Category Archives: Our Research

These are short reports about the research activities carried out at the SeRMN.
In them we describe the work done in collaboration with research groups, to summarize communications presented at scientific meetings, to report visits and stages at other laboratories or facilities, and to comment the meetings and workshops we have attended.

Interleaved Dual NMR Acquisition of Equivalent Transfer Pathways in TOCSY and HSQC experiments

Our Publications, Our Research

Nolis, P., Motiram-Corral, K., Pérez-Trujillo, M., & Parella, T. (2018). Interleaved Dual NMR Acquisition of Equivalent Transfer Pathways in TOCSY and HSQC experiments. ChemPhysChem. DOI: 10.1002/cphc.20180103

A dual NMR data acquisition strategy to handle and detect two active equivalent transfer pathways is presented and discussed. We illustrate the power of this time-efficient approach by collecting two different 2D spectra simultaneously in a single experiment: (i) TOCSY or HSQC-TOCSY spectra with different mixing times, (ii) F2-13C-coupled and decoupled HSQC spectra, (iii) conventional and pureshift HSQC spectra, and (iv) complementary HSQC and HSQC-TOCSY spectra.

Broadband homodecoupled Time-Shared 1H-13C and 1H-15N HSQC experiments

Our Publications, Our Research

Nolis, P., Motiram-Corral, K., Pérez-Trujillo, M., & Parella, T. (2018). Broadband homodecoupled Time-Shared 1H-13C and 1H-15N HSQC experiments. Journal Magnetic Resonance. DOI: 10.1016/j.jmr.2018.11.005

The concepts of pure-shift NMR and time-shared NMR are merged in a single NMR experiment. A 13C/15N time-shared version of the real-time BIRD-based broadband homodecoupled HSQC experiment is described. This time-efficient approach affords simultaneously 1H-13C and 1H-15N pure-shift HSQC spectra in a single acquisition, while achieving substantial gains in both sensitivity and spectral resolution. We also present a related 13C/15N-F2-coupled homodecoupled version of the CLIP-HSQC experiment for the simultaneous measurement of 1JCH and 1JNH from the simplified doublets observed along the direct dimension. Finally, a novel J-resolved HSQC experiment has been designed for the simple and automated determination of both 1JCH/1JNH from a 2D J-resolved spectrum.

Implementing one-shot multiple-FID acquisition into homonuclear and heteronuclear NMR experiments

Our Publications, Our Research

Motiram-Corral, K., Pérez-Trujillo, M., Nolis, P., & Parella, T. (2018). Implementing one-shot multiple-FID acquisition into homonuclear and heteronuclear NMR experiments. Chemical Communications. DOI: 10.1039/C8CC08065H

Multiple-FID acquisition (MFA) within the same scan is applied to acquire simultaneously multiple 2D spectra from a single NMR experiment. A discussion on the incorporation of the MFA strategy in several homonuclear and heteronuclear 2D pulse sequences is presented. As a proof of concept, a set of novel COSY, TOCSY and HMBC experiments are reported as a time-efficient solution in small-molecule NMR spectroscopy.

Exopolysaccharides from olive brines could reduce the adhesion of ETEC K88 to intestinal epithelial cells

Methods & Applications, Our Publications, Our Research, ,

“Exopolysaccharides from olive brines could reduce the adhesion of ETEC K88 to intestinal epithelial cells”  by Y. Zhu, G. Gonzalez-Ortiz, R. Jiménez-Díaz, M. Pérez-Trujillo, T. Parella, P. Lopez-Colom, SM Martín-Orúe. Food & function, 2018, 9, 3884-3894. DOI: https://doi.org/10.1039/c8fo00690c

This study aims to explore the biological functions of the isolated exopolysaccharides (EPSs) produced during the industrial fermentation of olives against enterotoxigenic E. coli (ETEC) K88. Exopolysaccharides were isolated from five industrial fermenters. Analysis of their monosaccharide composition by GLC revealed that the main components were glucose (27%–50%) and galactose (23%–33%) followed by rhamnose (4–23%) and arabinose (6–17%). The 1H NMR spectrum showed a very similar profile between samples, and a more in-depth analysis revealed the presence of an α-pyranose in the form of α-D-Glcp-(1→) and two different α-furanoses, with chemicals shift values, suggesting the presence of α-D-Glcf and α-D-Galf. Miniaturized in vitro tests demonstrated the ability of EPS samples to attach specifically to ETEC K88 (P < 0.05) with variable intensities. The competition test did not show the ability to block the ETEC K88 adhesion to IPEC-J2 cells; however, in the displacement test, all EPS samples were shown to effectively remove the pathogens attached to the cells (P < 0.01). These results suggest that the EPSs produced during the fermentation of table green olives could interfere with the attachment of opportunistic pathogens onto the intestinal epithelial cells. This would open the possibility of novel functional properties for this traditional Mediterranean fermented food and for the isolated EPSs as candidates for nutraceutics to be used in human and/or animal diets in the prevention and treatment of ETEC diarrhoea.

PhD Thesis: Development of Resolution-Enhanced NMR Techniques for Improved Small Molecules Structural Analysis

Methods & Applications, News from the SeRMN, Our Publications, Our Research

Last July 14th 2018 Núria Marcó defended her PhD Thesis entitled: Development of Resolution-Enhanced NMR Techniques for Improved Small Molecules Structural Analysis

 

The present doctoral thesis is framed within the field of Nuclear Magnetic Resonance (NMR) spectroscopy.

NMR spectroscopy is an analytic technique and, therefore, one of its main objectives is to unravel the correct structure of the molecules analyzed.This present doctoral thesis  is focused on this main objective. This work consists in a compendium of 7 publications, written in several prestigious scientific journals, that develop in depth the efficient and accurate determination of the constitution, configuration and conformation of small molecules thanks to the application of resolution improvements techniques.

In order to do that it is studied the accurate and efficient measurement of isotropic (homo- and heteronuclear scalar coupling constants) for the 2D structre determination, as well as the anisotropic parameters (RDCs, RCSAs and RQCs) for the 3D structure analysis. These anisotropic parameters allows us the discrimination of the different conformers of a molecule and can be found in weakly alignment media. PMMA gel provides an easy, reusable, and practical way to obtain this weakly alignment media. In this work, It has been researched the best way to get these anisotropic parameters, developing and adapting new pulse sequences to this type of media.

To get the correct structure (2D and 3D) it is important to obtain a precise and accurate measurement. In this thesis the great accuracy of isotropic and anisotropic parameters has been achieved through the use of resolution improvement techniques such as Pure-Shift, Spectral Aliasing and Non Uniform Sampling.

In addition it has been applied protocols for the easy automatization and measurement of coupling constants in isotropic and anisotropic media.

Also it has been design improved pulse sequences to achieve the measurement of longer- range heteronuclear connectivities that will  increase the amount of information that we will have available to do the structural analysis

Each experiment has been discussed from a methodological point of view. An assessment on its application has been also performed.

Pulse Programs and Data Set Examples:

Publication 1:
Extending long-range heteronuclear NMR connectivities by HSQMBC-COSY and HSQMBC-TOCSY experiments Saurí, J.; Marcó, N.; Williamson, R. T.; Martin, G. E.; Parella, T. J. Magn. Reson. 2015, 258, 25–32.
DOI 10.1016/j.jmr.2015.06.004

Pulse Program Code for Bruker:

Data set Example:

 

Publication 2:
Ultra high-resolution HSQC: Application to the efficient and accurate measurement of heteronuclear coupling constants  Marcó, N.; Fredi, A.; Parella, T. Chem. Commun. 2015, 51 (15), 3262–3265.
DOI 10.1039/C4CC10279G

Pulse Program Code for Bruker:

Data set Example:

 

Publication 3:
Isotropic/Anisotropic NMR Editing by Resolution-Enhanced NMR Spectroscopy Marcó, N.; Gil, R. R.; Parella, T. ChemPhysChem 2018, 19, 9, 1024-1029.
DOI: 10.1002/cphc.201800094

Pulse Programs Code for Bruker:

 

Publication 4:
Structural discrimination from in situ measurement of 1DCH and 2DHH residual dipolar coupling constants Marcó, N.; Gil, R. R.; Parella, T. Magn. Reson. Chem. 2017, 55 (6), 540–545.
DOI 10.1002/mrc.4575

Pulse Programs Code for Bruker:

Data set Example:

 

Publication 5:
Perfect 1JCH-resolved HSQC: Efficient measurement of one-bond proton-carbon coupling constants along the indirect dimension Marcó, N.; Souza, A. A.; Nolis, P.; Gil, R. R.; Parella, T. J. Magn. Reson. 2017, 276, 37–42.
DOI: 10.1016/j.jmr.2017.01.002

Pulse Programs Code for Bruker:

Data set Example:

 

Publication 6:
1JCH NMR Profile: Identification of key structural features and functionalities by visual observation and direct measurement of one-bond proton-carbon coupling constants Marcó, N.; Souza, A. A.; Nolis, P.; Cobas, C.; Gil, R. R.; Parella, T. J. Org. Chem. 2017, 82 (4), 2040–2044.
DOI: 10.1021/acs.joc.6b02873

Pulse Programs Code for Bruker:

 

Publication 7:
2JHH-resolved HSQC: Exclusive determination of geminal proton-proton coupling constants Marcó, N.; Nolis, P.; Gil, R. R.; Parella, T. J. Magn. Reson. 2017, 282, 18–26.
DOI: 10.1016/j.jmr.2017.06.014

Pulse Programs Code for Bruker:

 

Precise characterization of mycobacterial cell wall lipid PTTM

Methods & Applications, Our Publications, Our Research, , ,

“Molecule confirmation and structure characterization of pentatriacontatrienyl mycolate in Mycobacterium smegmatis” by M. Llorens-Fons, E. Julián, M. Luquin and M. Pérez-Trujillo. Chemistry and Physics of Lipids, 2018, Accepted Manuscript. DOI: https://doi.org/10.1016/j.chemphyslip.2017.12.006

Mycobacterium smegmatis is often used to study the different components of mycobacterial cell wall. Mycolic acids are important components of mycobacterial cell wall that have been associated with virulence. Recently, a novel lipid containing mycolic acids has been described in M. smegmatis. However, some uncertainties regarding the structure of this molecule named mycolate ester wax have been reported. The objective of this work was to perform an in depth structural study of this molecule for its precise characterization. Using 1H and 13C NMR spectroscopy, the molecular structure of mycolate ester wax found in M. smegmatis has been elucidated. The characterization was complemented with MS analyses. This molecule is formed by a carbon chain with three methyl substituted olefinic units and a mycolate structure with trans double bonds and cis cyclopropane rings. The present molecular study will facilitate the detection and identification of pentatriacontatrienyl mycolate (PTTM) in future studies by the performance of a simple 1D 1H NMR experiment.

Our Publications, Our Research, ,

Multiplicity-edited 1H-1H TOCSY experiment

Pau Nolis and Teodor Parella

Magnetic Resonance in Chemistry 2017 (DOI: 10.1002/mrc.4695)

Abstract

A 1H-1H TOCSY experiment incorporating 13C multiplicity information is proposed. In addition, broadband 1H homodecoupling in the indirect dimension can be implemented using a perfect BIRD module that affords exclusive 1H chemical shift evolution with full decoupling of all heteronuclear and homonuclear (including 2JHH) coupling constants. As a complement to the normal TOCSY and the recent PSYCHE-TOCSY experiments, this novel multiplicity-edited TOCSY experiment distinguishes between CH/CH3 (phased up) and CH2 (phased down) cross-peaks which facilitates resonance analysis and assignment.

SeRMN contribution to Symmetry 2017 Conference

NMR Events & Courses, Our Research, , , , ,

 

Some of the SeRMN staff  presented our last research work about chirality at The first International Conference on Symmetry, Symmetry 2017, that took place from16th to 18th October in Barcelona. Find below a summary of our contribution.

Míriam Pérez-Trujillo presented a lecture entitled: “Chiral Recognition by Dissolution Dynamic Nuclear Polarization NMR Spectroscopy”

Abstract: The recognition of enantiomeric molecules by chemical analytical techniques is still a challenge. A method based on d-DNP (dissolution dynamic nuclear polarization) NMR spectroscopy to study chiral recognition was described for the first time [1]. DNP allows boosting NMR sensitivity by several orders of magnitude, overcoming one of the main limitations of NMR spectroscopy [2]. A method integrating d-DNP and 13C NMR-aided enantiodifferentiation using chiral solvating agents (CSA) was developed, in which only the chiral analyte was hyperpolarized and selectively observed by NMR. The described method enhances the sensitivity of the conventional NMR-based procedure [3] and lightens the common problem of signal overlapping between analyte and CSA. As proof on concept, racemic metabolite 13C-labeled DL-methionine was enantiodifferentiated by a single-scan 13C NMR experiment. This method entails a step forward in the chiral recognition of small molecules by NMR spectroscopy; it opens new possibilities in situations where the sensitivity is limited, for example, when low analyte concentration available or when measurement of an insensitive nucleus required. The advantages and current limitations of the method, as well as future perspectives, are discussed.

NMR could improve the detection of “date rape” drug GHB

Methods & Applications, Our Publications, Our Research, , , ,

“Direct Monitoring of Exogenous γ-Hydroxybutyric Acid in Body Fluids by NMR Spectroscopy” by M. Palomino-Schätzlein, Y. Wang, A. Brailsford, T. Parella, D. Cowan, C. Legido-Quigley, M. Pérez-Trujillo. Anal. Chem., 2017, 89 (16), pp 8343–8350. DOI: http://dx.doi.org/10.1021/acs.analchem.7b01567

γ-Hydroxybutyric acid (GHB) is a popular drug increasingly associated with cases of drug-facilitated sexual assault (DFSA). Currently, expanding procedures of analysis and having forensic evidence of GHB intake in a long term are mandatory. Up to now, most studies have been performed using GC/MS and LC-MS as analytical platforms, which involve significant manipulation of the sample and, often, indirect measurements. In this work, procedures used in NMR-based metabolomics were applied to a GHB clinical trial on urine and serum. Detection, identification, and briefly quantification of the drug by NMR methods were surveyed, as well as the use of NMR-based metabolomics for the search of potential surrogate biomarkers of GHB consumption. Results demonstrated the suitability of NMR spectroscopy, as a robust nondestructive technique, to fast and directly monitor exogenous GHB in almost intact body fluids and its high potential in the search for metabolites associated with GHB intake. This initial work show some strengths of  NMR spectroscopy and standard methods routinely used in the NMR analysis of biological samples to approach the problem. These features could open up new interesting possibilities in future studies, complementing current procedures.

This work on media:   spectroscopynow.com  /  phys.org  / sciencedaily.com  /  canadafreepress.com / forensicmag.com  / cbinsights.com

NMR identification of monstrous mycobacterial lipids in cell wall of Mycobacterium abcessus

Methods & Applications, Our Publications, Our Research, , ,

” Trehalose polyphleates, external cell wall lipids in Mycobacterium abcessus, are associated with the formation of clumps with cording morphology, which have been associated with virulence” by M. Llorens-Fons, M. Pérez-Trujillo, E. Julián, C. Brambilla, F. Alcaide, T. F. Byrd and M. Luquin. Frontiers in Microbiology, 2017, 8:1402. DOI: http://dx.doi.org/10.3389/fmicb.2017.01402

Mycobacterium abscessus is a reemerging pathogen that causes pulmonary diseases similar to tuberculosis, which is caused by Mycobacterium tuberculosis. When grown in agar medium, M. abscessus strains generate rough (R) or smooth colonies (S). R morphotypes are more virulent than S morphotypes. In searching for the virulence factors responsible for this difference, R morphotypes have been found to form large aggregates (clumps) that, after being phagocytozed, result in macrophage death. Furthermore, the aggregates released to the extracellular space by damaged macrophages grow, forming unphagocytosable structures that resemble cords. In contrast, bacilli of the S morphotype, which do not form aggregates, do not damage macrophages after phagocytosis and do not form cords. Cording has also been related to the virulence of M. tuberculosis. A comparative study of the pattern and structure of mycolic acids was performed on R (cording) and S (non-cording) morphotypes derived from the same parent strains, and no differences were observed between morphotypes. Furthermore, cords formed by R morphotypes were disrupted with petroleum ether (PE), and the extracted lipids were analyzed by thin layer chromatography, nuclear magnetic resonance spectroscopy and mass spectrometry. Substantial amounts of trehalose polyphleates (TPP) were recovered as major lipids from PE extracts, and images obtained by transmission electron microscopy suggested that these lipids are localized to the external surfaces of cords and R bacilli. The structure of M. abscessus TPP was revealed to be similar to those previously described in Mycobacterium smegmatis. Although the exact role of TPP is unknown, our results demonstrated that TPP are not toxic by themselves and have a function in the formation of clumps and cords in M. abscessus, thus playing an important role in the pathogenesis of this species.