Protein and Peptide Letters - Volume 13, Issue 10, 2006

To assess the efficiency of two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and of twodimensional electrophoresis and ammoniacal silver staining (2D-E), different amounts of soybean trypsin inhibitor and horse myoglobin were added to amniotic fluid. In this model, a minimum of 5 to 10 ng of “artificial” biomarkers was detected.

The identification of the thermostability from the amino acid sequence information would be helpful in computational screening for thermostable proteins. We have developed a method to discriminate thermophilic and mesophilic proteins based on support vector machines. Using self-consistency validation, 5-fold cross-validation and independent testing procedure with other datasets, this module achieved overall accu Read More

In this study, we determine the mutation relation among 333 H5N1 hemagglutinins of influenza A viruses according to their amino acid and RNA codon sequences. Then, we calculate seven probabilistic numbers, which have been developed by us since 1999, for each amino acid in these hemagglutinins. With the seven numeric numbers as independents and the probability of occurrence of mutation at each hemagglutinin Read More

X-ray crystal structures of CYP102A1 (P450BM-3) have shown that PHE87 rotates upon substrate binding and is in contact with the heme cofactor. Analysis of substrate binding data combined with DFT calculations suggest that the ring is rotated into an unfavorable interaction with the heme and this could drive active site rearrangement.

A procedure to obtain endosperm protein extracts was standardized. After confirming the enrichment with nuclear proteins by immunodetection, the protein profiles of extracts from different seed development stages were compared by SDS-PAGE that showed the existence of several differentially expressed proteins.

Abstract: In this paper1 we present a novel framework for protein secondary structure prediction. In this prediction framework, firstly we propose a novel parameterized semi-probability profile, which combines single sequence with evolutionary information effectively. Secondly, different semi-probability profiles are respectively applied as network input to predict protein secondary structure. Then a comparison among these dif Read More

In the present study, it was found that intraperitoneal (i.p.) pre-injection of NG-nitro-L-arginine methyl ester (LNAME) significantly influenced the endomorphin-1 (EM-1) and endomorphin-2 (EM-2) induced antinociception. These effects could be inhibited or reversed by L-Arg or naloxone. Our results suggest that the modulatory effect of NO system on the mu-receptor evoked analgesia is different between the two mu receptor subtypes.

This paper proposes a novel method using protein residue conservation and evolution information, i.e., spatial sequence profile, sequence information entropy and evolution rate, to infer protein binding sites. Some predictors based on support vector machines (SVMs) algorithm are constructed to predict the role of surface residues in protein-protein interface. By combining protein residue characters, the prediction Read More

Spatial structure and conformational properties of the Dippu-AST 8 (allatostatin III) neuropeptide have been investigated by the molecular mechanics method. The conformational energy and geometrical parameters corresponding to the low-energy states of the molecule are obtained. A single backbone conformation with a very restricted set of Ser 3, Phe 4 and Leu 9 amino acids positions is observed for Dippu-AST 8 n Read More

Short peptides derived from the transmembrane sequence of NK activating receptors and associated molecules were tested in vitro for inhibition of NK cell cytotoxicity using a standard 51Cr release assay in the absence or presence of peptides. NKL23 cell line was used as the NK effector and the target was the NKL23 sensitive 721.221 cell line. NKp46, NKp30, NKG2D and CD3-ς peptides inhibited NK activity at higher concentra Read More

Nuclear translocation signal has been identified as a mediator of protein shuttling between nuclear and cytoplasm. Here we report that the combination of peptides from nuclear localization signal (NLS) and nuclear export signal (NES) of HIV-1 Rev have an antiviral activity against the Herpes virus of turkey and Marek's disease virus serotype 1.

We have previously isolated a cowpea seed defensin with potent antifungal activity. Here we report the cloning of its cDNA obtained from RT-PCR. The sequence of the deduced protein VUDEF exhibited homology to plant defensins. Northern analysis revealed that VUDEF mRNA is accumulated during cowpea seed development and its level increases in seedling tissues after exposure to fungal pathogen and cold.

Rings of rabbit aorta that were both incubated in a high concentration of D-glucose and contracted submaximally by phenylephrine showed significantly decreased endothelium-dependent relaxations induced by acetylcholine. The cGMP production of aorta rings was also reduced. Treatment with endomorphins (1-1000 nmol/L) restored acetylcholineinduced relaxations of aorta rings incubated in high glucose conce Read More

Tobacco plants were transformed with gene constructs encoding prepro-ConBr (Canavalia brasiliensis lectin). Transgenic plants confirmed by PCR expressed the recombinant protein as revealed by Western blot. However, the apparent molecular mass of the recombinant polypeptide (ca. 34 kDa) was higher than the native lectin (about 30 kDa), showing that further proteolytic processing of pro-ConBr was not detected.

Smu.1392c is a protein with 158 residues of uncharacterized function. Bioinformatics studies predict it is a putative acetyltransferase. In order to identify its exact function via structural studies, Smu.1392c gene was amplified from Streptococcus mutans genomic DNA and cloned into expression vector PET28a. Smu.1392c was crystallized and diffracted to a resolution of 3 Å in-house. The crystal belongs to R32 space g Read More