The source of oxygen in the reaction catalysed by collagen lysyl hydroxylase.

The synthetic peptides (Pro-Pro-Gly)5 and (Ile-Lys-Gly)5-Phe were hydroxylated with collagen prolyl hydroxylase and lysyl hydroxylase in an 18O2 atmosphere. The oxygen atoms in the hydroxy groups of hydroxyproline and hydroxylysine were 87% and 6.5% respectively derived from the atmospheric 18O2. The results are consistent with those reported previously for proline hydroxylation in vivo [Fujimoto & Tamiya (1962) Biochem. J. 84, 333-335; Prockop, Kaplan & Udenfriend (1962) Biochem. Biophys. Res. Commun. 9, 192-196; Fujimoto & Tamiya (1963) Biochem. Biophys. Res. Commun. 10, 498-501; Prockop, Kaplan & Udenfriend (1963) Arch. Biochem. Biophys. 101, 499-503] and in vitro [Cardinale, Rhoads & Udenfriend (1971) Biochem. Biophys. Res. Commun. 43, 537-543] and for lysine hydroxylation in vivo [Fujimoto & Tamiya (1963) Biochem. Biophys. Res. Commun. 10, 498-501]. In view of the similarities of these two oxygenase-type hydroxylation reactions the participation of intermediates is proposed, the oxygen atoms of which are exchangeable with those of water. The atmospheric oxygen atoms incorporated into the intermediate must be equilibrated with water oxygen atoms in the slower lysyl hydroxylase reaction.     

Towards a resolution on the inherent methodological weakness of the "effective number of codons used by a gene"

Recently Anders Fuglsang provided a modified way for calculating N(c) when biased discrepancy is present in a gene [Biochem. Biophys. Res. Commun. 317 (2004) 957]. Instead of taking the average codon homozygosity for each synonymous family type (as proposed by Wright) [Gene 87 (1990) 23] Fuglsang considered codon homozygosity of each amino acid individually. Marsashi and Najafabadi [Biochem. Biophys. Res. Commun. 324 (2004) 1] in their recent article demonstrated that the readjustment for overestimation at the level of individual amino acids results in loss of considerable amount of information. Immediately after the publication of Marsashi and Najafabadi, Fuglsang proposed that codon homozygosities can be calculated based on the classical population genetics [Biochem. Biophys. Res. Commun. 327 (2005) 1]. Though Fuglsang's approach is a novel one, it fails when any of the amino acids are absent in a gene. However, the inherent cause of overestimation at the level of individual amino acids is still obscured in the literature. Here in this communication we have presented a general condition where effective number of codons is overestimated using Wright's formula and also we propose a new way to calculate N(c), which is independent of amino acid composition.     

Oligomeric Aip2p/Dld2p modifies the protein conformation of both properly folded and misfolded substrates in vitro

Oligomeric actin-interacting protein 2 (Aip2p) [Nat. Struct. Biol. 2 (1995) 28]/D-lactate dehydrogenase protein 2 (Dld2p) [Yeast 15 (1999) 1377, Biochem. Biophys. Res. Commun. 295 (2002) 910] exhibits the unique grapple-like structure with an ATP-dependent opening [Biochem. Biophys. Res. Commun. 320 (2004) 1271], which is required for the F-actin conformation modifying activity in vitro and in vivo [Biochem. Biophys. Res. Commun. 319 (2004) 78]. To further investigate the molecular nature of oligomeric Aip2p/Dld2p, the substrate specificity of its binding and protein conformation modifying activity was examined. In the presence of 1mM ATP or AMP-PNP, oligomeric Aip2p/Dld2p bound to all substrates so far examined, and modified the conformation of actin, DNase I, the mature form of invertase, prepro-alpha-factor, pro-alpha-factor, and mitochondrial superoxide dismutase, as determined by the trypsin susceptibility assay. Of note, the activity could modify even the conformation of pathogenic highly aggregated polypeptides, such as recombinant prion protein in beta-sheet form, alpha-synuclein, and amyloid beta (1-42) in the presence of ATP. The in vivo protein conformation modifying activity, however, depends on the growth stage; the most significant substrate modification activity was observed in yeast cells at the log phase, suggesting the presence of a cofactor/s in yeast cells, where F-actin is supposed to be a major target in vivo. These data further support our previous notion that the oligomeric Aip2p/Dld2p may belong to an unusual class of molecular chaperones [Biochem. Biophys. Res. Commun. 320 (2004) 1271], which can target both properly folded and misfolded proteins in an ATP-dependent manner in vitro.     

Glucose regulation of beta-defensin-1 mRNA in human renal cells

We previously showed that beta-defensin-1 (BD-1), an anti-microbial peptide, is up-regulated during progressive hyperglycemia in the kidneys of the GK rat [R.A. Page, C.A. Morris, J.D. Williams, C.J. von Ruhland, A.N. Malik, Isolation of diabetes-associated kidney genes using differential display, Biochem. Biophys. Res. Commun. 232 (1997) 49-53, R.A. Page, A.N. Malik, Elevated levels of beta-defensin-1 mRNA in diabetic kidneys of GK rats, Biochem. Biophys. Res. Commun. 310 (2003) 513-521]. In this paper, we show that human beta-defensin-1 (hBD-1) mRNA is directly up-regulated by glucose in cultured human renal cells. hBD-1 mRNA levels increased by approximately 7-fold and approximately 4-fold in human embryonic kidney (HEK) cells and human mesangial cells (HMC) grown in 25mM glucose for four days, as determined by quantitative real-time PCR. Immunofluorescence showed that the hBD1 protein is located in the cytoplasm of HEK cells and transfected HMCs. The highest levels of hBD-1 mRNA were found in the kidney compared with 21 other human tissues. The increased expression of hBD-1 mRNA in cultured HMCs in high glucose suggests a role for hBD-1 in the molecular pathways induced during hyperglycemia.     

Hsp56 mRNA in Paracentrotus lividus embryos binds to a mitochondrial protein

We previously demonstrated that Paracentrotus lividus Hsp56 mitochondrial chaperonin is constitutively expressed during development, that it has a specific territorial distribution, both in normal and heat-shocked embryos, and that its amount increases after heat shock [Roccheri MC, Patti M, Agnello M, Gianguzza F, Carra E, Rinaldi AM. Localization of mitochondrial Hsp56 chaperonin during sea urchin development. Biochem Biophys Res Commun 2001;287:1093-98] and cadmium treatment [Roccheri MC, Agnello M, Boneventura R, Matranga V. Cadmium induces the expression of specific stress proteins in sea urchin embryos. Biochem Biophys Res Commun 2004;321:80-7]. In this study, we looked at Hsp56 mRNA during normal development and under stress conditions. The messenger is almost constantly expressed at all stages of development and its amount is steadily increased in stressed embryos. Moreover, we found, using T1 RNase protection assay, that the most proximal region of the 3'-UTR of the Hsp56 mRNA binds a 40 kDa protein: this factor is more abundant in the mitochondrial extract and, more specifically, in the outer membrane of the organelle.     

On the methodological weakness of 'the effective number of codons': a reply to Marashi and Najafabadi

In a recent publication [Biochem. Biophys. Res. Commun. 317 (2004) 957] it was proposed that the 'effective number of codons' (Nc) in a gene should be calculated by summing the individual amino acid Nc's using rounding whenever the codon homozygosities are lower than the reciprocal value of the number of members of the synonymous families. This led Marashi and Najafabadi to examine the consequences of individual re-adjustment when comparing observed Nc with the expected Nc under assumptions of no selection, and C=G and A=T [Biochem. Biophys. Res. Commun. 324 (2004) 1]. Clearly, the present methodology has some weaknesses; in this work, I discuss these in relation to the observations by Marashi and Najafabadi, and finally an alternative method for the calculation of Nc is introduced with the purpose of eliminating the need for re-adjustments.     

1 alpha,25-Dihydroxyvitamin D3 (calcitriol) stimulates proliferation of human circulating monocytes in vitro

Previous studies demonstrated that human circulating monocytes can proliferate in vitro when incubated with lectin-induced factor(s) from lymphocytes [(1985) Biochem. Biophys. Res. Commun., in press]. This study shows that human monocytes were induced to proliferate when incubated with 1 alpha,25-dihydroxyvitamin D3 (calcitriol) at physiological concentrations. The optimal dose was about 10 nM. Proliferative activity was examined both by measuring the [3H]thymidine incorporation and by counting cell nuclei. Among other derivatives of vitamin D3, 1 alpha,24R-dihydroxyvitamin D3 and 1 alpha,24R,25-trihydroxyvitamin D3 stimulated mitotic activity of monocytes. Addition of both calcitriol and lectin-stimulated lymphocyte-conditioned medium to the monocyte culture had an additional effect on the mitotic activity of monocytes.     

Inactivation of mitochondrial respiratory chain complex I leads mitochondrial nitric oxide synthase to become pro-oxidative

We recently demonstrated that mitochondrial nitric oxide synthase (mtNOS) functionally couples with mitochondrial respiratory chain complex I to produce nitric oxide [M.S. Parihar, R.R. Nazarewicz, E. Kincaid, U. Bringold, P. Ghafourifar, Association of mitochondrial nitric oxide synthase activity with respiratory chain complex I, Biochem. Biophys. Res. Commun. 366 (2008) 23-28] [1]. The present report shows that inactivation of complex I leads mtNOS to become pro-oxidative. Our findings suggest a crucial role for mtNOS in oxidative stress caused by mitochondrial complex I inactivation.     

In situ mechanical properties of the chondrocyte cytoplasm and nucleus

The way in which the nucleus experiences mechanical forces has important implications for understanding mechanotransduction. Knowledge of nuclear material properties and, specifically, their relationship to the properties of the bulk cell can help determine if the nucleus directly experiences mechanical loads, or if it is a signal transduction mechanism secondary to cell membrane deformation that leads to altered gene expression. Prior work measuring nuclear material properties using micropipette aspiration suggests that the nucleus is substantially stiffer than the bulk cell [Guilak, F., Tedrow, J.R., Burgkart, R., 2000. Viscoelastic properties of the cell nucleus. Biochem. Biophys. Res. Commun. 269, 781–786], whereas recent work with unconfined compression of single chondrocytes showed a nearly one-to-one correlation between cellular and nuclear strains [Leipzig, N.D., Athanasiou, K.A., 2008. Static compression of single chondrocytes catabolically modifies single-cell gene expression. Biophys. J. 94, 2412–2422]. In this study, a linearly elastic finite element model of the cell with a nuclear inclusion was used to simulate the unconfined compression data. Cytoplasmic and nuclear stiffnesses were varied from 1 to 7 kPa for several combinations of cytoplasmic and nuclear Poisson's ratios. It was found that the experimental data were best fit when the ratio of cytoplasmic to nuclear stiffness was 1.4, and both cytoplasm and nucleus were modeled as incompressible. The cytoplasmic to nuclear stiffness ratio is significantly lower than prior reports for isolated nuclei. These results suggest that the nucleus may behave mechanically different in situ than when isolated.     

Properties and distribution of the protein inhibitor (Mr 17,000) of protein kinase C.

Ca2+-dependent hydrophobic-interaction chromatography is a powerful tool for the identification and isolation of a variety of Ca2+-binding proteins which expose a hydrophobic site(s) in the presence of Ca2+ [Gopalakrishna & Anderson (1982) Biochem. Biophys. Res. Commun. 104, 830-836; Walsh, Valentine, Ngai, Carruthers & Hollenberg (1984) Biochem. J. 224, 117-127; McDonald & Walsh (1985) Biochem. J. 232, 559-567]. Using this approach, we isolated two potent and specific protein inhibitors of protein kinase C, of 17 kDa [McDonald & Walsh (1985) Biochem. J. 232, 559-567] and 12 kDa [McDonald & Walsh (1986) Biochem. Soc. Trans. 14, 585-586]. Although these inhibitors were purified by Ca2+-dependent hydrophobic-interaction chromatography and exhibit properties similar to those of calmodulin and related Ca2+-binding proteins, we were unable to demonstrate high-affinity Ca2+ binding to these inhibitors, using equilibrium dialysis. Protein kinase C exhibited half-maximal activity at 0.6 microM-Ca2+ in the presence of phospholipid and diacylglycerol, and complete inhibition by both inhibitors was observed over the range of Ca2+ concentrations examined (10 nM-10 microM). These observations suggest that the inhibitory action of these proteins does not require Ca2+. The inclusion of proteinase inhibitors during isolation of the kinase C inhibitors, as well as two-dimensional peptide mapping and amino acid analysis of the isolated proteins, suggested that the 12 kDa inhibitor is a proteolytic fragment of the 17 kDa protein which is generated during purification. Antibodies raised in rabbits against the bovine brain 17 kDa inhibitor were shown to be specific by Western immunoblotting and the competitive enzyme-linked immunosorbent assay method and were used to study the tissue and species distribution of this protein. The inhibitor was found to be present in several bovine, murine, avian and human tissues, consistent with a role in the regulation of a variety of physiological functions involving the widely distributed protein kinase C.     

Mechanism for action of electromagnetic fields on cells

A biophysical model for the action of oscillating electric fields on cells, presented by us before [Biochem. Biophys. Res. Commun. 272(3) (2000) 634-640], is extended now to include oscillating magnetic fields as well, extended to include the most active biological conditions, and also to explain why pulsed electromagnetic fields can be more active biologically than continuous ones. According to the present theory, the low frequency fields are the most bioactive ones. The basic mechanism is the forced-vibration of all the free ions on the surface of a cell's plasma membrane, caused by an external oscillating field. We have shown that this coherent vibration of electric charge is able to irregularly gate electrosensitive channels on the plasma membrane and thus cause disruption of the cell's electrochemical balance and function [Biochem. Biophys. Res. Commun. 272(3) (2000) 634-640]. It seems that this simple idea can be easily extended now and looks very likely to be able to give a realistic basis for the explanation of a wide range of electromagnetic field bioeffects.     

Activation of the binding of C1q to immune complexes by zinc

ZnSO4 promotes the binding of C1q to immune complexes over the same concentration range (10(-5)-10(-4) M) that it inhibits binding of C1 to cell-bound immunoglobulin [Biochem. Biophys. Res. Commun. (1981) 103, 856-862]. At higher concentrations (10(-3)-2 X 10(-2) M) ZnSO4 inhibited the binding of C1q to immune complexes, [Ki = (6 +/- 2) X 10(-3) M]. This inhibition could be correlated with a ZnSO4-induced change in the tryptophan fluorescence of C1q [delta F 25%, Kd = (9.9 +/- 1.0) X 10(-3) M].     

Type A allatostatins from Drosophila melanogaster and Diplotera puncata activate two Drosophila allatostatin receptors, DAR-1 and DAR-2, expressed in CHO cells

The type-A allatostatins A (AST-A) are a group of insect peptides with a common C-terminal motif Y/FXFGL-NH(2). The existence of at least four putative type A Drosophila melanogaster ASTs (called type A drostatins or DST-As) has been predicted from the sequence of a recently cloned DST-A preprohormone [C. Lenz et al. (2000) Biochem. Biophys. Res. Commun. 273, 126-1131]. SRPYSFGL-NH(2), (DST-3A), the only DST isolated from Drosophila so far, activated the first cloned DST-A GPCR (DAR-1) [N. Birgül et al. (1999) EMBO J. 18, 5892-5900]. A newly cloned orphan Dm GPCR, which shares 47% overall and 60% transmembrane region sequence identity with DAR-1, was classified as a second putative Dm DST-A receptor (DAR-2) [C. Lenz et al. (2000) Biochem. Biophys. Res. Commun. 273, 571-577]. Although activation of DAR-2 by DSTs has been postulated, no experimental evidence for that has been presented to date. In this study, we expressed both DAR-1 and DAR-2 in CHO cells and used a GTPgammaS and a Ca(2+) mobilization assay for pharmacological evaluation of the receptors. Synthetically prepared DST-As, as well as selected Diplotera punctata (cockroach) ASTs, activated DAR-1 and DAR-2 in both functional assays indicating ligand redundancy and cross species activity. Cell pretreatment with pertussis toxin led to some differences in the nature and magnitude of signaling pathways at the DAR-1 and DAR-2 receptors, suggesting possible differential coupling to cellular effector system(s) and distinct biological functions of each receptor in vivo.     

Nomenclature of lipoxins and related compounds derived from arachidonic acid and eicosapentaenoic acid

Oxygenated derivates of arachidonic acid and eicosapentaenoic acid which contain conjugated tetraene structures and are non-cyclized C20 carboxylic acids were first isolated and characterized from human and porcine leukocytes (Serhan, C.N. et al, 1984, Biochem. Biophys. Res. Commun. 118, 943-949; Wong, P.Y.-K., et al, 1985, Biochem. Biophys. Res. Commun. 126, 765-775). The trivial names lipoxins and lipoxenes have been introduced for compounds belonging to each of these series. Here, we propose that tetraene-containing compounds derived from arachidonic acid be denoted as lipoxins (LX) of the four series (i.e. lipoxin A4 or LXA4 and lipoxin B4 or LXB4) and those derived from eicosapentaenoic be termed lipoxins of the five series (i.e. lipoxin A5 or LXA5 and lipoxin B5 or LXB5).     

Synergism in mosquitocidal activity of 26 and 65 kDa proteins from Bacillus thuringiensis subsp. israelensis crystal

Three major protein components, 130, 65 and 26 kDa of solubilized Bacillus thuringiensis subsp. israelensis crystal were separated by gel filtration. The isolated 26 kDa protein is inactive against mosquito larvae at 6.4 μg/ml protein. The 65 kDa protein is also inactive towards mosquito larvae at low concentrations and shows but weak activity at higher concentrations. However, 26 and 65 kDa proteins simultaneously present at low concentrations exhibit high mosquitocidal activity. Similar synergistic effects are observed between 26 and 130 kDa proteins. These results differ from the findings of other investigators who have reported that a single protein component is sufficient for mosquitocidal activity [(1984) FEBS Lett. 175, 377-382; (1985) Biochem. Biophys. Res. Commun. 126, 961-965]. Our data suggest that the simultaneous presence of at least two proteins is required for activity.

Synergism Mosquitocidal activity Crystal protein     

Loss of the tyrosyl radical in mouse ribonucleotide reductase by (-)-epicatechin

The flavonoid (-)-epicatechin was previously demonstrated to interfere with tyrosine nitration by peroxynitrite [Biochem. Biophys. Res. Commun. 285 (2001) 782]. This effect was hypothesized to be based upon an interaction of epicatechin with a transiently generated tyrosyl radical. In the present study, using electron paramagnetic resonance, we demonstrate that (-)-epicatechin is capable of destabilizing the tyrosyl radical of the mouse ribonucleotide reductase R2 component. First-order rate constants for the disappearance of tyrosyl radical signals were 1 x 10(-4) and 2 x 10(-4)s(-1)for epicatechin and hydroxyurea, a well-known tyrosyl radical scavenger, respectively. In keeping with scavenging the ribonucleotide reductase tyrosyl radical, cellular production of deoxyribonucleotides and DNA synthesis were impaired by (-)-epicatechin in normal human keratinocytes and in human squamous carcinoma cells.     

Human platelets stimulated by thrombin produce platelet-activating factor (1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) when the degrading enzyme acetyl hydrolase is blocked.

It has been shown [Touqui, Jacquemin & Vargaftig (1983) Thromb. Haemostasis 50, 163; Touqui, Jacquemin & Vargaftig (1983) Biochem. Biophys. Res. Commun. 110, 890-893; Alam, Smith & Melvin (1983) Lipids 18, 534-538; Pieroni & Hanahan (1983) Arch. Biochem. Biophys. 224, 485-493] that rabbit platelets inactivate exogenous PAF (platelet-activating factor, PAF-acether) by a deacetylation-reacylation mechanism. The deacetylation step is catalysed by an acetyl hydrolase sensitive to the serine-hydrolase inhibitor PMSF (phenylmethanesulphonyl fluoride) [Touqui, Jacquemin, Dumarey & Vargaftig (1985) Biochim. Biophys. Acta 833, 111-118]. We report here that human platelets can produce PAF on thrombin stimulation. This production is marginal and transient, reaching a maximum at 10 min and decreasing thereafter. In contrast, 10-12 times more PAF is produced when platelets are treated with PMSF and stimulated with thrombin. Under these conditions, the maximum formation is observed at 30 min and no decline occurs for up to 60 min after stimulation. In addition, these platelets (treated with PMSF and stimulated with thrombin) incorporate exogenous labelled acetate in the 2-position of PAF, probably by an acetyltransferase-dependent mechanism. Production of PAF by human platelets during physiological stimulation can be demonstrated when PAF degradation is suppressed by the acetyl-hydrolase inhibitor PMSF.     

A stochastic model on DNA renaturation kinetics

A simple stochastic model on DNA renaturation kinetics in the presence and absence of cooperativity have been developed [the corresponding deterministic models have been explicitly treated in our previous work. Biochem Biophys Res Commun 293 (2002) 870-873]. Theoretical mean and variance of number of bases in single-stranded DNA (ssDNA), (which is of course a random variable) have been calculated and compared with the experimental values. The results showed that only the cooperative model correctly predicted the time t(m) at which variance becomes maximum whereas, the non-cooperative model overestimated it and thus proved the validity of the cooperative model. Some of the applications of this cooperative theory in resolving the problems of the central dogma of life, PCR etc. have also been discussed.     

Isolation and sequence determination of peptide components of atrial natriuretic factor

The independent isolation and sequence determination in our laboratories of three closely related Atrial Natriuretic Factor peptides from rat atria confirm the sequences of ANF peptides reported by Seidah et al and synthesized by Nutt et al [Proc. Natl. Acad. Sci., (1984) in press] and contain the sequences reported by Flynn et al [Biochem. Biophys. Res. Commun. (1983) 117: 859-865] and by Currie et al [Science (1984) 223: 67-69]. In addition, we provide proof for a C-terminal tyrosine rather than tyrosine amide in our isolated peptides.     

A 42,000-Da protein in rabbit tissues and in a glycogen synthase preparation cross-reacts with antibodies to glycogenin

Rabbit skeletal muscle glycogen previously has been shown to be covalently bound to a 40,000-Da protein ("glycogenin") via a novel glucosyl-tyrosine linkage [I.R. Rodriguez and W.J. Whelan (1985) Biochem. Biophys. Res. Commun. 132, 829-836]. Antibodies raised against rabbit skeletal muscle glycogenin cross-react with a similar protein present in rabbit heart and liver glycogens, as well as with a 42,000-Da "acceptor protein" present in high-speed supernatants of rabbit muscle, heart, retina, and liver. This 42,000-Da protein incorporates [U-14C]Glc when an ammonium sulfate fraction prepared from the tissue supernatants is incubated with UDP-[U-14C]Glc. The [U-14C]Glc incorporated can be removed quantitatively by treatment with amylolytic enzymes, indicating that the [U-14C]Glc incorporation represents elongation of a preexisting glucan attached to the acceptor protein. Furthermore, a commercial preparation of rabbit skeletal muscle glycogen synthase contains this 42,000-Da protein. We propose that the 42,000-Da protein represents the free form of glycogenin in tissues, with its covalently attached glucan chain(s) providing a "primed" elongation site for glycogen synthesis.