Identification of MicroRNAs Binding Site in the 3’Untranslated Region of Long Non-Coding RNA, MIR497HG: A Bioinformatic Prediction

@#Introduction: Prediction and identification of miRNAs target genes are crucial for understanding the biology of miRNAs. Amidst reported long-coding RNA (lncRNA), the microRNA 195-497 cluster host gene (MIR497HG) regulation is mediated by multiple non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). MIR497HG has been implicated as a tumour suppressor in various cancers. However, the impact of MIR497HG and its derived miRNAs is largely unknown and still needs to be further explored. Employing an experimental approach is often challenging since some lncRNAs are difficult to identify and isolate by the current isolation technique. Thus, bioinformatic tools are introduced to aid these problems. This study sought to search and identify the miRNAs targeting the 3’untranslated region (3’UTR) of MIR497HG. Methods: Here, bioinformatic tools were adopted to identify a unique list of miRNAs that potentially target the 3’UTR of MIR497HG. Results: A total of 57 candidate miRNAs that target the 3’UTR of MIR497HG were extracted using the miRDB. Meanwhile, STarMir predicted 291 miRNAs that potentially target the 3’UTR of MIR497HG. A common list of 36 miRNAs was obtained using the Venny 2.1.0 and further narrowed down using the LogitProb score of StarMir. Finally, a total 4 miRNAs (hsa-miR-3182, hsa-miR-7156-5p, hsa-miR-452-3p and hsa-miR-2117) were identified. The mRNA target of identified miRNAs was identified by TargetScan. Finally, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of mRNA target was done using Enrichr. Conclusion: This finding could be useful in understanding the complex interaction between MIR497HG and its regulatory miRNA. In addition, a comparative analysis of computational miRNA-target predictions is provided in this study would potentially lay the foundations for miRNAs to be used for biomarkers in cancer research.

Rational metabolic engineering of Corynebacterium glutamicum for efficient synthesis of L-glutamate / 生物工程学报

L-glutamic acid is the world's largest bulk amino acid product that is widely used in the food, pharmaceutical and chemical industries. Using Corynebacterium glutamicum G01 as the starting strain, the fermentation by-product alanine content was firstly reduced by knocking out the gene encoding alanine aminotransferase (alaT), a major by-product related to alanine synthesis. Secondly, since the α-ketoglutarate node carbon flow plays an important role in glutamate synthesis, the ribosome-binding site (RBS) sequence optimization was used to reduce the activity of α-ketoglutarate dehydrogenase and enhance the glutamate anabolic flow. The endogenous conversion of α-ketoglutarate to glutamate was also enhanced by screening different glutamate dehydrogenase. Subsequently, the glutamate transporter was rationally desgined to improve the glutamate efflux capacity. Finally, the fermentation conditions of the strain constructed using the above strategy were optimized in 5 L fermenters by a gradient temperature increase combined with a batch replenishment strategy. The glutamic acid production reached (135.33±4.68) g/L, which was 41.2% higher than that of the original strain (96.53±2.32) g/L. The yield was 55.8%, which was 11.6% higher than that of the original strain (44.2%). The combined strategy improved the titer and the yield of glutamic acid, which provides a reference for the metabolic modification of glutamic acid producing strains.

Interaction study of the antibacterial peptide urumin with the H1N1 HA protein of influenza A virus / 药学学报

Influenza A virus (H1N1) seriously affects the health of human and disrupts the development of global economic. The antimicrobial peptide urumin specifically binds to the conserved stem of the hemagglutinin (HA) protein of H1N1 virus, but its binding site and the mechanism of action are not clear. In this study, we investigated the possible binding sites and key amino acids for the interaction of urumin with HA protein by molecular docking and enzyme-linked immunosorbent assay (ELISA) experiments, suggesting that HA residues His32 (HA1), Asp19 (HA2), and Trp21 (HA2) are the key residues for the interaction of HA with urumin. Urumin's Arg4, Asn9, and Cys16 were associated with HA protein residues Asp19 (HA2), Trp21 (HA2), His32 (HA1), and Asn53 (HA2) form hydrogen bonding interactions, and Trp12 forms an aromatic π-stacking interaction with His32 (HA1) of HA, these interactions maintain the binding of urumin to HA protein. Wild-type HA and its alanine mutant [alanine substitutions His32 (HA1), Asp19 (HA2), and Trp21 (HA2)] were expressed in 293T cells. ELISA experiments showed that the affinity ability of urumin with HA wild-type was significantly higher than that of HA alanine mutant, suggesting that His32 (HA1), Asp19 (HA2), and Trp21 (HA2) may be the key residues for HA to interact with urumin. This study provides a theoretical and experimental basis for further modification and application of urumin.

ATP gatekeeper of Plasmodium protein kinase may provide the opportunity to develop selective antimalarial drugs with multiple targets

Malaria is one of the most devastating infectious diseases that caused millions of clinical cases annually despite decades of prevention efforts. Recent cases of Plasmodium falciparum resistance against the only remaining class of effective antimalarial (artemisinin) in South East Asia may soon pose a significant threat. Hence, the identification of new antimalarial compounds with a novel mode of action is necessary to curb this problem. Protein kinase has been implicated as a valid target for drug development in diseases such as cancer and diabetes in humans. A similar approach is now recognized for the treatment of protozoan-related disease including malaria. Few Plasmodium protein kinases that are not only crucial for their survival but also have unique structural features have been identified as a potential target for drug development. In this review, studies on antimalarial drug development exploiting the size of Plasmodium protein kinase ATP gatekeeper over the past 15 years are mainly discussed. The ATP-binding site of Plasmodium protein kinases such as Pf CDPK1, Pf CDPK4, Pf PKG, Pf PK7, and Pf PI4K showed great potential for selective and multi-target inhibitions owing to their smaller or unique ATP-gatekeeper amino acid subunits compared to that of human protein kinase. Hence it is a feasible solution to identify a new class of active antimalarial agents with a novel mode of action and longer clinical life-span.

Research progress on pyruvate dehydrogenase kinase inhibitors / 药学学报

Tumor cells can metabolize glucose through glycolysis to intermediates for biomacromolecule synthesis by inhibiting the activity of the pyruvate dehydrogenase complex (PDC) in mitochondria. In this process, pyruvate dehydrogenase kinases (PDKs) play a key role. The inhibition of the activity of PDKs can effectively block this metabolic pathway, activate mitochondrial oxidative metabolism, and induce tumor cell apoptosis. PDK inhibitors have become a research hotspot in medicinal chemistry, and novel structures targeting classical binding sites have been synthesized. In this paper, recent research progress on PDK inhibitors is reviewed to provide information on these latest entities and to explore their clinical applicability.

Effect of key notes of TCA cycle on L-glutamate production / 生物工程学报

Glutamic acid is an important amino acid with wide range of applications and huge market demand. Therefore, by performing transcriptome sequencing and re-sequencing analysis on Corynebacterium glutamicum E01 and high glutamate-producing strain C. glutamicum G01, we identified and selected genes with significant differences in transcription and gene levels in the central metabolic pathway that may have greatly influenced glutamate synthesis and further increased glutamic acid yield. The oxaloacetate node and α-ketoglutarate node play an important role in glutamate synthesis. The oxaloacetate node and α-ketoglutarate node were studied to explore effect on glutamate production. Based on the integrated strain constructed from the above experimental results, the growth rate in a 5-L fermenter was slightly lower than that of the original strain, but the glutamic acid yield after 48 h reached (136.1±5.53) g/L, higher than the original strain (93.53±4.52) g/L, an increase by 45.5%; sugar-acid conversion rate reached 58.9%, an increase of 13.7% compared to 45.2% of the original strain. The application of the above experimental strategy improved the glutamic acid yield and the sugar-acid conversion rate, and provided a theoretical basis for the metabolic engineering of Corynebacterium glutamicum.

ATP gatekeeper of Plasmodium protein kinase may provide the opportunity to develop selective antimalarial drugs with multiple targets

Malaria is one of the most devastating infectious diseases that caused millions of clinical cases annually despite decades of prevention efforts. Recent cases of Plasmodium falciparum resistance against the only remaining class of effective antimalarial (artemisinin) in South East Asia may soon pose a significant threat. Hence, the identification of new antimalarial compounds with a novel mode of action is necessary to curb this problem. Protein kinase has been implicated as a valid target for drug development in diseases such as cancer and diabetes in humans. A similar approach is now recognized for the treatment of protozoan-related disease including malaria. Few Plasmodium protein kinases that are not only crucial for their survival but also have unique structural features have been identified as a potential target for drug development. In this review, studies on antimalarial drug development exploiting the size of Plasmodium protein kinase ATP gatekeeper over the past 15 years are mainly discussed. The ATP-binding site of Plasmodium protein kinases such as Pf CDPK1, Pf CDPK4, Pf PKG, Pf PK7, and Pf PI4K showed great potential for selective and multi-target inhibitions owing to their smaller or unique ATP-gatekeeper amino acid subunits compared to that of human protein kinase. Hence it is a feasible solution to identify a new class of active antimalarial agents with a novel mode of action and longer clinical life-span.

Effects of calcium-binding sites in the S2–S3 loop on human and Nematostella vectensis TRPM2 channel gating processes / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

As a crucial signaling molecule, calcium plays a critical role in many physiological and pathological processes by regulating ion channel activity. Recently, one study resolved the structure of the transient receptor potential melastatin 2 (TRPM2) channel from Nematostella vectensis (nvTRPM2). This identified a calcium-binding site in the S2–S3 loop, while its effect on channel gating remains unclear. Here, we investigated the role of this calcium-binding site in both nvTRPM2 and human TRPM2 (hTRPM2) by mutagenesis and patch-clamp recording. Unlike hTRPM2, nvTRPM2 cannot be activated by calcium alone. Moreover, the inactivation rate of nvTRPM2 was decreased as intracellular calcium concentration was increased. In addition, our results showed that the four key residues in the calcium-binding site of S2–S3 loop have similar effects on the gating processes of nvTRPM2 and hTRPM2. Among them, the mutations at negatively charged residues (glutamate and aspartate) substantially decreased the currents of nvTRPM2 and hTRPM2. This suggests that these sites are essential for calcium-dependent channel gating. For the charge-neutralizing residues (glutamine and asparagine) in the calcium-binding site, our data showed that glutamine mutating to alanine or glutamate did not affect the channel activity, but glutamine mutating to lysine caused loss of function. Asparagine mutating to aspartate still remained functional, while asparagine mutating to alanine or lysine led to little channel activity. These results suggest that the side chain of glutamine has a less contribution to channel gating than does asparagine. However, our data indicated that both glutamine mutating to alanine or glutamate and asparagine mutating to aspartate accelerated the channel inactivation rate, suggesting that the calcium-binding site in the S2–S3 loop is important for calcium-dependent channel inactivation. Taken together, our results uncovered the effect of four key residues in the S2–S3 loop of TRPM2 on the TRPM2 gating process.

Estrogenic Activity of Sanguiin H-6 through Activation of Estrogen Receptor α Coactivator-binding Site

A popular approach for the study of estrogen receptor α inhibition is to investigate the protein-protein interaction between the estrogen receptor (ER) and the coactivator surface. In our study, we investigated phytochemicals from Rubus coreanus that were able to disrupt ERα and coactivator interaction with an ERα antagonist. The E-screen assay and molecular docking analysis were performed to evaluate the effects of the estrogenic activity of R. coreanus extract and its constituents on the MCF-7 human breast cancer cell line. At 100 µg/mL, R. coreanus extract significantly stimulated cell proliferation (574.57 ± 8.56%). Sanguiin H6, which was isolated from R. coreanus, demonstrated the strongest affinity for the ERα coactivator-binding site in molecular docking analysis, with a binding energy of

Effects of calcium-binding sites in the S2-S3 loop on human and Nematostella vectensis TRPM2 channel gating processes / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

As a crucial signaling molecule, calcium plays a critical role in many physiological and pathological processes by regulating ion channel activity. Recently, one study resolved the structure of the transient receptor potential melastatin 2 (TRPM2) channel from Nematostella vectensis (nvTRPM2). This identified a calcium-binding site in the S2-S3 loop, while its effect on channel gating remains unclear. Here, we investigated the role of this calcium-binding site in both nvTRPM2 and human TRPM2 (hTRPM2) by mutagenesis and patch-clamp recording. Unlike hTRPM2, nvTRPM2 cannot be activated by calcium alone. Moreover, the inactivation rate of nvTRPM2 was decreased as intracellular calcium concentration was increased. In addition, our results showed that the four key residues in the calcium-binding site of S2-S3 loop have similar effects on the gating processes of nvTRPM2 and hTRPM2. Among them, the mutations at negatively charged residues (glutamate and aspartate) substantially decreased the currents of nvTRPM2 and hTRPM2. This suggests that these sites are essential for calcium-dependent channel gating. For the charge-neutralizing residues (glutamine and asparagine) in the calcium-binding site, our data showed that glutamine mutating to alanine or glutamate did not affect the channel activity, but glutamine mutating to lysine caused loss of function. Asparagine mutating to aspartate still remained functional, while asparagine mutating to alanine or lysine led to little channel activity. These results suggest that the side chain of glutamine has a less contribution to channel gating than does asparagine. However, our data indicated that both glutamine mutating to alanine or glutamate and asparagine mutating to aspartate accelerated the channel inactivation rate, suggesting that the calcium-binding site in the S2-S3 loop is important for calcium-dependent channel inactivation. Taken together, our results uncovered the effect of four key residues in the S2-S3 loop of TRPM2 on the TRPM2 gating process.

Expression Analysis of Pyrenophora teres f. maculata-Responsive Loci in Hordeum vulgare

Abstract Pyrenophora teres f. maculata is the causal agent of barley spot form net blotch (SFNB), a major stubble-borne disease in many barley-growing areas worldwide. In plants, the Nucleotide-Binding Site-Leucine-Rich Repeat (NBS-LRR) gene family functions in immunity against a variety of pathogens and pests. From a pre-established set of NBS-type resistance gene candidates, we have selected three candidate genes, HvNBS10, HvNBS72 and HvNBS85, to analyze their possible involvement in P. teres f. maculata resistance. The studied genes were mapped on chromosomes 5H and 7H. Expression profiles using qRT-PCR, 48 hours after infection by P. teres. f. maculata, revealed that the transcription of all genes acted in the same direction (down-regulation) in both resistant and susceptible cultivars, although they showed a variation in transcript dosage. This result suggests that coordinated transcriptional responses of multiple barley NBS genes would be required to an efficient response against P. teres f. maculata. Moreover, the phylogenetic analysis revealed that the studied barley candidate R genes were characterized by a high homology with the barley Nbs2-Rdg2a gene conferring resistance to the fungus Pyrenophora graminea, suggesting a common origin of P. graminea and P. teres resistance genes in barley, following pathogens evolution. The genes characterized in the present study hold potential in elucidating the molecular pathways and developing novel markers associated with SFNB resistance in barley.

Dengue virus infection induces chromatin remodeling at locus AAEL006536 in the midgut of Aedes aegypti / La infección por virus dengue induce remodelación de la cromatina en el locus AAEL006536 en el intestino medio de Aedes aegypti

Abstract: Objective: To identify and characterize Aedes aegypti's AAEL006536 gene proximal upstream cis-regulatory sequences activated by dengue virus infection. Materials and methods: A. aegypti Rockefeller strain mosquitoes were blood fed or infected with dengue virus 2. Open chromatin profiling was then carried out in pools of midguts from each group of mosquitoes. Results: The proximal upstream region does not contain open chromatin sites in the midguts of blood-fed mosquitoes as detected by FAIRE-qPCR. In contrast, two cis-regulatory sites were identified in the same upstream region of dengue virus-infected mosquito midguts. The distal sequence contains STAT-, REL- and C/EBP-type transcription factor binding sites. Conclusion: The activation of two proximal cis-regulatory sequences, induced by dengue virus infection, is mediated by chromatin remodeling mechanisms. Binding sites suggest a dengue virus infection-induced participation of immunity transcription factors in the up-regulation of this gene. This suggests the participation of the AAEL006536 gene in the mosquito's antiviral innate immune response.

Resumen: Objetivo: Identificar y caracterizar las secuencias reguladoras activadas por la infección por virus dengue en la región proximal del gen AAEL006536 de Aedes aegypti. Material y métodos: Mosquitos de la cepa Rockefeller de A. aegypti se infectaron con virus dengue o se alimentaron con sangre. Se obtuvieron los perfiles de cromatina abierta del locus en los intestinos de cada uno de los grupos. Resultados: Se identificaron dos sitios reguladores solo en los intestinos de mosquitos infectados por virus dengue. El sitio distal contiene sitios de unión a factores de transcripción tipo REL, STAT y C/EBP. Conclusiones: La activación de dos sitios reguladores proximales está mediada por la remodelación de la cromatina. Los sitios de unión a factores de transcripción en el sitio regulador distal sugieren la participación de las vías de inmunidad en la regulación del gen. Esto sugiere la participación de este gen en la respuesta inmune del mosquito frente a la infección viral.

Study on Binding Characteristics of Aminocarboxyl Chelating Ligands for Metal Ions / 分析化学

The feasibility of frontal chromatography for determining the complexation stability constant KML and total mole of binding site Λo was demonstrated by the accuracy and precision binding experiments between metal ions (Cu2+, Ni2+ and Co2+) and chelating ligand (IDA), in which R2>0.98 and RSD Asp>Glu;binding strength of metal ions for chelate ligands followed Cu2+>Ni2+>Co2+;and the binding effect with NaAc-HAc buffer was the best.In aqueous solution, quantum computing of binding energy (ΔE) and gibbs free energy (ΔG) between chelating ligand and metal ion was performed at the M06/6-311++G (d, p) level.According to ΔE and ΔG, the binding rules between chelating ligand and metal ion were predicted theoretically.These rules were basically in agreement with above experimental results.The present work provided effective method for studying on binding characteristics of metal ions for aminocarboxyl chelating ligands, thus exhibited a good foundation for improving the stability of immobilized metal affinity chromatographic column and solving the leakage of metal ions from the column in the process of competitive elution.

Leucine-rich repeat kinase 2 inhibitor as Parkinson’s disease novel therapeutics: Research advances / 国际药学研究杂志

Parkinson’s disease PD is a common disease caused by multiple factors and characterized by pathological degeneration in the dopaminergic neural system. Based on its pathogenic factors, PD can be divided into several subtypes, so it is essential to develop therapeutic agents based on the main pathogenic factor of each subtype of PD. Recently it is confirmed that the mutation of leucine- rich repeat kinase 2 LRRK2 gene leads to increased activity of the LRRK2 notably, and then causes neurodegeneration. Thus developing LRRK2 inhibitors to modulate the kinase activity will be a novel therapy for the PD subtype which is caused by LRRK2 gene mutation. LRRK2, either a kinase or a GTPase, has two drug binding sites. Therefore, two types of LRRK2 inhibitors are being studied, one is the kinase inhibitor and the other is GTPase inhibitor. This paper summarizes the recent progress in the discovery and development of LRRK2 inhibitors.

Association between genetic variants in p53 binding sites and risks of breast cancer in Chinese population / 中华流行病学杂志

Objective To investigate the association between breast tissue specified variants in p53 binding sites and the risk of BC in Chinese women.Methods ChIP-seq database on p53 binding sites in MCF-7 cell lines was extracted to identify the possible variants in p53 target genes.A hospital-based case-control study was then performed to investigate the association between variants in p53 binding sites and the risk of BC in a Chinese women population.Results Three variants were identified from the bioinformatics analysis.A total of 1 274 BC cases and 1 255 frequency-matched cancer-free controls were included in this case-control study.The average age was comparable between the case and the control groups,with the P value as 0.318.Meanwhile,distributions on menopausal status,smoking and alcohol intake between cases and controls were similar with the P values as 0.539,0.258 and 0.131,respectively.The genotype distribution of rs1295925 was significantly different between the case and the control groups.Individuals that carrying rs1295925-CT and rs1295925-TT genotypes were significantly associated with an increased BC risk when compared with rs1295925-CC genotype after adjustment of age,menopausal status,smoking and alcohol intake (0R=1.32,95％ CI:1.07-1.62 and OR=1.41,95％CI:1.13-1.78,respectively).Positive associations were also observed under the allelic,dominant and additive models.Conclusion rs1295925 which located in VMP1 gene was associated with increased BC risk in the Chinese women population.

Association between genetic variants in p53 binding sites and risks of breast cancer in Chinese population / 中华流行病学杂志

Objective To investigate the association between breast tissue specified variants in p53 binding sites and the risk of BC in Chinese women.Methods ChIP-seq database on p53 binding sites in MCF-7 cell lines was extracted to identify the possible variants in p53 target genes.A hospital-based case-control study was then performed to investigate the association between variants in p53 binding sites and the risk of BC in a Chinese women population.Results Three variants were identified from the bioinformatics analysis.A total of 1 274 BC cases and 1 255 frequency-matched cancer-free controls were included in this case-control study.The average age was comparable between the case and the control groups,with the P value as 0.318.Meanwhile,distributions on menopausal status,smoking and alcohol intake between cases and controls were similar with the P values as 0.539,0.258 and 0.131,respectively.The genotype distribution of rs1295925 was significantly different between the case and the control groups.Individuals that carrying rs1295925-CT and rs1295925-TT genotypes were significantly associated with an increased BC risk when compared with rs1295925-CC genotype after adjustment of age,menopausal status,smoking and alcohol intake (0R=1.32,95％ CI:1.07-1.62 and OR=1.41,95％CI:1.13-1.78,respectively).Positive associations were also observed under the allelic,dominant and additive models.Conclusion rs1295925 which located in VMP1 gene was associated with increased BC risk in the Chinese women population.

Leucine-rich repeat kinase 2 inhibitor as Parkinson′s disease novel therapeutics:research advances / 国际药学研究杂志

Parkinson′s disease(PD)is a common disease caused by multiple factors and characterized by pathological degen?eration in the dopaminergic neural system. Based on its pathogenic factors,PD can be divided into several subtypes,so it is essential to develop therapeutic agents based on the main pathogenic factor of each subtype of PD. Recently it is confirmed that the mutation of leucine-rich repeat kinase 2(LRRK2)gene leads to increased activity of the LRRK2 notably,and then causes neurodegeneration. Thus developing LRRK2 inhibitors to modulate the kinase activity will be a novel therapy for the PD subtype which is caused by LRRK2 gene mutation. LRRK2,either a kinase or a GTPase,has two drug binding sites. Therefore,two types of LRRK2 inhibitors are being studied,one is the kinase inhibitor and the other is GTPase inhibitor. This paper summarizes the recent progress in the dis?covery and development of LRRK2 inhibitors.

Bioinformatic analysis of the hsa-miR-1908 upstream promoter region / 临床儿科杂志

Objective To predict the functions of hsa-miR-1908 promoter using various bioinformatic tools, and to provide clues for further study on transcriptional regulation mechanism of miR-1908 in human adipocytes. Methods The promoter se-quence of miR-1908 was obtained from Ensemble, and then the CpG islands and transcription factor binding sites were pre-dicted by a variety of online bioinformatic tools. Results The length of the miR-1908 promoter sequence was 1 458 bp. The CpG islands, which inhibited the transcription of miR-1908, were located at (438-756) bp, (836-937) bp and (979-1374) bp. Meanwhile, 15 transcription factor binding sites were found in the promoter sequence of miR-1908. Conclusions miRNA up-stream promoter related bioinformatics can not only improve the efficiency of microRNA promoter research, but also provide further important information on transcriptional regulation of miR-1908.

Identification of the binding region for interaction of optineurin with neural retina leucine / 中华实验眼科杂志

Background Gene encoding optineurin (OPTN) is a causative gene for glaucoma and amyotrophic lateral sclerosis,with a more expression in retina.Our previous study isolated OPTN-interacting proteins and identified that the gene encode the basic leucine zipper (bZIP) transcription factor neural retina leucine (NRL) zipper,a causative gene for retinitis pigmentosa,and further study demonstrated the interaction between OPTN and NRL proteins in nuclei of cultured HeLaS3 cells.Objective This study was to determine the protein binding site of OPTN necessary for NRL binding.Methods A deletion series of OPTN-expression plasmids were constructed and co-expressed with hemagglutinin (HA)-tagged NRL in HeLaS3 cells,respectively.The cytoplasmic and nuclear fractions were used to perform co-immunoprecipitate (CoIP) and Western blot with anti-tag antibodies.Results In the nuclear fractions of cells transfected with the del1 st,del2nd or del3rd plasmid,a band of coimmunoprecipitated HA-labelled NRL (HA-NRL) was detected.However,the del4th plasmid did not produce a band.The NRL band was not found in cytoplasmic fractions from transfected cells with any of the deletion plasmids or with the whole-length OPTN plasmid.Conclusions The protein binding site of OPTN necessary for NRL binding is determined.This result demonstrates the binding of Flag-OPTN and HA-NRL in HeLaS3 cells.A series of partial-deletion OPTN plasmids demonstrated that the tail region (423-577 amino acids) of OPTN was necessary for binding with NRL.

Effect of zinc and calcium ions on the rat kidney membrane-bound form of dipeptidyl peptidase IV.

Dipeptidyl peptidase IV (DPP-IV) is an ectopeptidase with many roles, and a target of therapies for different pathologies. Zinc and calcium produce mixed inhibition of porcine DPP-IV activity. To investigate whether these results may be generalized to mammalian DPP-IV orthologues, we purified the intact membrane-bound form from rat kidney. Rat DPP-IV hydrolysed Gly-Pro-p-nitroanilide with an average Vmax of 0.86±0.01 μmol min–1mL–1 and KM of 76±6 μM. The enzyme was inhibited by the DPP-IV family inhibitor L-threo-Ile-thiazolidide (Ki=64.0±0.53 nM), competitively inhibited by bacitracin (Ki=0.16±0.01 mM) and bestatin (Ki=0.23±0.02 mM), and irreversibly inhibited by TLCK (IC50 value of 1.20±0.11 mM). The enzyme was also inhibited by divalent ions like Zn2+ and Ca2+, for which a mixed inhibition mechanism was observed (Ki values of the competitive component: 0.15±0.01 mM and 50.0±1.05 mM, respectively). According to bioinformatic tools, Ca2+ ions preferentially bound to the β-propeller domain of the rat and human enzymes, while Zn2+ ions to the α-β hydrolase domain; the binding sites were essentially the same that were previously reported for the porcine DPP-IV. These data suggest that the cationic susceptibility of mammalian DPP-IV orthologues involves conserved mechanisms.