stress responses in which it unfolds ubiquitinated proteins to facilitate their degradation by the proteasome. P97 works in different cellular processes using alternative sets of cofactors and is implicated in multiple degenerative diseases. Ubiquitin regulatory X domain protein 1 (UBXD1) has been linked to pathogenesis and is unique amongst p97 cofactors because it interacts with both termini of p97. Its N-domain binds to the N-domain and N/D1 interface of p97 and regulates its ATPase activity. The PUB (peptide:N-glycanase and UBA or UBX-containing proteins) domain binds the p97 C-terminus, but how it controls p97 function is still unknown. Here we present the NMR structure of UBXD1-PUB together with binding studies, mutational analysis, and a model of UBXD1-PUB in complex with the p97 C-terminus. While the binding pocket is conserved among PUB domains, UBXD1-PUB features a unique loop and turn regions suggesting a role in coordinating interaction with downstream regulators and substrate processing
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10
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Staup AJ, De Silva IU, Catt JT, Tan X, Hammond RG, Johnson MA. Structure of the SARS-Unique Domain C From the Bat Coronavirus HKU4. Nat Prod Commun 2019; 14:1934578X19849202. [PMID: 32395093 PMCID: PMC7206560 DOI: 10.1177/1934578x19849202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/18/2019] [Indexed: 12/21/2022] Open
Abstract
Coronaviruses (CoVs) that cause infections such as severe acute respiratory syndrome
(SARS) and Middle East respiratory syndrome phylogenetically originate from bat CoVs. The
coronaviral nonstructural protein 3 (nsp3) has been implicated in viral replication,
polyprotein cleavage, and host immune interference. We report the structure of the C
domain from the SARS-Unique Domain of bat CoV HKU4. The protein has a frataxin fold,
consisting of 5 antiparallel β strands packed against 2 α helices. Bioinformatics analyses
and nuclear magnetic resonance experiments were conducted to investigate the function of
HKU4 C. The results showed that HKU4 C engages in protein-protein interactions with the
nearby M domain of nsp3. The HKU4 C residues involved in protein-protein interactions are
conserved in group 2c CoVs, indicating a conserved function.
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Affiliation(s)
- Andrew J Staup
- Department of Chemistry, 1720 2nd Avenue S. CHEM 201, University of Alabama at Birmingham, AL, USA
| | - Ivon U De Silva
- Department of Chemistry, 1720 2nd Avenue S. CHEM 201, University of Alabama at Birmingham, AL, USA
| | - Justin T Catt
- Department of Chemistry, 1720 2nd Avenue S. CHEM 201, University of Alabama at Birmingham, AL, USA
| | - Xuan Tan
- Department of Chemistry, 1720 2nd Avenue S. CHEM 201, University of Alabama at Birmingham, AL, USA
| | - Robert G Hammond
- Department of Chemistry, 1720 2nd Avenue S. CHEM 201, University of Alabama at Birmingham, AL, USA
| | - Margaret A Johnson
- Department of Chemistry, 1720 2nd Avenue S. CHEM 274, University of Alabama at Birmingham, AL, USA
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11
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Mohanty B, Hanson-Manful P, Finn TJ, Chambers CR, McKellar JLO, Macindoe I, Helder S, Setiyaputra S, Zhong Y, Mackay JP, Patrick WM. The uncharacterized bacterial protein YejG has the same architecture as domain III of elongation factor G. Proteins 2019; 87:699-705. [PMID: 30958578 DOI: 10.1002/prot.25687] [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: 11/13/2018] [Revised: 02/23/2019] [Accepted: 04/04/2019] [Indexed: 11/08/2022]
Abstract
InterPro family IPR020489 comprises ~1000 uncharacterized bacterial proteins. Previously we showed that overexpressing the Escherichia coli representative of this family, EcYejG, conferred low-level resistance to aminoglycoside antibiotics. In an attempt to shed light on the biochemical function of EcYejG, we have solved its structure using multinuclear solution NMR spectroscopy. The structure most closely resembles that of domain III from elongation factor G (EF-G). EF-G catalyzes ribosomal translocation and mutations in EF-G have also been associated with aminoglycoside resistance. While we were unable to demonstrate a direct interaction between EcYejG and the ribosome, the protein might play a role in translation.
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Affiliation(s)
- Biswaranjan Mohanty
- Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Paulina Hanson-Manful
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Thomas J Finn
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | | | - Ingrid Macindoe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Stephanie Helder
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Surya Setiyaputra
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Yichen Zhong
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Wayne M Patrick
- School of Biological Sciences, Victoria University, Wellington, New Zealand
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12
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Lisboa J, Celma L, Sanchez D, Marquis M, Andreani J, Guérois R, Ochsenbein F, Durand D, Marsin S, Cuniasse P, Radicella JP, Quevillon-Cheruel S. The C-terminal domain of HpDprA is a DNA-binding winged helix domain that does not bind double-stranded DNA. FEBS J 2019; 286:1941-1958. [PMID: 30771270 DOI: 10.1111/febs.14788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/21/2018] [Accepted: 02/14/2019] [Indexed: 12/15/2022]
Abstract
DNA-processing protein A, a ubiquitous multidomain DNA-binding protein, plays a crucial role during natural transformation in bacteria. Here, we carried out the structural analysis of DprA from the human pathogen Helicobacter pylori by combining data issued from the 1.8-Å resolution X-ray structure of the Pfam02481 domain dimer (RF), the NMR structure of the carboxy terminal domain (CTD), and the low-resolution structure of the full-length DprA dimer obtained in solution by SAXS. In particular, we sought a molecular function for the CTD, a domain that we show here is essential for transformation in H. pylori. Albeit its structural homology to winged helix DNA-binding motifs, we confirmed that the isolated CTD does not interact with ssDNA nor with dsDNA. The key R52 and K137 residues of RF are crucial for these two interactions. Search for sequences harboring homology to either HpDprA or Rhodopseudomonas palustris DprA CTDs led to the identification of conserved patches in the two CTD. Our structural study revealed the similarity of the structures adopted by these residues in RpDprA CTD and HpDprA CTD. This argues for a conserved, but yet to be defined, CTD function, distinct from DNA binding.
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Affiliation(s)
- Johnny Lisboa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Louisa Celma
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Dyana Sanchez
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Mathilde Marquis
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Raphael Guérois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Françoise Ochsenbein
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Stéphanie Marsin
- Institute of Cellular and Molecular Radiobiology, Institut François Jacob, CEA, Universités Paris Diderot and Paris-Sud, Fontenay aux Roses, France
| | - Philippe Cuniasse
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - J Pablo Radicella
- Institute of Cellular and Molecular Radiobiology, Institut François Jacob, CEA, Universités Paris Diderot and Paris-Sud, Fontenay aux Roses, France
| | - Sophie Quevillon-Cheruel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
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13
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Chen X, Smelter A, Moseley HNB. Automatic 13C chemical shift reference correction for unassigned protein NMR spectra. JOURNAL OF BIOMOLECULAR NMR 2018; 72:11-28. [PMID: 30097912 PMCID: PMC6209040 DOI: 10.1007/s10858-018-0202-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/01/2018] [Indexed: 05/09/2023]
Abstract
Poor chemical shift referencing, especially for 13C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamentally limits and even prevents effective study of biomacromolecules via NMR, including protein structure determination and analysis of protein dynamics. To solve this problem, we constructed a Bayesian probabilistic framework that circumvents the limitations of previous reference correction methods that required protein resonance assignment and/or three-dimensional protein structure. Our algorithm named Bayesian Model Optimized Reference Correction (BaMORC) can detect and correct 13C chemical shift referencing errors before the protein resonance assignment step of analysis and without three-dimensional structure. By combining the BaMORC methodology with a new intra-peaklist grouping algorithm, we created a combined method called Unassigned BaMORC that utilizes only unassigned experimental peak lists and the amino acid sequence. Unassigned BaMORC kept all experimental three-dimensional HN(CO)CACB-type peak lists tested within ± 0.4 ppm of the correct 13C reference value. On a much larger unassigned chemical shift test set, the base method kept 13C chemical shift referencing errors to within ± 0.45 ppm at a 90% confidence interval. With chemical shift assignments, Assigned BaMORC can detect and correct 13C chemical shift referencing errors to within ± 0.22 at a 90% confidence interval. Therefore, Unassigned BaMORC can correct 13C chemical shift referencing errors when it will have the most impact, right before protein resonance assignment and other downstream analyses are started. After assignment, chemical shift reference correction can be further refined with Assigned BaMORC. These new methods will allow non-NMR experts to detect and correct 13C referencing error at critical early data analysis steps, lowering the bar of NMR expertise required for effective protein NMR analysis.
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Affiliation(s)
- Xi Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40356, USA
- Department of Statistics, University of Kentucky, Lexington, KY, 40356, USA
| | - Andrey Smelter
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40356, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY, 40356, USA
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40356, USA
| | - Hunter N B Moseley
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40356, USA.
- Department of Statistics, University of Kentucky, Lexington, KY, 40356, USA.
- Markey Cancer Center, University of Kentucky, Lexington, KY, 40356, USA.
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY, 40356, USA.
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY, 40356, USA.
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14
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Serrano P, Hammond JA, Geralt M, Wüthrich K. Splicing Site Recognition by Synergy of Three Domains in Splicing Factor RBM10. Biochemistry 2018; 57:1563-1567. [PMID: 29450990 DOI: 10.1021/acs.biochem.7b01242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Splicing factor RBM10 and its close homologues RBM5 and RBM6 govern the splicing of oncogenes such as Fas, NUMB, and Bcl-X. The molecular architecture of these proteins includes zinc fingers (ZnFs) and RNA recognition motifs (RRMs). Three of these domains in RBM10 that constitute the RNA binding part of this splicing factor were found to individually bind RNAs with micromolar affinities. It was thus of interest to further investigate the structural basis of the well-documented high-affinity RNA recognition by RMB10. Here, we investigated RNA binding by combinations of two or three of these domains and discovered that a polypeptide containing RRM1, ZnF1, and RRM2 connected by their natural linkers recognizes a specific sequence of the Fas exon 6 mRNA with an affinity of 20 nM. Nuclear magnetic resonance structures of the RBM10 domains RRM1 and ZnF1 and the natural V354del isoform of RRM2 further confirmed that the interactions with RNA are driven by canonical RNA recognition elements. The well-known high-fidelity RNA splice site recognition by RBM10, and probably by RBM5 and RBM6, can thus be largely rationalized by a cooperative binding action of RRM and ZnF domains.
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Affiliation(s)
- Pedro Serrano
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - John A Hammond
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States.,Skaggs Institute for Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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15
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Vazquez L, e Lima LMTDR, Almeida MDS. Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus. PLoS One 2017; 12:e0182132. [PMID: 28750053 PMCID: PMC5531528 DOI: 10.1371/journal.pone.0182132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/12/2017] [Indexed: 11/18/2022] Open
Abstract
The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24-37) was identified as a transient structure (~20-30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered conformations.
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Affiliation(s)
- Leonardo Vazquez
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Marcius da Silva Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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16
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Birkou M, Chasapis CT, Marousis KD, Loutsidou AK, Bentrop D, Lelli M, Herrmann T, Carthy JM, Episkopou V, Spyroulias GA. A Residue Specific Insight into the Arkadia E3 Ubiquitin Ligase Activity and Conformational Plasticity. J Mol Biol 2017; 429:2373-2386. [PMID: 28647409 DOI: 10.1016/j.jmb.2017.06.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/15/2017] [Accepted: 06/15/2017] [Indexed: 12/17/2022]
Abstract
Arkadia (Rnf111) is an E3 ubiquitin ligase that plays a central role in the amplification of transforming growth factor beta (TGF-β) signaling responses by targeting for degradation the negative regulators of the pathway, Smad6 and Smad7, and the nuclear co-repressors Ski and Skil (SnoN). Arkadia's function in vivo depends on the really interesting new gene (RING)-H2 interaction with the E2 enzyme UbcH5b in order to ligate ubiquitin chains on its substrates. A conserved tryptophan (W972) in the C-terminal α-helix is widely accepted as essential for E2 recruitment and interaction and thus also for E3 enzymatic activity. The present NMR-driven study provides an atomic-level investigation of the structural and dynamical properties of two W972 Arkadia RING mutants, attempting to illuminate for the first time the differences between a functional and a nonfunctional mutant W972A and W972R, respectively. A TGF-β-responsive promoter driving luciferase was used to assay for Arkadia function in vivo. These experiments showed that the Arkadia W972A mutant has the same activity as wild-type (WT) Arkadia in enhancing TGF-β signaling responses, while W972R does not. Only minor structural differences exist between the W972A RING domain and WT-RING. In contrast, the W972R mutant hardly interacts with E2. The loss of function correlates with structural changes in the C-terminal α-helix and an increase in the distance between the Zn(II) ions. Our data show that the position occupied by W972 within WT Arkadia is critical for the function of RING and that it depends on the nature of the residue at this position.
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Affiliation(s)
- Maria Birkou
- Department of Pharmacy, University of Patras, GR-26504 Patras, Greece
| | | | | | | | - Detlef Bentrop
- Institute of Physiology II, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Moreno Lelli
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Torsten Herrmann
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Jonathon M Carthy
- Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Burlington Danes, London W12 0NN, UK
| | - Vasso Episkopou
- Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Burlington Danes, London W12 0NN, UK.
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17
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Hammond RG, Tan X, Johnson MA. SARS-unique fold in the Rousettus bat coronavirus HKU9. Protein Sci 2017; 26:1726-1737. [PMID: 28580734 PMCID: PMC5563143 DOI: 10.1002/pro.3208] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 12/28/2022]
Abstract
The coronavirus nonstructural protein 3 (nsp3) is a multifunctional protein that comprises multiple structural domains. This protein assists viral polyprotein cleavage, host immune interference, and may play other roles in genome replication or transcription. Here, we report the solution NMR structure of a protein from the “SARS‐unique region” of the bat coronavirus HKU9. The protein contains a frataxin fold or double‐wing motif, which is an α + β fold that is associated with protein/protein interactions, DNA binding, and metal ion binding. High structural similarity to the human severe acute respiratory syndrome (SARS) coronavirus nsp3 is present. A possible functional site that is conserved among some betacoronaviruses has been identified using bioinformatics and biochemical analyses. This structure provides strong experimental support for the recent proposal advanced by us and others that the “SARS‐unique” region is not unique to the human SARS virus, but is conserved among several different phylogenetic groups of coronaviruses and provides essential functions. PDB Code(s): 5UTV
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Affiliation(s)
- Robert G Hammond
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Xuan Tan
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Margaret A Johnson
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
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18
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Sugiki T, Kobayashi N, Fujiwara T. Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists. Comput Struct Biotechnol J 2017; 15:328-339. [PMID: 28487762 PMCID: PMC5408130 DOI: 10.1016/j.csbj.2017.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 02/07/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for structural studies of chemical compounds and biomolecules such as DNA and proteins. Since the NMR signal sensitively reflects the chemical environment and the dynamics of a nuclear spin, NMR experiments provide a wealth of structural and dynamic information about the molecule of interest at atomic resolution. In general, structural biology studies using NMR spectroscopy still require a reasonable understanding of the theory behind the technique and experience on how to recorded NMR data. Owing to the remarkable progress in the past decade, we can easily access suitable and popular analytical resources for NMR structure determination of proteins with high accuracy. Here, we describe the practical aspects, workflow and key points of modern NMR techniques used for solution structure determination of proteins. This review should aid NMR specialists aiming to develop new methods that accelerate the structure determination process, and open avenues for non-specialist and life scientists interested in using NMR spectroscopy to solve protein structures.
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Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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19
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Spiess HW. 50th Anniversary Perspective: The Importance of NMR Spectroscopy to Macromolecular Science. Macromolecules 2017. [DOI: 10.1021/acs.macromol.6b02736] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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20
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Smith AA. INFOS: spectrum fitting software for NMR analysis. JOURNAL OF BIOMOLECULAR NMR 2017; 67:77-94. [PMID: 28160196 DOI: 10.1007/s10858-016-0085-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/23/2016] [Indexed: 06/06/2023]
Abstract
Software for fitting of NMR spectra in MATLAB is presented. Spectra are fitted in the frequency domain, using Fourier transformed lineshapes, which are derived using the experimental acquisition and processing parameters. This yields more accurate fits compared to common fitting methods that use Lorentzian or Gaussian functions. Furthermore, a very time-efficient algorithm for calculating and fitting spectra has been developed. The software also performs initial peak picking, followed by subsequent fitting and refinement of the peak list, by iteratively adding and removing peaks to improve the overall fit. Estimation of error on fitting parameters is performed using a Monte-Carlo approach. Many fitting options allow the software to be flexible enough for a wide array of applications, while still being straightforward to set up with minimal user input.
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Affiliation(s)
- Albert A Smith
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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21
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Yadav DK, Lukavsky PJ. NMR solution structure determination of large RNA-protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:57-81. [PMID: 27888840 DOI: 10.1016/j.pnmrs.2016.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems. The new combination of NMR measurements with MD simulations and its potential will also be discussed. Application and combination of these various methods for structure determination of large RNPs will be illustrated with three large RNA-protein complexes (>40kDa) and other interesting complexes determined in the past six and a half years.
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Affiliation(s)
- Deepak Kumar Yadav
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Peter J Lukavsky
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic.
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22
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Woehl JL, Takahashi D, Herrera AI, Geisbrecht BV, Prakash O. (1)H, (15)N, and (13)C resonance assignments of Staphylococcus aureus extracellular adherence protein domain 4. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:301-5. [PMID: 27372920 PMCID: PMC5503465 DOI: 10.1007/s12104-016-9688-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/22/2016] [Indexed: 05/25/2023]
Abstract
The pathogenic bacterium Staphylococcus aureus has evolved to actively evade many aspects of the human innate immune system by expressing a series of secreted inhibitory proteins. Among these, the extracellular adherence protein (Eap) has been shown to inhibit the classical and lectin pathways of the complement system. By binding to complement component C4b, Eap is able to inhibit formation of the CP/LP C3 pro-convertase. Secreted full-length, mature Eap consists of four ~98 residue domains, all of which adopt a similar beta-grasp fold, and are connected through a short linker region. Through multiple biochemical approaches, it has been determined that the third and fourth domains of Eap are responsible for C4b binding. Here we report the backbone and side-chain resonance assignments of the 11.3 kDa fourth domain of Eap. The assignment data has been deposited in the BMRB database under the accession number 26726.
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Affiliation(s)
- Jordan L Woehl
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Daisuke Takahashi
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Alvaro I Herrera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA.
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23
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Mohanty B, Helder S, Silva APG, Mackay JP, Ryan DP. The Chromatin Remodelling Protein CHD1 Contains a Previously Unrecognised C-Terminal Helical Domain. J Mol Biol 2016; 428:4298-4314. [PMID: 27591891 DOI: 10.1016/j.jmb.2016.08.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
The packaging of eukaryotic DNA into nucleosomes, and the organisation of these nucleosomes into chromatin, plays a critical role in regulating all DNA-associated processes. Chromodomain helicase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodelling protein that is conserved throughout eukaryotes and has an ability to assemble and organise nucleosomes both in vitro and in vivo. This activity is involved in the regulation of transcription and is implicated in mammalian development and stem cell biology. CHD1 is classically depicted as possessing a pair of tandem chromodomains that directly precede a core catalytic helicase-like domain that is then followed by a SANT-SLIDE DNA-binding domain. Here, we have identified an additional conserved domain C-terminal to the SANT-SLIDE domain and determined its structure by multidimensional heteronuclear NMR spectroscopy. We have termed this domain the CHD1 helical C-terminal (CHCT) domain as it is comprised of five α-helices arranged in a variant helical bundle topology. CHCT has a conserved, positively charged surface and is able to bind DNA and nucleosomes. In addition, we have identified another group of proteins, the as yet uncharacterised C17orf64 proteins, as also containing a conserved CHCT domain. Our data provide new structural insights into the CHD1 enzyme family.
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Affiliation(s)
- Biswaranjan Mohanty
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia; Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Stephanie Helder
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia.
| | - Daniel P Ryan
- Department of Genome Sciences, The John Curtin School of Medical Research, Building 131, Garran Road, The Australian National University, Canberra, Australian Capital Territory, 2601, Australia.
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24
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Proudfoot A, Geralt M, Elsliger MA, Wilson IA, Wüthrich K, Serrano P. Dynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding. Structure 2016; 24:1372-1379. [PMID: 27396829 DOI: 10.1016/j.str.2016.05.013] [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: 01/19/2016] [Revised: 03/30/2016] [Accepted: 05/06/2016] [Indexed: 11/30/2022]
Abstract
The Gastrulation Brain Homeobox 1 (Gbx1) gene encodes the Gbx1 homeodomain that targets TAATTA motifs in double-stranded DNA (dsDNA). Residues Glu17 and Arg52 in Gbx1 form a salt bridge, which is preserved in crystal structures and molecular dynamics simulations of homologous homeodomain-DNA complexes. In contrast, our nuclear magnetic resonance (NMR) studies show that DNA binding to Gbx1 induces dynamic local polymorphisms, which include breaking of the Glu17-Arg52 salt bridge. To study this interaction, we produced a variant with Glu17Arg and Arg52Glu mutations, which exhibited the same fold as the wild-type protein, but a 2-fold reduction in affinity for dsDNA. Analysis of the NMR structures of the Gbx1 homeodomain in the free form, the Gbx1[E17R,R52E] variant, and a Gbx1 homeodomain-DNA complex showed that stabilizing interactions of the Arg52 side chain with the DNA backbone are facilitated by transient breakage of the Glu17-Arg52 salt bridge in the DNA-bound Gbx1.
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Affiliation(s)
- Andrew Proudfoot
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Joint Center for Structural Genomics, La Jolla, CA 92037, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Joint Center for Structural Genomics, La Jolla, CA 92037, USA
| | - Marc-Andre Elsliger
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Joint Center for Structural Genomics, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Joint Center for Structural Genomics, La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Joint Center for Structural Genomics, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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25
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Serrano P, Dutta SK, Proudfoot A, Mohanty B, Susac L, Martin B, Geralt M, Jaroszewski L, Godzik A, Elsliger M, Wilson IA, Wüthrich K. NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia. FEBS J 2016; 283:3870-3881. [PMID: 27154589 DOI: 10.1111/febs.13751] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/12/2016] [Accepted: 05/04/2016] [Indexed: 12/12/2022]
Abstract
For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs.
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Affiliation(s)
- Pedro Serrano
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Samit K Dutta
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew Proudfoot
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Biswaranjan Mohanty
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukas Susac
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Bryan Martin
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Michael Geralt
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Marc Elsliger
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A Wilson
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kurt Wüthrich
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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26
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Beuck C, Williamson JR, Wüthrich K, Serrano P. The acidic domain is a unique structural feature of the splicing factor SYNCRIP. Protein Sci 2016; 25:1545-50. [PMID: 27081926 DOI: 10.1002/pro.2935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/11/2016] [Accepted: 04/11/2016] [Indexed: 01/21/2023]
Abstract
The splicing factor SYNCRIP (hnRNP Q) is involved in viral replication, neural morphogenesis, modulation of circadian oscillation, and the regulation of the cytidine deaminase APOBEC1. It consists of three globular RNA-recognition motifs (RRM) domains flanked by an N-terminal acid-rich acidic sequence segment domain (AcD12-97 ) and a C-terminal domain containing an arginine-glycine-rich sequence motif (RGG/RXG box), which are located near to the N- and C-terminals, respectively. The acid-rich sequence segment is unique to SYNCRIP and the closely related protein hnRNP R, and is involved in interactions with APOBEC1. Here, we show that while AcD12-97 does not form a globular domain, structure-based annotation identified a self-folding globular domain with an all α-helix architecture, AcD24-107 . The NMR structure of AcD24-107 is fundamentally different from previously reported AcD molecular models. In addition to negatively charged surface areas, it contains a large hydrophobic cavity and a positively charged surface area as potential epitopes for intermolecular interactions.
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Affiliation(s)
- Christine Beuck
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, 92037.,Joint Center for Structural Genomics, http://www.jcsg.org
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037.,Joint Center for Structural Genomics, http://www.jcsg.org
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27
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Urbina P, Bersch B, De Angelis F, Derfoufi KM, Prévost M, Goormaghtigh E, Vandenbussche G. Structural and Functional Investigation of the Ag+/Cu+ Binding Domains of the Periplasmic Adaptor Protein SilB from Cupriavidus metallidurans CH34. Biochemistry 2016; 55:2883-97. [DOI: 10.1021/acs.biochem.6b00022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patricia Urbina
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Beate Bersch
- Institut
de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Fabien De Angelis
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Kheiro-Mouna Derfoufi
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Martine Prévost
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Erik Goormaghtigh
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
| | - Guy Vandenbussche
- Laboratory
for the Structure and Function of Biological Membranes, Center for
Structural Biology and Bioinformatics, Université Libre de Bruxelles, B-1050 Bruxelles, Belgium
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28
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Directional Phosphorylation and Nuclear Transport of the Splicing Factor SRSF1 Is Regulated by an RNA Recognition Motif. J Mol Biol 2016; 428:2430-2445. [PMID: 27091468 DOI: 10.1016/j.jmb.2016.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 01/21/2023]
Abstract
Multisite phosphorylation is required for the biological function of serine-arginine (SR) proteins, a family of essential regulators of mRNA splicing. These modifications are catalyzed by serine-arginine protein kinases (SRPKs) that phosphorylate numerous serines in arginine-serine-rich (RS) domains of SR proteins using a directional, C-to-N-terminal mechanism. The present studies explore how SRPKs govern this highly biased phosphorylation reaction and investigate biological roles of the observed directional phosphorylation mechanism. Using NMR spectroscopy with two separately expressed domains of SRSF1, we showed that several residues in the RNA-binding motif 2 interact with the N-terminal region of the RS domain (RS1). These contacts provide a structural framework that balances the activities of SRPK1 and the protein phosphatase PP1, thereby regulating the phosphoryl content of the RS domain. Disruption of the implicated intramolecular RNA-binding motif 2-RS domain interaction impairs both the directional phosphorylation mechanism and the nuclear translocation of SRSF1 demonstrating that the intrinsic phosphorylation bias is obligatory for SR protein biological function.
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29
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Stepanyuk GA, Serrano P, Peralta E, Farr CL, Axelrod HL, Geralt M, Das D, Chiu HJ, Jaroszewski L, Deacon AM, Lesley SA, Elsliger MA, Godzik A, Wilson IA, Wüthrich K, Salomon DR, Williamson JR. UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex. Acta Crystallogr D Struct Biol 2016; 72:497-511. [PMID: 27050129 PMCID: PMC4822562 DOI: 10.1107/s2059798316001248] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 01/19/2016] [Indexed: 01/14/2023] Open
Abstract
RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein-protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39-U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35-U2AF65 and RBM39-SF3b155, the RBM39-UHM-U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM-ULM binding interface, providing a rationale for the known specificity of UHM-ULM interactions. This study therefore establishes a structural basis for specific UHM-ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.
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Affiliation(s)
- Galina A. Stepanyuk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Eigen Peralta
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Carol L. Farr
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Debanu Das
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org
- Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093-0446, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Scott A. Lesley
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Marc-André Elsliger
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org
- Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093-0446, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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30
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Mohanty B, Silva APG, Mackay JP, Ryan DP. 1H, 13C and 15N resonance assignments of a C-terminal domain of human CHD1. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:31-34. [PMID: 26286320 DOI: 10.1007/s12104-015-9631-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/11/2015] [Indexed: 06/04/2023]
Abstract
Chromatin remodelling proteins are an essential family of eukaryotic proteins. They harness the energy from ATP hydrolysis and apply it to alter chromatin structure in order to regulate all aspects of genome biology. Chromodomain helicase DNA-binding protein 1 (CHD1) is one such remodelling protein that has specialised nucleosome organising abilities and is conserved across eukaryotes. CHD1 possesses a pair of tandem chromodomains that directly precede the core catalytic Snf2 helicase-like domain, and a C-terminal SANT-SLIDE DNA-binding domain. We have identified an additional conserved domain in the C-terminal region of CHD1. Here, we report the backbone and side chain resonance assignments for this domain from human CHD1 at pH 6.5 and 25 °C (BMRB No. 25638).
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Affiliation(s)
- Biswaranjan Mohanty
- School of Molecular Bioscience, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, NSW, 2006, Australia
- Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, 3052, Australia
| | - Ana P G Silva
- School of Molecular Bioscience, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, NSW, 2006, Australia
| | - Joel P Mackay
- School of Molecular Bioscience, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, NSW, 2006, Australia.
| | - Daniel P Ryan
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Building 131, Garran Road, Canberra, ACT, 2601, Australia.
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31
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Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL. Probabilistic validation of protein NMR chemical shift assignments. JOURNAL OF BIOMOLECULAR NMR 2016; 64:17-25. [PMID: 26724815 PMCID: PMC4744101 DOI: 10.1007/s10858-015-0007-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/20/2015] [Indexed: 05/05/2023]
Abstract
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data . ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/.
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Affiliation(s)
- Hesam Dashti
- Graduate Program in Biophysics, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Marco Tonelli
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Woonghee Lee
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - William M Westler
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Gabriel Cornilescu
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Eldon L Ulrich
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - John L Markley
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA.
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA.
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32
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Nuclear Magnetic Resonance Structure of a Novel Globular Domain in RBM10 Containing OCRE, the Octamer Repeat Sequence Motif. Structure 2015; 24:158-164. [PMID: 26712279 DOI: 10.1016/j.str.2015.10.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/09/2015] [Accepted: 10/15/2015] [Indexed: 12/12/2022]
Abstract
The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. Nuclear magnetic resonance structure determination showed that the RBM10 OCRE sequence motif is part of a 55-residue globular domain containing 16 aromatic amino acids, which consists of an anti-parallel arrangement of six β strands, with the first five strands containing complete or incomplete Tyr triplets. This OCRE globular domain is a distinctive component of RBM10 and is more widely conserved in RBM10s across the animal kingdom than the ubiquitous RNA recognition components. It is also found in the functionally related RBM5. Thus, it appears that the three-dimensional structure of the globular OCRE domain, rather than the 42-residue OCRE sequence motif alone, confers specificity on RBM10 intermolecular interactions in the spliceosome.
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33
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Kashyap M, Ganguly AK, Bhavesh NS. Structural delineation of stem-loop RNA binding by human TAF15 protein. Sci Rep 2015; 5:17298. [PMID: 26612539 PMCID: PMC4661536 DOI: 10.1038/srep17298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/28/2015] [Indexed: 11/09/2022] Open
Abstract
Human TATA binding protein associated factor 2 N (TAF15) and Fused in sarcoma (FUS) are nucleic acid binding proteins belonging to the conserved FET family of proteins. They are involved in diverse processes such as pre-mRNA splicing, mRNA transport, and DNA binding. The absence of information regarding the structural mechanism employed by the FET family in recognizing and discriminating their cognate and non-cognate RNA targets has hampered the attainment of consensus on modes of protein-RNA binding for this family. Our study provides a molecular basis of this RNA recognition using a combination of solution-state NMR spectroscopy, calorimetry, docking and molecular dynamics simulation. Analysis of TAF15-RRM solution structure and its binding with stem-loop RNA has yielded conclusive evidence of a non-canonical mode of RNA recognition. Rather than classical stacking interactions that occur across nitrogen bases and aromatic amino acids on ribonucleoprotein sites, moderate-affinity hydrogen bonding network between the nitrogen bases in the stem-loop RNA and a concave face on the RRM surface primarily mediate TAF15-RRM RNA interaction. We have compared the binding affinities across a set of single-stranded RNA oligonucleotides to conclusively establish that RNA binding is dependent upon structural elements in the RNA rather than sequence.
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Affiliation(s)
- Maruthi Kashyap
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110 067, New Delhi, India
| | - Akshay Kumar Ganguly
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110 067, New Delhi, India
| | - Neel Sarovar Bhavesh
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110 067, New Delhi, India
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34
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Didenko T, Proudfoot A, Dutta SK, Serrano P, Wüthrich K. Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination. Chemistry 2015; 21:12363-9. [PMID: 26227870 PMCID: PMC4576834 DOI: 10.1002/chem.201502544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/10/2022]
Abstract
High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data.
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Affiliation(s)
- Tatiana Didenko
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.jcsg.org
- Joint Center for Structural Genomics, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014
- GPCR-Network, 3430 S. Vermont Ave., TRF 105, Los Angeles, CA 90089-3301 (USA), Fax: (+1) 858-784-8014 http://gpcr.usc.edu
| | - Andrew Proudfoot
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.jcsg.org
- Joint Center for Structural Genomics, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014
| | - Samit Kumar Dutta
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.jcsg.org
- Joint Center for Structural Genomics, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.jcsg.org
- Joint Center for Structural Genomics, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA) http://www.jcsg.org. , ,
- Joint Center for Structural Genomics, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014. , ,
- GPCR-Network, 3430 S. Vermont Ave., TRF 105, Los Angeles, CA 90089-3301 (USA), Fax: (+1) 858-784-8014 http://gpcr.usc.edu. , ,
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-8014. , ,
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35
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Latge C, Cabral KMS, de Oliveira GAP, Raymundo DP, Freitas JA, Johanson L, Romão LF, Palhano FL, Herrmann T, Almeida MS, Foguel D. The Solution Structure and Dynamics of Full-length Human Cerebral Dopamine Neurotrophic Factor and Its Neuroprotective Role against α-Synuclein Oligomers. J Biol Chem 2015; 290:20527-40. [PMID: 26149686 PMCID: PMC4536457 DOI: 10.1074/jbc.m115.662254] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/02/2015] [Indexed: 11/06/2022] Open
Abstract
Cerebral dopamine neurotrophic factor (CDNF) is a promising therapeutic agent for Parkinson disease. As such, there has been great interest in studying its mode of action, which remains unknown. The three-dimensional crystal structure of the N terminus (residues 9-107) of CDNF has been determined, but there have been no published structural studies on the full-length protein due to proteolysis of its C-terminal domain, which is considered intrinsically disordered. An improved purification protocol enabled us to obtain active full-length CDNF and to determine its three-dimensional structure in solution. CDNF contains two well folded domains (residues 10-100 and 111-157) that are linked by a loop of intermediate flexibility. We identified two surface patches on the N-terminal domain that were characterized by increased conformational dynamics that should allow them to embrace active sites. One of these patches is formed by residues Ser-33, Leu-34, Ala-66, Lys-68, Ile-69, Leu-70, Ser-71, and Glu-72. The other includes a flexibly disordered N-terminal tail (residues 1-9), followed by the N-terminal portion of α-helix 1 (residues Cys-11, Glu-12, Val-13, Lys-15, and Glu-16) and residue Glu-88. The surface of the C-terminal domain contains two conserved active sites, which have previously been identified in mesencephalic astrocyte-derived neurotrophic factor, a CDNF paralog, which corresponds to its intracellular mode of action. We also showed that CDNF was able to protect dopaminergic neurons against injury caused by α-synuclein oligomers. This advises its use against physiological damages caused by α-synuclein oligomers, as observed in Parkinson disease and several other neurodegenerative diseases.
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Affiliation(s)
- Cristiane Latge
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Katia M S Cabral
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Guilherme A P de Oliveira
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Diana P Raymundo
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Julia A Freitas
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Laizes Johanson
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Luciana F Romão
- the UFRJ/Pólo Xerém, Universidade Federal do Rio de Janeiro 25245-390, Rio de Janeiro, Brazil
| | - Fernando L Palhano
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Torsten Herrmann
- the Institut des Sciences Analytiques, UMR 5280 CNRS, 5 rue de la Doua, 69100 Villeurbanne, France, and
| | - Marcius S Almeida
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil, the Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Debora Foguel
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil,
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36
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Dashti H, Lee W, Tonelli M, Cornilescu CC, Cornilescu G, Assadi-Porter FM, Westler WM, Eghbalnia HR, Markley JL. NMRFAM-SDF: a protein structure determination framework. JOURNAL OF BIOMOLECULAR NMR 2015; 62:481-95. [PMID: 25900069 PMCID: PMC4569665 DOI: 10.1007/s10858-015-9933-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/15/2015] [Indexed: 05/21/2023]
Abstract
The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR--from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm).
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Affiliation(s)
- Hesam Dashti
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Woonghee Lee
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Claudia C Cornilescu
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Fariba M Assadi-Porter
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - William M Westler
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Hamid R Eghbalnia
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
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37
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Guerry P, Duong VD, Herrmann T. CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO. JOURNAL OF BIOMOLECULAR NMR 2015; 62:473-480. [PMID: 25917899 DOI: 10.1007/s10858-015-9934-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/18/2015] [Indexed: 06/04/2023]
Abstract
UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved--including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO-ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications.
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Affiliation(s)
- Paul Guerry
- Institut des Sciences Analytiques, Centre de RMN à très Hauts Champs, Université de Lyon (UMR 5280 CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), 5 rue de la Doua, 69100, Villeurbanne, France
| | - Viet Dung Duong
- Institut des Sciences Analytiques, Centre de RMN à très Hauts Champs, Université de Lyon (UMR 5280 CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), 5 rue de la Doua, 69100, Villeurbanne, France
| | - Torsten Herrmann
- Institut des Sciences Analytiques, Centre de RMN à très Hauts Champs, Université de Lyon (UMR 5280 CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), 5 rue de la Doua, 69100, Villeurbanne, France.
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38
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Dutta SK, Serrano P, Geralt M, Axelrod HL, Xu Q, Lesley SA, Godzik A, Deacon AM, Elsliger MA, Wilson IA, Wüthrich K. Cofactor-induced reversible folding of Flavodoxin-4 from Lactobacillus acidophilus. Protein Sci 2015; 24:1600-8. [PMID: 26177955 DOI: 10.1002/pro.2743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 11/06/2022]
Abstract
Flavodoxins in combination with the flavin mononucleotide (FMN) cofactor play important roles for electron transport in prokaryotes. Here, novel insights into the FMN-binding mechanism to flavodoxins-4 were obtained from the NMR structures of the apo-protein from Lactobacillus acidophilus (YP_193882.1) and comparison of its complex with FMN. Extensive reversible conformational changes were observed upon FMN binding and release. The NMR structure of the FMN complex is in agreement with the crystal structure (PDB ID: 3EDO) and exhibits the characteristic flavodoxin fold, with a central five-stranded parallel β-sheet and five α-helices forming an α/β-sandwich architecture. The structure differs from other flavoproteins in that helix α2 is oriented perpendicular to the β-sheet and covers the FMN-binding site. This helix reversibly unfolds upon removal of the FMN ligand, which represents a unique structural rearrangement among flavodoxins.
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Affiliation(s)
- Samit Kumar Dutta
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Pedro Serrano
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Michael Geralt
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Herbert L Axelrod
- Joint Center for Structural Genomics, La Jolla, California, 92037.,SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, California, 94025
| | - Qingping Xu
- Joint Center for Structural Genomics, La Jolla, California, 92037.,SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, California, 94025
| | - Scott A Lesley
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037.,Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121
| | - Adam Godzik
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, 92037.,Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, 92093
| | - Ashley M Deacon
- Joint Center for Structural Genomics, La Jolla, California, 92037.,SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, California, 94025
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Ian A Wilson
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037.,Skaggs Institute for Chemical Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Kurt Wüthrich
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037.,Skaggs Institute for Chemical Biology, the Scripps Research Institute, La Jolla, California, 92037
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39
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Chandrashekaran IR, Mohanty B, Linossi EM, Dagley LF, Leung EWW, Murphy JM, Babon JJ, Nicholson SE, Norton RS. Structure and Functional Characterization of the Conserved JAK Interaction Region in the Intrinsically Disordered N-Terminus of SOCS5. Biochemistry 2015; 54:4672-82. [PMID: 26173083 DOI: 10.1021/acs.biochem.5b00619] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
SOCS5 can negatively regulate both JAK/STAT and EGF-receptor pathways and has therefore been implicated in regulating both the immune response and tumorigenesis. Understanding the molecular basis for SOCS5 activity may reveal novel ways to target key components of these signaling pathways. The N-terminal region of SOCS5 coordinates critical protein interactions involved in inhibition of JAK/STAT signaling, and a conserved region within the N-terminus of SOCS5 mediates direct binding to the JAK kinase domain. Here we have characterized the solution conformation of this conserved JAK interaction region (JIR) within the largely disordered N-terminus of SOCS5. Using nuclear magnetic resonance (NMR) chemical shift analysis, relaxation measurements, and NOE analysis, we demonstrate the presence of preformed structural elements in the JIR of mouse SOCS5 (mSOCS5175-244), consisting of an α-helix encompassing residues 224-233, preceded by a turn and an extended structure. We have identified a phosphorylation site (Ser211) within the JIR of mSOCS5 and have investigated the role of phosphorylation in modulating JAK binding using site-directed mutagenesis.
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Affiliation(s)
- Indu R Chandrashekaran
- †Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Biswaranjan Mohanty
- †Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Edmond M Linossi
- §The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Laura F Dagley
- §The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Eleanor W W Leung
- †Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - James M Murphy
- §The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Jeffrey J Babon
- §The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Sandra E Nicholson
- §The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Raymond S Norton
- †Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
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40
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Sethi A, Mohanty B, Ramasubbu N, Gooley PR. Structure of amylase-binding protein A of Streptococcus gordonii: a potential receptor for human salivary α-amylase enzyme. Protein Sci 2015; 24:1013-8. [PMID: 25739638 DOI: 10.1002/pro.2671] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/16/2015] [Accepted: 02/18/2015] [Indexed: 11/10/2022]
Abstract
Amylase-binding protein A (AbpA) of a number of oral streptococci is essential for the colonization of the dental pellicle. We have determined the solution structure of residues 24-195 of AbpA of Streptococcus gordonii and show a well-defined core of five helices in the region of 45-115 and 135-145. (13) Cα/β chemical shift and heteronuclear (15) N-{(1) H} NOE data are consistent with this fold and that the remainder of the protein is unstructured. The structure will inform future molecular experiments in defining the mechanism of human salivary α-amylase binding and biofilm formation by streptococci.
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Affiliation(s)
- Ashish Sethi
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Biswaranjan Mohanty
- Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Narayanan Ramasubbu
- Department of Oral Biology, 185 South Orange Ave, Rutgers School of Dental Medicine, Newark, New Jersey, 07103
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
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41
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Mewis RE, Green RA, Cockett MCR, Cowley M, Duckett SB, Green GGR, John R, Rayner PJ, Williamson DC. Strategies for the hyperpolarization of acetonitrile and related ligands by SABRE. J Phys Chem B 2015; 119:1416-24. [PMID: 25539423 PMCID: PMC4315046 DOI: 10.1021/jp511492q] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/22/2014] [Indexed: 01/18/2023]
Abstract
We report on a strategy for using SABRE (signal amplification by reversible exchange) for polarizing (1)H and (13)C nuclei of weakly interacting ligands which possess biologically relevant and nonaromatic motifs. We first demonstrate this via the polarization of acetonitrile, using Ir(IMes)(COD)Cl as the catalyst precursor, and confirm that the route to hyperpolarization transfer is via the J-coupling network. We extend this work to the polarization of propionitrile, benzylnitrile, benzonitrile, and trans-3-hexenedinitrile in order to assess its generality. In the (1)H NMR spectrum, the signal for acetonitrile is enhanced 8-fold over its thermal counterpart when [Ir(H)2(IMes)(MeCN)3](+) is the catalyst. Upon addition of pyridine or pyridine-d5, the active catalyst changes to [Ir(H)2(IMes)(py)2(MeCN)](+) and the resulting acetonitrile (1)H signal enhancement increases to 20- and 60-fold, respectively. In (13)C NMR studies, polarization transfers optimally to the quaternary (13)C nucleus of MeCN while the methyl (13)C is hardly polarized. Transfer to (13)C is shown to occur first via the (1)H-(1)H coupling between the hydrides and the methyl protons and then via either the (2)J or (1)J couplings to the respective (13)Cs, of which the (2)J route is more efficient. These experimental results are rationalized through a theoretical treatment which shows excellent agreement with experiment. In the case of MeCN, longitudinal two-spin orders between pairs of (1)H nuclei in the three-spin methyl group are created. Two-spin order states, between the (1)H and (13)C nuclei, are also created, and their existence is confirmed for Me(13)CN in both the (1)H and (13)C NMR spectra using the Only Parahydrogen Spectroscopy protocol.
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Affiliation(s)
- Ryan E. Mewis
- Centre for Hyperpolarisation
in Magnetic Resonance, University of York, Heslington, York, YO10
5DD, U.K.
| | - Richard A. Green
- Centre for Hyperpolarisation
in Magnetic Resonance, University of York, Heslington, York, YO10
5DD, U.K.
| | - Martin C. R. Cockett
- Centre for Hyperpolarisation
in Magnetic Resonance, University of York, Heslington, York, YO10
5DD, U.K.
| | - Michael
J. Cowley
- Centre for Hyperpolarisation
in Magnetic Resonance, University of York, Heslington, York, YO10
5DD, U.K.
| | - Simon B. Duckett
- Centre for Hyperpolarisation
in Magnetic Resonance, University of York, Heslington, York, YO10
5DD, U.K.
| | - Gary G. R. Green
- Centre for Hyperpolarisation
in Magnetic Resonance, University of York, Heslington, York, YO10
5DD, U.K.
| | - Richard
O. John
- Centre for Hyperpolarisation
in Magnetic Resonance, University of York, Heslington, York, YO10
5DD, U.K.
| | - Peter J. Rayner
- Centre for Hyperpolarisation
in Magnetic Resonance, University of York, Heslington, York, YO10
5DD, U.K.
| | - David C. Williamson
- Centre for Hyperpolarisation
in Magnetic Resonance, University of York, Heslington, York, YO10
5DD, U.K.
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42
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Dutta SK, Serrano P, Proudfoot A, Geralt M, Pedrini B, Herrmann T, Wüthrich K. APSY-NMR for protein backbone assignment in high-throughput structural biology. JOURNAL OF BIOMOLECULAR NMR 2015; 61:47-53. [PMID: 25428764 PMCID: PMC4305044 DOI: 10.1007/s10858-014-9881-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/18/2014] [Indexed: 05/12/2023]
Abstract
A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [(1)H,(1)H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.
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Affiliation(s)
- Samit Kumar Dutta
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Andrew Proudfoot
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Bill Pedrini
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Torsten Herrmann
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, Université de Lyon, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
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43
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Mohanty B, Serrano P, Geralt M, Wüthrich K. NMR structure determination of the protein NP_344798.1 as the first representative of Pfam PF06042. JOURNAL OF BIOMOLECULAR NMR 2015; 61:83-7. [PMID: 25430057 PMCID: PMC4304887 DOI: 10.1007/s10858-014-9878-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/17/2014] [Indexed: 05/13/2023]
Abstract
We present the NMR structure determination of the protein NP_344798.1, which forms a CCA-adding enzyme head-domain architecture and is the first structural representative of the Pfam protein family PF06042. Its structure can now serve as a template for homology modeling of the other 785 members of this protein family. With 191 residues, NP_344798.1 is the largest single-domain protein structure determined so far with the J-UNIO protocol for automated NMR structure determination. The present work thus also shows that J-UNIO based exclusively on automated projection spectroscopy (APSY) and 3D heteronuclear-resolved [1H,1H]-NOESY experiments, can successfully be used to obtain high-quality NMR structures of protein domains with up to 200 residues.
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Affiliation(s)
- Biswaranjan Mohanty
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics, (http://www.jcsg.org), La Jolla, CA 92037, USA. Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics, (http://www.jcsg.org), La Jolla, CA 92037, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics, (http://www.jcsg.org), La Jolla, CA 92037, USA
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44
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Jaudzems K, Pedrini B, Geralt M, Serrano P, Wüthrich K. J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4. JOURNAL OF BIOMOLECULAR NMR 2015; 61:65-72. [PMID: 25428766 PMCID: PMC4304919 DOI: 10.1007/s10858-014-9886-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/21/2014] [Indexed: 05/13/2023]
Abstract
The NMR structure of the 206-residue protein NP_346487.1 was determined with the J-UNIO protocol, which includes extensive automation of the structure determination. With input from three APSY-NMR experiments, UNIO-MATCH automatically yielded 77 % of the backbone assignments, which were interactively validated and extended to 97 %. With an input of the near-complete backbone assignments and three 3D heteronuclear-resolved [(1)H,(1)H]-NOESY spectra, automated side chain assignment with UNIO-ATNOS/ASCAN resulted in 77 % of the expected assignments, which was extended interactively to about 90 %. Automated NOE assignment and structure calculation with UNIO-ATNOS/CANDID in combination with CYANA was used for the structure determination of this two-domain protein. The individual domains in the NMR structure coincide closely with the crystal structure, and the NMR studies further imply that the two domains undergo restricted hinge motions relative to each other in solution. NP_346487.1 is so far the largest polypeptide chain to which the J-UNIO structure determination protocol has successfully been applied.
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Affiliation(s)
- Kristaps Jaudzems
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Bill Pedrini
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA. Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
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Barbet-Massin E, Pell AJ, Retel JS, Andreas LB, Jaudzems K, Franks WT, Nieuwkoop AJ, Hiller M, Higman V, Guerry P, Bertarello A, Knight MJ, Felletti M, Le Marchand T, Kotelovica S, Akopjana I, Tars K, Stoppini M, Bellotti V, Bolognesi M, Ricagno S, Chou JJ, Griffin RG, Oschkinat H, Lesage A, Emsley L, Herrmann T, Pintacuda G. Rapid proton-detected NMR assignment for proteins with fast magic angle spinning. J Am Chem Soc 2014; 136:12489-97. [PMID: 25102442 PMCID: PMC4156866 DOI: 10.1021/ja507382j] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
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Using a set of six 1H-detected
triple-resonance NMR
experiments, we establish a method for sequence-specific backbone
resonance assignment of magic angle spinning (MAS) nuclear magnetic
resonance (NMR) spectra of 5–30 kDa proteins. The approach
relies on perdeuteration, amide 2H/1H exchange,
high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling
the use of automated analysis. The method is validated with five examples
of proteins in different condensed states, including two microcrystalline
proteins, a sedimented virus capsid, and two membrane-embedded systems.
In comparison to contemporary 13C/15N-based
methods, this approach facilitates and accelerates the MAS NMR assignment
process, shortening the spectral acquisition times and enabling the
use of unsupervised state-of-the-art computational data analysis protocols
originally developed for solution NMR.
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Affiliation(s)
- Emeline Barbet-Massin
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 69100 Villeurbanne, France
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46
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Zhang Z, Porter J, Tripsianes K, Lange OF. Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta. JOURNAL OF BIOMOLECULAR NMR 2014; 59:135-45. [PMID: 24845473 DOI: 10.1007/s10858-014-9832-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/19/2014] [Indexed: 05/16/2023]
Abstract
We have developed a novel and robust approach for automatic and unsupervised simultaneous nuclear Overhauser effect (NOE) assignment and structure determination within the CS-Rosetta framework. Starting from unassigned peak lists and chemical shift assignments, autoNOE-Rosetta determines NOE cross-peak assignments and generates structural models. The approach tolerates incomplete and raw NOE peak lists as well as incomplete or partially incorrect chemical shift assignments, and its performance has been tested on 50 protein targets ranging from 50 to 200 residues in size. We find a significantly improved performance compared to established programs, particularly for larger proteins and for NOE data obtained on perdeuterated protein samples. X-ray crystallographic structures allowed comparison of Rosetta and conventional, PDB-deposited, NMR models in 20 of 50 test cases. The unsupervised autoNOE-Rosetta models were often of significantly higher accuracy than the corresponding expert-supervised NMR models deposited in the PDB. We also tested the method with unrefined peak lists and found that performance was nearly as good as for refined peak lists. Finally, demonstrating our method's remarkable robustness against problematic input data, we provided correct models for an incorrect PDB-deposited NMR solution structure.
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Affiliation(s)
- Zaiyong Zhang
- Department Chemie, Biomolecular NMR and Munich Center for Integrated Protein Science, Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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Serrano P, Geralt M, Mohanty B, Wüthrich K. NMR structures of α-proteobacterial ATPase-regulating ζ-subunits. J Mol Biol 2014; 426:2547-53. [PMID: 24838125 DOI: 10.1016/j.jmb.2014.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/30/2014] [Accepted: 05/02/2014] [Indexed: 11/27/2022]
Abstract
NMR structures of ζ-subunits, which are recently discovered α-proteobacterial F1F0-ATPase-regulatory proteins representing a Pfam protein family of 246 sequences from 219 species (PF07345), exhibit a four-helix bundle, which is different from all other known F1F0-ATPase inhibitors. Chemical shift mapping reveals a conserved ADP/ATP binding site in ζ-subunit, which mediates long-range conformational changes related to function, as revealed by the structure of the Paracoccus denitrificans ζ-subunit in complex with ADP. These structural data suggest a new mechanism of F1F0-ATPase regulation in α-proteobacteria.
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Affiliation(s)
- Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA.
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Biswaranjan Mohanty
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
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48
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Pedrini B, Serrano P, Mohanty B, Geralt M, Wüthrich K. NMR-profiles of protein solutions. Biopolymers 2013; 99:825-31. [PMID: 23839514 PMCID: PMC3960936 DOI: 10.1002/bip.22348] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 06/28/2013] [Indexed: 11/11/2022]
Abstract
NMR-Profiles are quantitative one-dimensional (1D) presentations of 2D [¹⁵N, ¹H]-correlation spectra used to monitor the quality of protein solutions prior to and during NMR structure determinations and functional studies. In our current use in structural genomics projects, an NMR-Profile is recorded at the outset of a structure determination, using a uniformly ¹⁵N-labeled microscale sample of the protein. We thus assess the extent to which polypeptide backbone resonance assignments can be achieved with given NMR techniques, for example, conventional triple resonance experiments or APSY-NMR. With the availability of sequence-specific polypeptide backbone resonance assignments in the course of the structure determination, an "Assigned NMR-Profile" is generated, which visualizes the variation of the ¹⁵N - ¹H correlation cross peak intensities along the sequence and thus maps the sequence locations of polypeptide segments for which the NMR line shapes are affected by conformational exchange or other processes. The Assigned NMR-Profile provides a guiding reference during later stages of the structure determination, and is of special interest for monitoring the protein during functional studies, where dynamic features may be modulated during physiological processes.
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Affiliation(s)
- Bill Pedrini
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, Schafmattstrasse 20, CH-8093 Zürich, Switzerland
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Biswaranjan Mohanty
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, Schafmattstrasse 20, CH-8093 Zürich, Switzerland
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Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL. Recommendations of the wwPDB NMR Validation Task Force. Structure 2013; 21:1563-70. [PMID: 24010715 PMCID: PMC3884077 DOI: 10.1016/j.str.2013.07.021] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 07/19/2013] [Accepted: 07/29/2013] [Indexed: 11/25/2022]
Abstract
As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment.
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Affiliation(s)
- Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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Schieborr U, Sreeramulu S, Elshorst B, Maurer M, Saxena K, Stehle T, Kudlinzki D, Gande SL, Schwalbe H. MOTOR: model assisted software for NMR structure determination. Proteins 2013; 81:2007-22. [PMID: 23852655 DOI: 10.1002/prot.24361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 06/26/2013] [Accepted: 06/28/2013] [Indexed: 11/06/2022]
Abstract
Eukaryotic proteins with important biological function can be partially unstructured, conformational flexible, or heterogenic. Crystallization trials often fail for such proteins. In NMR spectroscopy, parts of the polypeptide chain undergoing dynamics in unfavorable time regimes cannot be observed. De novo NMR structure determination is seriously hampered when missing signals lead to an incomplete chemical shift assignment resulting in an information content of the NOE data insufficient to determine the structure ab initio. We developed a new protein structure determination strategy for such cases based on a novel NOE assignment strategy utilizing a number of model structures but no explicit reference structure as it is used for bootstrapping like algorithms. The software distinguishes in detail between consistent and mutually exclusive pairs of possible NOE assignments on the basis of different precision levels of measured chemical shifts searching for a set of maximum number of consistent NOE assignments in agreement with 3D space. Validation of the method using the structure of the low molecular-weight-protein tyrosine phosphatase A (MptpA) showed robust results utilizing protein structures with 30-45% sequence identity and 70% of the chemical shift assignments. About 60% of the resonance assignments are sufficient to identify those structural models with highest conformational similarity to the real structure. The software was benchmarked by de novo solution structures of fibroblast growth factor 21 (FGF21) and the extracellular fibroblast growth factor receptor domain FGFR4 D2, which both failed in crystallization trials and in classical NMR structure determination.
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Affiliation(s)
- Ulrich Schieborr
- Johann Wolfgang Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
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