Characterization of 236 novel alleles at the HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 loci from China Marrow Donor Program

Two hundred and thirty-six novel human leukocyte antigen (HLA) alleles are described from volunteer donors of the China Marrow Donor Program: 71 HLA-A alleles, 79 HLA-B alleles, 43 HLA-C, 16 HLA-DRB1 alleles, 26 HLA-DQB1 and 1 HLA-DPB1. Two hundred and thirteen (90.3%) of the 236 novel alleles are single nucleotide substitution variants when compared with their most homologous allele. Seventy-eight of these single nucleotide variants are silent substitutions. The remaining novel alleles differ from their most similar allele by two to four nucleotide substitutions. Some of the novel alleles encode amino acid changes at positions not previously reported to be polymorphic, such as codons 57, 62, 67, 41 and 52 in HLA-A alleles; codons 133, 156, 201 and 215 in HLA-B alleles; codons 74, 208 and 225 in HLA-C; codons 25, 32 and 72 in HLA-DRB1; codons 20, 39 and 77 in HLA-DQB1.

Production of cloned calves by combination treatment of both donor cells and early cloned embryos with 5-aza-2/-deoxycytidine and trichostatin A

We previously reported that treatment of both donor cells and early cloned embryos with a combination of 0.01 μM 5-aza-2(/)-Deoxycytidine (5-aza-dC) and 0.05 μM trichostatin A (TSA) significantly improved development of cloned bovine embryos in vitro. In the present study, we investigated the effect of this combination treatment on the in vivo development potency and postnatal survivability of cloned calves. Blastocysts (77 and 82 blastocysts derived from untreated (control) and treated groups, respectively) were individually transferred to recipient cows. Relative to the control group, the combination treatment of both donor cells and early embryos with 5-aza-dC and TSA dramatically increased the cleavage rate (49.2 vs 63.6%, P < 0.05) at 24 h of culture, and blastocyst development rate on Days 6 and 7 of culture (18.8 vs 33.9% and 27.1 vs 38.5% respectively, P < 0.05). Although pregnancy rate did not differ 40 d after transfer, it was lower in the treated than control group 90 d after transfer (7.8 vs 29.3%, P < 0.05). In the control group, there were three calves born to 77 recipients (only two survived beyond 60 d), whereas in the treated group, 17 calves were born to 82 recipients, and 11 survived beyond 60 d. In conclusion, a combination treatment of donor cells and early cloned embryos with 5-aza-dC and TSA significantly enhanced development of somatic cell cloned bovine embryos in vivo; cloning efficiency (number of surviving calves at 60 d of birth/number of recipient cows) was increased from 2.6 to 13.4%.

The significance of neuroglobin in the brain

Since its discovery in 2000, neuroglobin (Nb) has been demonstrated to have an essential and conserved function in vertebrates with the consequential discovery of a neuroprotective role. Nb is a member of the globin superfamily and is predominantly expressed in neurons of the central and peripheral nervous system. Thorough studies have been performed to elucidate the molecular structure of Nb and its ligand binding characteristics. The precise physiological function and mechanism of action of Nb is beginning to be established, with a number of hypotheses having been put forward. While Nb shares an intrinsic affinity for low-molecular weight diatomic gases similar to other globins, the relatively low level of Nb expression in cerebral neurons places limitations on its potential to function as a reservoir for oxygen, especially during periods of acute ischemia. In vitro studies have suggested that the neuroprotective role of Nb may be due to its ability to scavenge reactive oxygen (ROS) and nitrogen (RNS) species. However other studies have proposed Nb as being part of a signalling chain that transmits the redox state of the cell that is protective against oxidative stress or that inhibits apoptosis. This review is intended to summarize the structural, genomic and functional data on neuroglobin to date, thereby providing perspectives for future research on these molecules that may have substantial biomedical implications.

Adaptive evolution of the mitochondrial ND6 gene in the domestic horse

Mitochondria play a crucial role in energy metabolism through oxidative phosphorylation. Organisms living at high altitudes are potentially influenced by oxygen deficits and cold temperatures. The severe environmental conditions can impact on metabolism and direct selection of mitochondrial DNA. As a wide-ranging animal, the domestic horse (Equus caballus) has developed various morphological and physiological characteristics for adapting to different altitudes. Thus, this is a good species for studying adaption to high altitudes at a molecular level. We sequenced the complete NADH dehydrogenase 6 gene (ND6) of 509 horses from 24 sampling locations. By comparative analysis of three horse populations living at different altitudes (>2200 m, 1200-1700 m, and <900 m), we found that the high-altitude population had the lowest genetic diversity and significant negative Tajima's D; both values declined with increasing elevation. Moreover, non-directional selection was identified for the ND6 gene by a tree-based relative ratio test (P = 0.007); the highest proportion of high-altitude horses was found distributed on the selected branches. We conclude that the high-altitude environment has directed adaptive evolution of the mitochondrial ND6 gene in the plateau horse.

[Thickness of the retinal nerve fiber layer in unilateral amblyopic patients with high myopia in children]

OBJECTIVE

To investigate the retina nerve fiber layer (RNFL) thickness in unilateral amblyopic patients with high myopia.

METHODS

Twenty-three cases (23 eyes) with unilateral high myopia amblyopia were tested by GD(X) ECC with laser polarized light scans in the posterior pole of retina, to measure the relative RNFL thickness according to papilla optical as a center, 3.2 mm as the diameter of outer ring, 2.4 mm as the diameter of inner ring. The relative RNFL thickness of high myopia amblyopia was compared with fellow eyes, normal eyes and high myopia respectively and statistics analysis.

RESULTS

TSNIT average, superior average and inferior average of RNFL in high myopia amblyopia became thinning (56.39 +/- 5.69, 68.30 +/- 10.16, 67.34 +/- 5.83), it showed statistically differences when compared with fellow eyes (t = 2.090, 2.243, 4.236) and normal eyes (t = 3.087, 1.025, 3.481) (P < 0.05). RNFL parameters were no statistically significant differences between high myopia amblyopia and simple high myopia (t = 0.872, 0.297, 0.658; P > 0.05). TSNIT average decreases with axial length in high myopia amblyopia and high myopia, there was inverse linear correlation between RNFL thickness and axial length (r = -0.462, -0.395; P < 0.05).

CONCLUSIONS

The RNFL thickness of unilateral high myopia amblyopia of children was thinner than normal, but there wasn't obvious compared with simple high myopia. The reasons for decreased best corrected vision of unilateral high myopia amblyopia in children still need further research.

Development in vitro and mitochondrial fate of interspecies cloned embryos

Although the technique of interspecies somatic cell nuclear transfer can be used to increase the population size of endangered mammals, the mitochondrial heteroplasmy in cloned embryos and animals makes this idea doubtful. In present study, goat-sheep cloned embryos were constructed by fusing goat foetal fibroblasts (GFFs) into sheep oocytes and then cultured in vitro to investigate the capability of sheep oocyte dedifferentiating GFF nucleus. Moreover, at each stage of 1- (immediately after fused), 2-, 4-, 8-, 16-cell, morula and blastocyst, the copy number of mtDNA from GFF and sheep oocyte was examined using real-time PCR. The results showed that: 7.4% of the fused cloned embryos can develop to the blastocyst stage; in the process of one cell to the morula stage, the copy number of two kinds of mtDNA was stable relatively; however, in the process of morula to the blastocyst stage, the decreasing in the copy number of GFF-derived mtDNA, while the increasing in sheep oocyte-derived, resulted in their ratio of decreasing sharply from 2.0 +/- 1.0% to 0.012 +/- 0.004%. This study demonstrates that: (i) the goat-sheep cloned embryos have the ability to develop to blastocyst in vitro; (ii) from the morula stage to the blastocyst stage of goat-sheep cloned embryos, goat derived mitochondria can be gradually replaced with those from sheep oocyte.

The effect of contact lens induced oedema on the accuracy of Goldmann tonometry in a mature population

AIM

To determine the effect of contact lens induced oedema on the accuracy of Goldmann tonometry measurements of intraocular pressure (IOP) in mature subjects.

METHODS

22 healthy subjects aged between 50 and 60 years were recruited. Corneal curvature, IOP, and central corneal thickness (CCT) were measured before and after two hours of monocular closed eye wear of a thick hydroxyethyl methacrylate (HEMA) contact lens. Measurements were then repeated at 20 minute intervals for one hour after lens removal.

RESULTS

Both CCT (+54.1 mum) and IOP (+2.7 mm Hg) increased significantly after lens wear (p<0.001, paired t test with Bonferroni correction). For the hour following lens removal, the measured IOP was correlated to the increase in CCT (r = 0.84, p<0.001), at a rate of 1.0 mm Hg/10 mum (95% confidence interval, 0.8 to 1.2 mm Hg/10 mum, linear mixed model analysis).

CONCLUSIONS

A relatively small increase in CCT from contact lens induced corneal oedema caused an overestimation error in Goldmann tonometry measurements of IOP in healthy mature subjects.

Role of interleukin (IL)-1 type 1 receptor in mycobacterial infection

It is important to gain a better understanding of IL-1-mediated signaling events in mycobacterial infection. In order to clarify the role of IL-1 receptor type 1 (IL-1 R1) in IL-1 R1, knockout (KO) mice were infected with either Mycobacterium tuberculosis H37Rv or Kurono strain by the respiratory route, and their ability to control mycobacterial growth, pulmonary granuloma formation, and cytokine mRNA expression was investigated. IL-1 R1 KO mice developed significantly larger (P< 0.01) granulomatous lesions with neutrophil infiltration in their lungs than wild-type mice did after infection with the M. tuberculosis Kurono strain. The number of mycobacterial colonies in lungs and spleen increased from five weeks post-infection. Interferon-y production by spleen cells was low in IL-1 R1 KO mice. It is concluded that the IL-1 R1 is essential for IL-1-mediated signaling events in mycobacterial infection.

Interaction of morin with CTMAB: aggregation and location in micellar

The aggregation and location of morin in CTMAB micellar solution was studied by light scattering spectra, electronic absorption spectra and pulsed FT NMR techniques. The difference in the light scattering property of morin with and without CTMAB proved that a large particle of the morin-CTMAB associate formed. Morin has a self-assembly tendency, but the assembly number is not high. With the increase of morin concentration, morin changed from a monomer to dimer. The hyperchromic and bathochromic effect of morin, with the increase in pH value or

Support vector machine approach for protein subcellular localization prediction

MOTIVATION

Subcellular localization is a key functional characteristic of proteins. A fully automatic and reliable prediction system for protein subcellular localization is needed, especially for the analysis of large-scale genome sequences.

RESULTS

In this paper, Support Vector Machine has been introduced to predict the subcellular localization of proteins from their amino acid compositions. The total prediction accuracies reach 91.4% for three subcellular locations in prokaryotic organisms and 79.4% for four locations in eukaryotic organisms. Predictions by our approach are robust to errors in the protein N-terminal sequences. This new approach provides superior prediction performance compared with existing algorithms based on amino acid composition and can be a complementary method to other existing methods based on sorting signals.

AVAILABILITY

A web server implementing the prediction method is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/.

SUPPLEMENTARY INFORMATION

Supplementary material is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/.

A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach

We have introduced a new method of protein secondary structure prediction which is based on the theory of support vector machine (SVM). SVM represents a new approach to supervised pattern classification which has been successfully applied to a wide range of pattern recognition problems, including object recognition, speaker identification, gene function prediction with microarray expression profile, etc. In these cases, the performance of SVM either matches or is significantly better than that of traditional machine learning approaches, including neural networks.The first use of the SVM approach to predict protein secondary structure is described here. Unlike the previous studies, we first constructed several binary classifiers, then assembled a tertiary classifier for three secondary structure states (helix, sheet and coil) based on these binary classifiers. The SVM method achieved a good performance of segment overlap accuracy SOV=76.2 % through sevenfold cross validation on a database of 513 non-homologous protein chains with multiple sequence alignments, which out-performs existing methods. Meanwhile three-state overall per-residue accuracy Q(3) achieved 73.5 %, which is at least comparable to existing single prediction methods. Furthermore a useful "reliability index" for the predictions was developed. In addition, SVM has many attractive features, including effective avoidance of overfitting, the ability to handle large feature spaces, information condensing of the given data set, etc. The SVM method is conveniently applied to many other pattern classification tasks in biology.

Distinct topologies of mono- and decavanadate binding and photo-oxidative cleavage in the sarcoplasmic reticulum ATPase

UV irradiation of the sarcoplasmic reticulum (SR) ATPase in the presence of vanadate cleaves the enzyme at either of two different sites. Under conditions favoring the presence of monovanadate, and in the presence of Ca(2+), ADP, and Mg(2+), cleavage results in two fragments of 71- and 38-kDa electrophoretic mobility. On the other hand, under conditions permitting formation of decavanadate, and in the absence of Ca(2+) and ADP, cleavage results in two fragments of 88- and 21-kDa electrophoretic mobility. The amino terminus resulting from cleavage is blocked and resistant to Edman degradation. However, the initial photo-oxidation product can be reduced with NaB(3)H(4,) resulting in incorporation of radioactive (3)H label. Extensive digestion of the labeled protein with trypsin then yields labeled peptides that are specific for the each of the photo-oxidation conditions, and can be sequenced after purification. Collection of the Edman reaction fractional products reveals the radioactive label and demonstrates that Thr(353) is the residue oxidized by monovanadate at the phosphorylation site (i.e. Asp(351)). Correct positioning of monovanadate at the phosphorylation site requires binding of Mg(2+) and ADP to the Ca(2+)-dependent conformation of the enzyme. Subsequent hydrolytic cleavage is likely assisted by the neighboring Asp(601), and yields the 71- and 38-kDa fragments. On the other hand, Ser(186) (and possibly the following three residues: Val(187), Ile(188), and Lys(189)) is the residue that is photo-oxidized by decavanadate in the absence of ADP. Hydrolytic cleavage of the oxidized product at this site is likely assisted by neighboring acidic residues, and yields the 88- and 21-kDa fragments. The bound decavanadate, which we find to produce steric interference with TNP-AMP binding, must therefore extend to the A domain (i.e. small cytosolic loop) in order to oxidize Ser(186). This protein conformation is only obtained in the absence of Ca(2+).

Activity of an alcohol-based hand gel against human adeno-, rhino-, and rotaviruses using the fingerpad method

OBJECTIVE

To assess the activity against three non-enveloped viruses (an adeno-, a rhino- and a rotavirus) of a gel containing 60% ethanol, using experimentally contaminated thumb- and fingerpads of 12 panelists, as per standard procedure E-1838-96 of the American Society of Testing and Materials.

DESIGN

Each digit received 10 microL of the test virus suspension. The inoculum from the thumbs was eluted immediately with 990 microL of Earle's balanced salt solution (EBSS) to assess the amount of virus on each digit (0-minute control). The inoculum on the fingers was allowed to dry (20-25 minutes), and virus was eluted from two fingerpads to determine the loss in virus infectivity upon drying (baseline titer). Then the dried inoculum on randomly selected fingers was exposed to 1 mL of the test product or standard hard water (200-ppm calcium carbonate) for 20 seconds. The virus remaining was eluted with 1 mL of EBSS, titrated to determine the amounts eliminated, and compared to the baseline titer.

RESULTS

Each digit received at least 10(4) plaque-forming units of virus in 10 microL. The amounts of adeno-, rhino-, and rotaviruses surviving the drying were 30%, 75%, and 42%, respectively. The product reduced the infectivity titers of the three viruses by 3 to >4 log10 when compared to a reduction of < or =1 log10 for the hard-water rinse.

CONCLUSION

The level of virus reduction by gel was statistically significantly higher than that seen with the water control. Evidence for such activity against non-enveloped viruses supports further investigation of the benefits of this product.

GCIP, a novel human grap2 and cyclin D interacting protein, regulates E2F-mediated transcriptional activity

Regulation of mammalian cell growth and proliferation is governed through receptor-mediated signaling networks that ultimately converge on the cell cycle machinery. Adaptor proteins play essential roles in the formation of intracellular signaling complexes, relaying extracellular signals from the plasma membrane to the nucleus of a cell. The leukocyte-specific adaptor protein Grap2 is a central linker protein in immune cell signaling and activation. Using Grap2 as bait protein, we identified a novel human protein, GCIP (Grap2 cyclin-D interacting protein). We found that GCIP bound to Grap2 in both yeast two-hybrid assays and in mammalian cells through binding to the COOH-terminal unique domain and SH3 domain (designated QC domain) of Grap2. GCIP also associated with cyclin D both in vitro and in vivo. The expression of GCIP was found in all human tissues examined with the highest level of expression in the heart, muscle, peripheral blood leukocytes, and brain. Furthermore, phosphorylation of retinoblastoma protein by cyclin D-dependent protein kinase was reduced and E2F1-mediated transcription activity was inhibited in cells transfected with GCIP. High level expression of GCIP in terminally differentiated tissues and the inhibition of E2F1 transcription activation suggest that GCIP could play an important role in controlling cell differentiation and proliferation.

Characterization of calcium, nucleotide, phosphate, and vanadate bound states by derivatization of sarcoplasmic reticulum ATPase with ThioGlo1

Sarcoplasmic reticulum vesicles were incubated with the maleimide-directed probe ThioGlo1, resulting in ATPase inactivation. Reacted ThioGlo1, revealed by its enhanced fluorescence, was found to be associated with the cytosolic but not with the membrane-bound region of the ATPase. The dependence of inactivation on ThioGlo1 concentration suggests derivatization of approximately four residues per ATPase, of which Cys(364), Cys(498), and Cys(636) were identified in prominently fluorescent peptide fragments. These cysteines reside within the phosphorylation and nucleotide-binding region of the ATPase. Accordingly, protection is observed in the presence of ATP, 2'(3')-O-(2,4,6-trinitrophenyl)adenosine 5'-diphosphate (TNP-AMP), or an fluoroisothiocyanate label of Lys(515). Furthermore, protection is observed in the presence of vanadate (or decavanadate), but not in the presence of phosphate. Labeling occurs equally well in the presence or in the absence of Ca(2+) and thapsigargin, excluding a role of the E1-to-E2 transition in the protective effect of vanadate. It is concluded that protection by vanadate is due to formation of a pentacoordinated orthovanadate complex at the phosphorylation site, corresponding to a stable transition state analog of the phosphorylation reaction, with intermediate characteristics of the EP1 and EP2 states. The lack of protection by phosphate is attributed to instability of its complex with the enzyme (EP2). These findings are discussed with respect to different structural images obtained from diffraction studies of ATPase in the presence or in the absence of Ca(2+) and/or decavanadate (Ogawa et al., 1998, Biophys. J. 75:41-52).

Molecular cloning and expression of human grap-2, a novel leukocyte-specific SH2- and SH3-containing adaptor-like protein that binds to gab-1

The SH2- and SH3-containing adaptor molecules serve to recruit cytosolic signal-transducing molecules to the activated receptor tyrosine kinases. In this study, we report the molecular cloning of a novel adaptor-like protein, Grap-2 (Grb-2 related adaptor protein 2), using the multisubstrate docking protein Gab-1 as bait in the yeast two-hybrid system. Sequence analysis revealed that Grap-2 contains a SH3-SH2-SH3 structure that has a high degree of sequence homology to those of the Grb-2 and Grap adaptor molecules. However, unlike in Grap and Grb-2, the SH2 and the C-terminal SH3 domains of Grap-2 are separated by a 120-amino-acid glutamine-rich sequence that shows no apparent homology to any known molecule or structural motif. The C-terminal SH3 domain of Grap-2 alone is sufficient to bind to Gab-1. Furthermore, Northern blot analysis demonstrated that Grap-2 has two major transcripts of 1.4 and 4.0 kb that can only be detected in tissues rich in leukocytes and in two leukemia cell lines. This highly restricted pattern of expression suggests that Grap-2 may participate in leukocyte-specific protein tyrosine kinase signaling.

The role of the thalamus and basal ganglia in parkinsonian tremor

The mechanism of parkinsonian tremor may involve a central oscillator, peripheral feedback to the central nervous system (CNS), or both. The thalamus or the globus pallidus is the most likely site for a central oscillator and would be predicted to generate thalamic tremor-related activity characterized, respectively, by calcium spike-associated bursts and by maximal tremor-related activity in the pallidal relay nucleus of thalamus. Thalamic spike trains demonstrate neither of these characteristics. However, cross-correlation, latency, and transfer function analysis indicate that sensory feedback is a critical element in the relationship between thalamic activity and parkinsonian tremor. Therefore, thalamic spike train activity is most consistent with parkinsonian tremor being mediated by peripheral inputs involved in either an unstable reflex loop or sensory modulation of a central oscillator.

[Effects of NPY microionophoresis on the units in nucleus tractus solitarius (NTS) responsive to baro- and chemoreceptor]

This experiment is designed to study the effects of NPY microionophoresis on the units in NTS responsive to baro- and chemoreceptor activiation at cellular level. In the experiment, it examined 62 units with spontaneous discharge in NTS. Among them, 34 were excited and 19 were inhibited by NPY microionophoresis. And other 9 units failed to respond to NPY microionophoresis. The units with the increase and decrease of discharge frequency to the activation of carotid baroreceptor showed excitation (16/21) and inhibition (7/11) respectively in response to NPY microionophoresis. The units with the increase (8/14) and decrease (5/9) of discharge frequency to the activation of carotid chemoreceptor mainly showed excitation.

Lys515-Lys492 cross-linking by DIDS interferes with substrate utilization by the sarcoplasmic reticulum ATPase

Sarcoplasmic reticulum (SR) Ca2+ ATPase was derivatized with 4,4'-diisothiocyanatostilbene-2,2'-sulfonic acid (DIDS), and complete enzyme inactivation was produced with a molecular stoichiometry of one DIDS per ATPase. It was determined by peptide analysis and sequencing that Lys492 and Lys515 were the ATPase residues derivatized by DIDS. Lack of electrophoretic resolution of the two peptide fragments that result from a single tryptic cut at Arg505 demonstrated that the two derivatized residues were cross-linked. Cross-linking of Lys492 and Lys515 by DIDS interfered with ATPase utilization of both ATP and p-nitrophenyl phosphate substrates, whereas derivatization of only Lys515 with fluorescein isothiocyanate interfered with ATPase utilization of ATP but not of p-nitrophenyl phosphate. Cross-linking with DIDS implies a distance of approximately 13 A between Lys492 and Lys515, which corresponds to the length of ATP bound in an extended configuration. Therefore, within the groove of the nucleotide binding domain, the ATP substrate is positioned with the adenosine moiety near Lys515 and its terminal phosphate near Lys492.

Synthesis of a radioactive azido derivative of thapsigargin and photolabeling of the sarcoplasmic reticulum ATPase

A thapsigargin C8-derivative (ZTG) was synthesized by acylating debutanoylthapsigargin with 4-azido[carboxyl-14C]benzoic acid. ZTG retains the inhibitory activity of thapsigargin (TG) with respect to the Ca2+ ATPase of sarcoplasmic reticulum (SR). Covalent ATPase labeling was obtained by photoactivation of the ZTG azido moiety under conditions optimized to reduce nonspecific association of ZTG with SR vesicles and to approximate a matching ZTG:ATPase stoichiometry. Specific photolabeling of the Ca2+ ATPase with ZTG was obtained with 30% efficiency and was competitively inhibited by TG. Analysis of the labeled protein and its proteolytic fragments demonstrates that the ZTG label is associated covalently with the membrane-bound portion of tryptic subfragment A1, which spans the sequence between Leu253 and Arg324 and includes segments of S3 and S4 in the stalk, the M3 and M4 transmembrane helices, and the intervening lumenal loop. This finding is in agreement with previous spectroscopic observations and mutational analysis.

Primary structure of bovine adenosine deaminase

Derivatized bovine adenosine deaminase is used in enzyme replacement therapy and as an adjunct to gene therapy against severe combined immunodeficiency syndrome. Although a gene sequence is known for human adenosine deaminase, the structure of the bovine enzyme has not been characterized. Structure studies using mass spectrometry are reported here that evaluate sequence, processing, post-translational modifications and the extent of homology between the human protein and its therapeutic surrogate.

Purification and characterization of proteasomes from Trypanosoma brucei

Proteasomes are multisubunit proteases that exist universally among eukaryotes. They have multiple proteolytic activities, and are believed to have important roles in regulating cell cycle, selective intracellular proteolysis, and antigen presentation. To determine the possible role that proteasomes may play in controlling the life cycle of African trypanosomes, we have isolated proteasomes from the bloodstream and the insect (procyclic) forms of Trypanosoma brucei by DEAE-cellulose chromatography and glycerol gradient fractionation in the presence of ATP. No 26 S proteasome homologs was identified in T. brucei under these experimental conditions. The proteasomes isolated from these two forms of T. brucei are very similar to the rat blood cell 20 S proteasome in their general appearance under the electron microscope. The profile of trypanosome proteasome subunits in sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) has eight visible protein bands with molecular weights ranging from 23 to 34 kDa, and cross-reacted very poorly with the anti-human 20 S proteasome antibodies on immunoblots. Two-dimensional gel electrophoresis of the parasite proteasomes shows a similar number of major subunits with pI's ranging from 4.5 to 7. Using a variety of fluorogenic peptides as substrates, the trypanosome proteasomes exhibited unusually high trypsin-like, but somewhat lower chymotrypsin-like activities, as compared to the rat 20 S proteasome. These proteolytic activities were, however, insensitive to phenylmethylsulfonyl fluoride (PMSF), tosyl-phenylalanine chloromethylketone (TPCK), tosyl-lysine chloromethylketone (TLCK) and trans-epoxy succinyl-L-leucylamido-(4 guanidino) butane (E-64), but the trypsin-like activity of trypanosome proteasomes was inhibited by leupeptin, an aldehyde known to inhibit the trypsin-like activity of mammalian proteasomes, thus ruling out possible contamination by other serine or cysteine proteases. Some quantitative differences in the substrate specificities between the proteasomes from bloodstream and procyclic forms were indicated, which may play a role in determining the differential protein turnovers at two different stages of development of T. brucei.

Cloning by functional complementation in Trypanosoma brucei

A procyclic Trypanosoma brucei double-knockout mutant lacking the ornithine decarboxylase (ODC) gene was transfected with a T. brucei genomic library in the expression vector pTSO-HYG4, which utilizes the PARP promoter and replicates extrachromosomally by virtue of a minicircle origin of replication. Transfectants which grew in the absence of exogenous putrescine, the product of the ODC-catalyzed reaction, were obtained at a frequency of 1.6 x 10(-7) and shown to restore ODC protein synthesis and enzymatic activity. Restriction enzyme patterns and Southern blot analysis of plasmids recovered from these cells and propagated in E. coli showed that the inserts contained a single copy of the T. brucei ODC gene. These results demonstrate for the first time the feasibility of identifying novel T. brucei genes by direct complementation of mutant T. brucei cell lines.

Mutation in the interdomain tether influences the stability and refolding of the enzyme rhodanese

Rhodanese is a single polypeptide chain of 293 amino acids that is folded into two globular domains of nearly equal size that are connected by a 16 amino acid tether. Two amino acids, Val-Asp (VD), were inserted into the interdomain tether through site-directed mutagenesis to produce the new interdomain sequence, E145PSRPEPAIFKAVDTLNR. The purified mutant protein, when unperturbed, was virtually indistiguishable in all properties tested and gave a specific activity that was at least 90% of the WT. However, the tether mutant was considerably less stable to perturbation compared with the WT enzyme. The interdomain hydrophobic surfaces in the mutant were more easily exposed, and the formation of intermediate folding states was facilitated. The rate of unassisted refolding was slightly less for the mutant, and the yield of active enzyme was somewhat reduced. The mutation introduced a new V8 proteinase cleavage site, but this site was not accessible in the native mutant which was as resistant to proteolysis as the WT enzyme. However, perturbation with low concentrations of urea that could form folding intermediate(s), allowed facile cleavage of the mutant to give fragments that appeared to represent the individual domains. In addition, the perturbed mutant could be proteolyzed close to one end of the polypeptide, a position that is far from the site of mutation, and which was not readily cleaved in the WT enzyme or the native form of the mutant. These results indicate that mutation in the interdomain tether can have dramatic effects on the stability and conformational transitions of rhodanese.

Rhodanese conformational changes permit oxidation to give disulfides that form in a kinetically determined sequence

When the structure of the monomeric enzyme rhodanese is perturbed by urea or SDS and heat, sulfhydryl assays combined with SDS gel analyses reveal that intrachain disulfides are formed rapidly. Two intrachain disulfide bonded species can be distinguished. One contains a single disulfide and comigrates on SDS gels with fully reduced rhodanese (Band I), while a second species contains two disulfides and migrates faster than the reduced enzyme (Band II). The kinetic path and identity of the participating sulfhydryl groups are suggested by the results with sulfhydryl mutants. On mild oxidation or perturbation, a single disulfide forms that involves two of the three sulfhydryl groups in C-terminal domain of the protein, i.e., two of the sulfhydryl groups from among the three residues: the active-site Cys-247, Cys-254 and Cys-263. These disulfides are the same as those that are formed upon oxidation of the native enzyme. The remaining sulfhydryl group of these three, in a kinetically slower process, can form a disulfide with Cys-63 which is in the N-terminal domain in native rhodanese. The resulting looped structure is so conformationally constrained that its shape and/or altered SDS binding gives rise to the 'fast' Band II on the SDS gels. The conformationally constrained species with two disulfides may be related to oxidized rhodanese species that are difficult to reduce.

Assay and purity control of minocycline by thin-layer chromatography using UV and fluorescence densitometry--a comparison with liquid chromatography

A thin-layer chromatography (TLC) method using UV and fluoresecence densitometry is described for the assay and purity control of minocycline (MC). With a mobile phase dichloromethane-methanol-water (57:35:8, v/v/v) and a silica gel thin-layer, previously sprayed with 10% m/v sodium edetate adjusted to pH 9.0, 4-epiminocycline and 7-didemethylminocycline were well separated from MC and from each other, 7-monodemethylminocycline and 6-deoxy-6-demethyltetracycline (6-DODMTC) were not separated from each other and were only partially separated from minocycline. 6-DODMTC was selectively determined by fluorescence densitometry, while quantification of other impurities and the assay of MC were performed by UV densitometry. Results obtained with qualitative TLC were compared with those obtained by a liquid chromatography (LC) method using a poly(styrene-divinylbenzene) copolymer stationary phase. The correlation coefficient for TLC and LC results was > 0.999. For TLC the relative standard deviation for the assay of MC at 1.25 mg ml-1 was < 3.0% (n = 4), while for LC it was < 1.0% (n = 4).

Synthesis and interaction of fluorescent thapsigargin derivatives with the sarcoplasmic reticulum ATPase membrane-bound region

Fluorescent derivatives of thapsigargin (TG) were synthesized by replacing the C8-butanoyl chain with a dansyl (DTG) or eosin (ETG) moiety. DTG and ETG retain the inhibitory effect of TG on the sarcoplasmic reticulum (SR) ATPase, displaying a 2 and 10 microM Ki, respectively. Steady state and lifetime fluorescence measurements are consistent with energy transfer between tryptophanyl residues assigned to the ATPase membrane-bound region and DTG. This phenomenon exhibits saturation behavior, occurs in the presence of DTG concentrations producing ATPase inhibition, and is partially prevented by inhibitory concentrations of TG. Although long range conformational effects of TG binding affect the fluorescence properties of endogenous tryptophans as well as of a fluorescein 5'-isothiocyanate (FITC) label of the ATPase extramembranous region, no significant energy transfer was detected between DTG and the FITC label. It is concluded that the inhibitors partition within the membrane and the binding domain resides within or near the membrane-bound region of the ATPase.

Hydrophobic surfaces that are hidden in chaperonin Cpn60 can be exposed by formation of assembly-competent monomers or by ionic perturbation of the oligomer

The oligomeric form (14-mer) of the chaperonin protein, Cpn60 (GroEL) from Eschericia coli, displays restricted hydrophobic surfaces and binds tightly one to two molecules of the fluorescent hydrophobic reporter, 1,1'-bi(4-anilino)naphthalene-5,5'-disulfonic acid (bisANS). The 14-mer is resistant to proteolysis by chymotrypsin, and none of the three sulfhydryl groups/monomer react with 6-iodoacetamidofluorescein. When monomers of Cpn60 that are folded and competent to participate in protein folding are formed by low concentrations of urea (< 2.5 M), the hydrophobic exposure increases to accommodate approximately 14 molecules of bisANS/14-mer, the binding affinity for bisANS decreases, and 1 sulfhydryl group/monomer reacts with 6-iodoacetamidofluorescein. These monomers display limited proteolysis by chymotrypsin at several points within a hydrophobic sequence centered around residue 250 to produce a relatively stable N-terminal fragment (approximately = to 26 kDa) and a partially overlapping C-terminal fragment (approximately = to 44 kDa). The exposure of hydrophobic surfaces is facilitated by ATPMg. Ions increase hydrophobic exposure more effectively than urea without dissociation of Cpn60. For example, subdenaturing concentrations of guanidinium chloride (< or = 0.75 M) or the stabilizing salt, guanidinium sulfate, as well as NaCl or KCl are effective. The trivalent cation, spermidine, induces maximum exposure at 5 mM. The results suggest that hydrophobic surfaces can be involved in stabilizing the oligomer and/or in binding proteins to be folded, and they are consistent with suggestions that amphiphilic structures, presenting hydrophobic surfaces within a charged context, would be particularly effective in binding to Cpn60.

Cysteine 254 can cooperate with active site cysteine 247 in reactivation of 5,5'-dithiobis(2-nitrobenzoic acid)-inactivated rhodanese as determined by site-directed mutagenesis

Sulfhydryl substitution mutants of rhodanese (thiosulfate:cyanide sulfurtransferase; EC 2.8.1.1) were used to determine whether the 4 cysteine residues in the native structure could cooperate in reactions. The sulfhydryl reactivity of persulfide-containing (ES) rhodanese was not significantly changed when cysteine residues at positions 63, 254, and 263 were replaced by serine, either individually or in combination. However, the sulfhydryl reactivity of persulfide-free (E) rhodanese was enhanced when Cys-254 was mutated. One sulfhydryl group, presumably the active site Cys-247, reacted rapidly in the E forms of these proteins with 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) or 4,4'-dipyridyl disulfide (4-PDS). After reaction with DTNB or 4-PDS, proteins with Cys-254 retained > 95% of their original activities as compared with Ser-254-containing proteins, which retained < 6% of their activities. Cyanide treatment could release thionitrobenzoate from rhodanese-thionitrobenzoate complexes with an approximate 1:1 stoichiometry. After this treatment, only the wild-type and C263S enzymes were fully active. Cyanide-treated rhodanese-thionitrobenzoate complexes of the C254S and C254S/C263S mutants could be fully reactivated using an exogenously added thiol, beta-mercaptoethanol. These results are consistent with the formation of a Cys-247-thiocyano derivative that is inactive but capable of being reactivated by intramolecular transfer of cyanide to Cys-254. In the absence of Cys-254, beta-mercaptoethanol can serve as the transferring sulfhydryl group.

Phosphorylation of aorta caldesmon by endogenous proteolytic fragments of protein kinase C

Endogenous caldesmon kinase activity in sheep aorta smooth muscle was purified and characterized. The enzyme was identified as a proteolytic fragment of protein kinase C by cross-reactivity with anti-protein kinase C antibodies, autophosphorylation, substrate specificity and the primary structure of the sites of phosphorylation on caldesmon. The enzyme phosphorylated aorta caldesmon both in native thin filaments and in the isolated state. Up to 2.9 mols of phosphate per mol of caldesmon were transferred. Prolonged incubation of caldesmon with the kinase resulted in phosphorylation of Ser-127, Ser-587, Ser-600, Ser-657, Ser-686, and Ser-726 (numbering corresponds to chicken gizzard caldesmon sequence). Ser-600 and Ser-587 were the major sites of phosphorylation containing more than 30% of phosphate transferred. Phosphorylation did not significantly affect the interaction of caldesmon with Ca(2+)-calmodulin. However, phosphorylation of both intact caldesmon and of its C-terminal fragment (658C), containing residues 658-756, significantly decreased their ability to inhibit acto-heavy meromyosin ATPase. This seems to be partially due to a decrease in the binding of caldesmon and 658C to actin-tropomyosin and partly due to an uncoupling of the binding-inhibition relationship.

Capsid assembly and involved function analysis of twelve core protein mutants of duck hepatitis B virus

The roles of different regions of the duck hepatitis B virus (DHBV) core protein on viral capsid assembly and related functions were examined. Twelve deletion and insertion mutations which covered 80% of the DHBV C open reading frame were constructed and expressed in Escherichia coli. The N-terminal region (amino acids 3 to 66) of DHBV core protein was important for its tertiary structure and function in E. coli. The expressed core mutants without this region apparently inhibited E. coli growth. The results of transmission electron microscopy of E. coli thin sections, capsid agarose gel, and sucrose gradient sedimentation demonstrated that a few DHBV core mutants with insertion in the N terminus and deletion in the C terminus retained the ability to form core-like particles in E. coli. However, other mutations in most of N-terminal and central regions strongly inhibited the self-assembly ability of DHBV core protein in E. coli. In addition, the mutant with a C-terminal region deletion (amino acids 181 to 228) lost most of the nucleic acid-binding activity of the DHBV core protein.

Identification of casein kinase II as a major endogeneous caldesmon kinase in sheep aorta smooth muscle

A caldesmon kinase activity was detected in an ATP extract of the myofibril-like pellet from sheep aorta. The enzyme was purified 745-fold and was identified as casein kinase II on the basis of molecular size, substrate specificity, and high sensitivity to heparin inhibition. Casein kinase II phosphorylated isolated caldesmon and caldesmon incorporated into native thin filaments, and transferred about 1 mol of phosphate per mol of caldesmon-h. Ser-73 was the main site phosphorylated by casein kinase II in chicken gizzard caldesmon. Phosphorylation of caldesmon reduced its affinity for smooth muscle myosin but had no effect upon the ability of caldesmon to inhibit the ATPase activity of actomyosin.