The role of sophisticated instruments in biological research: Examples from nuclear magnetic resonance

The development of NMR is described to illustrate the importance of new methodologies to solve biological problems.     

Proline Metabolism in Leishmania donovani Promastigotes*

Oxygen uptake of Leishmania donovani culture promastigotes was stimulated by L-proline and to a lesser extent by L-glutamate and L-arginine. L-proline reversed partially KCN-induced inhibition of respiration and completely, inhibition caused by malonate. Labeled proline, glutamate, alanine, and arginine were detected by thin layer chromatography in the free amino acid pool from cells incubated with L-proline-¹⁴C. Labeled tricarboxylic acid cycle intermediates, α-ketoglutarate, succinate, fumarate, malate, and oxaloacetate, also were found by this method in extracts from organisms incubated with L-proline-¹⁴C which contained also pyruvate. Cells incubated with malic acid-¹⁴C contained labeled alanine, glutamate, and arginine. Labeled L-proline was not found in promastigotes incubated with D-glucose-¹⁴C, although arginine, glutamate, and alanine were detected in extracts from these organisms. Indirect evidence for the presence of a NADP-dependent malic enzyme was obtained by Ochoa's method. All results suggest the presence of a proline-glutamate interconversion pathway in L. donovani promastigote culture forms.     

Glycoproteins Released by Leishmania donovani: Immunologic Relationships with Host and Bacterial Antigens and Preliminary Biochemical Analysis*

SYNOPSIS. The antigenically active glycoproteins (AAGP) released by Leishmania donovani strain 3S promastigotes into growth media and by amastigotes of this strain into the tissues, e.g. blood, of infected hamsters was found to consist of 6 to 7 antigenically distinct components. The antigenic activity of these glycoproteins was resistant to freeze-thawing, protease treatment, and purification by column chromatography using Sephadex G-100. This activity, however, was destroyed by Na periodate and altered by boiling; AAGP adhered firmly to Amicon filter (UM2). The antigenically active substances absorbed UV at 230, 260, 280 nm and gave positive Folin phenol, phenol sulfuric acid, and orcinol reactions. By gel diffusion, the component glycoproteins were found to form lines with concanavalin A and to give reactions of identity and partial identity with human red cells and Mycobacterium butyricum. The possible involvement of the antigenically active glycoproteins in pathogensis of kala azar is discussed.     

Chemical proteomics from a nuclear magnetic resonance spectroscopy perspective

Proteomics is the study of the protein complement of a genome and employs a number of newly emerging tools. One such tool is chemical proteomics, which is a branch of proteomics devoted to the exploration of protein function using both in vitro and in vivo chemical probes. Chemical proteomics aims to define protein function and mechanism at the level of directly observed protein–ligand interactions, whereas chemical genomics aims to define the biological role of a protein using chemical knockouts and observing phenotypic changes. Chemical proteomics is therefore traditional mechanistic biochemistry performed in a systems-based manner, using either activity- or affinity-based probes that target proteins related by chemical reactivities or by binding site shape/properties, respectively. Systems are groups of proteins related by metabolic pathway, regulatory pathway or binding to the same ligand. Studies can be based on two main types of proteome samples: pooled proteins (1 mixture of N proteins) or isolated proteins in a given system and studied in parallel (N single protein samples). Although the field of chemical proteomics originated with the use of covalent labeling strategies such as isotope-coded affinity tagging, it is expanding to include chemical probes that bind proteins noncovalently, and to include more methods for observing protein–ligand interactions. This review presents an emerging role for nuclear magnetic resonance spectroscopy in chemical proteomics, both in vitro and in vivo. Applications include: functional proteomics using cofactor fingerprinting to assign proteins to gene families; gene family-based structural characterizations of protein–ligand complexes; gene family-focused design of drug leads; and chemical proteomic probes using nuclear magnetic resonance SOLVE and studies of protein–ligand interactions in vivo.     

Application of proton nuclear magnetic resonance spectroscopy to the study of Cryptococcus and cryptococcosis

Proton nuclear magnetic resonance spectroscopy is a nondestructive technique that identifies chemicals in solution and in living cells. It has been used in cryptococcal research to identify the primary structure of capsular glucuronoxylomannans, link cellular apoptosis susceptibility (CAS) genes to positioning of residues on the mannose backbone of glucuronoxylomannan, and verify that the cryptococcal virulence determinant, phospholipase B, is elaborated in vivo. Promising clinical applications include speciation (Cryptococcus neoformans and Cryptococcus gattii), with preliminary evidence that varieties neoformans and grubii can also be distinguished, non-invasive diagnosis of cerebral cryptococcomas, and, in cases of meningitis, monitoring therapeutic response by analysis of cerebrospinal fluid.     

Chemoprevention of Leishmaniasis: In-vitro antiparasitic activity of dibenzalacetone,a synthetic curcumin analog leads to apoptotic cell death in Leishmania donovani

Curcumin is the major phenolic compound found in turmeric, a dry powder of rhizomes and roots of the plant, Curcuma longa L., which is widely used as spice and food colorant around the world, and in herbal medicinal practice in Asian countries. The present study reports the leishmanicidal activity of trans-dibenzalacetone (DBA), a synthetic monoketone analog of curcumin, against Leishmania donovani parasites. We for the first time report the antiproliferative effect of a curcumin analog (DBA) on the intracellular amastigotes of L. donovani, the clinically more relevant stage of the parasite than its promastigotes stage. The leishmanicidal effect of DBA was further confirmed by scanning and transmission electron microscopies. Cell growth was arrested in G0/G1 phase with increased concentration of cytosolic calcium and dissipation of mitochondrial membrane potential. Further, the unique trypanothione/trypanothione reductase (TR) system of Leishmania cells was significantly inhibited by DBA. This economically synthesizable simple monoketone analog of curcumin has the potential for field use against visceral leishmaniasis which is currently widespread in tropical and subtropical developing countries of the world. In conclusion, we have identified an analog of curcumin for potential applications against leishmaniasis, based on its strong antiparasitic activity and low toxicity. This curcumin analog compares favorably, at least in vitro, with the existing medication miltefosine.     

Leishmania donovani: In vitro culture and [1H] NMR characterization of amastigote-like forms

WhenLeishmania donovani promastigote forms, were cultured in TC-199 medium at 28°C and subsequently incubated at 38°C, they turned into aflagellate (amastogote-like) forms. A return of the incubation-culture temperature to 28°C these amastigote-like forms to revert to promastigotes. The amastigotes obtained by heat-shock, were viable and retained antigenic capacity being recognized by the sera of naturally infected patients. These forms, remained also capable of multiplying inside the J-774A. 1 macrophages. When the amastigote-like forms are kept in culture at 38°C retained their rounded appearance and their biological characteristics for more than 3 months subculturing every 6 days. These amastigote-like forms, when used for subcultures at 28°C, transformed into promastigotes capable of multiplying, as flagellate forms. The amastigotelike forms obtainedin vitro can be used in biochemical studies related to chemotherapy and immunology studies, as part of an effort to combat this parasite. The end-products of of glycolysis were studied in both the amastigote-like and promastigote forms ofL. donovani, by proton magnetic resonance analysis of the culture media. Alanine, succinate, and acetate, were predominant, and to a lesser extent pyruvate, glycine and D-lactate. Our results suggest that both forms ofLeishmania use different biochemical strategies to obtain their energy.     

The utility of nuclear magnetic resonance spectroscopy in assisted reproduction

Infertility affects approximately 15–20% of individuals of reproductive age worldwide. Over the last 40 years, assisted reproductive technology (ART) has helped millions of childless couples. However, ART is limited by a low success rate and risk of multiple gestations. Devising methods for selecting the best gamete or embryo that increases the ART success rate and prevention of multiple gestation has become one of the key goals in ART today. Special emphasis has been placed on the development of non-invasive approaches, which do not require perturbing the embryonic cells, as the current morphology-based embryo selection approach has shortcomings in predicting the implantation potential of embryos. An observed association between embryo metabolism and viability has prompted researchers to develop metabolomics-based biomarkers. Nuclear magnetic resonance (NMR) spectroscopy provides a non-invasive approach for the metabolic profiling of tissues, gametes and embryos, with the key advantage of having a minimal sample preparation procedure. Using NMR spectroscopy, biologically important molecules can be identified and quantified in intact cells, extracts or secretomes. This, in turn, helps to map out the active metabolic pathways in a system. The present review covers the contribution of NMR spectroscopy in assisted reproduction at various stages of the process.     

Identification and measurement of methylamines in elasmobranch tissues using proton nuclear magnetic resonance (1H-NMR) spectroscopy

Methylamines are frequently present in high concentrations in biological samples, but their separation and quantification are difficult. Data presented show that methylamines commonly occurring in biological material can be uniquely identified and quantified by proton nuclear magnetic resonance spectroscopy by recording spectra at both neutral and acid pH. Use of a high sensitivity probe permits this analysis even in the presence of high water concentrations, allowing accurate quantification with minimum preparative technique. The method was tested on tissues of the dogfish. Trimethylamine oxide was found in amounts ranging from 42 mmol kg⁻¹ fresh weight in liver, up to 115 mmol kg⁻¹ fresh weight in heart. Betaine was found to range from 10 mmol kg⁻¹ fresh weight in liver to 49 mmol kg⁻¹ fresh weight in brain. Creatine was not found in heart or liver, but was present in body wall muscle and in brain. Further analysis using high-performance liquid chromatography allowed determination of urea/methylamine ratios, which ranged from 1.9 in liver to 3.7 in body wall muscle. Accepted: 7 October 1997     

400 MHz proton nuclear magnetic resonance studies of the polar headgroup conformation of inositolphospholipids

400 MHz ¹H-resonances of 1-phosphatidyl-myoinositol (PI), PI 4-phosphate (DPI) and PI 4,5-bisphosphate (TPI) in CD₃OD were assigned. Proton resonances in the inositol moiety shift downfield with the increase in the number of the phosphate from PI to TPI. From the ¹H-¹H and ¹H-³¹P vicinal coupling constants, rotamer populations around bonds in the polar headgroups were calculated. The H-C(5)O-P bond at position 5 of the inositol moiety tends to assume a gauche form. The H-C(1)O-P and the H-C(4)O-P bonds are not so strongly restricted to the gauche form as the H-C(5)O-P bond. The conformation of the glycerol moiety in PI, DPI and TPI is similar to that in phosphotidylcholine (PC) and phosphatidylethanolamine (PE). The CH-CH₂O-P bond in the glycerol moiety assumes a trans form. The acyl chains prefer a gauche arrangement to each other around the CHCH₂OCOR bond.     

Quantitative in vivo nuclear magnetic resonance studies of hybridoma metabolism

Carbon-13 nuclear magnetic resonance (NMR) spectroscopy was used to study the metabolism of a murine hybridoma cell line at two feed glutamine concentrations, 4.0 and 1.7 mM. Carbon-13 labeling patterns were used in conjunction with nutrient uptake rates to calculate the metabolic fluxes through the glycolytic pathway, the pentose shunt, the malate shunt, lipid biosynthesis, and the tricarboxylic acid (TCA) cycle. Decreasing the feed glutamine concentration significantly decreased glutamine uptake but had little effect on glucose metabolism. A significant incrase in antibody productivity occurred upon decreasing the feed glutamine level. The increased antibody productivity in concert with decreased glutamine uptake and no apparent change in glucolytic metabolism suggests that antibody production was not energy limited. Metabolic flux calculations indicate that (1) approximately 92% of the glucose consumed proceeds directly through glycolysis with 8% channeled through the pentose shunt; (2) lipid biosynthesis appears to be greater than malate shunt activity; and (3) considerable exchange occurs between TCA cycle intermediates and amino acid metabolic pools, leading to substantial loss of (13)C label from the TCA cycle. These results illustrate that (13)NMR spectroscopy is a powerfulf tool in the calculation of metabolic fluxes, particularly for exchange pathways where no net flux occurs. (c) 1994 John Wiley & Sons, Inc.     

Protein dynamics by solid-state nuclear magnetic resonance spectroscopy: Peptide backbone of the coat protein in fd bacteriophage

¹³C and ¹⁵N chemical shift anisotropy and ¹⁵N¹H dipolar powder patterns from backbone sites of the coat protein in fd bacteriophage are not averaged by motion. This means that the polypeptide backbone of the protein has no large amplitude motions rapid compared to 10⁴ Hz. Relaxation studies on the ¹³C_α and ¹⁵N amide resonances indicate the presence of motions on the 10⁹ Hz timescale. These results are reconciled with a model where an otherwise rigid backbone undergoes small amplitude, rapid motions.     

A proton nuclear magnetic resonance study of the physical changes in growing plant cell walls

Changes in broadline proton nuclear magnetic resonance parameters of cell walls during growth of etiolated hypocotyls of bean (Phaseolus vulgaris L.) indicate that cell wall structure becomes more rigid during development. Most of the changes are completed in the first 6 cm below cotyledon insertion and are correlated with increased restriction of proton movements in regions of dense polymer packing.Abbreviations FID free induction decay - M₂ second moment - M_2interpair interpair second moment - NMR nuclear magnetic resonance - T_1D dipolar relaxation time - T₂ spin-spin relaxation time This work was supported by grants from Natural Sciences and Engineering Research Council of Canada to A.L.M., I.E.P.T. and M. Bloom.     

Localized proton magnetic resonance spectroscopy of lipids in adipose tissue at high spatial resolution in mice in vivo

We describe a localized proton magnetic resonance spectroscopy ((1)H-MRS) method for in vivo measurement of lipid composition in very small voxels (1.5 mm x 1.5 mm x 1.5 mm) in adipose tissue in mice. The method uses localized point-resolved spectroscopy to collect (1)H spectra from voxels in intra-abdominal white adipose tissue (WAT) and brown adipose tissue (BAT) deposits. Nonlinear least-squares fits of the spectra in the frequency domain allow for accurate calculation of the relative amount of saturated, monounsaturated, and polyunsaturated fatty acids. All spectral data are corrected for spin-spin relaxation. The data show BAT of NMRI mice to be significantly different from BAT of NMRI nu/nu mice in all aspects except for the fraction of monounsaturated fatty acids (FM); for WAT, only the FM is different. BAT and WAT of NMRI mice differ in the amount of saturated and di-unsaturated fatty acids. This method provides a potential tool for studying lipid metabolism in small animal models of disease during the initiation, progression, and manifestation of obesity-related disorders in vivo. Our results clearly demonstrate that localized (1)H-MRS of adipose tissue in vivo is possible at high spatial resolution with voxel sizes down to 3.4 ml.     

Determination of choline in erythrocytes using high-resolution proton nuclear magnetic resonance spectroscopy: Comparison with a choline oxidase method

Detailed operating conditions are reported for the determination of choline in human erythrocytes using proton nuclear magnetic resonance spectroscopy in conjunction with the inversion-recovery spin-echo pulse sequence. The results of the NMR method were in excellent agreement with those obtained using an enzymatic (choline oxidase) assay; however, they were approximately three times higher than those reported using gas chromatography/mass spectrometry techniques. The differences may be partly due to the method of preparing or sampling cells since there is a distribution of choline in cells of different ages. However, choline levels were not affected by the methods used in the present study for storing or preparing cells.     

Lipopolysaccharide‐bound structure of the antimicrobial peptide cecropin P1 determined by nuclear magnetic resonance spectroscopy

Antimicrobial peptides (AMPs) are components of the innate immune system and may be potential alternatives to conventional antibiotics because they exhibit broad‐spectrum antimicrobial activity. The AMP cecropin P1 (CP1), isolated from nematodes found in the stomachs of pigs, is known to exhibit antimicrobial activity against Gram‐negative bacteria. In this study, we investigated the interaction between CP1 and lipopolysaccharide (LPS), which is the main component of the outer membrane of Gram‐negative bacteria, using circular dichroism (CD) and nuclear magnetic resonance (NMR). CD results showed that CP1 formed an α‐helical structure in a solution containing LPS. For NMR experiments, we expressed ¹⁵N‐labeled and ¹³C‐labeled CP1 in bacterial cells and successfully assigned almost all backbone and side‐chain proton resonance peaks of CP1 in water for transferred nuclear Overhauser effect (Tr‐NOE) experiments in LPS. We performed ¹⁵N‐edited and ¹³C‐edited Tr‐NOE spectroscopy for CP1 bound to LPS. Tr‐NOE peaks were observed at the only C‐terminal region of CP1 in LPS. The results of structure calculation indicated that the C‐terminal region (Lys15–Gly29) formed the well‐defined α‐helical structure in LPS. Finally, the docking study revealed that Lys15/Lys16 interacted with phosphate at glucosamine I via an electrostatic interaction and that Ile22/Ile26 was in close proximity with the acyl chain of lipid A. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.     

Metabolic differentiation of Arabidopsis treated with methyl jasmonate using nuclear magnetic resonance spectroscopy

NMR spectroscopy combined with principal component analysis was applied to Arabidopsis thaliana treated with methyl jasmonate in order to obtain macroscopic metabolic changes caused by the treatment. As the first step several chromatographic and NMR spectroscopic techniques were utilized to identify metabolites of Arabidopsis. Sephadex LH-20 showed a high efficiency in the separation of phenolic metabolites in the plant. For identification of minor metabolites two-dimensional J-resolved NMR technique was directly applied to the plant extract and results in a number of elucidation of the metabolites of which signals overlap in ¹H NMR spectra. The chemical structure of the identified metabolites were confirmed by various two-dimensional NMR spectroscopy including correlated spectroscopy, heteronuclear single quantum coherence, and heternuclear multiple bond correlation. As next step, a statistical approach, principal component analysis based on projected J-resolved NMR spectra was performed for metabolic alteration of methyl jasmonate-treated Arabidopsis. The results show that methyl jasmonate caused an increase of flavonoids, fumaric acid, sinapoyl malate, sinigrin, tryptophan, valine, threonine, and alanine and a decrease of malic acid, feruloyl malate, glutamine, and carbohydrates after 24 h treatment.     

Folding determinants of disulfide bond forming protein B explored by solution nuclear magnetic resonance spectroscopy

The two-stage model for membrane protein folding postulates that individual helices form first and are subsequently packed against each other. To probe the two-stage model, the structures of peptides representing individual transmembrane helices of the disulfide bond forming protein B have been studied in trifluoroethanol solution as well as in detergent micelles using nuclear magnetic resonance (NMR) and circular dichroism spectroscopy. In TFE solution, peptides showed well-defined α-helical structures. Peptide structures in TFE were compared to the structures of full-length protein obtained by X-ray crystallography and NMR. The extent of α-helical secondary structure coincided well, lending support for the two-stage model for membrane protein folding. However, the conformation of some amino acid side chains differs between the structures of peptide and full-length protein. In micellar solution, the peptides also adopted a helical structure, albeit of reduced definition. Using measurements of paramagnetic relaxation enhancement, peptides were confirmed to be embedded in micelles. These observations may indicate that in the native protein, tertiary interactions additionally stabilize the secondary structure of the individual transmembrane helices.