Protein and Peptide Letters - Volume 15, Issue 6, 2008

A majority of column chromatographies use only selected salts, e.g., ammonium sulfate, NaCl, Citrate and phosphate in hydrophobic interaction chromatography (HIC) and NaCl in ion exchange and dye affinity chromatographies. Alternatively, a pH range below or above the neutral value is often used to reduce affinity interactions, e.g., in Protein-A or dye affinity column chromatography. Although these parameters are easil Read More

Intra-molecular electron transfer is a key process, which is of prime importance, in photosynthesis, mitochondrial electron transfer and the action of many multi-centre enzymes. This mini-review considers the possible mechanisms of intra-molecular electron transfer in proteins and reviews the recent developments relating to possible electron tunnelling and electron hopping processes within di-heme cytochrome c peroxidase.

We previously described a potent anthrax toxin inhibitor, based on a phage-library-selected peptide sequence, synthesized as a tetra-branched molecule on a lysine core and further modified for improvement of activity [Pini et al., Biochem. J., 2006, 395, 157]. This branched peptide had very low solubility because of several hydrophobic residues in the peptide sequence. This complicated molecule purification and manufacturi Read More

Peanut allergy is one of the most severe food allergies. One effort to alleviate this problem is to identify peanut germplasm with lower levels of allergens which could be used in conventional breeding to produce a less allergenic peanut cultivar. In this study, we identified one peanut line, GT-C9, lacking several seed proteins, which were identified as Ara h 3 isoforms by peptide sequencing and named iso-Ara h 3. Total seed pr Read More

Insect produce wide range of protein and peptides as a first fast defense line against pathogen infection. These agents act in different ways including insect immune system activation or by direct impact on the target tumor cells or viruses. It has been shown that some of the insect peptides suppress viral gene and protein expression, rybosilate DNA, whereas others cause membrane lysis, induce apoptosis or arrest Read More

Glycogen synthase kinase (GSK3) activity present in one cell is the consequence of the sum of the activities of two different proteins called GSK3α and GSK3β. These isoenzymes are coded by two different genes and share an almost identical sequence at their catalytic domain, but differ in the sequence of putative regulatory regions. In this review, we propose that glycine repeats present only in GSK3α may result in the differen Read More

The membrane protein type is an important feature in characterizing the overall topological folding type of a protein or its domains therein. Many investigators have put their efforts to the prediction of membrane protein type. Here, we propose a new approach, the bootstrap aggregating method or bragging learner, to address this problem based on the protein amino acid composition. As a demonstration, the benchmark Read More

To analysis the change of Deinococcus radiodurans extracellular proteins recovering from γ-irradiation, we examined extracellular proteome changes using two-dimensional polyacrylamide gel electrophoresis. Twenty-six spots on the gel of irradiated sample were showed significant changes compared with spots on the control gel. Using peptide mass fingerprinting via matrix-assisted laser desorption ionization-time o Read More

Two genes encoding a NAD+-dependent DNA ligase (LigA) and an ATP-dependent DNA ligase (LigB) were identified in the genome of the extremely radioresistant bacterium, Deinococcus radiodurans (DR). The recombinant enzymes expressed in Escherichia coli, were purified to homogeneity and characterized. The optimal temperature and pH value of the two DNA ligases were 60 °C and 7.0, respectively. Their optimal conce Read More

Pea lectin was exposed to a pH range of 7-13. It was observed that alkaline-unfolding resulted in a molten globule-like intermediate at pH 11. The structural stability of this alkaline unfolded molten globule-like state of pea lectin was studied in the presence of HFIP. Thermal studies showed that this state was more susceptible to thermal denaturation as compared to the native state and it became even more so in presence of HFIP.

The location of a protein in a cell is closely correlated with its biological function. Based on the concept that the protein subcellular location is mainly determined by its amino acid and pseudo amino acid composition (PseAA), a new algorithm of increment of diversity combined with support vector machine is proposed to predict the protein subcellular location. The subcellular locations of plant and non-plant proteins are inves Read More

The amidase from Sulfolobus solfataricus enantioselectively hydrolyzes S-ketoprofen amide to its corresponding acid. We identify three independent SsAH mutants that hydrolyze R-ketoprofen amide and built computational models of their three-dimensional structure. Interestingly the mutations do not specifically affect residues near the active site, or directly interacting with the substrate.

The 5S subunit of transcarboxylase was expressed and purified. Recent methods of NMR spectroscopy as transferred NOESY, INPHARMA and Saturation Transfer Difference (STD) NMR were used to investigate ligand binding of free biotin to the 5S protein. The binding epitope for biotin is very similar to that obtained at the 12S subunit of transcarboxylase, however no common binding site for pyruvate and biotin exists.

The phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) catalyzes the phosphorylation and transportation of its sugar substrates. A sugar-specific enzyme II complex involved in the PTS finally functions to translocate substrates across the membrane. A PTS EIIBfruc protein, a fructose specific EIIB subunit, from Escherichia coli has been cloned, expressed, refolded, purified, and crystallized. The synchrotron dat Read More

Heparin binding proteins (HBPs) from human seminal plasma (HSP) were obtained by heparin affinity and size exclusion chromatography. The aggregation/disaggregation of HBPs was followed by dynamic light scattering (DLS) in presence of various physiological ligands such as CaCl2, NaCl, EDTA, cholesterol, adenosine, D-glucose and D-fructose. The aggregation pattern of lactoferrin was also analyzed and compared. The st Read More

Previous structural studies based on the co-crystal of a complex between bovine pancreatic deoxyribonuclease I (bpDNase I) and a double-stranded DNA octamer d(GCGATCGC)2 have suggested the presence of a putative secondary active site near Ser43. In our present study, several crucial amino acid residues postulated in this putative secondary active site, including Thr14, Ser43, and His44 were selected for site-directed Read More

Human ankyrin repeat and suppressor of cytokine signaling box protein 9 (hASB9), a subunit of an Elongin Ccullin- SOCS box (ECS) E3 ubiquitin ligase complex, is believed to be involved in specific substrate-recognition for ubiquitination and degradation. In fact, this specific substrate-recognition is determined by the ankyrin repeats of hASB9 protein. Here, we have cloned and overexpressed the hASB9-2, the splice var Read More