Protein and Peptide Letters - Volume 17, Issue 5, 2010

The recognition of human leukocyte antigen (HLA) molecules by specific receptors is a crucial step in the regulation of natural killer (NK) cell function. Killer cell immunoglobulin-like receptor (KIR) 3DS1 is one of the activating receptors of NK cell and is implicated in slowing disease progression in HIV infection. KIR3DS1 play an important role in the outcome of multiple diseases associated with viral infections. In contr Read More

Histone deacetylase 6 (HDAC6) is a cytosolic enzyme that catalyzes deacetylation of several proteins. Acetylated tubulin has been recently identified as a physiological substrate of HDAC6. However in previous reports, all in vitro binding and enzymatic assays were accomplished with only partially purified protein samples. Therefore, it still remained unclear whether HDAC6 alone could interact with tubulin and catalyze dea Read More

We use approximate entropy and hydrophobicity patterns to predict G-protein-coupled receptors. Adaboost classifier is adopted as the prediction engine. A low homology dataset is used to validate the proposed method. Compared with the results reported, the successful rate is encouraging. The source code is written by Matlab.

MMP-7 is the smallest metalloproteinase. Its unregulated activities and existence in serum are recently known to be tightly related with life-threatening disease such as cardiac disease and several cancers. The protein production is thought to be useful for its characterization and antibody generation. Although many attempts at bacterial expressions have been conducted, they were recovered as insoluble and inac Read More

Cockroach infestations have been linked with allergic diseases such as asthma in humans. Bla g 5, sigma class glutathione S-transferase (GST), is the major cockroach allergen which has the highest IgE response value of all cockroach allergens. Although several cockroach allergens have been identified and cloned, information regarding their B ell and T cell IgE-binding epitopes is limited. In order to analyze the IgE binding epito Read More

Although cytoplasmic azoreductases have been purified and characterized from various bacteria, little evidence demonstrating that these azoreductases are directly involved in azo dye reduction in vivo is known. In order to evaluate the contribution of the enzyme to azo dye reduction in vivo, experiments were conducted to determine the effect of a recombinant cytoplasmic azoreductase (AzoA) from Enterococcus fae Read More

Ribosome display is a powerful cell-free technology to select a desired antibody together with its encoding mRNA. In this study, a human single-chain variable fragment (scFv) library was generated from the peripheral blood lymphocyte RNA of 10 ovarian cancer patients and then panned against bead-conjugated human PlGF, a protein that may contribute to the growth and metastasis of ovarian cancer. A selected scFv ant Read More

A multi-scale parameterization approach, factor analysis scales of generalized amino acid information combined with auto cross covariance, was used to develop quantitative sequence-activity models of peptides using support vector machines. The results demonstrated that this approach could well characterize sequence features of the peptides studied.

Based on enzyme sequence, using composite vectors with amino acid composition, low-frequency power spectral density, increment of diversity by combining a different form of pseudo amino acid composition to express the information of sequence, a support vector machine (SVM) for predicting enzyme subclasses is proposed. By the jackknife test, success rates of our algorithm are higher than other methods.

We describe the recombinant production of the human Y1 receptor from inclusion bodies of E. coli cultures. The in vitro refolding was carried out in the presence of lipids from bovine brain extracts. Y1 receptors in brain lipids compete for cellular receptors in competitive binding experiments.

Protein transduction therapy is a promising alternative to gene therapy, but has not previously been investigated for osteosarcoma. We here demonstrate efficient growth inhibition of human osteosarcoma cells using a p53 peptide. Our result suggests that protein transduction therapy has significant potential as a novel therapeutic approach for osteosarcoma.

Based on template hexapeptides Ac-Arg-Tyr-Tyr-Arg-Trp-Lys-NH2 and Ac-Arg-Tyr-Tyr-Arg-Ile-Lys-NH2 analogues and corresponding deacylated homologues were synthesized substituting ornithine, diaminobutanoic (Dab) and diaminopropanoic (Dap) acids for lysine at position 6. The aim was to investigate the effect of the newly synthesized compounds on the neurogenic contractions of isolated rat vas deferens. Ac-Arg-Tyr-Tyr Read More

The non-covalent interaction of reactive brilliant red (RBR) as a representative of sulfonic azo compounds with human serum albumin (HSA) was investigated by a combination of UV-VIS spectrometry, fluorophotometry, circular dichroism (CD) and isothermal titration calorimetry (ITC) technique. The thermodynamic characterization of the interaction was performed. The saturation binding numbers of RBR on peptide c Read More

Establishing codon usage biases are crucial for understanding the etiology of central nervous system neurodegenerative diseases (CNSNDD) especially Alzheimer's disease (AD) as well as genetic factors. G and C ending codons are strongly biased in the coding sequences of these proteins as a result of genomic GC composition constraints. On the other hand, codons that identified as translationally optimal in the major tren Read More

Two binary complexes (KAP2-C subunit and cAMP-bound KAP2) were built, to investigate molecular interaction. The binding sites of KAP2 include the acidic sequence motif (Asp73-Glu87), the inhibitor peptide/linker region (Arg93-Val118), and beta barrel of cAMP-binding domains (CBD-A/B). The binding surface on the C subunit anchoring KAP2 extends to the inhibitor binding site at the active site cleft (Glu127-Glu230), Pro243 Read More

The conformation of bovine serum fetuin (BSF) was examined over the pH 7.0-12.9 regions by circular dichroism, intrinsic fluorescence and ANS binding. We observed that at higher pH, BSF exists in alkaline unfolded state. Our results provided evidence that correlates simultaneous formation of secondary structure followed by accumulation of hydrophobic clusters.

Glutathione reductase was purified 34806-fold with a final yield of 85 % from the bovine kidney cortex. Some molecular and kinetic properties of purified enzyme are investigated. Product inhibition studies showed that the enzyme obeys ‘branched’ mechanism: KmNADPH 18 ± 3 μM and KmGSSG 65 ± 5 μM were determined.

Most of gene product similarity measurements concentrate on the information content of Gene Ontology (GO) terms or use a path-based similarity between GO terms, which may ignore other important information contained in the structure of the ontology. In our study, we integrate different GO similarity measure approaches to analyze the functional relationship of genes and gene products with a new triangle-based visualiza Read More