Protein and Peptide Letters - Volume 17, Issue 10, 2010

Aspartimide (Asi) formation is one of the most serious side reactions that can occur both during solid phase synthesis and storage of peptides containing aspartic acid. Although numerous studies on the mechanism of Asi formation conducted so far, the problem still remains unresolved and relatively little is known about the impact of this side reaction on biological properties of such modified peptides. In the present work we Read More

The single-stranded DNA-binding proteins are crucial in all kinds of DNA metabolic processes. Deinococcus SSB-like proteins are homodimers in nature and contain two OB folds per monomer, in contrast to other bacterial SSB proteins that are functionally active as homotetramers. We generated four truncated variants of DraSSB protein, based on its crystal structure (PDB code: 1SE8). Gel filtration showed that DraSSB, Read More

Characteristic peptides of the protein segments having common secondary folds are obtained for the I-sites library using maximal position specific probability scores. The secondary structures of these peptides are predicted deploying two best-known computational methods. These are validated with significant accuracy against the corresponding motifs. The characteristic peptides also match with those computed using Read More

There are different types of cyclins, which are active during the cell cycle and enable cyclin-dependent kinases to phosphorylate different substrates. Since there is not much similarity between amino acid sequences of cyclins, predicting these proteins is an important job. This paper presents a bioinformatics classifier to predict cyclins based on Chou's pseudo amino acid composition. Analysis of the results by StAR, w Read More

Discovering a protein motif is an important research topic in both bioinformatics and protein sciences. This paper presents a novel motif discovery algorithm which is capable of finding a motif set to represent a protein family. The algorithm involves an abstraction method of important features, a location-sensitive connection approach to link two features, and a repeated connection procedure to generate a motif set. The novel a Read More

Series of eight new monocyclic analogues of trypsin inhibitor SFTI-1 was synthesized by the solid phase method. In these analogues disulfide bridge Cys3 — Cys11 present in native inhibitor was replaced by different-sized carbonyl bridges formed by the amino groups of the side chain of Lys, Orn, Dab or Dap located in positions 3 and/or 11. All analogues appeared to be potent trypsin inhibitors. The values of association equilibrium Read More

The novel recombinant hirudin, r-RGD-hirudin, inhibits thrombin and platelet aggregation. Here, we reported over-expression of 15N-labeled r-RGD-hirudin by Pichia pastoris in minimal medium. After extensive optimization, the yield of active r-RGD-hirudin reached ~600 mg/L when the yeast cells were cultured in a fermenter. The purified 15N-labeled r-RGD-hirudin retained full biological activity and was uniformly labeled. Het Read More

Glutathionylation, covalently attaching glutathione(s) to cysteine residue(s) of a protein, has attracted great attention in recent years. The importance of glutathionylation was initially recognized for its role in protecting proteins from irreversible oxidation; however, more studies indicate that glutathionylation is also involved in redox regulation under both normal physiological conditions and oxidative stresses. Potential me Read More

To facilitate expression and purification of an analog of GLP-1 (mGLP-1), an intein system was employed in this study. A recombinant fusion protein, CBD-DnaB-mGLP-1, was constructed and expressed in the form of inclusion body. After refolding, the intein-mediated self-cleavage was triggered by pH and temperature shift. By using chitin beads column followed by single step purification, about 2.58 mg of mGLP-1 with the purity Read More

Triphala is an Ayurvedic herbal formulation consisting of equal parts of three myrobalans: Terminalia chebula, Terminalia bellerica and Emblica officinalis. We recently reported that chebulagic acid (CA) isolated from Terminalia chebula is a potent COX-2/5-LOX dual inhibitor. In this study, compounds isolated from Terminalia bellerica were tested for inhibition against COX and 5-LOX. One of the fractionated compounds sho Read More

Familial mediterranean fever (FMF) is a systemic disorder characterized by recurrent attacks of fever and polyserositis. In FMF, several pro-inflammatory cytokines, such as IL-6, have been found to be elevated during the attacks. In recent years, it is shown that some proteins originated from adipose tissue play important role in inflammatory process. One of them, adiponectin decreases the expression of adhesion molec Read More

Knowledge of apoptosis proteins plays an important role in understanding the mechanism of programmed cell death. Thus, annotating the function of apoptosis proteins is of significant value. Since the function of apoptosis proteins correlates with their subcellular location, the information about their subcellular location can be very useful in understanding their role in the process of programmed cell death. In the present study, w Read More

Flavonoids, also called vitamin P, are widely distributed in plants fulfilling many functions. Yeast α- glucosidase (YAGH; EC 3.2.1.20), as extensively used target protein for screening bioactive compounds from medicine plants, was selected to explore the possible mechanisms of multiple biological function of flavonoids. The results in this study indicated that flavonoids, as mixed-type inhibitors, quenched the intrinsic fluore Read More

In the current study, a mutant recombinant human interleukin-2 (MhIL-2) was generated using site-directed mutagenesis. The bacteria transformed with plasmid pET15b-MhIL-2 were cultured in LB medium containing 0.6mM IPTG for 8 hours at 27°C. Approximately 90% of His-MhIL-2 was efficiently expressed in soluble form. Purification efficiency was optimized using a number of strategies, including nickel ion chelating chr Read More

Apolipoprotein M (apoM) in human plasma is mainly associated with HDL. A retained signal peptide anchors apoM to the lipoproteins. To investigate the role of the signal peptide in the transfer of apoM from the synthesizing cell to the lipoproteins, wildtype apoM cDNA and the Q22A mutant, introducing a signal peptidase cleavage site, were used to stably transfect HEK293 cells, which intrinsically do not express apolipoprotein Read More

Glucagon-like peptide -1 (GLP-1) is an incretin hormone displaying glucose-dependent stimulation of insulin secretion and trophic effects on the pancreatic β-cells. However, GLP-1 is rapidly degraded to GLP-1(9-36) by dipeptidyl peptidase-IV (DPP-IV), which removes the N-terminal dipeptide His7-Ala8. The rapid inactivation of GLP-1 in the blood circulation limits its clinical application. Hence, we replaced the enzymatic hydroly Read More

PrkC is an important Ser/Thr membrane kinase of Staphylococcus aureus able to bind peptidoglycans through extra-cellular domains, denominated as PASTA. Upon peptidoglycan binding, PrkC is activated and stimulates bacterial growth and revival from latency. The entire extra-cellular region of PrkC (residues 378-664), containing three predicted PASTA domains and an extra-domain of unknown function, has been successfully cr Read More

Twelve peptides of the general X-SO2-D-Ser-Ala-Arg-OH formula (where X = methyl, phenyl, α-tolyl, p-tolyl, 4-methylbenzyl, 1-naphtyl, 2-naphtyl, 4-chlorophenyl, 4-bromophenyl, 2-mesityl, 2,4,6-triisopropylphenyl, 4-acetamidophenyl) were obtained and tested for their effect on the amidolytic activities of urokinase, thrombin, trypsin, plasmin, t-PA and kallikrein. 2,4,6-triisopropylphenyl-SO2-D-Ser-Ala-Arg-OH was the most select Read More

Interdomain binding has been shown to play an important role in the regulation of MAP kinase phosphatase 3 (MKP3), a phosphatase involved in control of ERK signalling pathways. In this study the residues in N- and C-terminal domains responsible for MKP3 interdomain binding are identified. Peptides from the N-terminal substrate-binding domain of MKP3 were assessed for their ability to bind the C-terminal catalytic domain u Read More