Computational Sequence Analysis of the Tissue Inhibitor of Metalloproteinase Family

The tissue inhibitor of metalloproteinase (TIMP) family regulates extracellular matrix turnover and tissue remodeling by forming tight-binding inhibitory complexes with matrix metalloproteinases (MMPs). MMPs and TIMPs have been implicated in many normal and pathological processes, such as morphogenesis, development, angiogenesis, and cancer metastasis. This minireview provides information that would aid in classification of the TIMP family and in understanding the similarities and differences among TIMP members according to the physical data, primary structure, and homology values. Calculations of molecular weight, isoelectric point values, and molar extinction coefficients are reported. This study also compares sequence similarities and differences among the TIMP members through calculations of homology within their individual loop regions and the mature region of the molecule. Lastly, this report examines structure–function relationships of TIMPs. Thorough knowledge of TIMP primary and tertiary structure would facilitate the uncovering of the molecular mechanisms underlying metalloproteinase, inhibitory activities and biological functions of TIMPs.     

Activation of human progelatinase A by collagenase and matrilysin: Activation of procollagenase by matrilysin

Proteolytic and nonproteolytic methods were used to investigate the mechanism(s) by which human fibroblast progelatinase A and fibroblast-type procollagenase can be activated. Both collagenase and matrilysin were able to activate progelatinase A, resulting in an amino terminus in gelatinase A of Tyr.⁸¹ The cleavage occurred distal to Cys⁷³ within the sequence of PR_CGNPDVAN⁸⁰-Y⁸¹NFFPRKP. While several nonproteolytic reagents were tested, only the heavy metal Hg() andp-chloromercuribenzoate (PCMB) were able to induce activation of progelatinase A and resulted in the conversion of the latent 72-kDa gelatinase A to an active form of about 64.5 kDa. Matrilysin was also able to activate procollagenase and resulted in an amino terminus in collagenase of Phe.⁸¹ These results suggest that fibroblast-type collagenase and matrilysin may be physiologically relevant activators of progelatinase A; the maintenance of latency and the process of activation for progelatinase A may occur through the cysteine-switch mechanism, and the proteolytic activation of procollagenase by matrilysin resulted in the same amino terminus as produced by stromelysin-1.Abbreviations APMA p-aminophenylmercuric acetate - Bistris [bis(2-hydroxyethyl)imino-tris(hydroxymethyl)methane] - CAPS 3-(cyclohexylamino)-1-propane sulfonic acid - DTNB 5,5-dithiobis(2-nitrobenzoic acid) - DTT dithiothreitol - EDTA ethylenediaminetetraacetic acid - GSSG oxidized glutathione - HFC human fibroblast-type collagenase, MMP-1 - HFG human fibroblast gelatinase A/72-kDa type IV collagenase, MMP-2 - HFS human fibroblast stromelysin-1, MMP-3 - MMP matrix metalloproteinase - MT-MMP membrane-type matrix metalloproteinase, MMP-14 - NEM N-ethylmaleimide - PCMB p-chloromercuribenzoate - PMA phenylmercuric acetate - PMC phenylmercuric acid - PMSF phenylmethanesulfonyl fluoride - PTH phenylthiohydantoin - RTT rat tail tendon - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis - Tes [tris(hydroxymethyl)-methyl-2-aminoethane sulfonic acid] - TIMP tissue inhibitor of metalloproteinase - Tris tris(hydroxymethyl)aminomethane - Tricine N-[tris(hydroxymethyl)methyl]glycine     

Molecular cloning and characterization of a cDNA encoding a novel cuticle protein from the Chinese oak Silkmoth, Antheraea pernyi.

In our research to identify gene involved in the cuticle protein, we cloned a novel cuticle protein gene, ApCP13, from the Chinese oak silkmoth, Antheraea pernyi, larvae cDNA library. The ApCP13 gene encodes a 120 amino acid polypeptide with a predicted molecular mass of 13 kDa and a pI of 4.01, and is intron-less gene. The ApCP13 contained a type-specific consensus sequence identifiable in other insect cuticle proteins and the deduced amino acid sequence of the ApCP13 cDNA is most homologous to another wild silkmoth, A. yamamai CP12 (86% protein sequence identity), followed by Bombyx mori LCP18 (35% protein sequence identity). Northern blot analysis revealed that the ApCP13 showed the epidermis-specific expression. This is the first report of cuticle protein gene in the wild silkmoth, A. pernyi.     

Sorption of polycyclic aromatic hydrocarbons (PAHs) by dietary fiber extracted from wheat bran

The unintentional ingestion of carcinogenic xenobiotic substances leads to the high risk of cancer. Dietary fiber (DF) may protect against cancer by sorbing such chemicals. To this end, the sorption of four polycyclic aromatic hydrocarbons (PAHs) to DF extracted from wheat bran (WB) was studied. The strong affinity of PAHs to DF and WB indicated the effective binding of PAHs, and their distribution coefficients (K_d) positively increased with the increase in hydrophobicity of the PAHs. The DF had much higher K_d values for all PAHs compared to those of the unprocessed WB. The DF extraction process removed hydrophilic residues, such as starch, from WB, and increased the roughness of DF surface. Loss of hydrophilic components from WB to DF led to much higher affinity of DF with PAHs than WB. The results indicate that the DF can effectively sorb and remove xenobiotics, thereby having the potential to lower carcinogenic risk to humans.     

Identification of putative biomarkers for type 2 diabetes using metabolomics in the Korea Association REsource (KARE) cohort

Introduction

Type 2 diabetes (T2D) is a multifactorial disease resulting from a complex interaction between environmental and genetic risk factors. Metabolomics provide a logical framework that reflects the functional endpoints of biological processes being triggered by genetic information and various external influences.

Objectives

Identification of metabolite biomarkers can shed insight into etiological pathways and improve the prediction of disease risk. Here, we aimed to identify serum metabolites as putative biomarkers for T2D and their association with genetic variants in the Korean population.

Methods

A targeted metabolomics approach was employed to quantify serum metabolites for 2240 participants in the Korea Association REsource (KARE) cohort. T2D-related metabolites were identified by statistical methods including multivariable linear and logistic regression, and were independently replicated in the Cooperative Health Research in the Region of Augsburg (KORA) cohort. Additionally, by combining a genome wide association study (GWAS) with metabolomics, genetic variants associated with the identified T2D-related metabolites were uncovered.

Results

123 metabolites were quantified from fasting serum samples and four metabolites, hexadecanoylcarnitine (C16), glycine, lysophosphatidylcholine acyl C18:2 (lysoPC a C18:2), and phosphatidylcholine acyl-alkyl C36:0 (PC ae C36:0), were significantly altered in T2D compared to non-T2D subjects (after the Bonferroni correction for multiple testing with P < 4.07E ? 04, α = 0.05). Among them, C16, glycine, and lysoPC a C18:2 were independently replicated in the KORA cohort. Alterations of these metabolites were associated with ten genetic loci including six that were previously implicated in T2D or obesity.

Conclusion

Using a targeted-metabolomics and in combination with GWAS approach, we identified three serum metabolites associated with risk of T2D in both the KARE and KORA cohort and discovered ten genetic variants in relation to the identified metabolites. These findings provide a better understanding to develop novel preventive strategies for T2D in the Korean population.

     

The role of BRD7 in embryo development and glucose metabolism

Bromodomain‐containing protein 7 (BRD7) is a member of bromodomain‐containing protein family and its function has been implicated in several diseases. We have previously shown that BRD7 plays a role in metabolic processes. However, the effect of BRD7 deficiency in glucose metabolism and its role in in vivo have not been fully revealed. Here, we report the essential role of BRD7 during embryo development. Mice homozygous for BRD7 led to embryonic lethality at mid‐gestation. Homozygous BRD7 knockout (KO) mice showed retardation in development, and eventually all BRD7 KO embryos died in utero prior to E16.5. Partial knockdown of Brd7 gene displayed mild changes in glucose metabolism.