Zinc and diabetes — clinical links and molecular mechanisms

Zinc is an essential trace element crucial for the function of more than 300 enzymes and it is important for cellular processes like cell division and apoptosis. Hence, the concentration of zinc in the human body is tightly regulated and disturbances of zinc homeostasis have been associated with several diseases including diabetes mellitus, a disease characterized by high blood glucose concentrations as a consequence of decreased secretion or action of insulin. Zinc supplementation of animals and humans has been shown to ameliorate glycemic control in type 1 and 2 diabetes, the two major forms of diabetes mellitus, but the underlying molecular mechanisms have only slowly been elucidated. Zinc seems to exert insulin-like effects by supporting the signal transduction of insulin and by reducing the production of cytokines, which lead to beta-cell death during the inflammatory process in the pancreas in the course of the disease. Furthermore, zinc might play a role in the development of diabetes, since genetic polymorphisms in the gene of zinc transporter 8 and in metallothionein (MT)-encoding genes could be demonstrated to be associated with type 2 diabetes mellitus. The fact that antibodies against this zinc transporter have been detected in type 1 diabetic patients offers new diagnostic possibilities. This article reviews the influence of zinc on the diabetic state including the molecular mechanisms, the role of the zinc transporter 8 and MT for diabetes development and the resulting diagnostic and therapeutic options.     

Malaria and ovalocytosis — molecular mimicry?

Two recently published reports have described findings which will have a profound impact on the understanding of molecular mechanisms of human resistance to malaria infection. In Melanesian ovalocytosis, a genetic polymorphism found in Papua New Guinea and parts of South East Asia, the red cells are highly resistant to invasion by various species of malaria parasite. The molecular nature of the defect in ovalocytic erythrocytes was not known. Recent reports by Liu et al., (Liu, S.-C., Zhai, S., Palek, J., Golan, D., Amato, D., Hassan, K., Nurse, G., Babona, D., Coetzer, T., Jarolim, P. Zaik, M. and Borwein, S. (1990) N. Engl. J. Med. 323, 1530–1538.) and Jones et al. (Jones, G.L., Edmundson, H.M., Wesche, D. and Saul, A. (1991) Biochim. Biophys. Acta 1096, 33–40.) have now identified the abnormality in the band 3 protein of ovalocytic red cell membranes. A major discovery in the Jones et al, study is the presence of an extended peptide at the N-terminus of ovalocyte band 3 protein. This novel 13 amino acid extended sequence is not found in the primary structure of normal band 3 protein and was suggested to be the cause of band 3 defect in ovalocytes. We have analyzed this extended sequence through Genbank using SWISS-PROT database and found that an almost identical sequence exists in a malaria parasite protein called RESA.     

Scrapie—Uncertainties,biology and molecular approaches

The study of the biology of scrapie in sheep is irretrievably associated with the genetics of the PrP gene in sheep. Control of susceptibility and resistance is so closely linked to certain alleles of the sheep PrP gene that no review on scrapie can avoid PrP genetics. Before the importance of PrP protein was discovered and before the influence of the gene itself on disease incidence was understood, it was clear there were some sheep which were more susceptible to natural scrapie than others and that this feature was heritable. These early observations have led to the development and use of PrP genotyping in sheep in what is probably the biggest genetic selection process ever attempted. The accompanying increase in surveillance has also discovered a novel type of scrapie, the subject of much speculation about its origin.     

α-Crystallin: molecular chaperone and protein surfactant

Bovine lens α-crystallin has recently been shown to function as a molecular chaperone by stabilizing proteins against heat denaturation (Horwitz, J. (1992) Proc. Natl. Acad. Sci. USA, 89, 10449–10453). An investigation, using a variety of physico-chemical methods, is presented into the mechanism of stabilization. α-Crystallin exhibits properties of a surfactant. Firstly, a plot of conductivity of α-crystallin versus concentration shows a distinct inflection in its profile, i.e., a critical micelle concentration (cmc), over a concentration range from 0.15 to 0.17 mM. Gel chromatographic and ¹H-NMR spectroscopic studies spanning the cmc indicate no change in the aggregated state of α-crystallin implying that a change in conformation of the aggregate occurs at the cmc. Secondly, spectrophotometric studies of the rate of heat-induced aggregation and precipitation of alcohol dehydrogenase (ADH), β_L- and γ-crystallin in the presence of α-crystallin and a variety of synthetic surfactants show that stabilization against precipitation results from hydrophobic interactions with α-crystallin and monomeric anionic surfactants. Per mole of subunit or monomer, α-crystallin is the most efficient at stabilization. α-Crystallin, however, does not preserve the activity of ADH after heating. After heat inactivation, gel permeation HPLC indicates that ADH and α-crystallin form a high molecular weight aggregate. Similar results are obtained following incubation of β_L- and γ-crystallin with α-crystallin. ¹H-NMR spectroscopy of mixtures of α- and β_L-crystallin, in their native states, reveals that the C-terminus of βB2-crystallin is involved in interaction with α-crystallin. In the case of γ- and α-crystallin mixtures, a specific interaction occurs between α-crystallin and the C-terminal region of γ_B-crystallin, an area which is known from the crystal structure to be relatively hydrophobic and to be involved in intermolecular interactions. The short, flexible C-terminal extensions of α-crystallin are not involved in specific interactions with these proteins. It is concluded that α-crystallin interacts with native proteins in a weak manner. Once a protein has become denatured, however, the soluble complex with α-crystallin cannot be readily dissociated. In the aging lens this finding may have relevance to the formation of high molecular weight crystallin aggregates.     

Crystal and molecular structures of substituted α-d-glucopyranosides

The crystal and molecular structures of methyl 2,4,6-tri-O-pivaloyl-α-d-glucopyranoside (1), methyl 4,6-O-(R)-benzylidene-2-O-pivaloyl-α-d-glucopyranoside (2), and methyl 4,6-O-(R)-benzylidene-2,3-di-O-pivaloyl-α-d-glucopyranoside (3) were determined by X-ray analysis. Crystals of 1 are orthorhombic, space group P2₁2₁2₁ with the unit cell a = 13.026(2), b = 16.832, c = 11.929(2) Å, Z = 4. Crystals of 2 are monoclinic, space group P2₁. The unit-cell parameters are a = 6.519(1), b = 14.664(4), c = 10.635(4) Å, β = 93.18(1)°, Z = 2. Crystals of 3 are orthorhombic, space group P2₁2₁2₁ with a = 10.006(3), b = 13.874(3), c = 18.527(5) Å, Z = 4. The structures were solved by MULTAN and refined by a full-matrix procedure to final values of R = 0.084 (1), 0.048 (2), and 0.069 (3). The pyranose ring in each compound adopts the ⁴C₁ conformation. The 1,3-dioxane rings in 2 and 3 show a chair conformation. The molecular packing in 1 is through the hydrogen bonds involving HO-3 and the 6-O-pivaloyl carbonyl group [HO-3 ⋯ O-9, 2.855(8) Å], which connect the molecules into a chain along

. The endocyclic oxygen atom is involved in an intermolecular hydrogen-bond with HO-3 [2.848(4) Å], joining molecules of 2 into the chains along

. There are no free hydroxyl groups in 3 and molecular packing reflects van der Waals interactions only.     

Direct molecular fishing in molecular partners investigation in protein–protein and protein–peptide interactions

An original experimental method of direct molecular fishing has been developed for identification of potential partners of protein–protein and protein–peptide interactions. It is based on combination of surface plasmon resonance technology (SPR), size exclusion and affinity chromatography and mass spectrometric identification of proteins (LC-MS/MS). Previously, we demonstrated applicability of this method for protein interactomics using experimental model system, as well as in the pilot study in the frame of the Human Proteome Project (HPP). In the present paper, this method was successfully applied to identify possible molecular partners of 7 target proteins encoded by genes of 18 chromosome (also in the frame of the HPP). Fishing on the affinity sorbents with immobilized target proteins as ligands was carried out using total lysate of human liver tissue as well as pooled sets of fractions (individual for each bait-protein) obtained by means of a combination of size exclusion chromatography and SPR analysis for the presence of potential prey-proteins in each fraction. As a result we obtained lists of possible molecular partners of all 7 proteins and performed a comparative evaluation of direct fishing specificity for these target proteins. Direct molecular fishing was also successfully used for search of potential protein partners interacting with different isoforms of amyloid-beta peptide, playing a key role in the development of Alzheimer’s disease. The synthetic peptides that are analogues of the metal-binding domain isoforms of beta-amyloid were used as molecular baits and the fishing was performed in various fractions of immortalized human neural cells. As a result, 13 potential partner proteins were identified in the cytosol fraction of the cells by fishing on amyloid-beta peptide (1-16).     

Enhancement of protonated molecular ions and ammonium·molecular ion complexes in direct-liquid-introduction-mass spectrometry of carbohydrates

Addition of ammonium acetate to the mobile phase in direct-liquid-introduction mass spectrometry enhances the abundance of the protonated molecular ion or ammonium·molecular ion complex for compounds of biological interest. The efficacy of the method was investigated by comparing mass spectra obtained, with and without ammonium acetate, for a variety of underivatized, per-O-acetylated, and per-O-alkylated carbohydrates, and for several underivatized peptides. The mass spectra of the per-O-alkylated carbohydrates obtained by direct-liquid-introduction mass spectrometry with ammonium acetate were also compared to those obtained by thermospray mass spectrometry.     

Are molecular haplotypes worth the time and expense? A cost-effective method for applying molecular haplotypes

Because current molecular haplotyping methods are expensive and not amenable to automation, many researchers rely on statistical methods to infer haplotype pairs from multilocus genotypes, and subsequently treat these inferred haplotype pairs as observations. These procedures are prone to haplotype misclassification. We examine the effect of these misclassification errors on the false-positive rate and power for two association tests. These tests include the standard likelihood ratio test (LRTstd) and a likelihood ratio test that employs a double-sampling approach to allow for the misclassification inherent in the haplotype inference procedure (LRTae). We aim to determine the cost-benefit relationship of increasing the proportion of individuals with molecular haplotype measurements in addition to genotypes to raise the power gain of the LRTae over the LRTstd. This analysis should provide a guideline for determining the minimum number of molecular haplotypes required for desired power. Our simulations under the null hypothesis of equal haplotype frequencies in cases and controls indicate that (1) for each statistic, permutation methods maintain the correct type I error; (2) specific multilocus genotypes that are misclassified as the incorrect haplotype pair are consistently misclassified throughout each entire dataset; and (3) our simulations under the alternative hypothesis showed a significant power gain for the LRTae over the LRTstd for a subset of the parameter settings. Permutation methods should be used exclusively to determine significance for each statistic. For fixed cost, the power gain of the LRTae over the LRTstd varied depending on the relative costs of genotyping, molecular haplotyping, and phenotyping. The LRTae showed the greatest benefit over the LRTstd when the cost of phenotyping was very high relative to the cost of genotyping. This situation is likely to occur in a replication study as opposed to a whole-genome association study.     

The crystal and molecular structure of α-laminaribiose octa-acetate

The crystal and molecular structure of octa-O-acetyl-α-laminaribiose is compared with those of disaccharides, and their acetylated derivatives, related to polysaccharides of the laminarin and curdlan type. Marked differences are found in the endo- and exo-cyclic torsion angles as well as in the molecular geometry of the glycosidic linkage. The conformation of AcO-6′ provides the first experimental evidence of the theoretically predicted gauche-trans-gauche⁻ conformation. This conformational change, together with the α-orientation of AcO-1, alters the overall shape of the molecule and influences the packing features. The effect of the acetylation is also examined in terms of calculated conformational energy maps.     

Biochemistry and molecular genetics of poly-γ-glutamate synthesis

Current research into poly-gamma-glutamate (PGA) and its biosynthesis is reviewed. In PGA-producing Bacillus subtilis, glutamate racemase supplies abundant DL-glutamate, the substrate for PGA synthesis. The pgsBCA genes of PGA-producing B. subtilis, which encode the membrane-associated PGA synthetase complex PgsBCA, were characterized and the enzyme complex was suggested to be an atypical amide ligase based on its structure and function. A novel reaction mechanism of PGA synthesis is proposed.     

3D-QSAR,molecular docking and molecular dynamics studies of a series of RORγt inhibitors

The discovery of clinically relevant inhibitors of retinoic acid receptor-related orphan receptor-gamma-t (RORγt) for autoimmune diseases therapy has proven to be a challenging task. In the present work, to find out the structural features required for the inhibitory activity, we show for the first time a three-dimensional quantitative structure–activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations for a series of novel thiazole/thiophene ketone amides with inhibitory activity at the RORγt receptor. The optimum CoMFA and CoMSIA models, derived from ligand-based superimposition I, exhibit leave-one-out cross-validated correlation coefficient (R²_cv) of .859 and .805, respectively. Furthermore, the external predictive abilities of the models were evaluated by a test set, producing the predicted correlation coefficient (R²_pred) of .7317 and .7097, respectively. In addition, molecular docking analysis was applied to explore the binding modes between the inhibitors and the receptor. MD simulation and MM/PBSA method were also employed to study the stability and rationality of the derived conformations, and the binding free energies in detail. The QSAR models and the results of molecular docking, MD simulation, binding free energies corroborate well with each other and further provide insights regarding the development of novel RORγt inhibitors with better activity.     

Effect of Zn ion on the structure and electronic states of Aβ nonamer: molecular dynamics and ab initio molecular orbital calculations

Aggregates of amyloid-beta proteins (Aβ) have been recognised to be intimately related to pathogenesis of Alzheimer’s disease (AD). Indeed, Aβ aggregates of various sizes from dimers to fibrils were found in the brains of AD patients, and these aggregates can be self-organised. Since abnormal accumulation of metal ions such as Zn, Cu and Fe was also observed in the brains, the association between Aβ aggregations and these metal ions has been studied widely. In the present study, to elucidate the influence of Zn ions on the stability of Aβ aggregates, we performed molecular dynamics (MD) simulations and ab initio fragment molecular orbital (FMO) calculations on the Aβ nonamers with and without Zn ions and investigated the change in its structure and electronic states induced by Zn ions at atomic and electronic levels. The MD simulations revealed that Aβ nonamer cannot keep its symmetry structure, whereas Aβ nonamer with Zn ions keeps the structure. The FMO results indicated that electrostatic interactions among the charged amino-acid residues of Aβ nonamer are significantly changed by the influence of Zn ions to stabilise Aβ nonamer. These results provide useful information for proposing novel compounds, which binds specifically to Aβ and inhibits the Aβ aggregation.     

α-Thalassaemia in Tunisia: some epidemiological and molecular data

Unlike the other haemoglobinopathies, few researches have been published concerning α-thalassaemia in Tunisia. The aim of the present work is to acquire further data concerning α-thalassaemia prevalence and molecular defects spectrum in Tunisia, by collecting and studying several kinds of samples carrying α-thalassaemia. The first survey conducted on 529 cord blood samples using cellulose acetate electrophoresis, have displayed the prevalence of 7.38% Hb Bart’s carriers at birth. Molecular analyses were conducted by PCR and DNA sequencing on 20 families’ cases from the above survey carrying the Hb Bart’s at birth and on 10 Hb H diseased patients. The results showed six α-globin gene molecular defects and were responsible for α-thalassaemia: -α^3.7, - -^MedI, α^TSaudi, α₂^{cd23GAG→Stop}, Hb Greone Hart: α₁^119CCT→TCT corresponding to 11 genotypes out of which two are responsible for Hb H disease (- -^Med/-α^3.7) and (α^TSaudiα/α^TSaudiα) and a newly described polymorphism: α^+6C→G. The geographical repartition of α-thal carriers showed that the -α^3.7 deletion is distributed all over the country, respectively the α^HphI and α^TSaudi seem to be more frequent in the central region of the northeast region. The haematological and clinical data showed a moderate phenotype with a late age of diagnosis for Hb H disease. This work had permitted, in addition to an overview on α-thalassaemia in the country, the optimization of protocols for α-thalassaemia detection in our lab, allowing further investigations concerning phenotype-genotype correlation in sickle cell disease or β-thalassaemia.     

Frequency and molecular types of deletional α-thalassemia in Egypt

Summary The frequency of deletional -thalassemia in the Egyptian population was estimated at 0.08 by DNA analysis of a newborn random sample. No ⁰ determinants were found. The most frequent ⁺ determinant was the –^3.7 type I in association with the medium allele at inter-zeta HVR. The –^4.2 and ^{anti 3.7} arrangements were found at very low frequencies.     

Biotechnology and molecular biology of the α-glucosidase inhibitor acarbose

The -glucosidase inhibitor acarbose, O-{4,6-dideoxy-4[1s-(1,4,6/5)-4,5,6-trihydroxy-3-hydroxymethyl-2-cyclohexen-1-yl]-amino--d-glucopyranosyl}-(14)-O--d-glucopyranosyl-(14)-d-glucopyranose, is produced in large-scale fermentation by the use of strains derived from Actinoplanes sp. SE50. It has been used since 1990 in many countries in the therapy of diabetes type II, in order to enable patients to better control blood sugar contents while living with starch-containing diets. Thus, it is one of the latest successful products of bacterial secondary metabolism to be introduced into the pharmaceutical world market. Cultures of Actinoplanes sp. also produce various other acarbose-like components, of which component C is hard to separate during downstream processing, which is one of the most modern work-up processes developed to date. The physiology, genetics and enzymology of acarbose biosynthesis and metabolism in the producer have been studied to some extent, leading to the proposal of a new pathway and metabolic cycle, the carbophore. These data could give clues for further biotechnological developments, such as the suppression of side-products, enzymological or biocombinatorial production of new metabolites and the engineering of production rates via genetic regulation in future.