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García-Jiménez MJ, Gil-Caballero S, Maza S, Corzana F, Juárez-Vicente F, Miles JR, Sakamoto K, Kadomatsu K, García-Domínguez M, de Paz JL, Nieto PM. Midkine Interaction with Chondroitin Sulfate Model Synthetic Tetrasaccharides and Their Mimetics: The Role of Aromatic Interactions. Chemistry 2021; 27:12395-12409. [PMID: 34213045 PMCID: PMC8457220 DOI: 10.1002/chem.202101674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 12/29/2022]
Abstract
Midkine (MK) is a neurotrophic factor that participates in the embryonic central nervous system (CNS) development and neural stem cell regulation, interacting with sulfated glycosaminoglycans (GAGs). Chondroitin sulfate (CS) is the natural ligand in the CNS. In this work, we describe the interactions between a library of synthetic models of CS‐types and mimics. We did a structural study of this library by NMR and MD (Molecular Dynamics), concluding that the basic shape is controlled by similar geometry of the glycosidic linkages. Their 3D structures are a helix with four residues per turn, almost linear. We have studied the tetrasaccharide‐midkine complexes by ligand observed NMR techniques and concluded that the shape of the ligands does not change upon binding. The ligand orientation into the complex is very variable. It is placed inside the central cavity of MK formed by the two structured beta‐sheets domains linked by an intrinsically disordered region (IDR). Docking analysis confirmed the participation of aromatics residues from MK completed with electrostatic interactions. Finally, we test the biological activity by increasing the MK expression using CS tetrasaccharides and their capacity in enhancing the growth stimulation effect of MK in NIH3T3 cells.
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Affiliation(s)
- María José García-Jiménez
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), cicCartuja, CSIC, Universidad de Sevilla, C/ Américo Vespucio, 49, 41092, Sevilla, Spain
| | - Sergio Gil-Caballero
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), cicCartuja, CSIC, Universidad de Sevilla, C/ Américo Vespucio, 49, 41092, Sevilla, Spain.,Current Address: Universitat de Girona, Edifici Jaume Casademont Porta E, Parc Científic, Girona, Spain
| | - Susana Maza
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), cicCartuja, CSIC, Universidad de Sevilla, C/ Américo Vespucio, 49, 41092, Sevilla, Spain
| | - Francisco Corzana
- Department of Chemistry, University of La Rioja, Logroño (La Rioja), Spain
| | - Francisco Juárez-Vicente
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, C/ Américo Vespucio, 24, 41092, Sevilla, Spain
| | - Jonathan R Miles
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), cicCartuja, CSIC, Universidad de Sevilla, C/ Américo Vespucio, 49, 41092, Sevilla, Spain
| | - Kazuma Sakamoto
- Institute for Glyco-core Research (iGCORE), Departments of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kenji Kadomatsu
- Institute for Glyco-core Research (iGCORE), Departments of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Mario García-Domínguez
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, C/ Américo Vespucio, 24, 41092, Sevilla, Spain
| | - José L de Paz
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), cicCartuja, CSIC, Universidad de Sevilla, C/ Américo Vespucio, 49, 41092, Sevilla, Spain
| | - Pedro M Nieto
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), cicCartuja, CSIC, Universidad de Sevilla, C/ Américo Vespucio, 49, 41092, Sevilla, Spain
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Oliveras À, Moll L, Riesco-Llach G, Tolosa-Canudas A, Gil-Caballero S, Badosa E, Bonaterra A, Montesinos E, Planas M, Feliu L. D-Amino Acid-Containing Lipopeptides Derived from the Lead Peptide BP100 with Activity against Plant Pathogens. Int J Mol Sci 2021; 22:ijms22126631. [PMID: 34205705 PMCID: PMC8233901 DOI: 10.3390/ijms22126631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/19/2022] Open
Abstract
From a previous collection of lipopeptides derived from BP100, we selected 18 sequences in order to improve their biological profile. In particular, analogues containing a D-amino acid at position 4 were designed, prepared, and tested against plant pathogenic bacteria and fungi. The biological activity of these sequences was compared with that of the corresponding parent lipopeptides with all L-amino acids. In addition, the influence of the length of the hydrophobic chain on the biological activity was evaluated. Interestingly, the incorporation of a D-amino acid into lipopeptides bearing a butanoyl or a hexanoyl chain led to less hemolytic sequences and, in general, that were as active or more active than the corresponding all L-lipopeptides. The best lipopeptides were BP475 and BP485, both incorporating a D-Phe at position 4 and a butanoyl group, with MIC values between 0.8 and 6.2 µM, low hemolysis (0 and 24% at 250 µM, respectively), and low phytotoxicity. Characterization by NMR of the secondary structure of BP475 revealed that the D-Phe at position 4 disrupts the α-helix and that residues 6 to 10 are able to fold in an α-helix. This secondary structure would be responsible for the high antimicrobial activity and low hemolysis of this lipopeptide.
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Affiliation(s)
- Àngel Oliveras
- LIPPSO, Department of Chemistry, Campus Montilivi, University of Girona, 17004 Girona, Spain; (À.O.); (G.R.-L.); (A.T.-C.)
| | - Luís Moll
- Laboratory of Plant Pathology, Institute of Food and Agricultural Technology-CIDSAV-XaRTA, Campus Montilivi, University of Girona, 17004 Girona, Spain; (L.M.); (E.B.); (A.B.); (E.M.)
| | - Gerard Riesco-Llach
- LIPPSO, Department of Chemistry, Campus Montilivi, University of Girona, 17004 Girona, Spain; (À.O.); (G.R.-L.); (A.T.-C.)
| | - Arnau Tolosa-Canudas
- LIPPSO, Department of Chemistry, Campus Montilivi, University of Girona, 17004 Girona, Spain; (À.O.); (G.R.-L.); (A.T.-C.)
| | - Sergio Gil-Caballero
- Serveis Tècnics de Recerca (NMR), Universitat de Girona, Parc Científic i Tecnològic de la UdG, Pic de Peguera 15, 17004 Girona, Spain;
| | - Esther Badosa
- Laboratory of Plant Pathology, Institute of Food and Agricultural Technology-CIDSAV-XaRTA, Campus Montilivi, University of Girona, 17004 Girona, Spain; (L.M.); (E.B.); (A.B.); (E.M.)
| | - Anna Bonaterra
- Laboratory of Plant Pathology, Institute of Food and Agricultural Technology-CIDSAV-XaRTA, Campus Montilivi, University of Girona, 17004 Girona, Spain; (L.M.); (E.B.); (A.B.); (E.M.)
| | - Emilio Montesinos
- Laboratory of Plant Pathology, Institute of Food and Agricultural Technology-CIDSAV-XaRTA, Campus Montilivi, University of Girona, 17004 Girona, Spain; (L.M.); (E.B.); (A.B.); (E.M.)
| | - Marta Planas
- LIPPSO, Department of Chemistry, Campus Montilivi, University of Girona, 17004 Girona, Spain; (À.O.); (G.R.-L.); (A.T.-C.)
- Correspondence: (M.P.); (L.F.)
| | - Lidia Feliu
- LIPPSO, Department of Chemistry, Campus Montilivi, University of Girona, 17004 Girona, Spain; (À.O.); (G.R.-L.); (A.T.-C.)
- Correspondence: (M.P.); (L.F.)
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Borrell M, Gil-Caballero S, Bietti M, Costas M. Site-Selective and Product Chemoselective Aliphatic C–H Bond Hydroxylation of Polyhydroxylated Substrates. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05423] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Margarida Borrell
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia Spain
| | - Sergio Gil-Caballero
- Serveis Tècnics de Recerca (NMR), Universitat de Girona, Parc científic i tecnològic de la UdG, Pic de Peguera 15, Girona E-17003, Catalonia, Spain
| | - Massimo Bietti
- Dipartimento di Scienze e Tecnologie Chimiche, Università “Tor Vergata”, Via della Ricerca Scientifica, 1 I-00133 Rome, Italy
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia Spain
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Armendáriz-Buil I, Gil-Caballero S, Guibert-Bayona MA, Martín-Rubio AM, Vicente de Vera-Floristán JM, Del Río-Manterola J. [Hypobaric spinal anesthesia in a large ventral hernia]. An Sist Sanit Navar 2019; 42:93-96. [PMID: 30895966 DOI: 10.23938/assn.0585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
High abdominal wall surgery may require general anesthesia but, in patients with high risk of difficult airway and respiratory complications, local or regional anesthesia is the choice whenever possible. Spinal anesthesia usually used (both isobaric and hyperbaric) could compromise the respiratory function due to blockade of the T6 metamere or higher. Hypobaric spinal anesthesia (HSA) at low doses (3.6 cc of 0.1% hypobaric bupivacaine plus 0.2 cc of 0.005% fentanyl) achieves sufficient analgesia with minimal motor blockade. We present the case of a patient with a large supraumbilical hernia with high risk of difficult airway and respiratory complications, who went through HSA. The patient did not report pain or dyspnea during the surgical procedure thus, HSA at low doses is an option to be taken into account in high abdominal wall surgery despite not having been described for this use.
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Affiliation(s)
- I Armendáriz-Buil
- F.E.A. anestesiología y reanimación. Hospital Reina Sofía. Tudela (Navarra).
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Domínguez-Rodríguez P, Reina JJ, Gil-Caballero S, Nieto PM, de Paz JL, Rojo J. Glycodendrimers as Chondroitin Sulfate Mimetics: Synthesis and Binding to Growth Factor Midkine. Chemistry 2017. [DOI: 10.1002/chem.201701890] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pedro Domínguez-Rodríguez
- Instituto de Investigaciones Químicas (IIQ); CSIC- Universidad de Sevilla; Américo Vespucio 49 41092 Seville Spain
| | - José J. Reina
- Instituto de Investigaciones Químicas (IIQ); CSIC- Universidad de Sevilla; Américo Vespucio 49 41092 Seville Spain
- Current address: Singular Research Centre in Chemical Biology and Molecular Materials (CIQUS); Organic Chemistry Department; University of Santiago de Compostela (USC); Santiago de Compostela Spain
| | - Sergio Gil-Caballero
- Instituto de Investigaciones Químicas (IIQ); CSIC- Universidad de Sevilla; Américo Vespucio 49 41092 Seville Spain
| | - Pedro M. Nieto
- Instituto de Investigaciones Químicas (IIQ); CSIC- Universidad de Sevilla; Américo Vespucio 49 41092 Seville Spain
| | - José L. de Paz
- Instituto de Investigaciones Químicas (IIQ); CSIC- Universidad de Sevilla; Américo Vespucio 49 41092 Seville Spain
| | - Javier Rojo
- Instituto de Investigaciones Químicas (IIQ); CSIC- Universidad de Sevilla; Américo Vespucio 49 41092 Seville Spain
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García-Jiménez MJ, Gil-Caballero S, Canales Á, Jiménez-Barbero J, de Paz JL, Nieto PM. Interactions between a Heparin Trisaccharide Library and FGF-1 Analyzed by NMR Methods. Int J Mol Sci 2017. [PMID: 28629128 PMCID: PMC5486114 DOI: 10.3390/ijms18061293] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
FGF-1 is a potent mitogen that, by interacting simultaneously with Heparan Sulfate Glycosaminoglycan HSGAG and the extracellular domains of its membrane receptor (FGFR), generates an intracellular signal that finally leads to cell division. The overall structure of the ternary complex Heparin:FGF-1:FGFR has been finally elucidated after some controversy and the interactions within the ternary complex have been deeply described. However, since the structure of the ternary complex was described, not much attention has been given to the molecular basis of the interaction between FGF-1 and the HSGAG. It is known that within the complex, the carbohydrate maintains the same helical structure of free heparin that leads to sulfate groups directed towards opposite directions along the molecular axis. The precise role of single individual interactions remains unclear, as sliding and/or rotating of the saccharide along the binding pocket are possibilities difficult to discard. The HSGAG binding pocket can be subdivided into two regions, the main one can accommodate a trisaccharide, while the other binds a disaccharide. We have studied and analyzed the interaction between FGF-1 and a library of trisaccharides by STD-NMR and selective longitudinal relaxation rates. The library of trisaccharides corresponds to the heparin backbone and it has been designed to interact with the main subsite of the protein.
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Affiliation(s)
- María José García-Jiménez
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja, CSIC and Universidad de Sevilla, Américo Vespucio, 49, 41092 Sevilla, Spain.
| | - Sergio Gil-Caballero
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja, CSIC and Universidad de Sevilla, Américo Vespucio, 49, 41092 Sevilla, Spain.
| | - Ángeles Canales
- Complutense University of Madrid, Fac CC Quim, Department Quim Organ 1, Avd Complutense S/N, E-28040 Madrid, Spain.
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain.
- Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain.
- Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain.
| | - José L de Paz
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja, CSIC and Universidad de Sevilla, Américo Vespucio, 49, 41092 Sevilla, Spain.
| | - Pedro M Nieto
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja, CSIC and Universidad de Sevilla, Américo Vespucio, 49, 41092 Sevilla, Spain.
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7
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Franco R, Gil-Caballero S, Ayala I, Favier A, Brutscher B. Probing Conformational Exchange Dynamics in a Short-Lived Protein Folding Intermediate by Real-Time Relaxation–Dispersion NMR. J Am Chem Soc 2017; 139:1065-1068. [DOI: 10.1021/jacs.6b12089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rémi Franco
- Institut
de Biologie Structurale, Université Grenoble Alpes, 71 Avenue
des Martyrs, 38044 Grenoble Cedex 9, France
- Commissariat à
l’Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
- Centre National
de Recherche Scientifique (CNRS), Grenoble, France
| | | | - Isabel Ayala
- Institut
de Biologie Structurale, Université Grenoble Alpes, 71 Avenue
des Martyrs, 38044 Grenoble Cedex 9, France
- Commissariat à
l’Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
- Centre National
de Recherche Scientifique (CNRS), Grenoble, France
| | - Adrien Favier
- Institut
de Biologie Structurale, Université Grenoble Alpes, 71 Avenue
des Martyrs, 38044 Grenoble Cedex 9, France
- Commissariat à
l’Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
- Centre National
de Recherche Scientifique (CNRS), Grenoble, France
| | - Bernhard Brutscher
- Institut
de Biologie Structurale, Université Grenoble Alpes, 71 Avenue
des Martyrs, 38044 Grenoble Cedex 9, France
- Commissariat à
l’Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
- Centre National
de Recherche Scientifique (CNRS), Grenoble, France
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Brutscher B, Felli IC, Gil-Caballero S, Hošek T, Kümmerle R, Piai A, Pierattelli R, Sólyom Z. NMR Methods for the Study of Instrinsically Disordered Proteins Structure, Dynamics, and Interactions: General Overview and Practical Guidelines. Adv Exp Med Biol 2015; 870:49-122. [PMID: 26387100 DOI: 10.1007/978-3-319-20164-1_3] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thanks to recent improvements in NMR instrumentation, pulse sequence design, and sample preparation, a panoply of new NMR tools has become available for atomic resolution characterization of intrinsically disordered proteins (IDPs) that are optimized for the particular chemical and spectroscopic properties of these molecules. A wide range of NMR observables can now be measured on increasingly complex IDPs that report on their structural and dynamic properties in isolation, as part of a larger complex, or even inside an entire living cell. Herein we present basic NMR concepts, as well as optimised tools available for the study of IDPs in solution. In particular, the following sections are discussed hereafter: a short introduction to NMR spectroscopy and instrumentation (Sect. 3.1), the effect of order and disorder on NMR observables (Sect. 3.2), particular challenges and bottlenecks for NMR studies of IDPs (Sect. 3.3), 2D HN and CON NMR experiments: the fingerprint of an IDP (Sect. 3.4), tools for overcoming major bottlenecks of IDP NMR studies (Sect. 3.5), 13C detected experiments (Sect. 3.6), from 2D to 3D: from simple snapshots to site-resolved characterization of IDPs (Sect. 3.7), sequential NMR assignment: 3D experiments (Sect. 3.8), high-dimensional NMR experiments (nD, with n>3) (Sect. 3.9) and conclusions and perspectives (Sect. 3.10).
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Affiliation(s)
- Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044, Grenoble Cedex 9, France.
| | - Isabella C Felli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy.
| | | | - Tomáš Hošek
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy
| | - Rainer Kümmerle
- Bruker BioSpin AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Alessandro Piai
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy
| | - Roberta Pierattelli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy.
| | - Zsófia Sólyom
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044, Grenoble Cedex 9, France
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9
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Gil-Caballero S, Favier A, Brutscher B. HNCA+, HNCO+, and HNCACB+ experiments: improved performance by simultaneous detection of orthogonal coherence transfer pathways. J Biomol NMR 2014; 60:1-9. [PMID: 25056271 DOI: 10.1007/s10858-014-9847-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/07/2014] [Indexed: 06/03/2023]
Abstract
Three experiments, BEST-TROSY HNCA+, HNCO+ and HNCACB+ are presented for sequential backbone resonance assignment of (13)C, (15)N labelled proteins. The novelty of these experiments with respect to conventional pulse sequences is the detection of additional orthogonal coherence transfer pathways that results in enhanced sensitivity for sequential correlations without significantly compromising the intensity of intra-residue correlation peaks. In addition, a 2-step phase cycle separates peaks originating from the orthogonal coherence transfer pathways in 2 sub-spectra, thus providing similar information as obtained from performing a pair of sequential and intra-residue correlation experiments.
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Affiliation(s)
- Sergio Gil-Caballero
- Institut de Biologie Structurale, Université Grenoble 1, 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
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