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Dehaloperoxidase (DHP) is a globular heme enzyme found in the marine worm Amphitrite ornatathat can catalyze the dehalogenation of halophenols to the corresponding quinones by using hydrogen peroxide as a cosubstrate. Its three-dimensional fold is surprisingly similar to that of the oxygen storage protein myoglobin (Mb). A key structural feature common to both DHP and Mb is the existence of multiple conformations of the distal histidine. In DHP, the conformational flexibility may be involved in promotion of substrate and cosubstrate entry and exit. Here we have explored the dynamics of substrate binding in DHP using Fourier transform infrared spectroscopy and flash photolysis. A number of discrete conformations at the active site were identified from the appearance of multiple CO absorbance bands in the infrared region of the spectrum. Upon photolysis at cryogenic temperatures, the CO molecules are trapped at docking sites within the protein matrix, as inferred from the appearance of several photoproduct bands characteristic of each site. Substrate binding stabilizes the protein by ∼20 kJ/mol. The low yield of substrate-bound DHP at ambient temperature points toward a steric inhibition of substrate binding by carbon monoxide. [ABSTRACT FROM AUTHOR]

We have combined Fourier transform infrared/temperature derivative (FTIR-TDS) spectroscopy at cryogenic temperatures and flash photolysis at ambient temperature to examine the effects of polar and bulky amino acid replacements of the highly conserved distal valine 68 in sperm whale myoglobin. In FTIR-TDS experiments, the CO ligand can serve as an internal voltmeter that monitors the local electrostatic field not only at the active site but also at intermediate ligand docking sites. Mutations of residue 68 alter size, shape, and electric field of the distal pocket, especially in the vicinity of the primary docking site (state B). As a consequence, the infrared bands associated with the ligand at site B are shifted. The effect is most pronounced in mutants with large aromatic side chains. Polar side chains (threonine or serine) have only little effect on the peak frequencies. Ligands that migrate toward more remote sites C and D give rise to IR bands with altered frequencies. TDS experiments separate the photoproducts according to their recombination temperatures. The rates and extent of ligand migration among internal cavities at cryogenic temperatures can be used to interpret geminate and bimolecular O[sub 2] and CO recombination at room temperature. The kinetics of geminate recombination can be explained by steric arguments alone, whereas both the polarity and size of the position 68 side chain play major roles in regulating bimolecular ligand binding from the solvent. [ABSTRACT FROM AUTHOR]

Background and Objectives: To optimize the pretreatment method of colorectal cancer tissue samples for metabolomics research based on solid-phase nuclear magnetic resonance (NMR). Methods and Study Design: The mucosal tissues of colorectal cancer were classified into five groups with a volume of 0.2 cm*0.2 cm*0.2 cm. The pretreatment methods for each group were as follows: I. Preservation with liquid nitrogen alone. Samples were also treated with liquid nitrogen for 10 (II), 20 (III), and 30 min (IV), respectively, immediately after isolation and then transferred to a -80°C refrigerator; V. Only -80°C refrigerator storage. No more than 30 minutes should pass between isolation and pretreatment of tumor samples. The tissue sample testing process was carried out on Bruker AVII-600 NMR Spectrometer. NMR signals were collected and analysed using partial least-squares discrimination analysis (PLS-DA) to explore the effects of different pretreatment methods on the metabolic changes of samples. Results: The levels of pelargonic acid, stearic acid, D-Ribose, heptadecanoic acid, pyruvic acid, succinate, sarcosine, glycine, creatine, and L-lactate in the group I (only liquid nitrogen) were significantly lower than the other groups (p<0.05); the content of glycerophosphocholine in the group I (only liquid nitrogen) was lower than that in the other groups (p=0.055). These indicated that the glucose and choline phospholipid metabolism levels of the liquid nitrogen group were significantly lower than those of the other four groups. Conclusions: Liquid nitrogen storage can stop the metabolic process of glucose and choline phospholipid in colorectal cancer tissue samples in vitro, thus maintaining the metabolic state of tissue samples in vivo as much as possible. [ABSTRACT FROM AUTHOR]

Background: Gastric cancer is the fourth most common cancer and the second most deadly cancer worldwide. Study on molecular mechanisms of carcinogenesis will play a significant role in diagnosing and treating gastric cancer. Metabolic profiling may offer the opportunity to understand the molecular mechanism of carcinogenesis and help to identify the potential biomarkers for the early diagnosis of gastric cancer.Methods: In this study, we reported the metabolic profiling of tissue samples on a large cohort of human gastric cancer subjects (n = 125) and normal controls (n = 54) based on (1)H nuclear magnetic resonance ((1)H NMR) together with multivariate statistical analyses (PCA, PLS-DA, OPLS-DA and ROC curve).Results: The OPLS-DA model showed adequate discrimination between cancer tissues and normal controls, and meanwhile, the model excellently discriminated the stage-related of tissue samples (stage I, 30; stage II, 46; stage III, 37; stage IV, 12) and normal controls. A total of 48 endogenous distinguishing metabolites (VIP > 1 and p < 0.05) were identified, 13 of which were changed with the progression of gastric cancer. These modified metabolites revealed disturbance of glycolysis, glutaminolysis, TCA, amino acids and choline metabolism, which were correlated with the occurrence and development of human gastric cancer. The receiver operating characteristic diagnostic AUC of OPLS-DA model between cancer tissues and normal controls was 0.945. And the ROC curves among different stages cancer subjects and normal controls were gradually improved, the corresponding AUC values were 0.952, 0.994, 0.998 and 0.999, demonstrating the robust diagnostic power of this metabolic profiling approach.Conclusion: As far as we know, the present study firstly identified the differential metabolites in various stages of gastric cancer tissues. And the AUC values were relatively high. So these results suggest that the metabolic profiling of gastric cancer tissues has great potential in detecting this disease and helping to understand its underlying metabolic mechanisms. [ABSTRACT FROM AUTHOR]

The quadruply hydrogen-bonded duplexes based on an imide-urea structure preorganized by three-center hydrogen bonds were found to associate via bifurcated hydrogen bonds. 1H NMR dilution experiments revealed the high stability of the homodimer in apolar solvent (Kdim> 105M–1in CDCl3) and enhancement of association ability due to electron-withdrawing substituent effects. The ready synthetic availability and adjustable association affinity via electronic effects may render these association units potentially applicable in constructing supramolecular architectures. [ABSTRACT FROM AUTHOR]

We have studied the temperature dependence of the IR stretch bands of carbon monoxide (CO) in the Xe 4 internal cavity of myoglobin mutant L29W-S108L at cryogenic temperatures. Pronounced changes of band areas and positions were analyzed quantitatively by using a simple dynamic model in which CO rotation in the cavity is constrained by a static potential. The librational dynamics of the CO causes a decrease of the total spectral area. A strong local electric field splits the CO stretch absorption into a doublet, indicating that CO can assume opposite orientations in the cavity. With increasing temperature, the two peaks approach each other, because the average angle of the CO with respect to the electric field increases. A combined classical and quantum-mechanical analysis precisely reproduces the observed temperature dependencies of both spectral area and peak shifts. It yields the height of the energy barrier between the two wells associated with opposite CO orientations, V[sub 0] ≈ 2 kJ/mol, and the frequency of oscillation within a well, ω ≈ 25 cm[sup -1]. The electric field in the protein cavity was estimated as 10 MV/cm. [ABSTRACT FROM AUTHOR]

The aim of the present study was to identify time-dependent changes in the expression of metabolic biomarkers during the various stages of oral carcinogenesis to provide an insight into the sequential mechanism of oral cancer development. An ¹H nuclear magnetic resonance (NMR)-based metabolomics approach was used to analyze the blood plasma samples of Sprague-Dawley rats exhibiting various oral lesions induced by the administration of 4-nitroquinoline-1-oxide (4NQO) in drinking water. The ¹H NMR spectra were processed by principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) to determine the metabolic differences between the three developmental stages of oral mucosa cancer (health, oral leukoplakia [OLK] and oral squamous cell carcinoma [OSCC]). The variable importance in projection (VIP) score derived from the PLS-DA model was used to screen for important metabolites, whose significance was further verified through analysis of variance (ANOVA). Data from the present study indicated that 4NQO-induced rat oral carcinogenesis produced oral pre-neoplastic and neoplastic lesions and provided an effective model for analyzing sequential changes in the ¹H NMR spectra of rat blood plasma. The ¹H NMR-based metabolomics approach clearly differentiates between healthy, OLK and OSSC rats in the PCA and PLS-DA models. Furthermore, lactic acid, choline, glucose, proline, valine, isoleucine, aspartic acid and 2-hydroxybutyric acid demonstrated VIP>1 in the PLS-D model and P<0.05 with ANOVA. It was also identified that increases in lactic acid, choline and glucose, and decreases in proline, valine, isoleucine, aspartic acid and 2-hydroxybutyric acid may be relative to the characteristic mechanisms of oral carcinogenesis. Therefore, these plasma metabolites may serve as metabolic biomarkers in oral carcinogenesis and assist in the early diagnosis and preventive treatment of oral cancer. [ABSTRACT FROM AUTHOR]

A strategy of using amide groups as the only functionality was developed to construct convergent heteroditopic cyclo[6]aramides that are able to strongly bind dibutylammonium chloride in chloroform (>105 M-1), leading to the formation of [2]pseudorotaxanes. [ABSTRACT FROM AUTHOR]

Background Rectal cancer is one of the most prevalent tumor types. Understanding the metabolic profile of rectal cancer is important for developing therapeutic approaches and molecular diagnosis. Methods Here, we report a metabonomics profiling of tissue samples on a large cohort of human rectal cancer subjects (n = 127) and normal controls (n = 43) using 1H nuclear magnetic resonance (1H NMR) based metabonomics assay, which is a highly sensitive and non-destructive method for the biomarker identification in biological systems. Principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and orthogonal projection to latent structure with discriminant analysis (OPLS-DA) were applied to analyze the 1H-NMR profiling data to identify the distinguishing metabolites of rectal cancer. Results Excellent separation was obtained and distinguishing metabolites were observed among the different stages of rectal cancer tissues (stage I = 35; stage II = 37; stage III = 37 and stage IV = 18) and normal controls. A total of 38 differential metabolites were identified, 16 of which were closely correlated with the stage of rectal cancer. The up-regulation of 10 metabolites, including lactate, threonine, acetate, glutathione, uracil, succinate, serine, formate, lysine and tyrosine, were detected in the cancer tissues. On the other hand, 6 metabolites, including myo-inositol, taurine, phosphocreatine, creatine, betaine and dimethylglycine were decreased in cancer tissues. These modified metabolites revealed disturbance of energy, amino acids, ketone body and choline metabolism, which may be correlated with the progression of human rectal cancer. Conclusion Our findings firstly identify the distinguishing metabolites in different stages of rectal cancer tissues, indicating possibility of the attribution of metabolites disturbance to the progression of rectal cancer. The altered metabolites may be as potential biomarkers, which would provide a promising molecular diagnostic approach for clinical diagnosis of human rectal cancer. The role and underlying mechanism of metabolites in rectal cancer progression are worth being further investigated. [ABSTRACT FROM AUTHOR]

Background: The biomarker identification of human esophageal cancer is critical for its early diagnosis and therapeutic approaches that will significantly improve patient survival. Specially, those that involves in progression of disease would be helpful to mechanism research. Methods: In the present study, we investigated the distinguishing metabolites in human esophageal cancer tissues (n = 89) and normal esophageal mucosae (n = 26) using a 1H nuclear magnetic resonance (1H-NMR) based assay, which is a highly sensitive and non-destructive method for biomarker identification in biological systems. Principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA) and orthogonal partial least-squares -discriminant anlaysis (OPLS-DA) were applied to analyse 1H-NMR profiling data to identify potential biomarkers. Results: The constructed OPLS-DA model achieved an excellent separation of the esophageal cancer tissues and normal mucosae. Excellent separation was obtained between the different stages of esophageal cancer tissues (stage II = 28; stage III = 45 and stage IV = 16) and normal mucosae. A total of 45 metabolites were identified, and 12 of them were closely correlated with the stage of esophageal cancer. The downregulation of glucose, AMP and NAD, upregulation of formate indicated the large energy requirement due to accelerated cell proliferation in esophageal cancer. The increases in acetate, short-chain fatty acid and GABA in esophageal cancer tissue revealed the activation of fatty acids metabolism, which could satisfy the need for cellular membrane formation. Other modified metabolites were involved in choline metabolic pathway, including creatinine, creatine, DMG, DMA and TMA. These 12 metabolites, which are involved in energy, fatty acids and choline metabolism, may be associated with the progression of human esophageal cancer. Conclusion: Our findings firstly identify the distinguishing metabolites in different stages of esophageal cancer tissues, indicating the attribution of metabolites disturbance to the progression of esophageal cancer. The potential biomarkers provide a promising molecular diagnostic approach for clinical diagnosis of human esophageal cancer and a new direction for the mechanism study. [ABSTRACT FROM AUTHOR]

A strategy for creating new association specificity of hydrogen-bonded duplexes by varying the spacings between neighboring hydrogen bonds is described. Incorporation of naphthalene-based residues has provided oligoamide strands that pair into duplexes sharing the same H-bonding sequences (e.g., DDAA) but differing in the spacings between their intermolecular hydrogen bonds, leading to homo- or heteroduplexes. The ability to manipulate association-specificity as demonstrated by this work may be extended to other multiple hydrogen bonded systems, thereby further enhancing the diversity of multiple hydrogen-bonded association units for constructing supramolecular structures. [ABSTRACT FROM AUTHOR]

Metabonomics using proton nuclear magnetic resonance (H-NMR) spectroscopy and multivariate data analysis of blood plasma samples can be used to characterize metabolic differences between healthy and diseased organisms, which can reveal important information about the causes of the disease. Here we evaluated whether the H-NMR-based metabonomic method can detect differences in blood plasma between healthy pregnant mice (outbred C57BL/6J strain) and pregnant mice injected with dexamethasone (Dex) to induce cleft palate. Both groups were injected with vitamin B. We found some metabolic differences from the 'outliers' among the mice, indicating that vitamin B protected against Dex-induced Cleft lip with or without palate (CLP) formation. [ABSTRACT FROM AUTHOR]

Two new kaempferol glycosides, 5hydroxy24hydroxyphenyl4oxo7αLrhamnopyranosyloxy4Hchromen3yl 2Oacetyl3OβDglucopyranosylαLrhamnopyranoside 1 and 5hydroxy24hydroxyphenyl4oxo7αLrhamnopyranosyloxy4Hchromen3yl βDglucopyranosyl1→26O2E34hydroxyphenylprop2enoylβDglucopyranosyl1→2βDglucopyranoside 2, along with ten known compounds, were isolated from the 95 EtOH extract of the whole plant of Androsace umbellata.The structures of the new glycosides were determined on the basis of detailed spectroscopic analyses, including 1D and 2DNMR, MS, and chemical methods. [ABSTRACT FROM AUTHOR]

Aromatic oligoamide macrocycles consisting of six to ten meta-linked residues were prepared based on bimolecular coupling/cyclization of a pentameric diamine and oligomeric diacid chlorides, and adopt folded conformations enforced by intramolecular three-center H-bonds. [ABSTRACT FROM AUTHOR]

The mini-hemoglobin from Cerebratulus lacteus (CerHb) belongs to a class of globins containing the polar Tyr-B10/Gln-E7 amino acid pair that normally causes low rates of O2 dissociation and ultra-high O2 affinity, which suggest O2 sensing or NO scavenging functions. CerHb, however, has high rates of O2 dissociation (kO2 ≈ 200–600 s-1) and moderate O2 affinity (KO2 ≈1 μM-1) as a result of a third polar amino acid in its active site, Thr-E11. When Thr-E11 is replaced by Val, kO2 decreases 1000-fold and KO2 increases 130-fold at pH 7.0, 20 °C. The mutation also shifts the stretching frequencies of both heme-bound and photodissociated CO, indicating marked changes of the electrostatic field at the active site. The crystal structure of Thr-E11 → Val CerHbO2 at 1.70 Å resolution is almost identical to that of the wild-type protein (root mean square deviation of 0.12 Å). The dramatic functional and spectral effects of the Thr-E11 → Val mutation are due exclusively to changes in the hydrogen bonding network in the active site. Replacing Thr-E11 with Val ‘frees’ the Tyr-B10 hydroxyl group to rotate toward and donate a strong hydrogen bond to the heme-bound ligand, causing a selective increase in O2 affinity, a decrease of the rate coefficient for O2 dissociation, a 40 cm-1 decrease in Vco of heme-bound CO, and an increase in ligand migration toward more remote intermediate sites. [ABSTRACT FROM AUTHOR]

Describes the ligand binding and protein dynamics in neuroglobin. Migration of photodissociated carbon dioxide in the distal heme pocket; Physiological functions of neuroglobin; Expression of neuroglobin in Escherichia coli strain.