scholarly journals Towards resolving the complex paramagnetic nuclear magnetic resonance (NMR) spectrum of small laccase: assignments of resonances to residue-specific nuclei

2021 ◽  
Vol 2 (1) ◽  
pp. 15-23
Author(s):  
Rubin Dasgupta ◽  
Karthick B. S. S. Gupta ◽  
Huub J. M. de Groot ◽  
Marcellus Ubbink
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Active Site ◽  
Nmr Spectra ◽  
Chemical Exchange ◽  
Streptomyces Coelicolor ◽  
Paramagnetic Nmr ◽  
Exchange Processes ◽  
Nuclear Magnetic

Abstract. Laccases efficiently reduce dioxygen to water in an active site containing a tri-nuclear copper centre (TNC). The dynamics of the protein matrix is a determining factor in the efficiency in catalysis. To probe mobility, nuclear magnetic resonance (NMR) spectroscopy is highly suitable. However, several factors complicate the assignment of resonances to active site nuclei in laccases. The paramagnetic nature causes large shifts and line broadening. Furthermore, the presence of slow chemical exchange processes of the imidazole rings of copper ligand results in peak doubling. A third complicating factor is that the enzyme occurs in two states, the native intermediate (NI) and resting oxidized (RO) states, with different paramagnetic properties. The present study aims at resolving the complex paramagnetic NMR spectra of the TNC of Streptomyces coelicolor small laccase (SLAC). With a combination of paramagnetically tailored NMR experiments, all eight His Nδ1 and Hδ1 resonances for the NI state are identified, as well as His Hβ protons for the RO state. With the help of second-shell mutagenesis, selective resonances are tentatively assigned to the histidine ligands of the copper in the type-2 site. This study demonstrates the utility of the approaches used for the sequence-specific assignment of the paramagnetic NMR spectra of ligands in the TNC that ultimately may lead to a description of the underlying motion.

scholarly journals Towards resolving the complex paramagnetic NMR spectrum of small laccase: Assignments of resonances to residue specific nuclei

2020 ◽  
Author(s):  
Rubin Dasgupta ◽  
Karthick B. S. S. Gupta ◽  
Huub J. M. de Groot ◽  
Marcellus Ubbink
Keyword(s):  
Active Site ◽  
Nmr Spectra ◽  
Chemical Exchange ◽  
Streptomyces Coelicolor ◽  
Paramagnetic Nmr ◽  
Line Broadening ◽  
Active Site Residues ◽  
Nmr Spectrum ◽  
Exchange Processes ◽  
Copper Ligands

Abstract. Laccases efficiently reduce dioxygen to water in an active site containing a tri-nuclear copper centre (TNC). One reason for its efficiency in catalysis of this complex reaction can be the presence of mobility of active site residues. To probe mobility, NMR spectroscopy is highly suitable. However, several factors complicate the assignment of resonances to active site nuclei in laccases. The paramagnetic nature causes large shifts and line broadening. Furthermore, the presence of slow chemical exchange processes of the imidazole rings of copper ligands result in peak doubling. A third complicating factor is that the enzyme occurs in two states, the native intermediate (NI) and resting oxidized (RO) states, with different paramagnetic properties. The present study aims at resolving the complex paramagnetic NMR spectra of the TNC of Streptomyces coelicolor small laccase (SLAC). With a combination of paramagnetically tailored NMR experiments, all eight His Nδ1 and Hδ1 resonances for the NI state are identified, as well as His Hβ protons for the RO state. With the help of second shell mutagenesis, selective resonances are tentatively assigned to the T2 histidines. This study demonstrates approaches that can be used for sequence specific assignment of the paramagnetic NMR spectra of ligands in the TNC that ultimately may lead to a description of the underlying motions.

Nuclear magnetic resonance studies of multi-site chemical exchange. I. Matrix formulation of the Bloch equations

1970 ◽  
Vol 48 (23) ◽  
pp. 3641-3653 ◽  
Author(s):  
L. W. Reeves ◽  
K. N. Shaw
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Chemical Exchange ◽  
Relaxation Times ◽  
Bloch Equations ◽  
Matrix Formulation ◽  
Exchange Processes ◽  
Site Exchange ◽  
Saturation Effects ◽  
Nuclear Magnetic

A concise matrix formulation of chemical exchange effects on a nuclear magnetic resonance (n.m.r.) spectrum using the Bloch equations is described. The method accommodates many-site exchange processes, site-dependent relaxation times, differing site populations, and saturation effects in a steady-state first-order spectrum. The simple two-site exchange system is analyzed in detail and saturation effects in this system are studied numerically. Alternative forms of the basic lineshape equation are derived, all of which are readily adapted to efficient computer calculations for complete lineshape fitting to obtain kinetic data for complicated chemical exchange processes.

scholarly journals Zero-Field Nuclear Magnetic Resonance of Chemically Exchanging Systems

2019 ◽  
Author(s):  
Danila Barskiy ◽  
Michael C. D. Tayler ◽  
Irene Marco-Rius ◽  
John Kurhanewicz ◽  
Daniel B. Vigneron ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
High Field ◽  
Nmr Spectra ◽  
Chemical Exchange ◽  
Chemical Shifts ◽  
Proton Exchange ◽  
Zero Field ◽  
Resonance Frequencies ◽  
Nuclear Magnetic

Zero- and ultralow-field (ZULF) nuclear magnetic resonance (NMR) is an emerging tool for precision chemical analysis. Unlike conventional (high-field) NMR, which relies on chemical shifts for molecular identification, zero-field analog reports <i>J</i>-spectra that depend on the nuclear spin-spin coupling topology of molecules under investigation. While chemical shifts are usually a small fraction of the resonance frequencies, <i>J</i>-spectra for various spin systems are completely different from each other. In this work, we use zero-field NMR to study dynamic chemical processes and investigate the influence of chemical exchange on ZULF NMR spectra. We develop a computation approach that allows quantitative calculation of ZULF NMR spectra in the presence of chemical exchange and apply it to study aqueous solutions of [<sup>15</sup>N]ammonium as a model system. In this system, proton exchange rates span more than three orders of magnitude depending on acidity (pH), as monitored by high-field and ZULF NMR. We show that chemical exchange substantially affects the <i>J</i>-coupled NMR spectra and, in some cases, can lead to degradation and complete disappearance of the spectral features. To demonstrate potential applications of ZULF NMR for chemistry and biomedicine, we show a ZULF NMR spectrum of [2-<sup>13</sup>C]pyruvic acid hyperpolarized via dissolution dynamic nuclear polarization (dDNP). The metabolism of pyruvate provides valuable biochemical information and its monitoring by zero-field NMR could give spectral resolution that is hard to achieve at high magnetic fields. We foresee applications of affordable and scalable ZULF NMR coupled with hyperpolarization modalities to study chemical exchange phenomena in vivo and in situations where high-field NMR detection is not possible to implement.<br>

scholarly journals Zero-Field Nuclear Magnetic Resonance of Chemically Exchanging Systems

2019 ◽  
Author(s):  
Danila Barskiy ◽  
Michael C. D. Tayler ◽  
Irene Marco-Rius ◽  
John Kurhanewicz ◽  
Daniel B. Vigneron ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
High Field ◽  
Nmr Spectra ◽  
Chemical Exchange ◽  
Chemical Shifts ◽  
Proton Exchange ◽  
Zero Field ◽  
Resonance Frequencies ◽  
Nuclear Magnetic

Zero- and ultralow-field (ZULF) nuclear magnetic resonance (NMR) is an emerging tool for precision chemical analysis. Unlike conventional (high-field) NMR, which relies on chemical shifts for molecular identification, zero-field analog reports <i>J</i>-spectra that depend on the nuclear spin-spin coupling topology of molecules under investigation. While chemical shifts are usually a small fraction of the resonance frequencies, <i>J</i>-spectra for various spin systems are completely different from each other. In this work, we use zero-field NMR to study dynamic chemical processes and investigate the influence of chemical exchange on ZULF NMR spectra. We develop a computation approach that allows quantitative calculation of ZULF NMR spectra in the presence of chemical exchange and apply it to study aqueous solutions of [<sup>15</sup>N]ammonium as a model system. In this system, proton exchange rates span more than three orders of magnitude depending on acidity (pH), as monitored by high-field and ZULF NMR. We show that chemical exchange substantially affects the <i>J</i>-coupled NMR spectra and, in some cases, can lead to degradation and complete disappearance of the spectral features. To demonstrate potential applications of ZULF NMR for chemistry and biomedicine, we show a ZULF NMR spectrum of [2-<sup>13</sup>C]pyruvic acid hyperpolarized via dissolution dynamic nuclear polarization (dDNP). The metabolism of pyruvate provides valuable biochemical information and its monitoring by zero-field NMR could give spectral resolution that is hard to achieve at high magnetic fields. We foresee applications of affordable and scalable ZULF NMR coupled with hyperpolarization modalities to study chemical exchange phenomena in vivo and in situations where high-field NMR detection is not possible to implement.<br>

scholarly journals Zero-Field Nuclear Magnetic Resonance of Chemically Exchanging Systems

2019 ◽  
Author(s):  
Danila Barskiy ◽  
Michael C. D. Tayler ◽  
Irene Marco-Rius ◽  
John Kurhanewicz ◽  
Daniel B. Vigneron ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
High Field ◽  
Nmr Spectra ◽  
Chemical Exchange ◽  
Chemical Shifts ◽  
Proton Exchange ◽  
Zero Field ◽  
Resonance Frequencies ◽  
Nuclear Magnetic

Zero- and ultralow-field (ZULF) nuclear magnetic resonance (NMR) is an emerging tool for precision chemical analysis. Unlike conventional (high-field) NMR, which relies on chemical shifts for molecular identification, zero-field analog reports <i>J</i>-spectra that depend on the nuclear spin-spin coupling topology of molecules under investigation. While chemical shifts are usually a small fraction of the resonance frequencies, <i>J</i>-spectra for various spin systems are completely different from each other. In this work, we use zero-field NMR to study dynamic chemical processes and investigate the influence of chemical exchange on ZULF NMR spectra. We develop a computation approach that allows quantitative calculation of ZULF NMR spectra in the presence of chemical exchange and apply it to study aqueous solutions of [<sup>15</sup>N]ammonium as a model system. In this system, proton exchange rates span more than three orders of magnitude depending on acidity (pH), as monitored by high-field and ZULF NMR. We show that chemical exchange substantially affects the <i>J</i>-coupled NMR spectra and, in some cases, can lead to degradation and complete disappearance of the spectral features. To demonstrate potential applications of ZULF NMR for chemistry and biomedicine, we show a ZULF NMR spectrum of [2-<sup>13</sup>C]pyruvic acid hyperpolarized via dissolution dynamic nuclear polarization (dDNP). The metabolism of pyruvate provides valuable biochemical information and its monitoring by zero-field NMR could give spectral resolution that is hard to achieve at high magnetic fields. We foresee applications of affordable and scalable ZULF NMR coupled with hyperpolarization modalities to study chemical exchange phenomena in vivo and in situations where high-field NMR detection is not possible to implement.<br>

scholarly journals P052 Nuclear magnetic resonance metabolomic profiling of IBD patients under anti-TNF treatment. Are the pathways network deregulated?

2020 ◽  
Vol 14 (Supplement_1) ◽  
pp. S160-S160
Author(s):  
S Notararigo ◽  
M Martin-Pastor ◽  
J E Dominguez Munoz ◽  
M Barreiro-de Acosta
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Nmr Spectra ◽  
Mononuclear Cells ◽  
High Rate ◽  
Resonance Spectroscopy ◽  
Serum Samples ◽  
Spectral Window ◽  
Metabolomic Study ◽  
Nuclear Magnetic

Abstract Background The deregulation of immune system cell response implies loss of T-cell apoptosis, high rate of proinflammatory cytokines production and subsequent exacerbate activation of TNF-α pathway. The use of biologic antibody decrease inflammation rate and symptoms, but it remains unclear if it has a direct effect on the pathways activation/inactivation on peripheral blood mononuclear cells (PBMCs). The aim of this study is evaluate the role of nuclear magnetic resonance spectroscopy (NMR) applied to the metabolomic study of serum samples isolated from fresh blood from inflammatory bowel disease (IBD) patients under IFX treatment to understand the activated/inactivated pathways of PBMCs. Methods A case–control study was performed. Inclusion criteria were IBD patients under IFX treatment. Blood samples were obtained in Crohn’s disease (CD) and ulcerative colitis (UC) patients before IFX and in healthy controls (CTRL). CD patients were divided into subgroups according to the gut affected, in Ileocolic (IC), ileum and colon. NMR samples of the serum were collected and measured according to Standard Operation Procedures. Three types of NMR spectra were measured for each serum sample (1Hnoepresat, 1Hcpmgpresat and 1HDfilterpresat). The signal in each NMR spectrum was integrated in a series of equidistant little portion of the spectrum called buckets of a constant width of 0.04 ppm, covering the complete 1H NMR spectral window from −5 to 14 ppm. Buckets in regions depleted from signal at the two extremes of the spectrum were discarded as well as those in the proximity of the water peak at ca. 4.7 ppm which was affected by the presaturation. The vectors corresponding to a number of samples of two or more groups can be rapidly analysed using Multivariant Statistical Analysis methods. Results Twenty-two IBD patients (12 CD and nine UC) were included, 10 CTRL were also included. The metabolomic analyses of the NMR spectra of the serum of the different patients and control groups by the fingerprinting and targeting profiling strategies provided OPLS-DA statistical models (Figure 1) that permitted the successful classification of certain groups of samples which are summarised in Table 1. Conclusion The results of this pilot NMR metabolomic study of serum samples of IBD found a series of spectral fingerprints that are able to discriminate between groups of patients CTRL and CD, which underlines its potential use for the diagnosis of the disease.

The metal nuclear magnetic resonance spectra of some tin(II) and lead(II) complexes with polydentate phosphines

1983 ◽  
Vol 61 (8) ◽  
pp. 1795-1799 ◽  
Author(s):  
Philip A. W. Dean
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Nmr Spectra ◽  
Narrow Range ◽  
Chemical Shifts ◽  
Nuclear Magnetic Resonance Spectra ◽  
Magnetic Resonance Spectra ◽  
Nuclear Magnetic

The previously reported 1:1 complexes formed in MeNO2, between M(SbF6)2 (M = Sn or Pb) and Ph2P(CH2)2PPh2, PhP[(CH2)2PPh2]2, MeC(CH2PPh2)3, P[(CH2)2PPh2]3, and [Formula: see text] have been studied by metal (119Sn or 207Pb) nmr. The metal chemical shifts span the comparatively narrow range of −586 to −792 ppm and 60 to −269 ppm, relative to the resonance of MMe4, for 119Sn and 207Pb nmr, respectively. The implications of these data regarding the denticity of the ligand in M(P[(CH2)2PPh2]3)2+ are discussed, and a comparison with the metal nmr spectra of related stannous and plumbous complexes is made.

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