1
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Manu VS, Olivieri C, Veglia G. Water irradiation devoid pulses enhance the sensitivity of 1H, 1H nuclear Overhauser effects. JOURNAL OF BIOMOLECULAR NMR 2023; 77:1-14. [PMID: 36534224 DOI: 10.1007/s10858-022-00407-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/22/2022] [Indexed: 05/03/2023]
Abstract
The nuclear Overhauser effect (NOE) is one of NMR spectroscopy's most important and versatile parameters. NOE is routinely utilized to determine the structures of medium-to-large size biomolecules and characterize protein-protein, protein-RNA, protein-DNA, and protein-ligand interactions in aqueous solutions. Typical [1H,1H] NOESY pulse sequences incorporate water suppression schemes to reduce the water signal that dominates 1H-detected spectra and minimize NOE intensity losses due to unwanted polarization exchange between water and labile protons. However, at high- and ultra-high magnetic fields, the excitation of the water signal during the execution of the NOESY pulse sequences may cause significant attenuation of NOE cross-peak intensities. Using an evolutionary algorithm coupled with artificial intelligence, we recently designed high-fidelity pulses [Water irrAdiation DEvoid (WADE) pulses] that elude water excitation and irradiate broader bandwidths relative to commonly used pulses. Here, we demonstrate that WADE pulses, implemented into the 2D [1H,1H] NOESY experiments, increase the intensity of the NOE cross-peaks for labile and, to a lesser extent, non-exchangeable protons. We applied the new 2D [1H,1H] WADE-NOESY pulse sequence to two well-folded, medium-size proteins, i.e., the K48C mutant of ubiquitin and the Raf kinase inhibitor protein. We observed a net increase of the NOE intensities varying from 30 to 170% compared to the commonly used NOESY experiments. The new WADE pulses can be easily engineered into 2D and 3D homo- and hetero-nuclear NOESY pulse sequences to boost their sensitivity.
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Affiliation(s)
- V S Manu
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 6-155 Jackson Hall, 312 Church St. SE, Minneapolis, MN, 55455, USA
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 6-155 Jackson Hall, 312 Church St. SE, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 6-155 Jackson Hall, 312 Church St. SE, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, 139 Smith Hall, Pleasant St. SE, Minneapolis, MN, 55455, USA.
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2
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Haller JD, Bodor A, Luy B. Pure shift amide detection in conventional and TROSY-type experiments of 13C, 15N-labeled proteins. JOURNAL OF BIOMOLECULAR NMR 2022; 76:213-221. [PMID: 36399207 PMCID: PMC9712348 DOI: 10.1007/s10858-022-00406-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Large coupling networks in uniformly 13C,15N-labeled biomolecules induce broad multiplets that even in flexible proteins are frequently not recognized as such. The reason is that given multiplets typically consist of a large number of individual resonances that result in a single broad line, in which individual components are no longer resolved. We here introduce a real-time pure shift acquisition scheme for the detection of amide protons which is based on 13C-BIRDr,X. As a result the full homo- and heteronuclear coupling network can be suppressed at low power leading to real singlets at substantially improved resolution and uncompromised sensitivity. The method is tested on a small globular and an intrinsically disordered protein (IDP) where the average spectral resolution is increased by a factor of ~ 2 and higher. Equally important, the approach works without saturation of water magnetization for solvent suppression and exchanging amide protons are not affected by saturation transfer.
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Affiliation(s)
- Jens D. Haller
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Hermann-Von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrea Bodor
- Institute of Chemistry, Analytical and BioNMR Laboratory, ELTE –Eötvös Loránd University, Pázmány Péter Sétány 1/A, 1117 Budapest, Hungary
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Hermann-Von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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3
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Kim J, Novakovic M, Jayanthi S, Lupulescu A, Kupče Ē, Grün JT, Mertinkus K, Oxenfarth A, Schwalbe H, Frydman L. The Extended Hadamard Transform: Sensitivity-Enhanced NMR Experiments Among Labile and Non-Labile 1 Hs of SARS-CoV-2-derived RNAs. Chemphyschem 2022; 23:e202100704. [PMID: 34968005 PMCID: PMC9015374 DOI: 10.1002/cphc.202100704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/29/2021] [Indexed: 11/09/2022]
Abstract
Hadamard encoded saturation transfer can significantly improve the efficiency of NOE-based NMR correlations from labile protons in proteins, glycans and RNAs, increasing the sensitivity of cross-peaks by an order of magnitude and shortening experimental times by ≥100-fold. These schemes, however, fail when tackling correlations within a pool of labile protons - for instance imino-imino correlations in RNAs or amide-amide correlations in proteins. Here we analyze the origin of the artifacts appearing in these experiments and propose a way to obtain artifact-free correlations both within the labile pool as well as between labile and non-labile 1 Hs, while still enjoying the gains arising from Hadamard encoding and solvent repolarizations. The principles required for implementing what we define as the extended Hadamard scheme are derived, and its clean, artifact-free, sensitivity-enhancing performance is demonstrated on RNA fragments derived from the SARS-CoV-2 genome. Sensitivity gains per unit time approaching an order of magnitude are then achieved in both imino-imino and imino-amino/aromatic protons 2D correlations; similar artifact-free sensitivity gains can be observed when carrying out extended Hadamard encodings of 3D NOESY/HSQC-type experiments. The resulting spectra reveal significantly more correlations than their conventionally acquired counterparts, which can support the spectral assignment and secondary structure determination of structured RNA elements.
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Affiliation(s)
- Jihyun Kim
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Sundaresan Jayanthi
- Department of Physics, Indian Institute of Space Science and Technology, Valiamala, 695 547, Thiruvananthapuram, Kerala, India
| | - Adonis Lupulescu
- "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, 30 Reactorului Street, 077125, Bucharest-Măgurele, Romania
| | - Ēriks Kupče
- Bruker UK, Banner Lane, Coventry, CV4 9GH, UK
| | - J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Klara Mertinkus
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, FrankfurtFrankfurt/Main, Germany
| | - Andreas Oxenfarth
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, FrankfurtFrankfurt/Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, FrankfurtFrankfurt/Main, Germany
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
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4
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Schmidt AB, Bowers CR, Buckenmaier K, Chekmenev EY, de Maissin H, Eills J, Ellermann F, Glöggler S, Gordon JW, Knecht S, Koptyug IV, Kuhn J, Pravdivtsev AN, Reineri F, Theis T, Them K, Hövener JB. Instrumentation for Hydrogenative Parahydrogen-Based Hyperpolarization Techniques. Anal Chem 2022; 94:479-502. [PMID: 34974698 PMCID: PMC8784962 DOI: 10.1021/acs.analchem.1c04863] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Andreas B. Schmidt
- Department of Radiology – Medical Physics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Killianstr. 5a, Freiburg 79106, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - C. Russell Bowers
- Department of Chemistry, University of Florida, 2001 Museum Road, Gainesville, Florida 32611, USA
- National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, Florida 32310, USA
| | - Kai Buckenmaier
- High-Field Magnetic Resonance Center, Max Planck Institute for Biological Cybernetics, Max-Planck-Ring 11, 72076, Tübingen, Germany
| | - Eduard Y. Chekmenev
- Intergrative Biosciences (Ibio), Department of Chemistry, Karmanos Cancer Institute (KCI), Wayne State University, 5101 Cass Ave, Detroit, MI 48202, United States
- Russian Academy of Sciences (RAS), Leninskiy Prospect, 14, 119991 Moscow, Russia
| | - Henri de Maissin
- Department of Radiology – Medical Physics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Killianstr. 5a, Freiburg 79106, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - James Eills
- Institute for Physics, Johannes Gutenberg University, D-55090 Mainz, Germany
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Helmholtz-Institut Mainz, 55128 Mainz, Germany
| | - Frowin Ellermann
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 14, 24118, Kiel, Germany
| | - Stefan Glöggler
- NMR Signal Enhancement Group Max Planck Institutefor Biophysical Chemistry Am Fassberg 11, 37077 Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration of UMG Von-Siebold-Str. 3A, 37075 Göttingen, Germany
| | - Jeremy W. Gordon
- Department of Radiology & Biomedical Imaging, University of California San Francisco, 185 Berry St., San Francisco, CA, 94158, USA
| | | | - Igor V. Koptyug
- International Tomography Center, SB RAS, 3A Institutskaya St., Novosibirsk 630090, Russia
| | - Jule Kuhn
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 14, 24118, Kiel, Germany
| | - Andrey N. Pravdivtsev
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 14, 24118, Kiel, Germany
| | - Francesca Reineri
- Dept. Molecular Biotechnology and Health Sciences, Via Nizza 52, University of Torino, Italy
| | - Thomas Theis
- Departments of Chemistry, Physics and Biomedical Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Kolja Them
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 14, 24118, Kiel, Germany
| | - Jan-Bernd Hövener
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 14, 24118, Kiel, Germany
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5
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Novakovic M, Battistel MD, Azurmendi HF, Concilio MG, Freedberg DI, Frydman L. The Incorporation of Labile Protons into Multidimensional NMR Analyses: Glycan Structures Revisited. J Am Chem Soc 2021; 143:8935-8948. [PMID: 34085814 PMCID: PMC8297728 DOI: 10.1021/jacs.1c04512] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Glycan structures
are often stabilized by a repertoire of hydrogen-bonded
donor/acceptor groups, revealing longer-lived structures that could
represent biologically relevant conformations. NMR provides unique
data on these hydrogen-bonded networks from multidimensional experiments
detecting cross-peaks resulting from through-bond (TOCSY) or through-space
(NOESY) interactions. However, fast OH/H2O exchange, and
the spectral proximity among these NMR resonances, hamper the use
of glycans’ labile protons in such analyses; consequently,
studies are often restricted to aprotic solvents or supercooled aqueous
solutions. These nonphysiological conditions may lead to unrepresentative
structures or to probing a small subset of accessible conformations
that may miss “active” glycan conformations. Looped,
projected spectroscopy (L-PROSY) has been recently shown to substantially
enhance protein NOESY and TOCSY cross-peaks, for 1Hs that
undergo fast exchange with water. This study shows that even larger
enhancements can be obtained for rapidly exchanging OHs in saccharides,
leading to the retrieval of previously undetectable 2D TOCSY/NOESY
cross-peaks with nonlabile protons. After demonstrating ≥300%
signal enhancements on model monosaccharides, these experiments were
applied at 1 GHz to elucidate the structural network adopted by a
sialic acid homotetramer, used as a model for α,2–8 linked
polysaccharides. High-field L-PROSY NMR enabled these studies at higher
temperatures and provided insight previously unavailable from lower-field
NMR investigations on supercooled samples, involving mostly nonlabile
nuclei. Using L-PROSY’s NOEs and other restraints, a revised
structural model for the homotetramer was obtained combining rigid
motifs and flexible segments, that is well represented by conformations
derived from 40 μs molecular dynamics simulations.
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Affiliation(s)
- Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Maria-Grazia Concilio
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
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6
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Sensitivity enhancement of homonuclear multidimensional NMR correlations for labile sites in proteins, polysaccharides, and nucleic acids. Nat Commun 2020; 11:5317. [PMID: 33087707 PMCID: PMC7577996 DOI: 10.1038/s41467-020-19108-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/17/2020] [Indexed: 12/02/2022] Open
Abstract
Multidimensional TOCSY and NOESY are central experiments in chemical and biophysical NMR. Limited efficiencies are an intrinsic downside of these methods, particularly when targeting labile sites. This study demonstrates that the decoherence imparted on these protons through solvent exchanges can, when suitably manipulated, lead to dramatic sensitivity gains per unit time in the acquisition of these experiments. To achieve this, a priori selected frequencies are encoded according to Hadamard recipes, while concurrently subject to looped selective inversion or selective saturation procedures. Suitable processing then leads to protein, oligosaccharide and nucleic acid cross-peak enhancements of ≈200–1000% per scan, in measurements that are ≈10-fold faster than conventional counterparts. The extent of these gains will depend on the solvent exchange and relaxation rates of the targeted sites; these gains also benefit considerably from the spectral resolution provided by ultrahigh fields, as corroborated by NMR experiments at 600 MHz and 1 GHz. The mechanisms underlying these experiments’ enhanced efficiencies are analyzed on the basis of three-way polarization transfer interplays between the water, labile and non-labile protons, and the experimental results are rationalized using both analytical and numerical derivations. Limitations as well as further extensions of the proposed methods, are also discussed. Here, the authors present an approach that enhances the sensitivity of basic 2D biomolecular NMR experiments like NOESY and TOCSY, when carried out in polysaccharides, proteins and nucleic acids. This method combines principles associated to quantum Anti-Zeno Effects and advanced data acquisition methods based on Hadamard multiplexing.
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7
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Novakovic M, Cousin SF, Jaroszewicz MJ, Rosenzweig R, Frydman L. Looped-PROjected SpectroscopY (L-PROSY): A simple approach to enhance backbone/sidechain cross-peaks in 1H NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 294:169-180. [PMID: 30064051 DOI: 10.1016/j.jmr.2018.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 05/08/2023]
Abstract
Cross-relaxation and isotropic mixing phenomena leading to the Nuclear Overhauser Effect (NOE) and to the TOCSY experiment, lie at the center of structural determinations by NMR. 2D TOCSY and NOESY exploit these polarization transfer effects to determine inter-site connectivities and molecular geometries under physiologically-relevant conditions. Among these sequences' drawback, particularly for the case of NOEs, are a lack of sensitivity arising from small structurally-relevant cross peaks. The present study explores the application of multiple Zeno-like projective measurements, to enhance the cross-peaks between spectrally distinct groups in proteins -in particular between amide and aliphatic protons. The enhancement is based on repeating the projection done by Ramsey or TOCSY blocks multiple times, in what we refer to as Looped, PROjected Spectroscopy (L-PROSY). This leads to a reset of the amide/aliphatic transfer processes; the initial slopes of the NOE- or J-transfer effects thus define the cross-peak growth, and a faster cross-peak buildup is achieved upon looping these transfers over the allotted time T1. These projections also help to better preserve the magnetization originating in the amides, resulting in an overall improvement in sensitivity. L-PROSY's usefulness is demonstrated by incorporating it into two widely used protein NMR experiments: 2D 15N-1H HMQC-NOESY and 15N-filtered 2D NOESY. Different parameters dictating the overall SNR improvement, particularly the protein correlation times and the amide-water chemical exchange rates, were examined, and L-PROSY's enhancements resulted for all tested proteins. The largest cross-peak enhancements were observed for unstructured proteins, where chemical exchanges with the solvent of the kind that tend to average out NOE cross-peaks in conventional NMR, boost L-PROSY's cross-peaks by replenishing the amide's magnetizations within each loop. Enhanced cross-peaks were also found in extensions involving TOCSY-based experiments when applied to proteins with unfolded segments.
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Affiliation(s)
- Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Samuel F Cousin
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michael J Jaroszewicz
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rina Rosenzweig
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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8
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Boros S, Gáspári Z, Batta G. Accurate NMR Determinations of Proton–Proton Distances. ANNUAL REPORTS ON NMR SPECTROSCOPY 2018:1-39. [DOI: 10.1016/bs.arnmr.2017.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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9
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Lehner F, Kudlinzki D, Richter C, Müller-Werkmeister HM, Eberl KB, Bredenbeck J, Schwalbe H, Silvers R. Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding. Chembiochem 2017; 18:2340-2350. [DOI: 10.1002/cbic.201700437] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Florian Lehner
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Denis Kudlinzki
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium; DKTK; German Cancer Research Center; DKFZ; Im Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Christian Richter
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | | | - Katharina B. Eberl
- Institute for Biophysics; Goethe University Frankfurt; Max-von-Laue-Strasse 1 60438 Frankfurt am Main Germany
| | - Jens Bredenbeck
- Institute for Biophysics; Goethe University Frankfurt; Max-von-Laue-Strasse 1 60438 Frankfurt am Main Germany
| | - Harald Schwalbe
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Robert Silvers
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- Present address: Francis Bitter Magnet Laboratory; Massachusetts Institute of Technology; Cambridge MA 02139 USA
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10
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Kew W, Bell NG, Goodall I, Uhrín D. Advanced solvent signal suppression for the acquisition of 1D and 2D NMR spectra of Scotch Whisky. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:785-796. [PMID: 28558164 PMCID: PMC5599976 DOI: 10.1002/mrc.4621] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
A simple and robust solvent suppression technique that enables acquisition of high-quality 1D 1 H nuclear magnetic resonance (NMR) spectra of alcoholic beverages on cryoprobe instruments was developed and applied to acquire NMR spectra of Scotch Whisky. The method uses 3 channels to suppress signals of water and ethanol, including those of 13 C satellites of ethanol. It is executed in automation allowing high throughput investigations of alcoholic beverages. On the basis of the well-established 1D nuclear Overhauser spectroscopy (NOESY) solvent suppression technique, this method suppresses the solvent at the beginning of the pulse sequence, producing pure phase signals minimally affected by the relaxation. The developed solvent suppression procedure was integrated into several homocorrelated and heterocorrelated 2D NMR experiments, including 2D correlation spectroscopy (COSY), 2D total correlation spectroscopy (TOCSY), 2D band-selective TOCSY, 2D J-resolved spectroscopy, 2D 1 H, 13 C heteronuclear single-quantum correlation spectroscopy (HSQC), 2D 1 H, 13 C HSQC-TOCSY, and 2D 1 H, 13 C heteronuclear multiple-bond correlation spectroscopy (HMBC). A 1D chemical-shift-selective TOCSY experiments was also modified. The wealth of information obtained by these experiments will assist in NMR structure elucidation of Scotch Whisky congeners and generally the composition of alcoholic beverages at the molecular level.
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Affiliation(s)
- Will Kew
- EastCHEM School of ChemistryUniversity of EdinburghKing's Buildings, David Brewster RoadEdinburghEH9 3FJUK
| | - Nicholle G.A. Bell
- EastCHEM School of ChemistryUniversity of EdinburghKing's Buildings, David Brewster RoadEdinburghEH9 3FJUK
| | - Ian Goodall
- The Scotch Whisky Research InstituteThe Robertson Trust Building, Research Avenue North, RiccartonEdinburghEH14 4APUK
| | - Dušan Uhrín
- EastCHEM School of ChemistryUniversity of EdinburghKing's Buildings, David Brewster RoadEdinburghEH9 3FJUK
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11
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Wirmer-Bartoschek J, Bendel LE, Jonker HRA, Grün JT, Papi F, Bazzicalupi C, Messori L, Gratteri P, Schwalbe H. Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding. Angew Chem Int Ed Engl 2017; 56:7102-7106. [DOI: 10.1002/anie.201702135] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 03/31/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Lars Erik Bendel
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Francesco Papi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Carla Bazzicalupi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Luigi Messori
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Paola Gratteri
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco; Salute del Bambino (NEUROFARBA); Università degli Studi di Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
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12
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Huang Y, Russu IM. Dynamic and Energetic Signatures of Adenine Tracts in a rA-dT RNA-DNA Hybrid and in Homologous RNA-DNA, RNA-RNA, and DNA-DNA Double Helices. Biochemistry 2017; 56:2446-2454. [PMID: 28430414 DOI: 10.1021/acs.biochem.6b01122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance spectroscopy and proton exchange are being used to characterize the opening reactions of individual base pairs in the RNA-DNA hybrid 5'-rGCGAUAAAAAGGCC-3'/5'-dGGCCTTTTTATCGC-3'. The hybrid contains a central tract of five rA-dT base pairs. The rates and the equilibrium constant of the opening reaction for each base pair are determined from the dependence of the exchange rates of imino protons on ammonia concentration, at 10 °C. The results are compared to those previously obtained by our laboratory for three homologous duplexes of the same base sequence (except for the appropriate T/U substitution), containing tracts of dA-rU, rA-rU, or dA-dT base pairs. The rA-dT tract is distinguished by an enhanced propensity of the base pairs to exist in the extrahelical state. The opening rates of rA-dT base pairs also exhibit a strong dependence on the location of the base pair in the structure; namely, as one advances into the tract, the opening rates of rA-dT base pairs gradually decrease. The local stability of each rA-dT base pair within the tract is the same as that of the corresponding rA-rU base pair in the homologous RNA-only duplex but differs from the stabilities of dA-dT and dA-rU base pairs in the other two duplexes (namely, dA-dT > rA-dT > dA-rU). These results demonstrate that, in nucleic acid double helices with the same base sequence, the opening dynamics and the energetics of individual base pairs are strongly influenced by the nature of the strand and by the structural context of the base pair.
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Affiliation(s)
- Yuegao Huang
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Irina M Russu
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University , Middletown, Connecticut 06459, United States
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13
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Wirmer-Bartoschek J, Bendel LE, Jonker HRA, Grün JT, Papi F, Bazzicalupi C, Messori L, Gratteri P, Schwalbe H. Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702135] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Lars Erik Bendel
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Francesco Papi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Carla Bazzicalupi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Luigi Messori
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Paola Gratteri
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco; Salute del Bambino (NEUROFARBA); Università degli Studi di Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
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14
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Izgu E, Fahrenbach A, Zhang N, Li L, Zhang W, Larsen AT, Blain JC, Szostak JW. Uncovering the thermodynamics of monomer binding for RNA replication. J Am Chem Soc 2015; 137:6373-82. [PMID: 25901790 PMCID: PMC4984997 DOI: 10.1021/jacs.5b02707] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Indexed: 01/07/2023]
Abstract
The nonenzymatic replication of primordial RNA is thought to have been a critical step in the origin of life. However, despite decades of effort, the poor rate and fidelity of model template copying reactions have thus far prevented an experimental demonstration of nonenzymatic RNA replication. The overall rate and fidelity of template copying depend, in part, on the affinity of free ribonucleotides to the RNA primer-template complex. We have now used (1)H NMR spectroscopy to directly measure the thermodynamic association constants, Kas, of the standard ribonucleotide monophosphates (rNMPs) to native RNA primer-template complexes. The binding affinities of rNMPs to duplexes with a complementary single-nucleotide overhang follow the order C > G > A > U. Notably, these monomers bind more strongly to RNA primer-template complexes than to the analogous DNA complexes. The relative binding affinities of the rNMPs for complementary RNA primer-template complexes are in good quantitative agreement with the predictions of a nearest-neighbor analysis. With respect to G:U wobble base-pairing, we find that the binding of rGMP to a primer-template complex with a 5'-U overhang is approximately 10-fold weaker than to the complementary 5'-C overhang. We also find that the binding of rGMP is only about 2-fold weaker than the binding of rAMP to 5'-U, consistent with the poor fidelity observed in the nonenzymatic copying of U residues in RNA templates. The accurate Ka measurements for ribonucleotides obtained in this study will be useful for designing higher fidelity, more effective RNA replication systems.
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Affiliation(s)
- Enver
Cagri Izgu
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Albert
C. Fahrenbach
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Earth-Life
Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Na Zhang
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Li Li
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Wen Zhang
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Aaron T. Larsen
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - J. Craig Blain
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Earth-Life
Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
St., Cambridge, Massachusetts 02138, United States
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15
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Školáková P, Foldynová-Trantírková S, Bednářová K, Fiala R, Vorlíčková M, Trantírek L. Unique C. elegans telomeric overhang structures reveal the evolutionarily conserved properties of telomeric DNA. Nucleic Acids Res 2015; 43:4733-45. [PMID: 25855805 PMCID: PMC4482068 DOI: 10.1093/nar/gkv296] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 03/25/2015] [Indexed: 11/16/2022] Open
Abstract
There are two basic mechanisms that are associated with the maintenance of the telomere length, which endows cancer cells with unlimited proliferative potential. One mechanism, referred to as alternative lengthening of telomeres (ALT), accounts for approximately 10–15% of all human cancers. Tumours engaged in the ALT pathway are characterised by the presence of the single stranded 5′-C-rich telomeric overhang (C-overhang). This recently identified hallmark of ALT cancers distinguishes them from healthy tissues and renders the C-overhang as a clear target for anticancer therapy. We analysed structures of the 5′-C-rich and 3′-G-rich telomeric overhangs from human and Caenorhabditis elegans, the recently established multicellular in vivo model of ALT tumours. We show that the telomeric DNA from C. elegans and humans forms fundamentally different secondary structures. The unique structural characteristics of C. elegans telomeric DNA that are distinct not only from those of humans but also from those of other multicellular eukaryotes allowed us to identify evolutionarily conserved properties of telomeric DNA. Differences in structural organisation of the telomeric DNA between the C. elegans and human impose limitations on the use of the C. elegans as an ALT tumour model.
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Affiliation(s)
- Petra Školáková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic
| | - Silvie Foldynová-Trantírková
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic Institute of Parasitology, Academy of Sciences of the Czech Republic, Branisovska, 31, 375 05 Ceske Budejovice, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
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16
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Usachev KS, Efimov SV, Kolosova OA, Filippov AV, Klochkov VV. High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles. JOURNAL OF BIOMOLECULAR NMR 2015; 61:227-34. [PMID: 25430060 DOI: 10.1007/s10858-014-9885-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/20/2014] [Indexed: 05/22/2023]
Abstract
PG-1 adopts a dimeric structure in dodecylphosphocholine (DPC) micelles, and a channel is formed by the association of several dimers but the molecular mechanisms of the membrane damage by non-α-helical peptides are still unknown. The formation of the PG-1 dimer is important for pore formation in the lipid bilayer, since the dimer can be regarded as the primary unit for assembly into the ordered aggregates. It was supposed that only 12 residues (RGGRL-CYCRR-RFCVC-V) are needed to endow protegrin molecules with strong antibacterial activity and that at least four additional residues are needed to add potent antifungal properties. Thus, the 16-residue protegrin (PG-2) represents the minimal structure needed for broad-spectrum antimicrobial activity encompassing bacteria and fungi. As the peptide conformation and peptide-to-membrane binding properties are very sensitive to single amino acid substitutions, the solution structure of PG-2 in solution and in a membrane mimicking environment are crucial. In order to find evidence if the oligomerization state of PG-1 in a lipid environment will be the same or not for another protegrins, we investigate in the present work the PG-2 NMR solution structure in the presence of perdeuterated DPC micelles. The NMR study reported in the present work indicates that PG-2 form a well-defined structure (PDB: 2MUH) composed of a two-stranded antiparallel β-sheet when it binds to DPC micelles.
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Affiliation(s)
- K S Usachev
- Kazan Federal University, Kremlevskaya, 18, Kazan, 420008, Russian Federation,
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17
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Kellish PC, Kumar S, Mack TS, Spano MN, Hennig M, Arya DP. Multivalent Amino Sugars to Recognize Different TAR RNA Conformations. MEDCHEMCOMM 2014; 5:1235-1246. [PMID: 27076899 PMCID: PMC4828046 DOI: 10.1039/c4md00165f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neomycin dimers synthesized using "click chemistry" with varying functionality and length in the linker region have been shown to be effective in targeting the HIV-1 TAR RNA region of the HIV virus. TAR (Transactivation Response) RNA region, a 59 base pair stem loop structure located at the 5'-end of all nascent viral transcripts interacts with its target, a key regulatory protein, Tat, and necessitates the replication of HIV-1 virus. Ethidium bromide displacement and FRET competition assays have revealed nanomolar binding affinity between neomycin dimers and wildtype TAR RNA while in case of neomycin, only a weak binding was detected. Here, NMR and FID-based comparisons reveal an extended binding interface for neomycin dimers involving the upper stem of the TAR RNA thereby offering an explanation for increased affinities. To further explore the potential of these modified aminosugars we have extended binding studies to include four TAR RNA mutants that display conformational differences with minimal sequence variation. The differences in binding between neomycin and neomycin dimers is characterized with TAR RNA mutants that include mutations to the bulge region, hairpin region, and both the bulge and hairpin regions. Our results demonstrate the effect of these mutations on neomycin binding and our results show that linker functionalities between dimeric units of neomycin can distinguish between the conformational differences of mutant TAR RNA structures.
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Affiliation(s)
- Patrick C. Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Todd S. Mack
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | | | - Mirko Hennig
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
- NUBAD, LLC, 900B West Faris Rd., Greenville, SC 29605
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18
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Zhang J, Russu IM. Site-Resolved Structural Energetics of the T7 Concatemer Junction. Biochemistry 2014; 53:4806-13. [DOI: 10.1021/bi500393q] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jie Zhang
- Department of Chemistry and
Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Irina M. Russu
- Department of Chemistry and
Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
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19
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Zweytick D, Japelj B, Mileykovskaya E, Zorko M, Dowhan W, Blondelle SE, Riedl S, Jerala R, Lohner K. N-acylated peptides derived from human lactoferricin perturb organization of cardiolipin and phosphatidylethanolamine in cell membranes and induce defects in Escherichia coli cell division. PLoS One 2014; 9:e90228. [PMID: 24595074 PMCID: PMC3940911 DOI: 10.1371/journal.pone.0090228] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 01/31/2014] [Indexed: 11/18/2022] Open
Abstract
Two types of recently described antibacterial peptides derived from human lactoferricin, either nonacylated or N-acylated, were studied for their different interaction with membranes of Escherichia coli in vivo and in model systems. Electron microscopy revealed striking effects on the bacterial membrane as both peptide types induced formation of large membrane blebs. Electron and fluorescence microscopy, however demonstrated that only the N-acylated peptides partially induced the generation of oversized cells, which might reflect defects in cell-division. Further a different distribution of cardiolipin domains on the E. coli membrane was shown only in the presence of the N-acylated peptides. The lipid was distributed over the whole bacterial cell surface, whereas cardiolipin in untreated and nonacylated peptide-treated cells was mainly located at the septum and poles. Studies with bacterial membrane mimics, such as cardiolipin or phosphatidylethanolamine revealed that both types of peptides interacted with the negatively charged lipid cardiolipin. The nonacylated peptides however induced segregation of cardiolipin into peptide-enriched and peptide-poor lipid domains, while the N-acylated peptides promoted formation of many small heterogeneous domains. Only N-acylated peptides caused additional severe effects on the main phase transition of liposomes composed of pure phosphatidylethanolamine, while both peptide types inhibited the lamellar to hexagonal phase transition. Lipid mixtures of phosphatidylethanolamine and cardiolipin revealed anionic clustering by all peptide types. However additional strong perturbation of the neutral lipids was only seen with the N-acylated peptides. Nuclear magnetic resonance demonstrated different conformational arrangement of the N-acylated peptide in anionic and zwitterionic micelles revealing possible mechanistic differences in their action on different membrane lipids. We hypothesized that both peptides kill bacteria by interacting with bacterial membrane lipids but only N-acylated peptides interact with both charged cardiolipin and zwitterionic phosphatidylethanolamine resulting in remodeling of the natural phospholipid domains in the E. coli membrane that leads to defects in cell division.
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Affiliation(s)
- Dagmar Zweytick
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Graz, Austria
- * E-mail:
| | - Bostjan Japelj
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Eugenia Mileykovskaya
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, Texas, United States of America
| | - Mateja Zorko
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, Texas, United States of America
| | - Sylvie E. Blondelle
- Department of Biochemistry, Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Sabrina Riedl
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Graz, Austria
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Karl Lohner
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Graz, Austria
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20
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Every AE, Russu IM. Opening dynamics of 8-oxoguanine in DNA. J Mol Recognit 2013; 26:175-80. [PMID: 23456741 DOI: 10.1002/jmr.2262] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/18/2012] [Accepted: 12/22/2012] [Indexed: 12/15/2022]
Abstract
8-oxoguanine is a major lesion of genomic DNA that results from oxidation of guanine by reactive oxygen species. The repair of this lesion is initiated by 8-oxoguanine glycosylases, which excise the damaged base by "flipping" it outside the DNA double helix. The molecular mechanisms involved in the specific recognition of the damaged base by the enzyme are not yet fully understood. Several models have proposed that, in DNA, the base pair between 8-oxoguanine and cytosine may possess altered dynamic properties that could help the enzyme locate the lesion and could favor the selective extra-helical flipping of the damaged base. To test this proposal, we have characterized the spontaneous opening of the base pair between 8-oxoguanine and cytosine in a DNA double helix using NMR spectroscopy and proton exchange. The results show that the rate of spontaneous opening of 8-oxoguanine and the lifetime of the base in the extra-helical state are the same as those of a canonical guanine-cytosine base pair, in the same base sequence context. This finding suggests that the opening dynamics of 8-oxoguanine, when paired with cytosine in DNA, does not play a significant role in the recognition of the lesion by glycosylases.
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Affiliation(s)
- Alicia E Every
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
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21
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Roth BM, Ishimaru D, Hennig M. The core microprocessor component DiGeorge syndrome critical region 8 (DGCR8) is a nonspecific RNA-binding protein. J Biol Chem 2013; 288:26785-99. [PMID: 23893406 DOI: 10.1074/jbc.m112.446880] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MicroRNA (miRNA) biogenesis follows a conserved succession of processing steps, beginning with the recognition and liberation of an miRNA-containing precursor miRNA hairpin from a large primary miRNA transcript (pri-miRNA) by the Microprocessor, which consists of the nuclear RNase III Drosha and the double-stranded RNA-binding domain protein DGCR8 (DiGeorge syndrome critical region protein 8). Current models suggest that specific recognition is driven by DGCR8 detection of single-stranded elements of the pri-miRNA stem-loop followed by Drosha recruitment and pri-miRNA cleavage. Because countless RNA transcripts feature single-stranded-dsRNA junctions and DGCR8 can bind hundreds of mRNAs, we explored correlations between RNA binding properties of DGCR8 and specific pri-miRNA substrate processing. We found that DGCR8 bound single-stranded, double-stranded, and random hairpin transcripts with similar affinity. Further investigation of DGCR8/pri-mir-16 interactions by NMR detected intermediate exchange regimes over a wide range of stoichiometric ratios. Diffusion analysis of DGCR8/pri-mir-16 interactions by pulsed field gradient NMR lent further support to dynamic complex formation involving free components in exchange with complexes of varying stoichiometry, although in vitro processing assays showed exclusive cleavage of pri-mir-16 variants bearing single-stranded flanking regions. Our results indicate that DGCR8 binds RNA nonspecifically. Therefore, a sequential model of DGCR8 recognition followed by Drosha recruitment is unlikely. Known RNA substrate requirements are broad and include 70-nucleotide hairpins with unpaired flanking regions. Thus, specific RNA processing is likely facilitated by preformed DGCR8-Drosha heterodimers that can discriminate between authentic substrates and other hairpins.
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Affiliation(s)
- Braden M Roth
- From the Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
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22
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Sun P, Jiang X, Jiang B, Zhang X, Liu M. Biomolecular ligands screening using radiation damping difference WaterLOGSY spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2013; 56:285-290. [PMID: 23740293 DOI: 10.1007/s10858-013-9748-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
Water-ligand observed via gradient spectroscopy (WaterLOGSY) is a widely used nuclear magnetic resonance method for ligand screening. The crucial procedure for the effectiveness of WaterLOGSY is selective excitation of the water resonance. The selective excitation is conventionally achieved by using long selective pulse, which causes partial saturation of the water magnetization leading to reduction of sensitivity, in addition to time consuming and error prone. Therefore, many improvements have been made to enhance the sensitivity and robustness of the method. Here we propose an alternative selective excitation scheme for WaterLOGSY by utilizing radiation damping effect. The pulse scheme starts simply with a hard inversion pulse, instead of selective pulse or pulse train, followed by a pulse field gradient to control the radiation damping effect. The rest parts of the pulse scheme are similar to conventional WaterLOGSY. When the gradient pulse is applied immediately after the inversion pulse, the radiation damping effect is suppressed, and all of the magnetization is inversed. When the gradient pulse and the inversion pulse are about 10-20 ms apart, the radiation damping effect remains active and drives the water magnetization toward +z-axis, resulting in selective non-inversion of the water magnetization. By taking the differences of the spectra obtained under these two conditions, one should get the result of WaterLOGSY. The method is demonstrated to be simple, robust and sensitive for ligand screening.
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Affiliation(s)
- Peng Sun
- Wuhan Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
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23
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Krishnan VV, Murali N. Radiation damping in modern NMR experiments: progress and challenges. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 68:41-57. [PMID: 23398972 PMCID: PMC3644564 DOI: 10.1016/j.pnmrs.2012.06.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 06/07/2012] [Indexed: 05/12/2023]
Affiliation(s)
- V V Krishnan
- Department of Chemistry, California State University, Fresno, CA 93740, USA.
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24
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Ishimaru D, Plant EP, Sims AC, Yount BL, Roth BM, Eldho NV, Pérez-Alvarado GC, Armbruster DW, Baric RS, Dinman JD, Taylor DR, Hennig M. RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus. Nucleic Acids Res 2012; 41:2594-608. [PMID: 23275571 PMCID: PMC3575852 DOI: 10.1093/nar/gks1361] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis.
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Affiliation(s)
- Daniella Ishimaru
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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Shishmarev D, Otting G. Radiation damping on cryoprobes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 213:76-81. [PMID: 21955524 DOI: 10.1016/j.jmr.2011.08.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/01/2011] [Accepted: 08/30/2011] [Indexed: 05/31/2023]
Abstract
Radiation damping on 600 and 800 MHz cryoprobes was investigated. The phase angle β between a vector 90° phase shifted to the precessing magnetization and the rf field induced in the coil was found to depend markedly on whether an FID was being acquired or not. The magnitude of the radiation damping field was sufficiently strong to restore 95% of the equilibrium water magnetization of a 90% H2O sample in a 5 mm sample tube within about 5 ms following a 165° pulse. This can be exploited in water flip-back versions of NOESY and TOCSY experiments of proteins, but care must be taken to limit the effect of the radiation damping field from the water on the Ha protons. Long water-selective pulses can be applied only following corrections. We developed a program for correcting pulse shapes if β is non-zero. The WATERGATE scheme is shown to be insensitive to imperfections introduced by radiation damping.
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Affiliation(s)
- Dmitry Shishmarev
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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26
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Ball KA, Phillips AH, Nerenberg PS, Fawzi NL, Wemmer DE, Head-Gordon T. Homogeneous and heterogeneous tertiary structure ensembles of amyloid-β peptides. Biochemistry 2011; 50:7612-28. [PMID: 21797254 DOI: 10.1021/bi200732x] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interplay of modern molecular simulation and high-quality nuclear magnetic resonance (NMR) experiments has reached a fruitful stage for quantitative characterization of structural ensembles of disordered peptides. Amyloid-β 1-42 (Aβ42), the primary peptide associated with Alzheimer's disease, and fragments such as Aβ21-30 are both classified as intrinsically disordered peptides (IDPs). We use a variety of NMR observables to validate de novo molecular dynamics simulations in explicit water to characterize the tertiary structure ensemble of Aβ42 and Aβ21-30 from the perspective of their classification as IDPs. Unlike the Aβ21-30 fragment that conforms to expectations of an IDP that is primarily extended, we find that Aβ42 samples conformations reflecting all possible secondary structure categories and spans the range of IDP classifications from collapsed structured states to highly extended conformations, making it an IDP with a far more heterogeneous tertiary ensemble.
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Affiliation(s)
- K Aurelia Ball
- Graduate Group in Biophysics, University of California, Berkeley, California 94720, United States
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27
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Huang Y, Weng X, Russu IM. Enhanced base-pair opening in the adenine tract of a RNA double helix. Biochemistry 2011; 50:1857-63. [PMID: 21250663 DOI: 10.1021/bi1014997] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Proton exchange and nuclear magnetic resonance spectroscopy are being used to characterize the kinetics and energetics of base-pair opening in two nucleic acid double helices. One is the RNA duplex 5'-r(GCGAUAAAAAGGCC)-3'/5'-r(GGCCUUUUUAUCGC)-3', which contains a central tract of five AU base pairs. The other is the homologous DNA duplex with a central tract of five AT base pairs. The rates and the equilibrium constants of the opening reaction of each base pair are measured from the dependence of the exchange rates of imino protons on ammonia concentration, at 10 °C. The results reveal that the tract of AU base pairs in the RNA duplex differs from the homologous tract of AT base pairs in DNA in several ways. The rates of opening of AU base pairs in RNA are high and increase progressively along the tract, reaching their largest values at the 3'-end of the tract. In contrast, the opening rates of AT base pairs in DNA are much lower than those of AU base pairs. Within the tract, the largest opening rate is observed for the AT base pair at the 5'-end of the tract. These differences in opening kinetics are paralleled by differences in the stabilities of individual base pairs. All AU base pairs in the RNA are less stable than the AT base pairs in the DNA. The presence of the tract enhances these differences by increasing the stability of AT base pairs in DNA while decreasing the stability of AU base pairs in RNA. Due to these divergent trends, along the tracts, the AU base pairs become progressively less stable than AT base pairs. These findings demonstrate that tracts of AU base pairs in RNA have specific dynamic and energetic signatures that distinguish them from similar tracts of AT base pairs in DNA.
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Affiliation(s)
- Yuegao Huang
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
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28
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Walrant A, Correia I, Jiao CY, Lequin O, Bent EH, Goasdoué N, Lacombe C, Chassaing G, Sagan S, Alves ID. Different membrane behaviour and cellular uptake of three basic arginine-rich peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:382-93. [DOI: 10.1016/j.bbamem.2010.09.009] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 11/30/2022]
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29
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Huang Y, Weng X, Russu IM. Structural energetics of the adenine tract from an intrinsic transcription terminator. J Mol Biol 2010; 397:677-88. [PMID: 20132823 DOI: 10.1016/j.jmb.2010.01.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/25/2010] [Accepted: 01/27/2010] [Indexed: 11/26/2022]
Abstract
Intrinsic transcription termination sites generally contain a tract of adenines in the DNA template that yields a tract of uracils at the 3' end of the nascent RNA. To understand how this base sequence contributes to termination of transcription, we have investigated two nucleic acid structures. The first is the RNA-DNA hybrid that contains the uracil tract 5'-rUUUUUAU-3' from the tR2 intrinsic terminator of bacteriophage lambda. The second is the homologous DNA-DNA duplex that contains the adenine tract 5'-dATAAAAA-3'. This duplex is present at the tR2 site when the DNA is not transcribed. The opening and the stability of each rU-dA/dT-dA base pair in the two structures are characterized by imino proton exchange and nuclear magnetic resonance spectroscopy. The results reveal concerted opening of the central rU-dA base pairs in the RNA-DNA hybrid. Furthermore, the stability profile of the adenine tract in the RNA-DNA hybrid is very different from that of the tract in the template DNA-DNA duplex. In the RNA-DNA hybrid, the stabilities of rU-dA base pairs range from 4.3 to 6.5 kcal/mol (at 10 degrees C). The sites of lowest stability are identified at the central positions of the tract. In the template DNA-DNA duplex, the dT-dA base pairs are more stable than the corresponding rU-dA base pairs in the hybrid by 0.9 to 4.6 kcal/mol and, in contrast to the RNA-DNA hybrid, the central base pairs have the highest stability. These results suggest that the central rU-dA/dT-dA base pairs in the adenine tract make the largest energetic contributions to transcription termination by promoting both the dissociation of the RNA transcript and the closing of the transcription bubble. The results also suggest that the high stability of dT-dA base pairs in the DNA provides a signal for the pausing of RNA polymerase at the termination site.
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Affiliation(s)
- Yuegao Huang
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
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30
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Huang Y, Chen C, Russu IM. Dynamics and stability of individual base pairs in two homologous RNA-DNA hybrids. Biochemistry 2009; 48:3988-97. [PMID: 19296713 DOI: 10.1021/bi900070f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nuclear magnetic resonance spectroscopy and proton exchange have been used to characterize two RNA-DNA hybrids from the tR2 intrinsic transcription terminator site of phage lambda. The hybrids have the same base sequence [5'-GGCGCAGGCC(T/U)(T/U)CC-3'/5'-GGAAGGCC(T/U)GCGCC-3'] but differ from each other by an interchange of DNA and RNA strands. The opening of single base pairs in the two hybrids is characterized by measuring the rates of exchange of imino protons with solvent protons as a function of the concentration of a proton acceptor (ammonia base) at 10 degrees C. The free energy change in the opening reaction provides a measure of the stability of the base pair, while the rates of opening and closing define the base pair dynamics. The results demonstrate that, within the same base sequence context, dA-rU base pairs are less stable than dT-rA base pairs. The differences in stability are enhanced when two dA-rU base pairs are located next to each other in the hybrid structure. For the G-C base pairs, the rates of opening and closing and the stability are affected by the base sequence context and by the nature of the sugar moiety attached to the guanine. The dominant feature of the base sequence is the proximity of the dA-rU base pair, which destabilizes the G-C base pair when the guanine is located on the DNA strand. Two G-C base pairs (namely, those in the fourth and 10th positions) exhibit large differences in their opening and closing rates between the two hybrids, while maintaining the same stability. These results provide the first demonstration that, for RNA-DNA hybrid structures with the same base sequence, the opening dynamics and the stability of individual base pairs are strongly influenced by the chemical nature of each strand.
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Affiliation(s)
- Yuegao Huang
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA
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31
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Galanth C, Abbassi F, Lequin O, Ayala-Sanmartin J, Ladram A, Nicolas P, Amiche M. Mechanism of antibacterial action of dermaseptin B2: interplay between helix-hinge-helix structure and membrane curvature strain. Biochemistry 2009; 48:313-27. [PMID: 19113844 DOI: 10.1021/bi802025a] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dermaseptin B2 (Drs B2) is a 33-residue-long cationic, alpha-helical antimicrobial peptide endowed with membrane-damaging activity against a broad spectrum of microorganisms, including bacteria, yeasts, fungi, and protozoa, but its precise mechanism of action remained ill-defined. A detailed characterization of peptide-membrane interactions of Drs B2 was undertaken in comparison with a C-terminal truncated analogue, [1-23]-Drs B2, that was virtually inactive on bacteria despite retaining the cationic charge of the full-length peptide. Both peptides were tested on living cells using membrane permeabilization assays and on large unilamellar and multilamellar phospholipid vesicles composed of binary lipid mixtures by dye leakage assay, fluorescence spectroscopy, circular dichroism, and differential scanning calorimetry and also on SDS micelles using NMR spectroscopy. The results indicate that Drs B2 induces a strong perturbation of anionic lipid bilayers, resides at the hydrocarbon core-water interface, parallel to the plane of the membrane, and interacts preferentially with the polar head groups and glycerol backbone region of the anionic phospholipids, as well as the region of the lipid acyl chain near the bilayer surface. The interfacial location of Drs B2 induces a positive curvature of the bilayer and clustering of anionic lipids, consistent with a carpet mechanism, that may lead to the formation of mixed peptide-phospholipid toroidal, transient pores and membrane permeation/disruption once a threshold peptide accumulation is reached. In constrast, the truncated [1-23]-Drs B2 analogue interacts at the head group level without penetrating and perturbing the hydrophobic core of the bilayer. NMR study in SDS micelles showed that [1-23]-Drs B2 adopts a well-defined helix encompassing residues 2-20, whereas Drs B2 was previously found to adopt helical structures interrupted around the Val(9)-Gly(10) segment. Thus the antibacterial activity of Drs B2 depends markedly on a threshold number of hydrophobic residues to be present on both extremities of the helix. In a membrane environment with a strong positive curvature strain, Drs B2 can adopt a flexible helix-hinge-helix structure that facilitates the concomitant insertion of the strongly hydrophobic N- and C-termini of the peptide into the acyl core of the membrane.
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Affiliation(s)
- Cécile Galanth
- Peptidome de la Peau des Amphibiens, UPMC Universite Paris 06, CNRS FRE 2852, F-75005 Paris, France.
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Rehm S, Han S, Hassani I, Sokocevic A, Jonker HRA, Engels JW, Schwalbe H. The high resolution NMR structure of parvulustat (Z-2685) from Streptomyces parvulus FH-1641: comparison with tendamistat from Streptomyces tendae 4158. Chembiochem 2009; 10:119-27. [PMID: 19067455 DOI: 10.1002/cbic.200800547] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The protein parvulustat (Z-2685) from Streptomyces parvulus comprises 78 amino acids and functions as a highly efficient alpha-amylase inhibitor. Parvulustat shares 29.6 % overall amino acid sequence identity to the well-known alpha-amylase inhibitor tendamistat. Among the conserved residues are the two disulfide bridges (C9-C25, C43-C70) and the active-site motif (W16, R17, Y18). Here, we report the high-resolution NMR structure of parvulustat based on NOEs, J couplings, chemical shifts and hydrogen-exchange data. In addition, we studied the dynamical properties of parvulustat by heteronuclear relaxation measurements. We compare the structure of parvulustat with the structure of tendamistat in terms of secondary structure elements, charges and hydrophobicity. The overall structural composition is very similar, but there are distinct differences including the active-site region. These structural and dynamical differences indicate that for parvulustat an induced-fit mechanism for binding to alpha-amylase might take place, since the structure of tendamistat does not change upon binding to alpha-amylase.
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Affiliation(s)
- Stephan Rehm
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann-Wolfgang-Goethe University, Max-von-Laue-Strasse 7, Frankfurt am Main, Germany
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33
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Lipay JM, Mihailescu MR. NMR spectroscopy and kinetic studies of the quadruplex forming RNA r(UGGAGGU). MOLECULAR BIOSYSTEMS 2009; 5:1347-55. [DOI: 10.1039/b911555b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Li Y, Gao X, Chen L. GroEL Recognizes an Amphipathic Helix and Binds to the Hydrophobic Side. J Biol Chem 2008; 284:4324-31. [PMID: 19074438 DOI: 10.1074/jbc.m804818200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GroEL is an essential Escherichia coli molecular chaperon that uses ATP to facilitate correct folding of a range of proteins in a cell. Central to the GroEL substrate diversity is how GroEL recognizes the substrates. The interaction between GroEL and substrate has been proposed to be largely hydrophobic because GroEL interacts with proteins in non-native conformations but not in native forms. Analysis of GroEL substrate proteins reveals that one of its main substrates are proteins with alphabeta folding domains, suggesting that GroEL may stabilize the collapsed alphabeta core by binding to hydrophobic surfaces that are usually buried between the alpha and beta elements. In this study, we characterize the interaction between GroEL and a peptide derived from our previous selection via a phage display method. NMR studies map the peptide-binding site to the region containing Helices H and I, which is consistent with evidence that this region comprises the primary substrate-binding site. The peptide is largely unstructured in solution but adopts a helical conformation when bound to the GroEL apical domain with a moderate affinity (K(d) = 17.1 +/- 2.5 microm). The helical conformation aligns residues to form an amphipathic structure, and the hydrophobic side of this amphipathic helix interacts with GroEL as suggested by fluorescence quenching studies. Together with previous structural studies on the GroEL-peptide complexes, our work supports the notion that the amphipathic secondary elements in the substrate proteins may be the structural motif recognized by GroEL.
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Affiliation(s)
- Yali Li
- Interdisciplinary Biochemistry Program and the Departments of Chemistry and Biology, Indiana University, Bloomington, Indiana 47405, USA
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35
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Guichard G, Violette A, Chassaing G, Miclet E. Solution structure determination of oligoureas using methylene spin state selective NMR at 13C natural abundance. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:918-924. [PMID: 18720449 DOI: 10.1002/mrc.2271] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Ability of N,N'-linked oligoureas containing proteinogenic side chains to adopt a stable helix conformation in solution has been described recently. NMR as well as circular dichroism (CD) spectroscopies were employed to gain insight into their specific fold. It is herein proposed to extend the structural information available on these peptidomimetics by an advantageous use of a methylene spin state selective NMR experiment. Homodecoupling provided by the pulse scheme made it possible to readily measure conformation-dependent (3)J(HH) constants that are difficult if not impossible to obtain with standard NMR experiments. Adding those couplings to the NMR restraints improved the quality of the structure calculations significantly, as judged by a ca 30% decrease of the root mean square deviation (RMSD) obtained over an ensemble of 20 structures. Moreover, accurate determination of individual (1)J(CH) couplings within each methylene group revealed uniform values throughout the oligourea sequence, with (1)J(CH) systematically slightly larger for the pro-S hydrogen than for the pro-R. As shown in this study, the methylene spin state selective NMR experiment displays a good intrinsic sensitivity and could therefore provide valuable structural information at (13)C natural abundance for peptidomimetic molecules and foldamers bearing diastereotopic methylene protons.
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Affiliation(s)
- Gilles Guichard
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Immunologie et Chimie Thérapeutique, 15, Rue Descartes, Strasbourg F-67084, France
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Tolkatchev D, Malik S, Vinogradova A, Wang P, Chen Z, Xu P, Bennett HPJ, Bateman A, Ni F. Structure dissection of human progranulin identifies well-folded granulin/epithelin modules with unique functional activities. Protein Sci 2008; 17:711-24. [PMID: 18359860 DOI: 10.1110/ps.073295308] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Progranulin is a secreted protein with important functions in several physiological and pathological processes, such as embryonic development, host defense, and wound repair. Autosomal dominant mutations in the progranulin gene cause frontotemporal dementia, while overexpression of progranulin promotes the invasive progression of a range of tumors, including those of the breast and the brain. Structurally, progranulin consists of seven-and-a-half tandem repeats of the granulin/epithelin module (GEM), several of which have been isolated as discrete 6-kDa GEM peptides. We have expressed all seven human GEMs using recombinant DNA in Escherichia coli. High-resolution NMR showed that only the three GEMs, hGrnA, hGrnC, and hGrnF, contain relatively well-defined three-dimensional structures in solution, while others are mainly mixtures of poorly structured disulfide isomers. The three-dimensional structures of hGrnA, hGrnC, and hGrnF contain a stable stack of two beta-hairpins in their N-terminal subdomains, but showed a more flexible C-terminal subdomain. Interestingly, of the well-structured GEMs, hGrnA demonstrated potent growth inhibition of a breast cancer cell line, while hGrnF was stimulatory. Poorly folded peptides were either weakly inhibitory or without activity. The functionally active and structurally well-characterized human hGrnA offers a unique opportunity for detailed structure-function studies of these important GEM proteins as novel members of mammalian growth factors.
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Affiliation(s)
- Dmitri Tolkatchev
- Bio-NMR and Protein Research Laboratory, Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada
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Abstract
This chapter reviews the methodologies for RNA structure determination by liquid-state nuclear magnetic resonance (NMR). The routine production of milligram quantities of isotopically labeled RNA remains critical to the success of NMR-based structure studies. The standard method for the preparation of isotopically labeled RNA for structural studies in solution is in vitro transcription from DNA oligonucleotide templates using T7 RNA polymerase and unlabeled or isotopically labeled nucleotide triphosphates (NTPs). The purification of the desired RNA can be performed by either denaturing polyacrylamide gel electrophoresis (PAGE) or anion-exchange chromatography. Our basic strategy for studying RNA in solution by NMR is outlined. The topics covered include RNA resonance assignment, restraint collection, and the structure calculation process. Selected examples of NMR spectra are given for a correctly folded 30 nucleotide-containing RNA.
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Hennig M, Munzarova ML, Bermel W, Scott LG, Sklenar V, Williamson JR. Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA. J Am Chem Soc 2007; 128:5851-8. [PMID: 16637654 PMCID: PMC2556634 DOI: 10.1021/ja060165t] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long-range scalar 5J(H1',F) couplings were observed in 5-fluoropyrimidine-substituted RNA. We developed a novel S3E-19F-alpha,beta-edited NOESY experiment for quantitation of these long-range scalar 5J(H1',F) couplings, where the J-couplings can be extracted from inspection of intraresidual (H1',H6) NOE cross-peaks. Quantum chemical calculations were exploited to investigate the relation between scalar couplings and conformations around the glycosidic bond in oligonucleotides. The theoretical dependence of the observed 5J(H1',F) couplings on the torsion angle chi can be described by a generalized Karplus relationship. The corresponding density functional theory (DFT) analysis is outlined. Additional NMR experiments facilitating the resonance assignments of 5-fluoropyrimidine-substituted RNAs are described, and chemical shift changes due to altered shielding in the presence of fluorine-19 (19F) are presented.
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Affiliation(s)
- Mirko Hennig
- Department of Molecular Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, MB 33, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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40
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Hennig M, Scott LG, Sperling E, Bermel W, Williamson JR. Synthesis of 5-fluoropyrimidine nucleotides as sensitive NMR probes of RNA structure. J Am Chem Soc 2007; 129:14911-21. [PMID: 17990877 DOI: 10.1021/ja073825i] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymatic synthesis methods for the fluorinated 5'-triphosphate analogues 5F-UTP and 5F-CTP have been developed to facilitate 19F-labeling of RNAs for biophysical studies. HIV-2 TAR RNAs were synthesized using these analogues by in vitro transcription reactions using T7 RNA polymerase. The uniform incorporation of 5F-U or 5F-C analogues into HIV-2 TAR RNA transcripts does not significantly alter the RNA structure or thermodynamic stability. Fluorine observed homonuclear 19F-19F and heteronuclear 19F-1H NOE experiments providing selective distance information are presented and discussed. The availability of efficient synthesis of 5F-UTP, and for the first time, 5F-CTP, will facilitate the use of 5F-labeled RNAs in structural, ligand binding, and dynamic studies of RNAs using the advantages of 19F-labeling.
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Affiliation(s)
- Mirko Hennig
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 173 Ashley Avenue, P.O. Box 250509, Charleston, South Carolina 29425, USA.
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41
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Every AE, Russu IM. Probing the role of hydrogen bonds in the stability of base pairs in double-helical DNA. Biopolymers 2007; 87:165-73. [PMID: 17636510 DOI: 10.1002/bip.20811] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Aromatic stacking and hydrogen bonding between nucleobases are two of the key interactions responsible for stabilization of DNA double-helical structures. The present work aims at defining the specific contributions of these interactions to the stability of individual base pairs in DNA. The two DNA double helices investigated are formed, respectively, by the palindromic base sequences 5'-dCCAACGTTGG-3' and 5'-dCGCAGATCTGCG-3'. The strength of the N==H...N inter-base hydrogen bond in each base pair is characterized from the measurement of the protium-deuterium fractionation factor of the corresponding imino proton using NMR spectroscopy. The structural stability of each base pair is evaluated from the exchange rate of the imino proton, measured by NMR. The results reveal that the fractionation factors of the imino protons in the two DNA double helices investigated fall within a narrow range of values, between 0.92 and 1.0. In contrast, the free energies of structural stabilization for individual base pairs span 3.5 kcal/mol, from 5.2 to 8.7 kcal/mol (at 15 degrees C). These findings indicate that, in the two DNA double helices investigated, the strength of N==H...N inter-base hydrogen bonds does not change significantly depending on the nature or the sequence context of the base pair. Hence, the variations in structural stability detected by proton exchange do not involve changes in the strength of inter-base hydrogen bonds. Instead, the results suggest that the energetic identity of a base pair is determined by the number of inter-base hydrogen bonds, and by the stacking interactions with neighboring base pairs.
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Affiliation(s)
- Alicia E Every
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
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42
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Horst R, Wider G, Fiaux J, Bertelsen EB, Horwich AL, Wüthrich K. Proton-proton Overhauser NMR spectroscopy with polypeptide chains in large structures. Proc Natl Acad Sci U S A 2006; 103:15445-50. [PMID: 17032756 PMCID: PMC1622842 DOI: 10.1073/pnas.0607141103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The use of 1H-1H nuclear Overhauser effects (NOE) for structural studies of uniformly deuterated polypeptide chains in large structures is investigated by model calculations and NMR experiments. Detailed analysis of the evolution of the magnetization during 1H-1H NOE experiments under slow-motion conditions shows that the maximal 1H-1H NOE transfer is independent of the overall rotational correlation time, even in the presence of chemical exchange with the bulk water, provided that the mixing time is adjusted for the size of the structure studied. 1H-1H NOE buildup measurements were performed for the 472-kDa complex of the 72-kDa cochaperonin GroES with a 400-kDa single-ring variant of the chaperonin GroEL (SR1). These experiments demonstrate that multidimensional NOESY experiments with cross-correlated relaxation-enhanced polarization transfer and transverse relaxation-optimized spectroscopy elements can be applied to structures of molecular masses up to several hundred kilodaltabs, which opens new possibilities for studying functional interactions in large maromolecular assemblies in solution.
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Affiliation(s)
- Reto Horst
- *Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Gerhard Wider
- *Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Jocelyne Fiaux
- *Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Eric B. Bertelsen
- Howard Hughes Medical Institute and Department of Genetics, Yale University School of Medicine, New Haven, CT 06510; and
| | - Arthur L. Horwich
- Howard Hughes Medical Institute and Department of Genetics, Yale University School of Medicine, New Haven, CT 06510; and
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Kurt Wüthrich
- *Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
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Lequin O, Ladram A, Chabbert L, Bruston F, Convert O, Vanhoye D, Chassaing G, Nicolas P, Amiche M. Dermaseptin S9, an alpha-helical antimicrobial peptide with a hydrophobic core and cationic termini. Biochemistry 2006; 45:468-80. [PMID: 16401077 DOI: 10.1021/bi051711i] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dermaseptins S are closely related peptides with broad-spectrum antibacterial activity that are produced by the skin of the South American hylid frog, Phyllomedusa sauvagei. These peptides are polycationic (Lys-rich), alpha-helical, and amphipathic, with their polar/charged and apolar amino acids on opposing faces along the long axis of the helix cylinder. The amphipathic alpha-helical structure is believed to enable the peptides to interact with membrane bilayers, leading to permeation and disruption of the target cell. We have identified new members of the dermaseptin S family that do not resemble any of the naturally occurring antimicrobial peptides characterized to date. One of these peptides, designated dermaseptin S9, GLRSKIWLWVLLMIWQESNKFKKM, has a tripartite structure that includes a hydrophobic core sequence encompassing residues 6-15 (mean hydrophobicity, +4.40, determined by the Liu-Deber scale) flanked at both termini by cationic and polar residues. This structure is reminiscent of that of synthetic peptides originally designed as transmembrane mimetic models and that spontaneously become inserted into membranes [Liu, L., and Deber, C. M. (1998) Biopolymers 47, 41-62]. Dermaseptin S9 is a potent antibacterial, acting on gram-positive and gram-negative bacteria. The structure of dermaseptin S9 in aqueous solution and in TFE/water mixtures was analyzed by circular dichroism and two-dimensional NMR spectroscopy combined with molecular dynamics calculations. Dermaseptin S9 is aggregated in water, but a monomeric nonamphipathic alpha-helical conformation, mostly in residues 6-21, is stabilized by the addition of TFE. These results, combined with membrane permeabilization assays and surface plasmon resonance analysis of the peptide binding to zwitterionic and anionic phospholipid bilayers, demonstrate that spatial segregation of hydrophobic and hydrophilic/charged residues on opposing faces along the long axis of a helix is not essential for the antimicrobial activity of cationic alpha-helical peptides.
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Affiliation(s)
- Olivier Lequin
- Synthèse, structure et fonction de molécules bioactives, UMR 7613 CNRS, Université Pierre et Marie Curie, Case Courrier 45, 4 Place Jussieu, 75252 Paris Cedex 05, France
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Mátyus E, Monticelli L, Kövér KE, Xu Z, Blaskó K, Fidy J, Tieleman DP. Structural investigation of syringomycin-E using molecular dynamics simulation and NMR. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 35:459-67. [PMID: 16544138 DOI: 10.1007/s00249-006-0053-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Revised: 02/16/2006] [Accepted: 02/20/2006] [Indexed: 11/26/2022]
Abstract
Syringomycin-E (SR-E) is a cyclic lipodepsinonapeptide produced by certain strains of the bacterium Pseudomonas syringae pv. syringae. It shows inhibitory effects against many fungal species, including human pathogens. Its primary biological target is the plasma membrane, where it forms channels comprised of at least six SR-E molecules. The high-resolution structure of SR-E and the structure of the channels are currently not known. In this paper, we investigate in atomic detail the molecular features of SR-E in water by NMR and in water and octane by molecular dynamics simulation (MD). We built a model of the peptide and examined its structure in water and octane in 200 ns MD simulations both with and without distance restraints derived from NMR NOE data. The resulting trajectories show good agreement with the measured NOEs and circular dichroism data from the literature and provide atomistic models of SR-E that are an important step toward a better understanding of the antifungal and antibacterial activity of this peptide.
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Affiliation(s)
- E Mátyus
- Institute of Biophysics and Radiation Biology, Semmelweis University, 1444, Budapest, Hungary.
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Balayssac S, Burlina F, Convert O, Bolbach G, Chassaing G, Lequin O. Comparison of Penetratin and Other Homeodomain-Derived Cell-Penetrating Peptides: Interaction in a Membrane-Mimicking Environment and Cellular Uptake Efficiency†. Biochemistry 2006; 45:1408-20. [PMID: 16445283 DOI: 10.1021/bi0518390] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antennapedia and other homeoproteins have the unique ability to efficiently translocate across biological membranes, a property that is mediated by the third helix of the homeodomain. To analyze the effects of sequence divergence in the homeodomain, we have compared the cellular uptake efficiencies and interaction properties in a membrane-mimicking environment of four peptides corresponding to the third helix sequence of Antennapedia, Engrailed-2, HoxA-13, and Knotted-1. NMR studies revealed that these peptides adopt helical conformations in SDS micelles. Their localization with respect to the micelle was investigated using Mn(2+) as a paramagnetic probe. Peptides are positioned parallel to the micelle surface, but subtle differences in the depth of immersion were observed. Using a recently developed method for quantification of CPP cellular uptake based on MALDI-TOF mass spectrometry, all of these peptides were found to translocate into cells but with large differences in their uptake efficiencies. The peptide with the highest uptake efficiency was found to be the least deeply inserted within the micelle, indicating that electrostatic surface interactions may be a major determinant for membrane translocation. A new cell-penetrating peptide derived from Knotted-1 homeodomain with improved uptake properties compared to penetratin is introduced here.
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Affiliation(s)
- Stéphane Balayssac
- Synthèse, Structure et Fonction de Molécules Bioactives, UMR 7613 CNRS, Université Pierre et Marie Curie, boîte 45, 4 place Jussieu, 75252 Paris Cedex 05, France
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Fohrer J, Hennig M, Carlomagno T. Influence of the 2'-hydroxyl group conformation on the stability of A-form helices in RNA. J Mol Biol 2005; 356:280-7. [PMID: 16376377 DOI: 10.1016/j.jmb.2005.11.043] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 11/09/2005] [Accepted: 11/14/2005] [Indexed: 11/18/2022]
Abstract
The 2'-hydroxyl group plays fundamental roles in both the structure and the function of RNA, and is the major determinant of the conformational and thermodynamic differences between RNA and DNA. Here, we report a conformational analysis of 2'-OH groups of the HIV-2 TAR RNA by means of NMR scalar coupling measurements in solution. Our analysis supports the existence of a network of water molecules spanning the minor groove of an RNA A-form helix, as has been suggested on the basis of a high-resolution X-ray study of an RNA duplex. The 2'-OH protons of the lower stem nucleotides of the TAR RNA project either towards the O3' or towards the base, where the 2'-OH group can favorably participate in H-bonding interactions with a water molecule situated in the nucleotide base plane. We observe that the k(ex) rate of the 2'-OH proton with the bulk solvent anti-correlates with the base-pair stability, confirming the involvement of the 2'-OH group in a collective network of H-bonds, which requires the presence of canonical helical secondary structure. The methodology and conformational analysis presented here are broadly applicable and facilitate future studies aimed to correlate the conformation of the 2'-OH group with both the structure and the function of RNA and RNA-ligand complexes.
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Affiliation(s)
- Jörg Fohrer
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Halskau O, Underhaug J, Frøystein NA, Martínez A. Conformational flexibility of alpha-lactalbumin related to its membrane binding capacity. J Mol Biol 2005; 349:1072-86. [PMID: 15913646 DOI: 10.1016/j.jmb.2005.04.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Revised: 04/04/2005] [Accepted: 04/12/2005] [Indexed: 10/25/2022]
Abstract
Different folding states of the small, globular milk protein bovine alpha-lactalbumin (BLA) induced by the anionic surfactant sodium dodecylsulphate (SDS) have been examined by fluorescence spectroscopy, CD and NMR. The solution structure of the protein in the absence of SDS was also determined, indicating fluidity even under native conditions. BLA is partly denatured to a molten globule (MG)-like state by micromolar concentrations of SDS, and the transitions from native to MG-like state are dependent on pH, the protein being more sensitive to the surfactant at pH 6.5. As indicated by measurements of the intrinsic emission fluorescence, the tertiary structure disappears at lower concentrations of SDS than most of the secondary structure, as estimated from CD data. The MG-like state induced by low concentrations of SDS is not observable by NMR, and is probably fluctuating and/or aggregating. At higher concentrations of SDS above the critic concentration of micelles, an NMR-observable state reappears. This micelle-associated conformer was partially assigned, and found to bear strong resemblance to the acid-tri-fluoroethanol state, retaining weakened versions of the A and C helix of native BLA. We discuss the results in terms of the inherent flexibility of the protein, and its ability to form multiple folding states and to bind to membranes. Also, we propose that proteins with stable MG-like conformers can have these states stabilized by low levels of compounds with surfactant properties in vivo.
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Affiliation(s)
- Oyvind Halskau
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
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48
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Venkitaramani DV, Fulton DB, Andreotti AH, Johansen KM, Johansen J. Solution structure and backbone dynamics of Calsensin, an invertebrate neuronal calcium-binding protein. Protein Sci 2005; 14:1894-901. [PMID: 15937283 PMCID: PMC2253341 DOI: 10.1110/ps.051412605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Calsensin is an EF-hand calcium-binding protein expressed by a subset of peripheral sensory neurons that fasciculate into a single tract in the leech central nervous system. Calsensin is a 9-kD protein with two EF-hand calcium-binding motifs. Using multidimensional NMR spectroscopy we have determined the solution structure and backbone dynamics of calcium-bound Calsensin. Calsensin consists of four helices forming a unicornate-type four-helix bundle. The residues in the third helix undergo slow conformational exchange indicating that the motion of this helix is associated with calciumbinding. The backbone dynamics of the protein as measured by (15)N relaxation rates and heteronuclear NOEs correlate well with the three-dimensional structure. Furthermore, comparison of the structure of Calsensin with other members of the EF-hand calcium-binding protein family provides insight into plausible mechanisms of calcium and target protein binding.
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Affiliation(s)
- Deepa V Venkitaramani
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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The Solution Structure of a Cyclic Analog of Neuropeptide Y with High Y1 Receptor Affinity by NMR, CD and MD Simulations. Int J Pept Res Ther 2005. [DOI: 10.1007/s10989-004-4708-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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50
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Plant EP, Pérez-Alvarado GC, Jacobs JL, Mukhopadhyay B, Hennig M, Dinman JD. A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal. PLoS Biol 2005; 3:e172. [PMID: 15884978 PMCID: PMC1110908 DOI: 10.1371/journal.pbio.0030172] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Accepted: 03/14/2005] [Indexed: 12/16/2022] Open
Abstract
A wide range of RNA viruses use programmed -1 ribosomal frameshifting for the production of viral fusion proteins. Inspection of the overlap regions between ORF1a and ORF1b of the SARS-CoV genome revealed that, similar to all coronaviruses, a programmed -1 ribosomal frameshift could be used by the virus to produce a fusion protein. Computational analyses of the frameshift signal predicted the presence of an mRNA pseudoknot containing three double-stranded RNA stem structures rather than two. Phylogenetic analyses showed the conservation of potential three-stemmed pseudoknots in the frameshift signals of all other coronaviruses in the GenBank database. Though the presence of the three-stemmed structure is supported by nuclease mapping and two-dimensional nuclear magnetic resonance studies, our findings suggest that interactions between the stem structures may result in local distortions in the A-form RNA. These distortions are particularly evident in the vicinity of predicted A-bulges in stems 2 and 3. In vitro and in vivo frameshifting assays showed that the SARS-CoV frameshift signal is functionally similar to other viral frameshift signals: it promotes efficient frameshifting in all of the standard assay systems, and it is sensitive to a drug and a genetic mutation that are known to affect frameshifting efficiency of a yeast virus. Mutagenesis studies reveal that both the specific sequences and structures of stems 2 and 3 are important for efficient frameshifting. We have identified a new RNA structural motif that is capable of promoting efficient programmed ribosomal frameshifting. The high degree of conservation of three-stemmed mRNA pseudoknot structures among the coronaviruses suggests that this presents a novel target for antiviral therapeutics.
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Affiliation(s)
- Ewan P Plant
- 1Department of Cell Biology and Molecular Genetics, University of MarylandCollege Park, MarylandUnited States of America
| | - Gabriela C Pérez-Alvarado
- 2Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research InstituteLa Jolla, CaliforniaUnited States of America
| | - Jonathan L Jacobs
- 1Department of Cell Biology and Molecular Genetics, University of MarylandCollege Park, MarylandUnited States of America
| | - Bani Mukhopadhyay
- 1Department of Cell Biology and Molecular Genetics, University of MarylandCollege Park, MarylandUnited States of America
| | - Mirko Hennig
- 2Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research InstituteLa Jolla, CaliforniaUnited States of America
| | - Jonathan D Dinman
- 1Department of Cell Biology and Molecular Genetics, University of MarylandCollege Park, MarylandUnited States of America
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