Protein and Peptide Letters - Volume 18, Issue 12, 2011

Protein aggregation during expression, purification, storage, or transfer into requisite assay buffers hampers the use of proteins for in vitro studies. The formation of these aggregates represents a major obstacle in the study of biological activity and also restricts the spectrum of protein products being available for the biomedical applications. The catalytic light chain of botulinum neurotoxin type A undergoes autocatalysis and agg Read More

Cyclophilin A (CyPA) is a cytosolic receptor of immunosuppressive drug cyclosporin A (CsA) which possesses peptidyl-prodyl cis/trans isomerase (PPIase) activity. The recombinant human CyPA (rhCyPA) gene has been expressed in E. coli M15. Purification was performed using salting-out, as well as Sephacryl S-100 and DEAE-Sepharose CL-6B column chromatography. The molecular weight is about 18 kDa, confirmed by SDS- Read More

Glutamate dehydrogenase (GDH) enzyme is recently being reported to be present in the nucleus in addition to the mitochondria in a number of organisms. Here we investigated the distribution of GDH in liver and brain tissues of chicken. Polyclonal anti-GDH antibody against bovine GDH was raised by us, which was later shown to be immunereactive to chicken GDH. The nuclear and the mitochondrial extracts from liver and br Read More

Galanin is a neuropeptide that is widely distributed in the central and peripheral nervous systems. In a previous study, we showed that a small cell lung carcinoma (SCLC) cell line, SBC-3A, released progalanin but not galanin, and that progalanin was then converted to galanin(1-20), the active form. Because the galanin(1-20) had undergone hydrolysis at Arg and Lys residues, the protease concerned was surmised to have a try Read More

This article describes a novel method for predicting ligand-binding sites of proteins. This method uses only 8 structural properties as input vector to train 9 random forest classifiers which are combined to predict binding residues. These predicted binding residues are then clustered into some predicted ligand-binding sites. According to our measurement criterion, this method achieved a success rate of 0.914 in the bound state Read More

For a protein, an important characteristic is its location or compartment in a cell. This is because a protein has to be located in its proper position in a cell to perform its biological functions. Therefore, predicting protein subcellular location is an important and challenging task in current molecular and cellular biology. In this paper, based on AdaBoost.ME algorithm and Chou's PseAAC (pseudo amino acid composition), a new comput Read More

Protein-splicing inteins are widespread in nature and have found many applications in protein research and engineering. The mechanism of protein splicing typically requires a nucleophilic amino acid residue at both position 1 (first residue of intein) and position +1 (first residue after intein), however it was not clear whether or how the three different nucleophilic residues (Cys, Ser, and Thr) would work differently at these two Read More

In this study, physicochemical scale (P-scale), was recruited as a novel set of physicochemical descriptors derived from component analysis on four short of physicochemical properties variables (hydrophobic, electronic, steric and hydrogen bond contribution) of 20 coded amino acids, By using partial least squares (PLS), we applied P-scale for the study of quantitative structure-activity relationship models (QASRs) on three angio Read More

Comprehensive knowledge of thermophilic mechanisms about some organisms whose optimum growth temperature (OGT) ranges from 50 to 80 °C degree plays a major role for helping to design stable proteins. How to predict function-unknown proteins to be thermophilic is a long but not fairly resolved problem. Chaos game representation (CGR) can investigate hidden patterns in protein sequences, and also can visually re Read More

Heme-regulated eukaryotic initiation factor 2α kinase (HRI) functions under conditions of heme shortage caused by blood diseases such as erythropoietic protoporphyria and β-thalassemia, and retains the heme:globin ratio at 1:1 by sensing the heme concentration in reticulocytes. This HRI function is regulated by various factors including autophosphorylation and protein-protein interactions. A heat-shock protein control Read More

A series of novel compounds with N-phosphoryl peptide modification at the C-4 position on podophyllotoxin were synthesized and evaluated for their cytotoxicity in vitro against K562 cell lines. Among these compounds 5c, 5f and 5k exhibited better cytotoxicity (IC50 = 5.5 μM, 2.1 μM, and 3.1 μM, respectively) than podophyllotoxin and etoposide. Further study on compound 5f using flow cytometry analysis indicated that the an Read More

Mussels Mytilus coruscus can adhere to various solid surface in the presence of moisture. Mussel foot protein-3 (mfp-3) has been suggested as the main adhesive protein in the plaques closest to the adhesion interface and been the focus of substantial biomaterials development research within the last decade. The byssal plaques of M. coruscus were accumulated and variants of a family known as mcofp3 (Mytilus coruscus foot p Read More

Due to their critical involvement in the execution of the malaria parasite developmental pattern both in the mosquito vector and in the human host, Plasmodium calcium-dependent protein kinases (CDPKs) are considered promising candidates for the development of new tools to block malaria transmission. We report here that the phenothiazine trifluoperazine non-competitively inhibits Plasmodium falciparum CDPK4 in the micr Read More

The superoxide anion radical is a highly reactive toxic species produced during the metabolic processes. A number of copper (II) complexes with amino acids and peptides are known to show superoxide dismutase (SOD) like activity. The design and application of synthetic low molecular weight metal complexes as SOD mimics have received considerable attention during the last decade. A variety of di- and tri-peptides containin Read More

Several variants of Saccharomyces cerevisiae triosephosphate isomerase (yTIM) were studied to determine how mutations of conserved and non-conserved Cys residues affect the enzyme. Wild-type yTIM has two buried free cysteines: Cys 41 (non-conserved) and the invariant Cys 126. Single-site mutants, containing substitutions of these cysteines with Ala, Val, or Ser (the three most conservative changes for a buried Cys, acc Read More