1
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Dong Y, Bonin JP, Devant P, Liang Z, Sever AIM, Mintseris J, Aramini JM, Du G, Gygi SP, Kagan JC, Kay LE, Wu H. Structural transitions enable interleukin-18 maturation and signaling. Immunity 2024; 57:1533-1548.e10. [PMID: 38733997 PMCID: PMC11236505 DOI: 10.1016/j.immuni.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/28/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
Several interleukin-1 (IL-1) family members, including IL-1β and IL-18, require processing by inflammasome-associated caspases to unleash their activities. Here, we unveil, by cryoelectron microscopy (cryo-EM), two major conformations of the complex between caspase-1 and pro-IL-18. One conformation is similar to the complex of caspase-4 and pro-IL-18, with interactions at both the active site and an exosite (closed conformation), and the other only contains interactions at the active site (open conformation). Thus, pro-IL-18 recruitment and processing by caspase-1 is less dependent on the exosite than the active site, unlike caspase-4. Structure determination by nuclear magnetic resonance uncovers a compact fold of apo pro-IL-18, which is similar to caspase-1-bound pro-IL-18 but distinct from cleaved IL-18. Binding sites for IL-18 receptor and IL-18 binding protein are only formed upon conformational changes after pro-IL-18 cleavage. These studies show how pro-IL-18 is selected as a caspase-1 substrate, and why cleavage is necessary for its inflammatory activity.
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Affiliation(s)
- Ying Dong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Jeffrey P Bonin
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Pascal Devant
- Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhuoyi Liang
- Bioscience and Biomedical Engineering Thrust, Brain and Intelligence Research Institute, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China
| | - Alexander I M Sever
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - James M Aramini
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Gang Du
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Stephen P Gygi
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Lewis E Kay
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada.
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
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2
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Mineev KS, Chernykh MA, Motov VV, Prudnikova DA, Pavlenko DM, Kuzmenkov AI, Peigneur S, Tytgat J, Vassilevski AA. A scorpion toxin affecting sodium channels shows double cis-trans isomerism. FEBS Lett 2023; 597:2358-2368. [PMID: 37501371 DOI: 10.1002/1873-3468.14705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Scorpion α-toxins (α-NaTx) inhibiting the inactivation of voltage-gated sodium channels (Nav ) are a well-studied family of small proteins. We previously showed that the structure of α-NaTx specificity module responsible for selective Nav binding is governed by an interplay between the nest and niche protein motifs. Here, we report the solution structure of the toxin Lqq4 from the venom of the scorpion Leiurus quinquestriatus. Unexpectedly, we find that this toxin presents an ensemble of long-lived structurally distinct states. We unequivocally assign these states to the alternative configurations (cis-trans isomers) of two peptide bonds: V56-P57 and C17-G18; neither of the cis isomers has been described in α-NaTx so far. We argue that the native conformational space of α-NaTx is wider than assumed previously.
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Affiliation(s)
- Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail A Chernykh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladislav V Motov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Daria A Prudnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Daniil M Pavlenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey I Kuzmenkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Jan Tytgat
- Toxicology and Pharmacology, KU Leuven, Belgium
| | - Alexander A Vassilevski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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3
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Kornilov FD, Slonimskiy YB, Lunegova DA, Egorkin NA, Savitskaya AG, Kleymenov SY, Maksimov EG, Goncharuk SA, Mineev KS, Sluchanko NN. Structural basis for the ligand promiscuity of the neofunctionalized, carotenoid-binding fasciclin domain protein AstaP. Commun Biol 2023; 6:471. [PMID: 37117801 PMCID: PMC10147662 DOI: 10.1038/s42003-023-04832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/10/2023] [Indexed: 04/30/2023] Open
Abstract
Fasciclins (FAS1) are ancient adhesion protein domains with no common small ligand binding reported. A unique microalgal FAS1-containing astaxanthin (AXT)-binding protein (AstaP) binds a broad repertoire of carotenoids by a largely unknown mechanism. Here, we explain the ligand promiscuity of AstaP-orange1 (AstaPo1) by determining its NMR structure in complex with AXT and validating this structure by SAXS, calorimetry, optical spectroscopy and mutagenesis. α1-α2 helices of the AstaPo1 FAS1 domain embrace the carotenoid polyene like a jaw, forming a hydrophobic tunnel, too short to cap the AXT β-ionone rings and dictate specificity. AXT-contacting AstaPo1 residues exhibit different conservation in AstaPs with the tentative carotenoid-binding function and in FAS1 proteins generally, which supports the idea of AstaP neofunctionalization within green algae. Intriguingly, a cyanobacterial homolog with a similar domain structure cannot bind carotenoids under identical conditions. These structure-activity relationships provide the first step towards the sequence-based prediction of the carotenoid-binding FAS1 members.
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Affiliation(s)
- Fedor D Kornilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Daria A Lunegova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Anna G Savitskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
| | - Sergey Yu Kleymenov
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 26 Vavilov Street, 119334, Moscow, Russia
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119991, Moscow, Russia
| | - Sergey A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia.
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
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4
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Bozin TN, Berdyshev IM, Chukhontseva KN, Karaseva MA, Konarev PV, Varizhuk AM, Lesovoy DM, Arseniev AS, Kostrov SV, Bocharov EV, Demidyuk IV. NMR structure of emfourin, a novel protein metalloprotease inhibitor: Insights into the mechanism of action. J Biol Chem 2023; 299:104585. [PMID: 36889586 PMCID: PMC10124921 DOI: 10.1016/j.jbc.2023.104585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Emfourin (M4in) is a protein metalloprotease inhibitor recently discovered in the bacterium Serratia proteamaculans and the prototype of a new family of protein protease inhibitors with an unknown mechanism of action. Protealysin-like proteases (PLPs) of the thermolysin family are natural targets of emfourin-like inhibitors widespread in bacteria and known in archaea. The available data indicate the involvement of PLPs in interbacterial interaction as well as bacterial interaction with other organisms and likely in pathogenesis. Arguably, emfourin-like inhibitors participate in the regulation of bacterial pathogenesis by controlling PLP activity. Here, we determined the 3D structure of M4in using solution NMR spectroscopy. The obtained structure demonstrated no significant similarity to known protein structures. This structure was used to model the M4in-enzyme complex and the complex model was verified by small-angle X-ray scattering. Based on the model analysis, we propose a molecular mechanism for the inhibitor, which was confirmed by site-directed mutagenesis. We show that two spatially close flexible loop regions are critical for the inhibitor-protease interaction. One region includes aspartic acid forming a coordination bond with catalytic Zn2+ of the enzyme and the second region carries hydrophobic amino acids interacting with protease substrate binding sites. Such an active site structure corresponds to the noncanonical inhibition mechanism. This is the first demonstration of such a mechanism for protein inhibitors of thermolysin family metalloproteases, which puts forward M4in as a new basis for the development of antibacterial agents relying on selective inhibition of prominent factors of bacterial pathogenesis belonging to this family.
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Affiliation(s)
- Timur N Bozin
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia; National Research Centre "Kurchatov Institute", Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Igor M Berdyshev
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ksenia N Chukhontseva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Maria A Karaseva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Petr V Konarev
- Shubnikov Institute of Crystallography of the Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia
| | - Anna M Varizhuk
- Moscow Institute of Physics and Technology, State University, Dolgoprudny, Russia
| | - Dmitry M Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Kostrov
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Moscow Institute of Physics and Technology, State University, Dolgoprudny, Russia
| | - Ilya V Demidyuk
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia.
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5
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Kornilov FD, Shabalkina AV, Lin C, Volynsky PE, Kot EF, Kayushin AL, Lushpa VA, Goncharuk MV, Arseniev AS, Goncharuk SA, Wang X, Mineev KS. The architecture of transmembrane and cytoplasmic juxtamembrane regions of Toll-like receptors. Nat Commun 2023; 14:1503. [PMID: 36932058 PMCID: PMC10023784 DOI: 10.1038/s41467-023-37042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
Toll-like receptors (TLRs) are the important participants of the innate immune response. Their spatial organization is well studied for the ligand-binding domains, while a lot of questions remain unanswered for the membrane and cytoplasmic regions of the proteins. Here we use solution NMR spectroscopy and computer simulations to investigate the spatial structures of transmembrane and cytoplasmic juxtamembrane regions of TLR2, TLR3, TLR5, and TLR9. According to our data, all the proteins reveal the presence of a previously unreported structural element, the cytoplasmic hydrophobic juxtamembrane α-helix. As indicated by the functional tests in living cells and bioinformatic analysis, this helix is important for receptor activation and plays a role, more complicated than a linker, connecting the transmembrane and cytoplasmic parts of the proteins.
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Affiliation(s)
- F D Kornilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - A V Shabalkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Cong Lin
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, Jilin, China
| | - P E Volynsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- Institute of Cytology of Russian Academy of Sciences, Tikhoretsky 4, 194064, Saint Petersburg, Russia
| | - E F Kot
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - A L Kayushin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - V A Lushpa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - M V Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - S A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, Jilin, China.
- School of Applied Chemistry and Engineering, University of Science and Technology of China, 230026, Hefei, Anhui, China.
| | - K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
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6
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Lushpa VA, Baleeva NS, Goncharuk SA, Goncharuk MV, Arseniev AS, Baranov MS, Mineev KS. Spatial Structure of nanoFAST in the Apo State and in Complex with its Fluorogen HBR-DOM2. Int J Mol Sci 2022; 23:ijms231911361. [PMID: 36232662 PMCID: PMC9570328 DOI: 10.3390/ijms231911361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022] Open
Abstract
NanoFAST is a fluorogen-activating protein and can be considered one of the smallest encodable fluorescent tags. Being a shortened variant of another fluorescent tag, FAST, nanoFAST works nicely only with one out of all known FAST ligands. This substantially limits the applicability of this protein. To find the reason for such a behavior, we investigated the spatial structure and dynamics of nanoFAST, both in the apo state and in the complex with its fluorogen molecule, using the solution NMR spectroscopy. We showed that the truncation of FAST did not affect the structure of the remaining part of the protein. Our data suggest that the deleted N-terminus of FAST destabilizes the C-terminal domain in the apo state. While it does not contact the fluorogen directly, it serves as a free energy reservoir that enhances the ligand binding propensity of the protein. The structure of nanoFAST/HBR-DOM2 complex reveals the atomistic details of nanoFAST interactions with the rhodanine-based ligands and explains the ligand specificity. NanoFAST selects ligands with the lowest dissociation constants, 2,5-disubstituted 4-hydroxybenzyldienerhodainines, which allow the non-canonical intermolecular CH–N hydrogen bonding and provide the optimal packing of the ligand within the hydrophobic cavity of the protein.
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Affiliation(s)
- Vladislav A. Lushpa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, School of Biological and Medical Physics, Dolgoprudny 141701, Russia
| | - Nadezhda S. Baleeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, School of Biological and Medical Physics, Dolgoprudny 141701, Russia
| | - Marina V. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | | | - Mikhail S. Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Correspondence: (M.S.B.); (K.S.M.)
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, School of Biological and Medical Physics, Dolgoprudny 141701, Russia
- Correspondence: (M.S.B.); (K.S.M.)
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7
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Lushpa VA, Goncharuk MV, Lin C, Zalevsky AO, Talyzina IA, Luginina AP, Vakhrameev DD, Shevtsov MB, Goncharuk SA, Arseniev AS, Borshchevskiy VI, Wang X, Mineev KS. Modulation of Toll-like receptor 1 intracellular domain structure and activity by Zn 2+ ions. Commun Biol 2021; 4:1003. [PMID: 34429510 PMCID: PMC8385042 DOI: 10.1038/s42003-021-02532-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/06/2021] [Indexed: 12/27/2022] Open
Abstract
Toll-like receptors (TLRs) play an important role in the innate immune response. While a lot is known about the structures of their extracellular parts, many questions are still left unanswered, when the structural basis of TLR activation is analyzed for the TLR intracellular domains. Here we report the structure and dynamics of TLR1 toll-interleukin like (TIR) cytoplasmic domain in crystal and in solution. We found that the TLR1-TIR domain is capable of specific binding of Zn with nanomolar affinity. Interactions with Zn are mediated by cysteine residues 667 and 686 and C667 is essential for the Zn binding. Potential structures of the TLR1-TIR/Zn complex were predicted in silico. Using the functional assays for the heterodimeric TLR1/2 receptor, we found that both Zn addition and Zn depletion affect the activity of TLR1, and C667A mutation disrupts the receptor activity. Analysis of C667 position in the TLR1 structure and possible effects of C667A mutation, suggests that zinc-binding ability of TLR1-TIR domain is critical for the receptor activation. Lushpa et al report the structure and dynamics of the TLR1 toll-interleukin like (TIR) cytoplasmic domain in both crystal and solution. They demonstrate that the TLR1 TIR domain is capable of specific binding of Zn with nanomolar affinity, which appears to be critical for receptor activation, and provide potential structures TLR1-TIR/Zn complex based on in silico data.
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Affiliation(s)
- Vladislav A Lushpa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Marina V Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Cong Lin
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Arthur O Zalevsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Irina A Talyzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | | | | | - Sergey A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Valentin I Borshchevskiy
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China.,Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, China
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia. .,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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8
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Goncharuk SA, Artemieva LE, Tabakmakher VM, Arseniev AS, Mineev KS. CARD domain of rat RIP2 kinase: Refolding, solution structure, pH-dependent behavior and protein-protein interactions. PLoS One 2018; 13:e0206244. [PMID: 30352081 PMCID: PMC6198988 DOI: 10.1371/journal.pone.0206244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/09/2018] [Indexed: 02/06/2023] Open
Abstract
RIP2, one of the RIP kinases, interacts with p75 neurotrophin receptor, regulating the neuron survival, and with NOD1 and NOD2 proteins, causing the innate immune response against gram-negative and gram-positive bacteria via its caspase recruitment domain (CARD). This makes RIP2 a prospective target for novel therapies, aimed to modulate the inflammatory diseases and neurogenesis/neurodegeneration. Several studies report the problems with the stability of human RIP2 CARD and its production in bacterial hosts, which is a prerequisite for the structural investigation with solution NMR spectroscopy. In the present work, we report the high yield production and refolding protocols and resolve the structure of rat RIP2 CARD. The structure reveals the important differences to the previously published conformation of the homologous human protein. Using solution NMR, we characterized the intramolecular mobility and pH-dependent behavior of RIP2 CARD, and found the propensity of the protein to form high-order oligomers at physiological pH while being monomeric under acidic conditions. The oligomerization of protein may be explained, based on the electrostatic properties of its surface. Analysis of the structure and sequences of homologous proteins reveals the residues which are significant for the unusual fold of RIP2 CARD domains from different species. The high-throughput protein production/refolding protocols and proposed explanation for the protein oligomerization, provide an opportunity to design the stabilized variants of RIP2 CARD, which could be used to study the structural details of RIP2/NOD1/NOD2 interaction and perform the rational drug design.
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Affiliation(s)
- Sergey A. Goncharuk
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Institutsky per., Dolgoprudnyi, Russian Federation
| | - Lilya E. Artemieva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Institutsky per., Dolgoprudnyi, Russian Federation
| | - Valentin M. Tabakmakher
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Moscow, Russian Federation
| | - Alexander S. Arseniev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Institutsky per., Dolgoprudnyi, Russian Federation
| | - Konstantin S. Mineev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Institutsky per., Dolgoprudnyi, Russian Federation
- * E-mail:
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9
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Kuldyushev NA, Mineev KS, Berkut AA, Peigneur S, Arseniev AS, Tytgat J, Grishin EV, Vassilevski AA. Refined structure of BeM9 reveals arginine hand, an overlooked structural motif in scorpion toxins affecting sodium channels. Proteins 2018; 86:1117-1122. [DOI: 10.1002/prot.25583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/27/2018] [Accepted: 07/04/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Nikita A. Kuldyushev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow Russia
- Moscow Institute of Physics and Technology (State University); Moscow Russia
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow Russia
- Moscow Institute of Physics and Technology (State University); Moscow Russia
| | - Antonina A. Berkut
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow Russia
- Moscow Institute of Physics and Technology (State University); Moscow Russia
| | - Steve Peigneur
- Toxicology and Pharmacology; University of Leuven; Leuven Belgium
| | - Alexander S. Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow Russia
- Moscow Institute of Physics and Technology (State University); Moscow Russia
| | - Jan Tytgat
- Toxicology and Pharmacology; University of Leuven; Leuven Belgium
| | - Eugene V. Grishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow Russia
| | - Alexander A. Vassilevski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow Russia
- Moscow Institute of Physics and Technology (State University); Moscow Russia
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10
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Larsen EK, Olivieri C, Walker C, V S M, Gao J, Bernlohr DA, Tonelli M, Markley JL, Veglia G. Probing Protein-Protein Interactions Using Asymmetric Labeling and Carbonyl-Carbon Selective Heteronuclear NMR Spectroscopy. Molecules 2018; 23:E1937. [PMID: 30081441 PMCID: PMC6205158 DOI: 10.3390/molecules23081937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 11/23/2022] Open
Abstract
Protein-protein interactions (PPIs) regulate a plethora of cellular processes and NMR spectroscopy has been a leading technique for characterizing them at the atomic resolution. Technically, however, PPIs characterization has been challenging due to multiple samples required to characterize the hot spots at the protein interface. In this paper, we review our recently developed methods that greatly simplify PPI studies, which minimize the number of samples required to fully characterize residues involved in the protein-protein binding interface. This original strategy combines asymmetric labeling of two binding partners and the carbonyl-carbon label selective (CCLS) pulse sequence element implemented into the heteronuclear single quantum correlation (¹H-15N HSQC) spectra. The CCLS scheme removes signals of the J-coupled 15N⁻13C resonances and records simultaneously two individual amide fingerprints for each binding partner. We show the application to the measurements of chemical shift correlations, residual dipolar couplings (RDCs), and paramagnetic relaxation enhancements (PRE). These experiments open an avenue for further modifications of existing experiments facilitating the NMR analysis of PPIs.
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Affiliation(s)
- Erik K Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Manu V S
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Madison, WI 53706, USA.
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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11
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Lesovoy DM, Mineev KS, Bragin PE, Bocharova OV, Bocharov EV, Arseniev AS. NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 69:165-179. [PMID: 29063258 DOI: 10.1007/s10858-017-0146-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
In the case of soluble proteins, chemical shift mapping is used to identify the intermolecular interfaces when the NOE-based calculations of spatial structure of the molecular assembly are impossible or impracticable. However, the reliability of the membrane protein interface mapping based on chemical shifts or other relevant parameters was never assessed. In the present work, we investigate the predictive power of various NMR parameters that can be used for mapping of helix-helix interfaces in dimeric TM domains. These parameters are studied on a dataset containing three structures of helical dimers obtained for two different proteins in various membrane mimetics. We conclude that the amide chemical shifts have very little predictive value, while the methyl chemical shifts could be used to predict interfaces, though with great care. We suggest an approach based on conversion of the carbon NMR relaxation parameters of methyl groups into parameters of motion, and one of such values, the characteristic time of methyl rotation, appears to be a reliable sensor of interhelix contacts in transmembrane domains. The carbon NMR relaxation parameters of methyl groups can be measured accurately and with high sensitivity and resolution, making the proposed parameter a useful tool for investigation of protein-protein interfaces even in large membrane proteins. An approach to build the models of transmembrane dimers based on perturbations of methyl parameters and TMDOCK software is suggested.
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Affiliation(s)
- D M Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
| | - K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
| | - P E Bragin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Lomonosov Moscow State University, Leninskiye Gory, 1, Moscow, Russian Federation, 119991
| | - O V Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
| | - E V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997.
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700.
- National Research Centre "Kurchatov Institute", Kurchatov Complex of NBICS-technologies, Akad. Kurchatova Sqr., 1, Moscow, Russian Federation, 123182.
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997
- Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700
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12
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Park S, Phukan PD, Zeeb M, Martinez-Yamout MA, Dyson HJ, Wright PE. Structural Basis for Interaction of the Tandem Zinc Finger Domains of Human Muscleblind with Cognate RNA from Human Cardiac Troponin T. Biochemistry 2017; 56:4154-4168. [PMID: 28718627 PMCID: PMC5560242 DOI: 10.1021/acs.biochem.7b00484] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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The human muscleblind-like
proteins (MBNL) regulate tissue-specific
splicing by targeting cardiac troponin T and other pre-mRNAs; aberrant
targeting of CUG and CCUG repeat expansions frequently accompanies
the neuromuscular disease myotonic dystrophy. We show, using biolayer
interferometry (Octet) and NMR spectroscopy, that the zinc finger
domains of MBNL isoform 1 (MBNL1) are necessary and sufficient for
binding CGCU sequences within the pre-mRNA of human cardiac troponin
T. Protein constructs containing zinc fingers 1 and 2 (zf12) and zinc
fingers 3 and 4 (zf34) of MBNL1 each fold into a compact globular
tandem zinc finger structure that participates in RNA binding. NMR
spectra show that the stoichiometry of the interaction between zf12
or zf34 and the CGCU sequence is 1:1, and that the RNA is single-stranded
in the complex. The individual zinc fingers within zf12 or zf34 are
nonequivalent: the primary RNA binding surface is formed in each pair
by the second zinc finger (zf2 or zf4), which interacts with the CGCU
RNA sequence. The NMR structure of the complex between zf12 and a
15-base RNA of sequence 95GUCUCGCUUUUCCCC109, containing a single
CGCU element, shows the single-stranded RNA wrapped around zf2 and
extending to bind to the C-terminal helix. Bases C101, U102, and U103
make well-defined and highly ordered contacts with the protein, whereas
neighboring bases are less well-ordered in the complex. Binding of
the MBNL zinc fingers to cardiac troponin T pre-mRNA is specific and
relatively simple, unlike the complex multiple dimer–trimer
stoichiometries postulated in some previous studies.
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Affiliation(s)
- Sangho Park
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Priti Deka Phukan
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Markus Zeeb
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maria A Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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13
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Spatial structure of TLR4 transmembrane domain in bicelles provides the insight into the receptor activation mechanism. Sci Rep 2017; 7:6864. [PMID: 28761155 PMCID: PMC5537299 DOI: 10.1038/s41598-017-07250-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/26/2017] [Indexed: 01/16/2023] Open
Abstract
Toll-like receptors (TLRs) play a key role in the innate and adaptive immune systems. While a lot of structural data is available for the extracellular and cytoplasmic domains of TLRs, and a model of the dimeric full-length TLR3 receptor in the active state was build, the conformation of the transmembrane (TM) domain and juxtamembrane regions in TLR dimers is still unclear. In the present work, we study the transmembrane and juxtamembrane parts of human TLR4 receptor using solution NMR spectroscopy in a variety of membrane mimetics, including phospholipid bicelles. We show that the juxtamembrane hydrophobic region of TLR4 includes a part of long TM α-helix. We report the dimerization interface of the TM domain and claim that long TM domains with transmembrane charged aminoacids is a common feature of human toll-like receptors. This fact is analyzed from the viewpoint of protein activation mechanism, and a model of full-length TLR4 receptor in the dimeric state has been proposed.
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14
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Wang LP, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ, Pande VS. Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. J Phys Chem B 2017; 121:4023-4039. [PMID: 28306259 PMCID: PMC9724927 DOI: 10.1021/acs.jpcb.7b02320] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.
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Affiliation(s)
- Lee-Ping Wang
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - Keri A McKiernan
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Joseph Gomes
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Kyle A Beauchamp
- Counsyl, Inc. , South San Francisco, California 94080, United States
| | - Teresa Head-Gordon
- Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering, and Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
- Chemical Sciences Division, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Julia E Rice
- IBM Almaden Research Center, IBM Research , San Jose, California 95120, United States
| | - William C Swope
- IBM Almaden Research Center, IBM Research , San Jose, California 95120, United States
| | - Todd J Martínez
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
- PULSE Institute, Stanford University , Stanford, California 94305, United States
- SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Vijay S Pande
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
- Departments of Computer Science, Structural Biology, and Program in Biophysics, Stanford University , Stanford, California 94305, United States
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15
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Catazaro J, Periago J, Shortridge MD, Worley B, Kirchner A, Powers R, Griep MA. Identification of a Ligand-Binding Site on the Staphylococcus aureus DnaG Primase C-Terminal Domain. Biochemistry 2017; 56:932-943. [PMID: 28125218 PMCID: PMC6476306 DOI: 10.1021/acs.biochem.6b01273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interface between the DnaG primase C-terminal domain (CTD) and the N-terminal domain of DnaB helicase is essential for bacterial DNA replication because it allows coordinated priming of DNA synthesis at the replication fork while the DNA is being unwound. Because these two proteins are conserved in all bacteria and distinct from those in eukaryotes, their interface is an attractive antibiotic target. To learn more about this interface, we determined the solution structure and dynamics of the DnaG primase CTD from Staphylococcus aureus, a medically important bacterial species. Comparison with the known primase CTD structures shows there are two biologically relevant conformations, an open conformation that likely binds to DnaB helicase and a closed conformation that does not. The S. aureus primase CTD is in the closed conformation, but nuclear magnetic resonance (NMR) dynamic studies indicate there is considerable movement in the linker between the two subdomains and that N564 is the most dynamic residue within the linker. A high-throughput NMR ligand affinity screen identified potential binding compounds, among which were acycloguanosine and myricetin. Although the affinity for these compounds and adenosine was in the millimolar range, all three bind to a common pocket that is present only on the closed conformation of the CTD. This binding pocket is at the opposite end of helices 6 and 7 from N564, the key hinge residue. The identification of this binding pocket should allow the development of stronger-binding ligands that can prevent formation of the CTD open conformation that binds to DnaB helicase.
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Affiliation(s)
| | | | | | - Bradley Worley
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Andrew Kirchner
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Mark A. Griep
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
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16
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Lee CJ, Liang X, Wu Q, Najeeb J, Zhao J, Gopalaswamy R, Titecat M, Sebbane F, Lemaitre N, Toone EJ, Zhou P. Drug design from the cryptic inhibitor envelope. Nat Commun 2016; 7:10638. [PMID: 26912110 PMCID: PMC4773385 DOI: 10.1038/ncomms10638] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/05/2016] [Indexed: 11/09/2022] Open
Abstract
Conformational dynamics plays an important role in enzyme catalysis, allosteric regulation of protein functions and assembly of macromolecular complexes. Despite these well-established roles, such information has yet to be exploited for drug design. Here we show by nuclear magnetic resonance spectroscopy that inhibitors of LpxC--an essential enzyme of the lipid A biosynthetic pathway in Gram-negative bacteria and a validated novel antibiotic target--access alternative, minor population states in solution in addition to the ligand conformation observed in crystal structures. These conformations collectively delineate an inhibitor envelope that is invisible to crystallography, but is dynamically accessible by small molecules in solution. Drug design exploiting such a hidden inhibitor envelope has led to the development of potent antibiotics with inhibition constants in the single-digit picomolar range. The principle of the cryptic inhibitor envelope approach may be broadly applicable to other lead optimization campaigns to yield improved therapeutics.
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Affiliation(s)
- Chul-Jin Lee
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Xiaofei Liang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Qinglin Wu
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Javaria Najeeb
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jinshi Zhao
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Ramesh Gopalaswamy
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Marie Titecat
- Inserm, Univ. Lille, CHU Lille, Institut Pasteur de Lille, CNRS, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Florent Sebbane
- Inserm, Univ. Lille, CHU Lille, Institut Pasteur de Lille, CNRS, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nadine Lemaitre
- Inserm, Univ. Lille, CHU Lille, Institut Pasteur de Lille, CNRS, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Eric J Toone
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.,Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.,Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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17
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Melnikova DN, Mineev KS, Finkina EI, Arseniev AS, Ovchinnikova TV. A novel lipid transfer protein from the dill Anethum graveolens L.: isolation, structure, heterologous expression, and functional characteristics. J Pept Sci 2015; 22:59-66. [PMID: 26680443 DOI: 10.1002/psc.2840] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/31/2015] [Accepted: 11/06/2015] [Indexed: 11/09/2022]
Abstract
A novel lipid transfer protein, designated as Ag-LTP, was isolated from aerial parts of the dill Anethum graveolens L. Structural, antimicrobial, and lipid binding properties of the protein were studied. Complete amino acid sequence of Ag-LTP was determined. The protein has molecular mass of 9524.4 Da, consists of 93 amino acid residues including eight cysteines forming four disulfide bonds. The recombinant Ag-LTP was overexpressed in Escherichia coli and purified. NMR investigation shows that the Ag-LTP spatial structure contains four α-helices, forming the internal hydrophobic cavity, and a long C-terminal tail. The measured volume of the Ag-LTP hydrophobic cavity is equal to ~800 A(3), which is much larger than those of other plant LTP1s. Ag-LTP has weak antifungal activity and unpronounced lipid binding specificity but effectively binds plant hormone jasmonic acid. Our results afford further molecular insight into biological functions of LTP in plants.
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Affiliation(s)
- Daria N Melnikova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia
| | - Konstantin S Mineev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia
| | - Ekaterina I Finkina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia
| | - Alexander S Arseniev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia
| | - Tatiana V Ovchinnikova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia
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18
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Mineev KS, Goncharuk SA, Arseniev AS. Toll-like receptor 3 transmembrane domain is able to perform various homotypic interactions: An NMR structural study. FEBS Lett 2014; 588:3802-7. [DOI: 10.1016/j.febslet.2014.08.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/27/2014] [Accepted: 08/27/2014] [Indexed: 11/26/2022]
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19
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Tuttle LM, Dyson HJ, Wright PE. Side chain conformational averaging in human dihydrofolate reductase. Biochemistry 2014; 53:1134-45. [PMID: 24498949 PMCID: PMC3985697 DOI: 10.1021/bi4015314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The three-dimensional structures
of the dihydrofolate reductase
enzymes from Escherichia coli (ecDHFR or ecE) and Homo sapiens (hDHFR or hE) are very similar, despite a rather
low level of sequence identity. Whereas the active site loops of ecDHFR
undergo major conformational rearrangements during progression through
the reaction cycle, hDHFR remains fixed in a closed loop conformation
in all of its catalytic intermediates. To elucidate the structural
and dynamic differences between the human and E. coli enzymes, we conducted a comprehensive analysis of side chain flexibility
and dynamics in complexes of hDHFR that represent intermediates in
the major catalytic cycle. Nuclear magnetic resonance relaxation dispersion
experiments show that, in marked contrast to the functionally important
motions that feature prominently in the catalytic intermediates of
ecDHFR, millisecond time scale fluctuations cannot be detected for
hDHFR side chains. Ligand flux in hDHFR is thought to be mediated
by conformational changes between a hinge-open state when the substrate/product-binding
pocket is vacant and a hinge-closed state when this pocket is occupied.
Comparison of X-ray structures of hinge-open and hinge-closed states
shows that helix αF changes position by sliding between the
two states. Analysis of χ1 rotamer populations derived
from measurements of 3JCγCO and 3JCγN couplings
indicates that many of the side chains that contact helix αF
exhibit rotamer averaging that may facilitate the conformational change.
The χ1 rotamer adopted by the Phe31 side chain depends
upon whether the active site contains the substrate or product. In
the holoenzyme (the binary complex of hDHFR with reduced nicotinamide
adenine dinucleotide phosphate), a combination of hinge opening and
a change in the Phe31 χ1 rotamer opens the active
site to facilitate entry of the substrate. Overall, the data suggest
that, unlike ecDHFR, hDHFR requires minimal backbone conformational
rearrangement as it proceeds through its enzymatic cycle, but that
ligand flux is brokered by more subtle conformational changes that
depend on the side chain motions of critical residues.
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Affiliation(s)
- Lisa M Tuttle
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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20
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Foroozandeh M, Giraudeau P, Jeannerat D. A toolbox of HSQC experiments for small molecules at high 13C-enrichment. Artifact-free, fully 13C-homodecoupled and JCC-encoding pulse sequences. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:808-814. [PMID: 24123384 DOI: 10.1002/mrc.4019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/18/2013] [Accepted: 09/10/2013] [Indexed: 06/02/2023]
Abstract
A set of modified HSQC experiments designed for the study of (13)C-enriched small molecules is introduced. It includes an improved sensitivity-enhanced HSQC experiment eliminating signal artifacts because of high-order (13)C magnetization terms generated at high (13)C enrichment. A broadband homonuclear (13)C decoupling sequence based on Zangger and Sterk's method simplifies the complex (13)C-(13)C multiplet structure in the F1 dimension of HSQC. When recording spectra at high resolution, the combination with a multiple-site modulation of the selective pulse outperforms the constant-time HSQC in terms of sensitivity and reliability. Finally, two pulse sequences reintroducing selected J(CC) couplings with selective pulses facilitate their assignments and measurements either in the splitting of the resulting doublets or by modulation of the signal amplitude. A sample of uniformly 92% (13)C-enriched cholesterol is used as an example.
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Affiliation(s)
- Mohammadali Foroozandeh
- Department of Organic Chemistry, University of Geneva, 30 Quai E. Ansermet, 1211, Geneva 4, Switzerland
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21
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Tuttle LM, Dyson HJ, Wright PE. Side-chain conformational heterogeneity of intermediates in the Escherichia coli dihydrofolate reductase catalytic cycle. Biochemistry 2013; 52:3464-77. [PMID: 23614825 DOI: 10.1021/bi400322e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli dihydrofolate reductase (DHFR) provides a paradigm for the integrated study of the role of protein dynamics in enzyme function. Previous studies of backbone and side chain dynamics have yielded unprecedented insights into the mechanism by which DHFR progresses through the structural changes that occur during its catalytic cycle. Here we report a comprehensive study of the χ1 rotamer populations of the aromatic and γ-methyl containing residues for complexes of the catalytic cycle, based on NMR measurement of (3)JCγCO and (3)JCγN coupling constants. We report conformational and dynamic information for eight distinct complexes, where transitions between rotamer wells may occur on a broad picosecond to millisecond time scale. This large volume of (3)J data has allowed us to fit new Karplus parameterizations for aromatic side chains and to select the best available of previously determined parameters for Ile, Thr, and Val. The (3)JCγCO and (3)JCγN coupling constants are found to be extremely sensitive measures of side chain χ1 rotamers and to give important insights into the extent of conformational averaging. For a subset of residues in DHFR, the extent of rotamer averaging is invariant to the nature of the bound ligand, while for other residues the rotamer averaging differs in one or more complexes of the enzymatic cycle. These variable-averaging residues are generally located near the active site, but the phenomenon extends into the adenosine binding domain. For several residues, the rotamer populations in different DHFR complexes appear to depend on whether the complex is in the closed or occluded state, and some residues are exquisitely sensitive to small changes in the nature of the bound ligand.
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Affiliation(s)
- Lisa M Tuttle
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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22
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Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy has come a long way in characterizing the structure and function of biological molecules since the first one-dimensional spectrum of protein was recorded about 30 years ago. To date (September 1, 2012), there are 9,521 solution NMR structures in the Protein Data Bank, compared to 74,009 determined by crystallographic methods. Unlike X-ray and electron microscopy (EM) methods, which are based on the concepts of Fourier optics and image reconstruction, structure determination by NMR involves measuring structural restraints and finding structural solutions that satisfy the restraints. Although the NMR approach is much less direct in a physical sense, it has proven itself over the years to be capable of de novo structure determination at high precision. Moreover, the method is highly versatile and can be used in a variety of ways for addressing mechanistic questions. NMR measurements of protein internal dynamics and protein-protein or protein-ligand interaction are directly relevant to function in vivo because the molecules are often in physiological buffer conditions. The method can also be applied to investigate protein-folding intermediates, conformational changes, as well as intrinsically unfolded proteins. Recently, along with X-ray and EM, solution NMR has entered a state of rapid growth for structural studies of membrane proteins, already demonstrating its feasibility in de novo structure determination of membrane-embedded ion channels and receptors. As the hardware advances rapidly, especially in cryogenic probes that have much higher sensitivity, the sample concentration required for solution NMR investigation is decreasing, hopefully soon to a concentration level at which nonspecific protein aggregation is no longer an issue. After three decades of improvement in spectrometer technology, NMR pulse experiments, isotope labeling schemes, and structure determination software, we believe that solution NMR will truly enter the production phase in the next decade to answer biological questions of high impact, and to become more versatile than ever in complementing X-ray and EM in investigating protein structure and function.
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Affiliation(s)
- James J Chou
- Jack and Eileen Connors Structural Biology Laboratory, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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23
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Claridge JK, Schnell JR. Bacterial production and solution NMR studies of a viral membrane ion channel. Methods Mol Biol 2012; 831:165-79. [PMID: 22167674 DOI: 10.1007/978-1-61779-480-3_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Advances in solution nuclear magnetic resonance (NMR) methodology that enable studies of very large proteins have also paved the way for studies of membrane proteins that behave like large proteins due to the added weight of surfactants. Solution NMR has been used to determine the high-resolution structures of several small, membrane proteins dissolved in detergent micelles and small bicelles. However, the usual difficulties with membrane proteins in producing, purifying, and stabilizing the proteins away from native membranes remain, requiring intensive screening efforts. Low levels of heterologous expression can be the most detrimental aspect to studying membrane proteins. This is exacerbated for NMR studies because of the costs of isotopically enriched media. Thus, solution NMR studies have tended to focus on relatively small, membrane proteins that can be expressed into inclusion bodies and refolded. Here, we describe the methods used to produce, purify, and refold the proton channel M2 into detergent micelles, and the procedures used to determine chemical shift assignments and the atomic level structure of the closed form of the homotetrameric channel.
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Traaseth NJ, Veglia G. Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 211:18-24. [PMID: 21482162 PMCID: PMC3328402 DOI: 10.1016/j.jmr.2011.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/10/2011] [Accepted: 03/14/2011] [Indexed: 05/15/2023]
Abstract
We present a new method that combines carbonyl-selective labeling with frequency-selective heteronuclear recoupling to resolve the spectral overlap of magic angle spinning (MAS) NMR spectra of membrane proteins in fluid lipid membranes with broad lines and high redundancy in the primary sequence. We implemented this approach in both heteronuclear (15)N-(13)C(α) and homonuclear (13)C-(13)C dipolar assisted rotational resonance (DARR) correlation experiments. We demonstrate its efficacy for the membrane protein phospholamban reconstituted in fluid PC/PE/PA lipid bilayers. The main advantage of this method is to discriminate overlapped (13)C(α) resonances by strategically labeling the preceding residue. This method is highly complementary to (13)C(i-1)(')-(15)N(i)-(13)C(i)(α) and (13)C(i-1)(α)-(15)N(i-1)-(13)C(i)(') experiments to distinguish inter-residue spin systems at a minimal cost to signal-to-noise.
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Affiliation(s)
- Nathaniel J. Traaseth
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55445
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55445
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55445
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25
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Hansen DF, Kay LE. Determining Valine Side-Chain Rotamer Conformations in Proteins from Methyl 13C Chemical Shifts: Application to the 360 kDa Half-Proteasome. J Am Chem Soc 2011; 133:8272-81. [DOI: 10.1021/ja2014532] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
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26
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Xiong K, Zwier MC, Myshakina NS, Burger VM, Asher SA, Chong LT. Direct observations of conformational distributions of intrinsically disordered p53 peptides using UV Raman and explicit solvent simulations. J Phys Chem A 2011; 115:9520-7. [PMID: 21528875 DOI: 10.1021/jp112235d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report the first experimental measurements of Ramachandran Ψ-angle distributions for intrinsically disordered peptides: the N-terminal peptide fragment of tumor suppressor p53 and its P27S mutant form. To provide atomically detailed views of the conformational distributions, we performed classical, explicit-solvent molecular dynamics simulations on the microsecond time scale. Upon binding its partner protein, MDM2, wild-type p53 peptide adopts an α-helical conformation. Mutation of Pro27 to serine results in the highest affinity yet observed for MDM2-binding of the p53 peptide. Both UV resonance Raman spectroscopy (UVRR) and simulations reveal that the P27S mutation decreases the extent of PPII helical content and increases the probability for conformations that are similar to the α-helical MDM2-bound conformation. In addition, UVRR measurements were performed on peptides that were isotopically labeled at the Leu26 residue preceding the Pro27 in order to determine the conformational distributions of Leu26 in the wild-type and mutant peptides. The UVRR and simulation results are in quantitative agreement in terms of the change in the population of non-PPII conformations involving Leu26 upon mutation of Pro27 to serine. Finally, our simulations reveal that the MDM2-bound conformation of the peptide is significantly populated in both the wild-type and mutant isolated peptide ensembles in their unbound states, suggesting that MDM2 binding of the p53 peptides may involve conformational selection.
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Affiliation(s)
- Kan Xiong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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27
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Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:1-61. [PMID: 21241883 DOI: 10.1016/j.pnmrs.2010.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/24/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Cyril Dominguez
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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28
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Gans P, Hamelin O, Sounier R, Ayala I, Durá MA, Amero CD, Noirclerc-Savoye M, Franzetti B, Plevin MJ, Boisbouvier J. Stereospecific isotopic labeling of methyl groups for NMR spectroscopic studies of high-molecular-weight proteins. Angew Chem Int Ed Engl 2010; 49:1958-62. [PMID: 20157899 DOI: 10.1002/anie.200905660] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Pierre Gans
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA/CNRS/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex, France
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29
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A single destabilizing mutation (F9S) promotes concerted unfolding of an entire globular domain in gammaS-crystallin. J Mol Biol 2010; 399:320-30. [PMID: 20382156 DOI: 10.1016/j.jmb.2010.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 03/30/2010] [Accepted: 04/01/2010] [Indexed: 11/22/2022]
Abstract
Conformational change and aggregation of native proteins are associated with many serious age-related and neurological diseases. gammaS-Crystallin is a highly stable, abundant structural component of vertebrate eye lens. A single F9S mutation in the N-terminal domain of mouse gammaS-crystallin causes the severe Opj cataract, with disruption of cellular organization and appearance of fibrillar structures in the lens. Although the mutant protein has a near-native fold at room temperature, significant increases in hydrogen/deuterium exchange rates were observed by NMR for all the well-protected beta-sheet core residues throughout the entire N-terminal domain of the mutant protein, resulting in up to a 3.5-kcal/mol reduction in the free energy of the folding/unfolding equilibrium. No difference was detected for the C-terminal domain. At a higher temperature, this effect further increases to allow for a much more uniform exchange rate among the N-terminal core residues and those of the least well-structured surface loops. This suggests a concerted unfolding intermediate of the N-terminal domain, while the C-terminal domain stays intact. Increasing concentrations of guanidinium chloride produced two transitions for the Opj mutant, with an unfolding intermediate at approximately 1 M guanidinium chloride. The consequence of this partial unfolding, whether by elevated temperature or by denaturant, is the formation of thioflavin T staining aggregates, which demonstrated fibril-like morphology by atomic force microscopy. Seeding with the already unfolded protein enhanced the formation of fibrils. The Opj mutant protein provides a model for stress-related unfolding of an essentially normally folded protein and production of aggregates with some of the characteristics of amyloid fibrils.
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30
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Gans P, Hamelin O, Sounier R, Ayala I, Durá M, Amero C, Noirclerc-Savoye M, Franzetti B, Plevin M, Boisbouvier J. Stereospecific Isotopic Labeling of Methyl Groups for NMR Spectroscopic Studies of High-Molecular-Weight Proteins. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905660] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Tonelli M, Masterson LR, Cornilescu G, Markley JL, Veglia G. One-sample approach to determine the relative orientations of proteins in ternary and binary complexes from residual dipolar coupling measurements. J Am Chem Soc 2009; 131:14138-9. [PMID: 19764746 DOI: 10.1021/ja904766g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a procedure that supports the acquisition of (1)H-(15)N residual dipolar coupling (RDC) values for individual subunits in binary or ternary protein assemblies from a single experimental sample. Our method relies on asymmetric labeling of each subunit with the following scheme: species A uniformly with (15)N, species B uniformly with (15)N and (13)C, and species C uniformly with (15)N but selectively with (13)C' or (13)C(alpha). Because only a single sample is required, the approach obviates the need for preparing multiple samples and eliminates potential errors introduced from differences in sample conditions. Because numerous biological processes rely on protein assemblies or transient interactions, this method should be well suited for a wide range of future applications.
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Affiliation(s)
- Marco Tonelli
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA
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32
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Clarkson MW, Lei M, Eisenmesser EZ, Labeikovsky W, Redfield A, Kern D. Mesodynamics in the SARS nucleocapsid measured by NMR field cycling. JOURNAL OF BIOMOLECULAR NMR 2009; 45:217-25. [PMID: 19641854 PMCID: PMC2728245 DOI: 10.1007/s10858-009-9347-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 06/26/2009] [Indexed: 05/19/2023]
Abstract
Protein motions on all timescales faster than molecular tumbling are encoded in the spectral density. The dissection of complex protein dynamics is typically performed using relaxation rates determined at high and ultra-high field. Here we expand this range of the spectral density to low fields through field cycling using the nucleocapsid protein of the SARS coronavirus as a model system. The field-cycling approach enables site-specific measurements of R (1) at low fields with the sensitivity and resolution of a high-field magnet. These data, together with high-field relaxation and heteronuclear NOE, provide evidence for correlated rigid-body motions of the entire beta-hairpin, and corresponding motions of adjacent loops with a time constant of 0.8 ns (mesodynamics). MD simulations substantiate these findings and provide direct verification of the time scale and collective nature of these motions.
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Affiliation(s)
- Michael W. Clarkson
- Department of Biochemistry and Howard Hughes Medical Institute, MS009 Brandeis University, Waltham, MA 02452 USA
| | - Ming Lei
- Department of Biochemistry and Howard Hughes Medical Institute, MS009 Brandeis University, Waltham, MA 02452 USA
| | - Elan Z. Eisenmesser
- Department of Biochemistry and Howard Hughes Medical Institute, MS009 Brandeis University, Waltham, MA 02452 USA
| | - Wladimir Labeikovsky
- Department of Biochemistry and Howard Hughes Medical Institute, MS009 Brandeis University, Waltham, MA 02452 USA
| | - Alfred Redfield
- Department of Biochemistry, MS009 Brandeis University, Waltham, MA 02452 USA
| | - Dorothee Kern
- Department of Biochemistry and Howard Hughes Medical Institute, MS009 Brandeis University, Waltham, MA 02452 USA
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33
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Bryce DL, Autschbach J. Relativistic hybrid density functional calculations of indirect nuclear spin–spin coupling tensors — Comparison with experiment for diatomic alkali metal halides,. CAN J CHEM 2009. [DOI: 10.1139/v09-040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The accurate calculation of the isotropic (Jiso) and anisotropic (ΔJ) parts of indirect nuclear spin–spin coupling tensors is a stringent test for quantum chemistry, particularly for couplings involving heavy isotopes where relativistic effects and relativity – electron correlation cross terms are expected to play an important role. Experimental measurements on diatomic molecules in the gas phase offer ideal data for testing the success of computational approaches, since the data are essentially free from intermolecular effects, and precise coupling anisotropies may be reliably extracted in favourable cases. On the basis of available experimental molecular-beam coupling-tensor parameters for diatomic alkali metal halides, we tabulate known values of Jiso and, taking rotational–vibrational corrections to the direct dipolar coupling constant into account, precise values of ΔJ are determined for the ground rovibrational state. First-principles calculations of the coupling tensors were performed using a recently developed program based on hybrid density functional theory using the two-component relativistic zeroth-order regular approximation (ZORA). Experimental trends in Jiso and ΔJ are reproduced with correlation coefficients of 0.993 and 0.977, respectively. Periodic trends in the coupling constants and their dependence on the product of the atomic numbers of the coupled nuclei are discussed. Finally, the hybrid functional method is also successfully tested against experimental data for a series of polyatomic xenon fluorides and group-17 fluorides.
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Affiliation(s)
- David L. Bryce
- Department of Chemistry and Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry, State University of New York at Buffalo, New York 14260-3000, USA
| | - Jochen Autschbach
- Department of Chemistry and Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry, State University of New York at Buffalo, New York 14260-3000, USA
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34
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Functional and structural characterization of a dense core secretory granule sorting domain from the PC1/3 protease. Proc Natl Acad Sci U S A 2009; 106:7408-13. [PMID: 19376969 DOI: 10.1073/pnas.0809576106] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several peptide hormones are initially synthesized as inactive precursors. It is only on entry of these prohormones and their processing proteases into dense core secretory granules (DCSGs) that the precursors are cleaved to generate their active forms. Prohormone convertase (PC)1/3 is a processing protease that is targeted to DCSGs. The signal for targeting PC1/3 to DCSGs resides in its carboxy-terminal tail (PC1/3(617-753)), where 3 regions (PC1/3(617-625), PC1/3(665-682), and PC1/3(711-753)) are known to aid in sorting and membrane association. In this article, we have determined a high-resolution structure of the extreme carboxy-terminal sorting domain, PC1/3(711-753) in micelles by NMR spectroscopy. PC1/3(711-753) contains 2 alpha helices located between residues 722-728 and 738-750. Functional assays demonstrate that the second helix (PC1/3(738-750)) is necessary and sufficient to target a constitutively secreted protein to granules, and that L(745) anchors a hydrophobic patch that is critical for sorting. Also, we demonstrate that calcium binding by the second helix of PC1/3(711-753) promotes aggregation of the domain via the hydrophobic patch centered on L(745). These results provide a structure-function analysis of a DCSG-sorting domain, and reveal the importance of a hydrophobic patch and calcium binding in controlling the sorting of proteins containing alpha helices to DCSGs.
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35
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Barnwal RP, Atreya HS, Chary KVR. Chemical shift based editing of CH3 groups in fractionally 13C-labelled proteins using GFT (3, 2)D CT-HCCH-COSY: stereospecific assignments of CH3 groups of Val and Leu residues. JOURNAL OF BIOMOLECULAR NMR 2008; 42:149-154. [PMID: 18810645 DOI: 10.1007/s10858-008-9273-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 08/18/2008] [Indexed: 05/26/2023]
Abstract
We propose a (3, 2)D CT-HCCH-COSY experiment to rapidly collect the data and provide significant dispersion in the spectral region containing (13)C-(1)H cross peaks of CH(3) groups belonging to Ala, Ile, Leu, Met, Thr and Val residues. This enables one to carry out chemical shift based editing and grouping of all the (13)C-(1)H cross peaks of CH(3) groups belonging to Ala, Ile, Leu, Met, Thr and Val residues in fractionally (10%) (13)C-labelled proteins, which in turn aids in the sequence-specific resonance assignments in general and side-chain resonance assignments in particular, in any given protein. Further, we demonstrate the utility of this experiment for stereospecific assignments of the pro-R and pro-S methyl groups belonging to the Leu and Val residues in fractionally (10%) (13)C-labelled proteins. The proposed experiment opens up a wide range of applications in resonance assignment strategies and structure determination of proteins.
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Affiliation(s)
- Ravi Pratap Barnwal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
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36
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Whitley MJ, Zhang J, Lee AL. Hydrophobic core mutations in CI2 globally perturb fast side-chain dynamics similarly without regard to position. Biochemistry 2008; 47:8566-76. [PMID: 18656953 DOI: 10.1021/bi8007966] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein dynamics is currently an area of intense research because of its importance as complementary information to the huge quantity of available data relating protein structure and function. Because it is usually the influence of dynamics on function that is studied, the physical determinants of the distribution of flexibility in proteins have not been explored as thoroughly. In the present NMR study, an expanded suite of five (2)H relaxation experiments was used to characterize the picosecond-to-nanosecond side-chain dynamics of chymotrypsin inhibitor 2 (CI2) and five hydrophobic core mutants, some of which are members of the folding nucleus. Because CI2 is a homologue of the serine protease inhibitor eglin c, which has already been extensively characterized in terms of its dynamics, it was possible to compare not only side-chain dynamics but also the responses of these dynamics to analogous mutations. Remarkably, each of the five core mutations in CI2 led to similar and reproducible increases in side-chain flexibility throughout the entire structure. Although the expanded suite of (2)H relaxation experiments does not affect model selection for the vast majority of residues, it did enable the detection of increasing levels of nanosecond-scale motions in CI2's reactive site binding loop as the L68 side chain was progressively shortened by mutation. Collectively, we observed that the CI2 mutants are more dynamically similar to each other than to the more rigid wild-type CI2, from which we propose that wild-type CI2 has been optimized to a specific level of rigidity which may aid in its function as a serine protease inhibitor. We also observed that the pattern of side-chain dynamics of CI2 is quantitatively similar to eglin c, but that this similarity is lost upon mutating both proteins at an equivalent position. Finally, (15)N relaxation was used to characterize the backbone dynamics of wild-type and mutant CI2. Interestingly, mutation at folding nucleus positions led to widespread increases in backbone flexibility, whereas non-folding-nucleus positions led to increases in flexibility in the C-terminal half of the protein only.
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Affiliation(s)
- Matthew J Whitley
- Department of Biochemistry & Biophysics, School of Medicine, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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37
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Masterson LR, Tonelli M, Markley JL, Veglia G. Simultaneous detection and deconvolution of congested NMR spectra containing three isotopically labeled species. J Am Chem Soc 2008; 130:7818-9. [PMID: 18512910 DOI: 10.1021/ja802701w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a procedure for isolating subspectra corresponding to individual protein or peptide components in a ternary mixture or complex. Each of the three-component species is labeled differently: species A uniformly with 15N, species B uniformly with 15N and 13C, and species C uniformly with 15N but selectively with 13C' or 13Calpha. By using the dual carbon label selective HSQC (DCLS-HSQC) pulse sequence and exploiting differences in 1J 15N-13C coupling patterns to filter selected 15N resonances from detection during a constant time period, a subspectrum from each species can be generated from three spectra acquired from a single sample. Many important biological pathways involve dynamic interactions among members of multicomponent protein assemblies, and this approach offers a powerful way to monitor such processes.
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Affiliation(s)
- Larry R Masterson
- Department of Chemistry and Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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38
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Tonelli M, Masterson LR, Hallenga K, Veglia G, Markley JL. Carbonyl carbon label selective (CCLS) 1H-15N HSQC experiment for improved detection of backbone 13C-15N cross peaks in larger proteins. JOURNAL OF BIOMOLECULAR NMR 2007; 39:177-85. [PMID: 17828465 PMCID: PMC4452135 DOI: 10.1007/s10858-007-9185-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 08/06/2007] [Accepted: 08/07/2007] [Indexed: 05/15/2023]
Abstract
We present a highly sensitive pulse sequence, carbonyl carbon label selective (1)H-(15)N HSQC (CCLS-HSQC) for the detection of signals from (1)H-(15)N units involved in (13)C'-(15)N linkages. The CCLS-HSQC pulse sequence utilizes a modified (15)N CT evolution period equal to 1/( [Formula: see text]) ( approximately 33 ms) to select for (13)C'-(15)N pairs. By collecting CCLS-HSQC and HNCO data for two proteins (8 kDa ubiquitin and 20 kDa HscB) at various temperatures (5-40 degrees C) in order to vary correlation times, we demonstrate the superiority of the CCLS-HSQC pulse sequence for proteins with long correlation times (i.e. higher molecular weight). We then show that the CCLS-HSQC experiment yields assignments in the case of a 41 kDa protein incorporating pairs of (15)N- and (13)C'-labeled amino acids, where a TROSY 2D-HN(CO) had failed. Although the approach requires that the (1)H-(15)N HSQC cross peaks be observable, it does not require deuteration of the protein. The method is suitable for larger proteins and is less affected by conformational exchange than HNCO experiments, which require a longer period of transverse (15)N magnetization. The method also is tolerant to the partial loss of signal from isotopic dilution (scrambling). This approach will be applicable to families of proteins that have been resistant to NMR structural and dynamic analysis, such as large enzymes, and partially folded or unfolded proteins.
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Affiliation(s)
- Marco Tonelli
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Larry R. Masterson
- Departments of Chemistry and Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Klaas Hallenga
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Gianluigi Veglia
- Departments of Chemistry and Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - John L. Markley
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
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39
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Lee BM, Buck-Koehntop BA, Martinez-Yamout MA, Dyson HJ, Wright PE. Embryonic neural inducing factor churchill is not a DNA-binding zinc finger protein: solution structure reveals a solvent-exposed beta-sheet and zinc binuclear cluster. J Mol Biol 2007; 371:1274-89. [PMID: 17610897 PMCID: PMC1994575 DOI: 10.1016/j.jmb.2007.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 11/20/2022]
Abstract
Churchill is a zinc-containing protein that is involved in neural induction during embryogenesis. At the time of its discovery, it was thought on the basis of sequence alignment to contain two zinc fingers of the C4 type. Further, binding of an N-terminal GST-Churchill fusion protein to a particular DNA sequence was demonstrated by immunoprecipitation selection assay, suggesting that Churchill may function as a transcriptional regulator by sequence-specific DNA binding. We show by NMR solution structure determination that, far from containing canonical C4 zinc fingers, the protein contains three bound zinc ions in novel coordination sites, including an unusual binuclear zinc cluster. The secondary structure of Churchill is also unusual, consisting of a highly solvent-exposed single-layer beta-sheet. Hydrogen-deuterium exchange and backbone relaxation measurements reveal that Churchill is unusually dynamic on a number of time scales, with the exception of regions surrounding the zinc coordinating sites, which serve to stabilize the otherwise unstructured N terminus and the single-layer beta-sheet. No binding of Churchill to the previously identified DNA sequence could be detected, and extensive searches using DNA sequence selection techniques could find no other DNA sequence that was bound by Churchill. Since the N-terminal amino acids of Churchill form part of the zinc-binding motif, the addition of a fusion protein at the N terminus causes loss of zinc and unfolding of Churchill. This observation most likely explains the published DNA-binding results, which would arise due to non-specific interaction of the unfolded protein in the immunoprecipitation selection assay. Since Churchill does not appear to bind DNA, we suggest that it may function in embryogenesis as a protein-interaction factor.
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Affiliation(s)
- Brian M Lee
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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40
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Cicero DO, Contessa GM, Pertinhez TA, Gallo M, Katsuyama AM, Paci M, Farah CS, Spisni A. Solution structure of ApaG from Xanthomonas axonopodis pv. citri reveals a fibronectin-3 fold. Proteins 2007; 67:490-500. [PMID: 17256769 DOI: 10.1002/prot.21277] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
ApaG proteins are found in a wide variety of bacterial genomes but their function is as yet unknown. Some eukaryotic proteins involved in protein-protein interactions, such as the human polymerase delta-interacting protein (PDIP38) and the F Box A (FBA) proteins, contain ApaG homology domains. We have used NMR to determine the solution structure of ApaG protein from the plant pathogen Xanthomonas axonopodis pv. citri (ApaG(Xac)) with the aim to shed some light on its molecular function. ApaG(Xac) is characterized by seven antiparallel beta strands forming two beta sheets, one containing three strands (ABE) and the other four strands (GFCC'). Relaxation measurements indicate that the protein has a quite rigid structure. In spite of the presence of a putative GXGXXG pyrophosphate binding motif ApaG(Xac) does not bind ATP or GTP, in vitro. On the other hand, ApaG(Xac) adopts a fibronectin type III (Fn3) fold, which is consistent with the hypothesis that it is involved in mediating protein-protein interactions. The fact that the proteins of ApaG family do not display significant sequence similarity with the Fn3 domains found in other eukaryotic or bacterial proteins suggests that Fn3 domain may have arisen earlier in evolution than previously estimated.
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Affiliation(s)
- Daniel O Cicero
- Department of Chemical Science and Technology, University of Rome, Tor Vergata, Italy
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41
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Call ME, Schnell JR, Xu C, Lutz RA, Chou JJ, Wucherpfennig KW. The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor. Cell 2006; 127:355-68. [PMID: 17055436 PMCID: PMC3466601 DOI: 10.1016/j.cell.2006.08.044] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 07/23/2006] [Accepted: 08/11/2006] [Indexed: 11/29/2022]
Abstract
The T cell receptor (TCR) alphabeta heterodimer communicates ligand binding to the cell interior via noncovalently associated CD3gammaepsilon, CD3deltaepsilon, and zetazeta dimers. While structures of extracellular components of the TCR-CD3 complex are known, the transmembrane (TM) domains that mediate assembly have eluded structural characterization. Incorporation of the zetazeta signaling module is known to require one basic TCRalpha and two zetazeta aspartic acid TM residues. We report the NMR structure of the zetazeta(TM) dimer, a left-handed coiled coil with substantial polar contacts. Mutagenesis experiments demonstrate that three polar positions are critical for zetazeta dimerization and assembly with TCR. The two aspartic acids create a single structural unit at the zetazeta interface stabilized by extensive hydrogen bonding, and there is evidence for a structural water molecule (or molecules) within close proximity. This structural unit, representing only the second transmembrane dimer interface solved to date, serves as a paradigm for the assembly of all modules involved in TCR signaling.
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MESH Headings
- Amino Acid Sequence
- Aspartic Acid/chemistry
- Dimerization
- Humans
- Hydrogen Bonding
- Membrane Proteins/chemistry
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis
- Nuclear Magnetic Resonance, Biomolecular
- Peptides/chemistry
- Peptides/metabolism
- Protein Binding
- Protein Conformation
- Protein Engineering
- Protein Structure, Tertiary
- Receptor-CD3 Complex, Antigen, T-Cell/chemistry
- Receptor-CD3 Complex, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
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Affiliation(s)
- Matthew E. Call
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason R. Schnell
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Chenqi Xu
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Regina A. Lutz
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - James J. Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kai W. Wucherpfennig
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
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42
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Fuentes EJ, Gilmore SA, Mauldin RV, Lee AL. Evaluation of energetic and dynamic coupling networks in a PDZ domain protein. J Mol Biol 2006; 364:337-51. [PMID: 17011581 DOI: 10.1016/j.jmb.2006.08.076] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 08/17/2006] [Accepted: 08/26/2006] [Indexed: 11/21/2022]
Abstract
A number of computational and experimental studies have identified intramolecular communication "pathways" or "networks" important for transmitting allostery. Here, we have used mutagenesis and NMR relaxation methods to investigate the scope and nature of the communication networks found in the second post-synaptic density-95/discs large/zonula occludens-1 (PDZ) domain of the human protein tyrosine phosphatase 1E protein (hPTP1E) (PDZ2). It was found that most mutations do not have a significant energetic contribution to peptide ligand binding. Three mutants that showed significant changes in binding also displayed context-dependent dynamic effects. Both a mutation at a partially exposed site (H71Y) and a buried core position (I35V) had a limited response in side-chain (2)H-based dynamics when compared to wild-type PDZ2. In contrast, a change at a second core position (I20F) that had previously been shown to be part of an energetic and dynamic network, resulted in extensive changes in side-chain dynamics. This response is reminiscent to that seen previously upon peptide ligand binding. These results shed light on the nature of the PDZ2 dynamic network and suggest that position 20 in PDZ2 acts as a "hub" that is energetically and dynamically critical for transmitting changes in dynamics throughout the PDZ domain.
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Affiliation(s)
- Ernesto J Fuentes
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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43
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Wickstrom L, Okur A, Song K, Hornak V, Raleigh DP, Simmerling CL. The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure. J Mol Biol 2006; 360:1094-107. [PMID: 16797585 PMCID: PMC4805113 DOI: 10.1016/j.jmb.2006.04.070] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Revised: 04/27/2006] [Accepted: 04/28/2006] [Indexed: 11/19/2022]
Abstract
The 36 residue villin headpiece helical subdomain (HP36) is one of the fastest cooperatively folding proteins, folding on the microsecond timescale. HP36's simple three helix topology, fast folding and small size have made it an attractive model system for computational and experimental studies of protein folding. Recent experimental studies have explored the denatured state of HP36 using fragment analysis coupled with relatively low-resolution spectroscopic techniques. These studies have shown that there is apparently only a small tendency to form locally stabilized secondary structure. Here, we complement the experimental studies by using replica exchange molecular dynamics with explicit solvent to investigate the structural features of these peptide models of unfolded HP36. To ensure convergence, two sets of simulations for each fragment were performed with different initial structures, and simulations were continued until these generated very similar final ensembles. These simulations reveal low populations of native-like structure and early folding events that cannot be resolved by experiment. For each fragment, calculated J-coupling constants and helical propensities are in good agreement with experimental trends. HP-1, corresponding to residues 41 to 53 and including the first alpha-helix, contains the highest helical population. HP-3, corresponding to residues 62 through 75 and including the third alpha-helix, contains a small population of helical turn residing at the N terminus while HP-2, corresponding to residues 52 through 61 and including the second alpha-helix, formed little to no structure in isolation. Overall, HP-1 was the only fragment to adopt a native-like conformation, but the low population suggests that formation of significant structure only occurs after formation of specific tertiary interactions.
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Affiliation(s)
- Lauren Wickstrom
- Biochemistry and Structural Biology Program, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
| | - Asim Okur
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA
| | - Kun Song
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA
| | - Viktor Hornak
- Center for Structural Biology, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA
| | - Daniel P. Raleigh
- Biochemistry and Structural Biology Program, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA
- Graduate Program in Biophysics, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
| | - Carlos L. Simmerling
- Biochemistry and Structural Biology Program, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA
- Center for Structural Biology, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA
- Computational Science Center, Brookhaven National Laboratory, Upton NY 11973, USA
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44
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Sanders CR, Sönnichsen F. Solution NMR of membrane proteins: practice and challenges. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44 Spec No:S24-40. [PMID: 16826539 DOI: 10.1002/mrc.1816] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
This review focuses upon the application of solution NMR methods to multispan integral membrane proteins, particularly with respect to determination of global folds by this approach. Practical methods are described along with the special difficulties that confront the application of solution NMR to proteins that dwell in the netherworld of the lipid bilayer.
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Affiliation(s)
- Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232-8725, USA.
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45
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Wu Z, Delaglio F, Wyatt K, Wistow G, Bax A. Solution structure of (gamma)S-crystallin by molecular fragment replacement NMR. Protein Sci 2005; 14:3101-14. [PMID: 16260758 PMCID: PMC2253246 DOI: 10.1110/ps.051635205] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 09/02/2005] [Accepted: 09/04/2005] [Indexed: 10/25/2022]
Abstract
The solution structure of murine gammaS-crystallin (gammaS) has been determined by multidimensional triple resonance NMR spectroscopy, using restraints derived from two sets of dipolar couplings, recorded in different alignment media, and supplemented by a small number of NOE distance restraints. gammaS consists of two topologically similar domains, arranged with an approximate twofold symmetry, and each domain shows close structural homology to closely related (approximately 50% sequence identity) domains found in other members of the gamma-crystallin family. Each domain consists of two four-strand "Greek key" beta-sheets. Although the domains are tightly anchored to one another by the hydrophobic surfaces of the two inner Greek key motifs, the N-arm, the interdomain linker and several turn regions show unexpected flexibility and disorder in solution. This may contribute entropic stabilization to the protein in solution, but may also indicate nucleation sites for unfolding or other structural transitions. The method used for solving the gammaS structure relies on the recently introduced molecular fragment replacement method, which capitalizes on the large database of protein structures previously solved by X-ray crystallography and NMR.
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Affiliation(s)
- Zhengrong Wu
- Building 5, Room 126, NIH, Bethesda, MD 20892-0520, USA
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46
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Oxenoid K, Chou JJ. The structure of phospholamban pentamer reveals a channel-like architecture in membranes. Proc Natl Acad Sci U S A 2005; 102:10870-5. [PMID: 16043693 PMCID: PMC1182456 DOI: 10.1073/pnas.0504920102] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2005] [Indexed: 11/18/2022] Open
Abstract
Contraction and relaxation of heart muscle cells is regulated by cycling of calcium between cytoplasm and sarcoplasmic reticulum. Human phospholamban (PLN), expressed in the sarcoplasmic reticulum membrane as a 30-kDa homopentamer, controls cellular calcium levels by a mechanism that depends on its phosphorylation. Since PLN was discovered approximately 30 years ago, extensive studies have aimed to explain how it influences calcium pumps and to determine whether it acts as an ion channel. We have determined by solution NMR methods the atomic resolution structure of an unphosphorylated PLN pentamer in dodecylphosphocholine micelles. The unusual bellflower-like assembly is held together by leucine/isoleucine zipper motifs along the membrane-spanning helices. The structure reveals a channel-forming architecture that could allow passage of small ions. The central pore gradually widens toward the cytoplasmic end as the transmembrane helices twist around each other and bend outward. The dynamic N-terminal amphipathic helices point away from the membrane, perhaps facilitating recognition and inhibition of the calcium pump.
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Affiliation(s)
- Kirill Oxenoid
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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47
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Möller HM, Martinez-Yamout MA, Dyson HJ, Wright PE. Solution Structure of the N-terminal Zinc Fingers of the Xenopus laevis double-stranded RNA-binding Protein ZFa. J Mol Biol 2005; 351:718-30. [PMID: 16051273 DOI: 10.1016/j.jmb.2005.06.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 06/03/2005] [Accepted: 06/08/2005] [Indexed: 10/25/2022]
Abstract
Several zinc finger proteins have been discovered recently that bind specifically to double-stranded RNA. These include the mammalian JAZ and wig proteins, and the seven-zinc finger protein ZFa from Xenopus laevis. We have determined the solution structure of a 127 residue fragment of ZFa, which consists of two zinc finger domains connected by a linker that remains unstructured in the free protein in solution. The first zinc finger consists of a three-stranded beta-sheet and three helices, while the second finger contains only a two-stranded sheet and two helices. The common structures of the core regions of the two fingers are superimposable. Each finger has a highly electropositive surface that maps to a helix-kink-helix motif. There is no evidence for interactions between the two fingers, consistent with the length (24 residues) and unstructured nature of the intervening linker. Comparison with a number of other proteins shows similarities in the topology and arrangement of secondary structure elements with canonical DNA-binding zinc fingers, with protein interaction motifs such as FOG zinc fingers, and with other DNA-binding and RNA-binding proteins that do not contain zinc. However, in none of these cases does the alignment of these structures with the ZFa zinc fingers produce a consistent picture of a plausible RNA-binding interface. We conclude that the ZFa zinc fingers represent a new motif for the binding of double-stranded RNA.
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Affiliation(s)
- Heiko M Möller
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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48
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Whitson SR, LeStourgeon WM, Krezel AM. Solution structure of the symmetric coiled coil tetramer formed by the oligomerization domain of hnRNP C: implications for biological function. J Mol Biol 2005; 350:319-37. [PMID: 15936032 DOI: 10.1016/j.jmb.2005.05.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2005] [Revised: 04/28/2005] [Accepted: 05/03/2005] [Indexed: 11/16/2022]
Abstract
During active cell division, heterogeneous nuclear ribonucleoprotein (hnRNP) C is one of the most abundant proteins in the nucleus. hnRNP C exists as a stable tetramer that binds about 230 nucleotides of pre-mRNA and functions in vivo to package nascent transcripts and nucleate assembly of the 40 S hnRNP complex. Previous studies have shown that monomers lacking or possessing mutant oligomerization domains bind RNA with low affinity, strongly suggesting a cooperative protomer-RNA binding mode. In order to understand the role of the oligomerization domain in defining the biological functions and structure of hnRNP C tetramers, we have determined the high-resolution NMR structure of the oligomerization interface that is formed at the core of the complex, examining specific molecular interactions that drive assembly and contribute to the structural integrity of the tetramer. The determined structure reveals an antiparallel four-helix coiled coil, where classically described knobs-into-holes packing interactions at interhelical contact surfaces are optimized so that side-chains interdigitate to create an even distribution of hydrophobic surfaces along the core. While the stoichiometry of the complex appears to be primarily specified by occlusion of hydrophobic surfaces, particularly the interfacial residue L198, from solvent, helix orientation is primarily determined by electrostatic attractions across helix interfaces. The creation of potential interaction surfaces for other hnRNP C domains along the coiled coil exterior and the assembly of oligomerization interfaces in an antiparallel orientation shape the tertiary fold of full-length monomers and juxtapose RNA-binding elements at distal surfaces of the tetrameric complex in the quaternary assembly. In addition, we discuss the specific challenges encountered in structure determination of this symmetric oligomer by NMR methods, specifically in sorting ambiguous interatomic distance constraints into classes that define different elements of the coiled coil structure.
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Affiliation(s)
- Stefanie R Whitson
- Department of Biological Sciences, 465 21st Ave. South, Vanderbilt University, Nashville, TN 37232, USA
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49
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Fürst J, Schedlbauer A, Gandini R, Garavaglia ML, Saino S, Gschwentner M, Sarg B, Lindner H, Jakab M, Ritter M, Bazzini C, Botta G, Meyer G, Kontaxis G, Tilly BC, Konrat R, Paulmichl M. ICln159 folds into a pleckstrin homology domain-like structure. Interaction with kinases and the splicing factor LSm4. J Biol Chem 2005; 280:31276-82. [PMID: 15905169 DOI: 10.1074/jbc.m500541200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ICln is a multifunctional protein involved in regulatory mechanisms as different as membrane ion transport and RNA splicing. The protein is water-soluble, and during regulatory volume decrease after cell swelling, it is able to migrate from the cytosol to the cell membrane. Purified, water-soluble ICln is able to insert into lipid bilayers to form ion channels. Here, we show that ICln159, a truncated ICln mutant, which is also able to form ion channels in lipid bilayers, belongs to the pleckstrin homology (PH) domain superfold family of proteins. The ICln PH domain shows unusual properties as it lacks the electrostatic surface polarization seen in classical PH domains. However, similar to many classical PH domain-containing proteins, ICln interacts with protein kinase C, and in addition, interacts with cAMP-dependent protein kinase and cGMP-dependent protein kinase type II but not cGMP-dependent protein kinase type Ibeta. A major phosphorylation site for all three kinases is Ser-45 within the ICln PH domain. Furthermore, ICln159 interacts with LSm4, a protein involved in splicing and mRNA degradation, suggesting that the ICln159 PH domain may serve as a protein-protein interaction platform.
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Affiliation(s)
- Johannes Fürst
- Department of Physiology and Medical Physics, Innsbruck Medical University, Fritz-Pregl Strasse 3, A-6020 Innsbruck, Austria
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50
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Legge GB, Martinez-Yamout MA, Hambly DM, Trinh T, Lee BM, Dyson HJ, Wright PE. ZZ domain of CBP: an unusual zinc finger fold in a protein interaction module. J Mol Biol 2004; 343:1081-93. [PMID: 15476823 DOI: 10.1016/j.jmb.2004.08.087] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Revised: 08/24/2004] [Accepted: 08/27/2004] [Indexed: 11/17/2022]
Abstract
CREB-binding protein (CBP) is a large, multi-domain protein that provides a multitude of binding sites for transcriptional coactivators. The site of interaction of the tumor suppressor p53 and the oncoprotein E1A with CBP/p300 has been identified with the third cysteine-histidine-rich (CH3) domain, which incorporates two zinc-binding motifs, ZZ and TAZ2. We show that these two domains fold independently and do not interact in solution. Our experiments demonstrate conclusively that the interaction of p53 and E1A with the CH3 domain resides exclusively in the TAZ2 domain, with no contribution from the ZZ domain. We report also the three-dimensional solution structure of the ZZ domain of murine CBP. The 52 residue ZZ domain contains two twisted antiparallel beta-sheets and a short alpha-helix, and binds two zinc ions. The identity of the zinc coordinating ligands was resolved unambiguously using NMR spectroscopy of the ZZ domain substituted with (113)Cd. One zinc ion is coordinated tetrahedrally via two CXXC motifs to four cysteine side-chains, and the second zinc ion is coordinated tetrahedrally by a third CXXC motif, together with an unusual HXH motif coordinating via the N(epsilon2) atom of His40 and the N(delta1) atom of His-42. The first zinc cluster of the ZZ domain is strictly conserved, whereas the second zinc cluster shows variability in the position of the two histidine residues, reflecting the wide variety of molecules that incorporate ZZ domains. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains; however, its biological function is unclear. Mapping of the positions of conserved residues onto the calculated structures reveals a face containing exposed aromatic and hydrophobic side-chains, while the opposite face contains a series of conserved charged or hydrophilic groups. These homologies suggest that the ZZ domain is involved in ligand binding or molecular scaffolding, with specificity provided by the variability of the sequence that contains the helix in the murine CPB ZZ domain structure.
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Affiliation(s)
- Glen B Legge
- Department of Molecular Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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