Proton NMR spectroscopy of Alcaligenes cytochrome c556

A high molecular-weight c-type cytochrome was purified from Alcaligenes faecalis ATCC 8750. Its weight was 40,000 daltons by sodium dodecyl sulfate-gel electrophoresis. Heme content was determined to be one heme per 40,000 daltons. Proton nuclear magnetic resonance-NMR-spectroscopy determined that the ferrous form is low spin. The detection of a methyl resonance at -3 ppm in the ferrous form indicated that methionine is a heme ligand in this state. The NMR spectrum of the ferric form at pH 7.2 revealed hyperfine shifted methyl resonances at 67.79, 63.17, 57.71, and 50.46 ppm. The large downfield shifts observed are indicative of high spin character. The ferric spectrum was pH-sensitive, indicating two pH-linked structural transitions with estimated pKs at 6.0 and 10.5. The first is interpreted as due to the ionization of a heme propionate. The second is interpreted as the acquisition of a strong field ligand and the subsequent conversion to a low spin ferric form. The ferricytochrome did not form complexes with cyanide, azide, or fluoride at pH 5.2 or 7.9.     

Proton NMR spectroscopy of cytochrome c-554 from Alcaligenes faecalis

Cytochrome c-554 from the bacterium Alcaligenes faecalis (ATCC 8750) is a respiratory electron-transport protein homologous to other members of the cytochrome c family. Its structure has been studied by 1H NMR spectroscopy in both the ferric and ferrous states. The ferric spectrum is characterized by downfield hyperfine-shifted heme methyl resonances at 46.25, 43.60, 38.40, and 36.73 ppm (25 degrees C, pH 7.1). Chemical shifts of these resonances change with temperature opposite to expectations derived from Curie's law. The pH behavior of the hyperfine-shifted resonances titrates with a pK of 6.3 that has been interpreted as due to ionization of a heme propionate. In the ferrous state, heme methyl, meso, and thioether bridge resonances have been observed and assigned. All aromatic proteins have been assigned according to the side chain of origin, and the structural environment about the sole tryptophan residue has been examined. The electron-transfer rate between ferric and ferrous forms has been estimated to be on the order of 3 X 10(8) M-1 s-1, which is the largest such self-exchange rate yet observed for a cytochrome.     

Multiple forms of sulfmyoglobin as detected by 1H nuclear magnetic resonance spectroscopy

The proton nuclear magnetic resonance spectrum of sulfmyoglobin prepared in standard fashion reveals the presence of three forms, A, B, and C, with different chemical reactivity. Conditions for some interconversions of these forms are given. The 1H NMR spectra of the different forms show similar patterns. It appears that the differences between forms involve chemical modification on the porphyrin periphery. The altered heme can be extracted from FeIII(CN) sulfmyoglobin C to give a stable green substance.     

Proton NMR assignments of systemin

Complete proton NMR assignments have been made for a synthetic 18-amino acid peptide named systemin, which functions as a wound-induced polypeptide hormone in tomato plants, and three of its derivatives. The wild-type peptide and this synthetic homolog have equivalent activities in their functional roles as systemic inducing signals in tomato plants. Proton NMR studies were carried out to characterize the solution properties of systemin. A variety of homonuclear proton NMR experiments at both 500 and 600 MHz were utilized in making these assignments, which have resulted in additional structural information. Whereas these results provide no evidence for persistence of common secondary (helix, sheet) or tertiary structural elements in the systemin polypeptide, there is evidence for two distinct molecular conformations at the carboxy terminus.     

In-cell NMR spectroscopy

Structural studies by in-cell nuclear magnetic resonance are a developing new field of research, and their objective is to obtain structural information of proteins and other biological macromolecules in the cytoplasm of Escherichia coli cells. The major limitation of in-cell experiments is cell lysis that occurs during the experiments. In this article, we describe how inhibition of autologous expression by rifampicin at a high concentration decreases cell lysis in E. coli. We suggest that rifampicin is acting in the programmed cell death gene system MazEF, which is triggered by stress conditions and ultimately leads to cell lysis.     

Proton NMR studies of vesicles incorporating glycophorin

The effects of incorporation of glycophorin. the major sialoglycoprotein or the human crythrocyte membrane, on the lipid of small vesicles have been studied using proton NMR and electron microscopy. In contrast to the incorporation of other peptides, the major effect is apparently the clustering of vesicles without fusion. The relative mobility of lipids of the vesicle. monitored by changes in proton spin-lattice time, is only moderately effected by the presence of protein. The methylene protons of the lipid chains are subject to a somewhat greater restriction of motion following the incorporation of glycophorin than are the protons of the head group.     

High-Resolution Proton NMR Studies of Lymphocyte Extracts

Anatomic imaging is now a well-developed application of magnetic resonance. Greater capabilities for physiologic characterization should become possible by concomitant application of spectroscopic methods. High-resolution in vitro spectroscopy must first provide a framework upon which in vivo and diagnostic interpretation may be based. Biochemical profiles consisting of quantitation of extracted aqueous metabolites and lipids of particular cells or organs establish an in vitro glossary for what may be found in the intact cell or living subject. A large variety of amino acids, intermediary metabolites, membrane precursors, and nucleotides are detectable in extracts of human peripheral blood lymphocytes, and significant changes in intracellular concentrations have been monitored after lectin-induced activation. Corresponding changes in lipid profile have also been noted. An increasing variety of other cells and tissues are being similarly characterized. Despite its limitations, NMR analysis possesses the unique prospect of providing a noninvasive and nondestructive source of biochemical information.     

NMR spectroscopy of G-quadruplexes

G-rich DNA and RNA sequences can form four-stranded structures called G-quadruplexes. Such structures have gained significant interest in the past decade with increasing evidence of their biological role. G-quadruplex structures can be polymorphic and dynamic. NMR spectroscopy has played an important role in G-quadruplex research. Here we review on the application of NMR techniques to study structure, dynamics and interaction of G-quadruplexes.     

Proton NMR study of erythrocytes of essential hypertensives

Proton NMR studies (saturation transfer experiments and longitudinal relaxation time determinations) indicate that substantial differences exist between erythrocytes of essential hypertensives and normotensive subjects. A higher degree of intracellular organization has been found for the hypertensives and several factors are proposed as contributing to the observed behaviour.     

Proton NMR studies of myohemerythrin from Themiste zostericola

 One- and two-dimensional NMR experiments have been carried out on different forms of myohemerythrin (MHr), a monomeric 13.9-kDa oxygen carrier, focusing on paramagnetically shifted proton resonances. Compared to the corresponding forms of octameric hemerythrin (Hr), all of the MHr forms exhibit spectra with better resolution and signal-to-noise ratios. The metMHr spectra allow the differentiation of the signals from the N_δ-H protons of the five N_ε-coordinated His ligands and those from the bridging Asp and Glu ligands. The 1D spectra of deoxyMHr exhibit a number of relatively sharp features including three solvent-exchangeable peaks that account for five protons. One of these His N-H protons exchanges more slowly with solvent than the other four and is assigned to His 54, which, by analogy to the crystal structure of deoxyHr, is the only His ligand that is hydrogen-bonded to an amino acid residue, Glu24 in this case. One-dimensional NOE results on the non-exchangeable signals clearly show the connectivities among the α and β protons of the bridging Asp111, and the α, β, and γ protons of the bridging Glu58 ligands. One-dimensional NOE experiments performed on the N-H proton signals of the coordinated His ligands, together with the COSY results, help to identify the geminal β protons of the His ligands. Upon the binding of N₃ ^– to one of the Fe(II) sites in deoxyMHr, the overlapping His N_δ-H proton signals observed in the deoxyMHr spectrum are resolved into individual signals; these have been correlated to the corresponding signals in deoxyMHr by saturation transfer experiments. Similarly, all five His N-H protons are resolved in the ¹H NMR spectrum of the deoxy form of the single point mutant L103N MHr. However, all five N-H protons readily exchange with solvent, indicating that the mutation affects the hydrogen-bonding interaction between His54 and Glu24. Received: 20 May 1996 / Accepted: 24 October 1996     

In-cell NMR spectroscopy.

The recent development of "in-cell NMR" techniques by two independent groups has demonstrated that NMR spectroscopy can be used to characterize the conformation and dynamics of biological macromolecules inside living cells. In this article, we describe different methods and discuss current and future applications as well as critical parameters of this new technique. We show experimental results, compare them with traditional in vitro experiments, and demonstrate that differences between the in vitro and the in vivo state of a macromolecule exist and can be detected and characterized.     

A proton nuclear magnetic resonance study of sulfmyoglobin cyanide

The proton nuclear magnetic resonance spectrum of sulfmyoglobin cyanide was studied at 400 MHz. The position of a methyl-group resonance at low field is consistent with a chlorin-like structure for the prosthetic group. The proton NMR spectrum of the cyanide derivative of the purified prosthetic group which decomposes upon extraction from the protein was found to be the same as that of the cyanide derivative of the prosthetic group extracted from myoglobin and a sample prepared from hemin-Cl.     

Proton magnetic resonance spectroscopy in diagnostics of epilepsy

Present paper presents proton MRS investigation results. The investigation was carried out with Magnetom Vision device. Twenty-five patients in the age of 20-44 years suffering with generalization epileptic fits validated by EEG (no visible changes on MRT) were examined. In all cases independently on the localization of the changes, decreasing of NAA and increasing of Cho were recorded. At one side temporal lobe injury recorded by EEG at the damaged part decreasing of NAA/Cr and NAA/Cho + Cr ratios were registered. Patients with bilateral changes registered by EEG showed non-equal changes of metabolite concentration on both sides. Examination of patients suffering with distinct symptoms of temple epileptics has shown ipsilaterality decrease of NAA and Cr concentration. But on the injured side NAA/Cr ratio decrease was more distinct. In general, the laterality was recorded in 14 patients out of 22 with pathological changes registered by proton MRS and in 10 patients out of 14 the above mentioned changes corresponds to the side of the fit initiation. In the patients with bilaterality changes NAA/Cr ratio asymmetry was recorded in all cases, but the most distinctly in the medium part of the temple lobe. Comparison of data recorded in 8 patients suffering with one side fit complex has shown significant asymmetry of metabolites which was observed in ipsilaterality and contra laterality NAA ratio obtained in hippocampal areas. Difference in NAA ratio obtained between left and right sides are 19-25%. Left-right ratio of other metabolites corresponded to that ratio in the control group and was symmetrical.     

Proton correlation NMR studies of metabolism in Rhodopseudomonas palustris

A 1H correlation NMR study is reported, on the metabolism of a photosynthetic bacterium, Rhodopseudomonas palustris, in dark and light anaerobic conditions. Alkali treatment as well as sonication of the cells were employed to follow the process of accumulation and decomposition of poly-beta-hydroxybutyrate (PHB) which is the reserve material for the bacterium. It was shown that synthesis of PHB from trans-crotonate proceeds in the granules of the cells. It was also demonstrated that under anaerobic light conditions photometabolism and glycolysis generally compete with concomitant synthesis and decomposition of PHB, respectively, and that glycolysis gradually replaces photometabolism with aging of the cells. In contrast, glycolysis is always predominant in the dark and PHB is primarily used as the carbon source. It was observed that photo-induced transport of beta-hydroxybutyrate through the membrane occurs when photometabolism and glycolysis are equally active in the light. The implications of this observation are briefly discussed.     

Proton NMR spectroscopic studies of dipeptidase in human erythrocytes

In studies on human erythrocyte metabolism in situ, high resolution (400 MHz)¹H spin-echo NMR spectroscopy was used to follow the time dependence of hydrolysis of glycylglycine and L-cysteinylglycine in intact cells and their lysates. The concentration dependence of the hydrolysis of L-cysteinylglycine was described by a rectangular hyperbola with K_m, 3.5 ± 0.6 mmol/llysate and V_max, 64.2 ± 3.2 mmol/llysate/h. We demonstrated that glycylglycine readily enters the erythrocyte and we introduce a means of analysing the data from the coupled reaction sequence; the sequence consists of transport followed by enzyme catalysed hydrolysis.     

High Resolution Proton NMR Spectroscopy of Multiple Sclerosis Lesions

Abstract: Tissue from postmortem multiple sclerosis and normal control brains was extracted with perchloric acid and analysed using proton NMR spectroscopy. The content of N -acetyl-derived groups (the sum of N -acetylaspartate, acetate, and N -acetylaspartylglutamate) was decreased in multiple sclerosis plaques compared with normal control white matter (mean, 4.36 vs. 6.64 µmol/g wet weight). In normal appearing white matter adjacent to plaques a corresponding decrease was seen, with no change in white matter distant from plaques. A decrease in the content of total creatine was observed in multiple sclerosis plaques in comparison with normal control white matter (mean, 4.64 vs. 6.56 µmol/g wet weight), which correlated strongly with the decrease in N -acetyl-derived groups. No changes in other metabolites such as total choline or myo -inositol were seen. The decreases in content of N -acetyl-derived groups are in agreement with observations from in vivo proton NMR spectroscopy in multiple sclerosis patients. The decrease in total creatine is in contrast to most of the observations made in vivo where total creatine is assumed to be unchanged and metabolite levels are often expressed as a total creatine ratio. The use of a total creatine ratio in vivo could lead to an underestimation of reductions in N -acetylaspartate and an apparent increase in other metabolites in the multiple sclerosis lesion.     

Structural proteomics by NMR spectroscopy

Structural proteomics is one of the powerful research areas in the postgenomic era, elucidating structure-function relationships of uncharacterized gene products based on the 3D protein structure. It proposes biochemical and cellular functions of unannotated proteins and thereby identifies potential drug design and protein engineering targets. Recently, a number of pioneering groups in structural proteomics research have achieved proof of structural proteomic theory by predicting the 3D structures of hypothetical proteins that successfully identified the biological functions of those proteins. The pioneering groups made use of a number of techniques, including NMR spectroscopy, which has been applied successfully to structural proteomics studies over the past 10 years. In addition, advances in hardware design, data acquisition methods, sample preparation and automation of data analysis have been developed and successfully applied to high-throughput structure determination techniques. These efforts ensure that NMR spectroscopy will become an important methodology for performing structural proteomics research on a genomic scale. NMR-based structural proteomics together with x-ray crystallography will provide a comprehensive structural database to predict the basic biological functions of hypothetical proteins identified by the genome projects.     

In-cell biochemistry using NMR spectroscopy

Biochemistry and structural biology are undergoing a dramatic revolution. Until now, mostly in vitro techniques have been used to study subtle and complex biological processes under conditions usually remote from those existing in the cell. We developed a novel in-cell methodology to post-translationally modify interactor proteins and identify the amino acids that comprise the interaction surface of a target protein when bound to the post-translationally modified interactors. Modifying the interactor proteins causes structural changes that manifest themselves on the interacting surface of the target protein and these changes are monitored using in-cell NMR. We show how Ubiquitin interacts with phosphorylated and non-phosphorylated components of the receptor tyrosine kinase (RTK) endocytic sorting machinery: STAM2 (Signal-transducing adaptor molecule), Hrs (Hepatocyte growth factor regulated substrate) and the STAM2-Hrs heterodimer. Ubiquitin binding mediates the processivity of a large network of interactions required for proper functioning of the RTK sorting machinery. The results are consistent with a weakening of the network of interactions when the interactor proteins are phosphorylated. The methodology can be applied to any stable target molecule and may be extended to include other post-translational modifications such as ubiquitination or sumoylation, thus providing a long-awaited leap to high resolution in cell biochemistry.