Kinetic comparison of caiman ε-crystallin and authentic lactate dehydrogenases of vertebrates

Kinetic comparison of -crystallins isolated from the avian and reptilian species and the authentic lactate dehydrogenases (LDHs) was undertaken in order to clarify the identities of these structural lens proteins in relation to their enzymatic activity. Caiman -crystallin similar to the previously characterized duck -crystallin appeared to possess a genuine and stable LDH activity as detected by nitro blue tetrazolium staining on polyacrylamide gels and conventional kinetic assays. Kinetic parameters for pyruvate,l-lactate, NAD⁺, and three structural analogues of the coenzyme in this -crystallin catalyzed reaction were also determined and compared. Despite the structural similarities between -crystallins and chicken heart LDH, differences in charge and kinetic properties have been revealed by native isozyme electrophoresis and kinetic analysis as examined by initial velocity and substrate inhibition studies. It is found that the kinetic data analyzed for caiman -crystallin were more fitted with a compulsory ordered Bi-Bi sequential mechanism similar to those for the authentic LDHs and duck -crystallin. Caiman -crystallin has for the first time been established as a heart-type LDH based on the kinetic analysis and comparison with the authentic heart- and muscle-type LDHs from pig and chicken.     

Determination of the primary sequence of the duck αD globin mRNA and comparison of all adult duck and chick globin mRNA sequences

The nucleotide sequence of the duck α^D globin mRNA was determined. Its main feature is an exceptionally short 3′ non-coding segment of only 46 nucleotides, placed after the coding sequence of 141 codons. The last of the 6 adult globin mRNA of duck and chicken being thus sequenced, a comparison of all their features has become possible. Comparing the duck α^D mRNA to the related sequence in the chicken, we found greater homology than comparing it to the linked α^A globin sequence in the same species. Extensive homology can be found for a same globin chain α^A, α^D or β in between different avian species including also the goose and the ostrich; the avian α globin chains show a lower degree of sequence conservation in between species than the β chains. In contrast, within one species the three globin sequences have further diverged. The divergence between the α^A and α^D globin within a same species point to individual functional specificity and hence independent evolution and suggest that a mechanism of ‘gene conversion’ did not operate in between the avian α globin genes. Two segments of the amino acid sequence which we named ‘A^α’ and ‘B^α’ remain homologous in all avian α globins; two other regions ‘A^β’ and ‘B^β’ are identical in between the β globins. Segment A is placed at the 5′ end of exon II, and segment B at the 3′ end of the same exon; some amino acids in those segments are involved in the Heme binding site. Being almost identical in all know mammalian and avian globins of the α respectively the β type, regions A and B seem to represent the best conserved sequences in adult globin mRNA maintained during the divergence of species.     

Binding of γ-crystallin substrate prevents the binding of copper and zinc ions to the molecular chaperone α-crystallin

α-Crystallin is a small heat shock protein and molecular chaperone. Binding of Cu2+ and Zn2+ ions to α-crystallin leads to enhanced chaperone function. Sequestration of Cu2+ by α-crystallin prevents metal-ion mediated oxidation. Here we show that binding of human γD-crystallin (HGD, a natural substrate) to human αA-crystallin (HAA) is inversely related to the binding of Cu2+/Zn2+ ions: The higher the amount of bound HGD, the lower the amount of bound metal ions. Thus, in the aging lens, depletion of free HAA will not only lower chaperone capacity but also lower Cu2+ sequestration, thereby promoting oxidation and cataract.     

A comparison of structural relationships among α-crystallin, human Hsp27, γ-crystallins and βB2-crystallin

The 3D structures of α-crystallin, a major eye lens protein, and related small heat shock proteins are unresolved. It has been assumed that α-crystallin is primarily a β-sheet globular protein similar to γ-crystallin (Siezen and Argos, Biochim. Biophys. Acta, 1983, 748, 56–67) containing sequence repeats in its two domains (Wistow, FEBS Lett. 1985, 181, 1–6). Positional flexibility of amino acid residues and far UV-circular dichroism spectroscopy were used to investigate structural relationships among these proteins. The utility of flexibility plots for predicting protein structure is demonstrated by the excellent correlation of these plots with the known 3D X-ray structures of β/γ-crystallins. Similar analyses of α-crystallin subunits, αA and αB, and human heat shock protein 27 show that the C-terminal domains and connecting segments of these proteins are very similar while the N-terminal domains have significant structural differences. Unlike β/γ-crystallins, both Hsp27 and α-crystallin subunits are asymmetrical with highly flexible C-terminal domains. Flexibility is considered essential for protein functional activity. Therefore, the C-terminal region may play an active role in α-crystallin and small heat shock protein function. Differences in flexibility profiles and estimated secondary structure distribution in α-crystallin by three recent/updated algorithms from far UV-CD spectra support our predicted 3D structure and the concept that α-crystallin and members of β/γ-superfamily are structurally dissimilar.     

A comparison of the size and shape of β-limit dextrin and amylopectin using pulsed field-gradient nuclear magnetic resonance and analytical ultracentrifugation

The size and shape of β-limit dextrin have been investigated by using pulsed, field-gradient nuclear magnetic resonance and analytical ultracentrifugation. In addition, the β-limit dextrin has been compared with the amylopectin from which it was derived by enzymic hydrolysis. When measuring size and shape, dimethyl sulfoxide was used as the solvent, in order to avoid problems of polymer agggregation. The results suggest that β-limit dextrin is an oblate ellipsoid with an axial ratio of ∼5:1, and the corresponding amylopectin molecule is even flatter. This indicates that the linear segments beyond the final branch-points of amylopectin lie in the plane of its branched core. The study also demonstrated that the density of packing of polymer chains in this branched core is much greater than at the periphery of amylopectin, and that the latter region is the location of the great majority of the nonreducing chains cleaved by beta amylase. Furthermore, the different sized molecules in amylopectin samples appear to undergo the same degree of degradation by this enzyme.     

The kinetics of interconversion of intermediates of the reaction of pig muscle lactate dehydrogenase with oxidized nicotinamide–adenine dinucleotide and lactate

Oxamate competes with pyruvate for the substrate binding site on the E(NADH) complex of pig skeletal muscle lactate dehydrogenase. When this enzyme was mixed with saturating concentrations of NAD(+) and lactate in a stopped-flow rapid-reaction spectrophotometer there was no transient accumulation of enzyme complexes with the reduced nucleotide. The steady-state rate of formation of free NADH was reached within the dead-time of the instrument (3ms). When oxamate was added to inhibit the steady state and to uncouple the equilibration: [Formula: see text] through the rapid formation of E(NADH) (Oxamate), the rate of formation of E(NADH) could be measured by observation of the first turnover. This pH-dependent transient is controlled by the rate of dissociation of pyruvate and the fraction of the enzyme in the form E(NADH) (Pyruvate).     

A comparison of the interfacial interactions of the apoprotein from high density lipoprotein and β-casein with phospholipids

The conformations adopted by β-casein and the total apoprotein from serum high density lipoprotein when spread at the air-water interface are compared; the monolayer data are consistent with the apoprotein being α-helical and the β-casein being disordered with segments distributed in loops and trains. The penetration of these hydrophobic proteins into phosphatidylcholine monolayers in different physical states was investigated. More protein can penetrate into monolayers when they are in the liquid-expanded state; for penetration at constant total surface area the lateral compressibility of the lipid is an important factor. The charge and conformation of the polar group of the phospholipid does not have a major influence on the interaction. The mixed films of lipid and protein have a mosaic structure; probably the β-casein is in a compressed state whereas the apoprotein is extended as α-helices in the plane of the interface. The chain-length dependences of the interaction of the apoprotein with phosphatidylcholine monolayers and bilayers are different; when the apoprotein binds to bilayers of shorter-chain phosphatidylcholines it alters the shape of the lipid-water interface whereas with monolayers the interface remains planar throughout.     

Process and molecular data of branched 1,3-β-D-glucans in comparison with Xanthan

Bioreactor cultivations were carried out with Schizophyllum commune and Xanthomonas campestris. Influence of process parameters and downstream processing on molecular data (molecular weight, intrinsic and shear viscosity) of the secreted exopolysaccharide are shown. Glucan formation of S. commune was enhanced by oxygen limitation. Depending on the type of agitator used, a maximum glucan formation rate of 0.12 kg/(m³ · h) was reached. During cultivation molecular weight and intrinsic viscosity went through a broad maximum with maximum data of 1.3 10⁷ g/mol and 15,400 cm³/g, respectively. After substrate consumption glucan degrading enzymes (glucananses) were released by S. commune. For washing out low molecular substances and concentrating cellfree glucan solutions cross-flow filtration technique with hollow fiber cartridges (molecular cut-off 100,000) were used. After this procedure the shear and intrinsic viscosity were decreased. In contrast to Xanthan, shear viscosity of glucan solutions was not affected by a change in pH from 2 to 12. The intrinsic viscosity of aqueous Xanthan and glucan solutions was opposingly altered by adding salt.List of Symbols A number of capillaries - C ^*g/(dm³ · h) formation rate - D ^–1 shear rate - k Pa/sⁿ consistency index - n flow behaviour index - MW g/mol molecular weight - R m radius - t h time - V dm³ volume - Y yield coefficient - mPas shear viscosity - [] cm³/g intrinsic viscosity - Pa shear stress Indices PS polysaccharide - X cell mass - S substrate - m maximum Dedicated to Prof. Dr. Fritz Wagner on his 60th birthday     

Comprehensive analysis of the molecular docking of small molecule inhibitors to the Aβ1–40 peptide and its Osaka-mutant: insights into the molecular mechanisms of Aβ-peptide inhibition

Abstract

Alzheimer’s disease (AD) is the most common form of age-related neurodegeneration occurs because of deposition of proteins in the form of extracellular plaques containing aggregated amyloid beta (Aβ) peptide and intracellular neurofibrillary tangles composed of aggregated microtubule-binding protein tau. Amyloid aggregation process can be enhanced by several familial AD-associated mutations in Aβ peptide. In this study, we have unravelled the interactions of 40 small molecule inhibitors with the Osaka-mutant of Aβ_1–40 peptide at atomic level and characterized modes of their binding to mutant Aβ by docking approaches. We have also compared docking energies of these inhibitors with Osaka-mutant with those previously determined for the wild-type and Iowa-mutant peptides and discussed in light of the peptide conformations and non-covalent interactions. We have also discussed inhibition mechanisms of these three peptides. Our analyses revealed that these small molecules can efficiently inhibit Osaka-mutant. The binding modes of drugs with these three peptides are markedly different and so are the mechanisms of inhibition of these three peptides. Overall analysis of the data reveals that binding energy of Iowa-mutant drug complex is lowest and most stable which is followed wild-type peptide-drug complex followed by Osaka-mutant drug complex.

Communicated by Ramaswamy H. Sarma     

A comparison of the crosslinking abilities of glutaraldehyde,formaldehyde and α-hydroxyadipaldehyde with bovine serum albumin and casein

Summary The crosslinking effects of formaldehyde, -hydroxyadipaldehyde and glutaraldehyde have been compared by various techniques. Using a micro-Ouchterlony technique with an aldehyde treated bovine serum albumin-rabbit anti-bovine serum albumin system it was found that glutaraldehyde prevented precipitin line formation except at very high titres of antibody. The effects of formaldehyde and -hydroxyadipaldehyde were less marked. Cellulose acetate electrophoresis of aldehyde treated bovine serum albumin showed an increase in mobility compared with the untreated protein. Starch gel electrophoresis of aldehyde fixed liver slices showed no protein loss after glutaraldehyde fixation whereas the other aldehydes permitted proteins to be extracted. Polyacrylamide gel electrophoresis of the aldehyde treated bovine serum albumin showed a little change in mobility after formaldehyde and -hydroxyadipaldehyde treatment and a little polymer formation. Glutaraldehyde on the other hand produced much polymer. These findings were confirmed by gel filtration with Sephadex G-200. Intermolecular crosslinking with glutaraldehyde was dependant on the aldehyde concentration.     

The molecular weight of the basic polypetide chain αB2 of α-crystallin

The molecular weights calculated from the amino acid sequences of the A and B chains of the lens protein -crystallin differ only slightly (19830 and 20070, respectively). SDS gel electrophoresis of these chains and comparison with marker proteins yield apparent molecular weights of 19500 for A and 22500 for B. The discrepancy between the value of 22500 and the real molecular weight of 20070 for B vanishes by the combined use of SDS and 6 M urea in the polyacrylamide gels.     

Linking the molecular evolution of avian beta (β) keratins to the evolution of feathers

Feathers of today's birds are constructed of beta (β)-keratins, structural proteins of the epidermis that are found solely in reptiles and birds. Discoveries of \"feathered dinosaurs\" continue to stimulate interest in the evolutionary origin of feathers, but few studies have attempted to link the molecular evolution of their major structural proteins (β-keratins) to the appearance of feathers in the fossil record. Using molecular dating methods, we show that before the appearance of Anchiornis (～155 Million years ago (Ma)) the basal β-keratins of birds began diverging from their archosaurian ancestor ～216?Ma. However, the subfamily of feather β-keratins, as found in living birds, did not begin diverging until ～143?Ma. Thus, the pennaceous feathers on Anchiornis, while being constructed of avian β-keratins, most likely did not contain the feather β-keratins found in the feathers of modern birds. Our results demonstrate that the evolutionary origin of feathers does not coincide with the molecular evolution of the feather β-keratins found in modern birds. More likely, during the Late Jurassic, the epidermal structures that appeared on organisms in the lineage leading to birds, including early forms of feathers, were constructed of avian β-keratins other than those found in the feathers of modern birds. Recent biophysical studies of the β-keratins in feathers support the view that the appearance of the subfamily of feather β-keratins altered the biophysical nature of the feather establishing its role in powered flight.     

A mutant α-amylase with only part of the catalytic domain and its structural implication

A truncated mutant α-amylase, Xa-S2, was obtained from Xanthomonas campestris wild type α-amylases (Xa-WT) through random mutagenesis that contained 167 amino acid residues (approx 65% shorter than that of Xa-WT). Secondary structure prediction implied that Xa-S2, would be unable to form the whole (β/α)₈-barrel catalytic domain and did not have the three conserved catalytic residues of wild type α-amylase, but it still displays the starch-hydrolyzing activity. Xa-S2 was prepared, characterized and compared to the recombinant wild-type enzymes. The K _m for starch was 32 mg/ml; activity was optimal at pH 6.2 and 30°C. In contrast, the K _m for starch of Xa-WT was 8 mg/ml and optimal enzyme activity was at pH 6.0–6.2 and 45–50°C. Our results suggested that Xa-S2 is a new amylase with a minimal catalytic domain for hydrolyzing substrates with of α-1,4-glucosidic bonds. T. Ke and X. D. Ma contributed equally to this work     

Molecular modeling and spectroscopic studies of semustine binding with DNA and its comparison with lomustine–DNA adduct formation

Chloroethyl nitrosoureas constitute an important family of cancer chemotherapeutic agents, used in the treatment of various types of cancer. They exert antitumor activity by inducing DNA interstrand cross-links. Semustine, a chloroethyl nitrosourea, is a 4-methyl derivative of lomustine. There exist some interesting reports dealing with DNA-binding properties of chloroethyl nitrosoureas; however, underlying mechanism of cytotoxicity caused by semustine has not been precisely and completely delineated. The present work focuses on understanding semustine–DNA interaction to comprehend its anti-proliferative action at molecular level using various spectroscopic techniques. Attenuated total reflection–Fourier transform infrared (ATR-FTIR) spectroscopy is used to determine the binding site of semustine on DNA. Conformational transition in DNA after semustine complexation is investigated using circular dichroism (CD) spectroscopy. Stability of semustine–DNA complexes is determined using absorption spectroscopy. Results of the present study demonstrate that semustine performs major-groove-directed DNA alkylation at guanine residues in an incubation-time–drug-concentration-dependent manner. CD spectral outcomes suggest partial transition of DNA from native B-conformation to C-form. Calculated binding constants (K_a) for semustine and lomustine interactions with DNA are 1.53?×?10³ M^?1 and 8.12?×?10³ M^?1, respectively. Moreover, molecular modeling simulation is performed to predict preferential binding orientation of semustine with DNA that corroborates well with spectral outcomes. Results based on comparative study of DNA-binding properties of semustine and lomustine, presented here, may establish a correlation between molecular structure and cytotoxicity of chloroethyl nitrosoureas that may be instrumental in the designing and synthesis of new nitrosourea therapeutics possessing better efficacy and fewer side effects.     

Tissue culture fixation with diimidoesters—IV. A comparison between adipimidate and aldehydes of their effects on cell size and morphology

The effects of fixation with dimethyladipimidate (DMA) on cell size and morphology were compared with those from aldehydes (glutaraldehyde, formaldehyde) using African green monkey kidney CV1 cells. Fixation with any of the three fixatives makes the cells resistant to any considerable size alteration. Glutaraldehyde has the strongest stabilizing effect, formaldehyde occupies an intermediate position while DMA forms the least cross-links of all. Morphologically (phase contrast microscopy), DMA-fixed and aldehydes-fixed cells stained with haematoxylin/eosin were similar except that with DMA the nuclei exhibit a granular thread-like structure with apparent granular nucleolei. This was also observed in isolated nuclei. Furthermore, in DMA-fixed unstained cells the cytoplasmic filament bundles are very distinct. This feature is not present to the same extent in aldehydes-fixed cells. Data from stained CV1 monolayers, from determinations of free amino groups and from gel electrophoresis show that DMA fixation does not preclude a subsequent reaction with glutaraldehyde or formaldehyde.     

The parasitoid complex of Parthenolecanium corni Bouché in the city of Tbilisi and its surroundings and comparison with some other European countries

The European fruit lecanium (EFL), Parthenolecanium corni Bouché (Hemiptera: Coccoidea), is a common and harmful soft scale, which attacks Fraxinus oxycarpa Willd. and other ornamental and orchard plants in Tbilisi, Georgia. This study investigates the phenology, degree of plant damage and effect of parasitoids on this scale in Tbilisi, a densely populated area. We present data on the 32 species of chalcidoid parasitoids recorded from EFL in Georgia and south-eastern Europe. The scale is heavily parasitized in Tbilisi, but we did not find any variation in seasonal abundance. The most common parasitoid of EFL was Blastothrix longipennis (Hymenoptera: Encyrtidae).     

Expression of βA3/A1-crystallin in the developing and adult rat eye

Crystallins are very abundant structural proteins of the lens and are also expressed in other tissues. We have previously reported a spontaneous mutation in the rat βA3/A1-crystallin gene, termed Nuc1, which has a novel, complex, ocular phenotype. The current study was undertaken to compare the expression pattern of this gene during eye development in wild type and Nuc1 rats by in situ hybridization (ISH) and immunohistochemistry (IHC). βA3/A1-crystallin expression was first detected in the eyes of both wild type and Nuc1 rats at embryonic (E) day 12.5 in the posterior portion of the lens vesicle, and remained limited to the lens fibers throughout fetal life. After birth, βA3/A1-crystallin expression was also detected in the neural retina (specifically in the astrocytes and ganglion cells) and in the retinal pigmented epithelium (RPE). This suggested that βA3/A1-crystallin is not only a structural protein of the lens, but has cellular function(s) in other ocular tissues. In summary, expression of βA3/A1-crystallin is controlled differentially in various eye tissues with lens being the site of greatest expression. Similar staining patterns, detected by ISH and IHC, in wild type and Nuc1 animals suggest that functional differences in the protein, rather than changes in mRNA/protein level of expression, likely account for developmental abnormalities in Nuc1.