Protein and Peptide Letters - Volume 14, Issue 2, 2007

Inactivation of RNA molecules by sequence-specific endoribonucleolytic cleavage is a subtle mechanism by which cells coordinate, regulate and adapt their complex gene expression patterns. This special issue entitled “Highly Sequence-Specific Endoribonucleases” highlights the latest findings in the field of RNA recognition and cleavage by sequence-specific endoribonucleases. The aim of this issue is not to provide an e Read More

Inactivation of RNA molecules by sequence-specific endoribonucleolytic cleavage is a subtle mechanism by which cells regulate gene expression. Sequence-specific endoribonucleases can recognize and cleave particular phosphodiester bonds confined within hundreds/thousands of chemically similar bonds. Here, we present a comparative analysis of the mechanisms used by endoribonucleases to select and cleave their target Read More

Toxin-antitoxin systems were discovered as plasmid auxiliary maintenance cassettes. In recent years, an increasing amount of structural and functional information has become available about the proteins involved, allowing the understanding of bacterial cell growth inhibition by the toxins on a molecular level. A well-studied TA system is formed by the proteins Kid and Kis, encoded by the parD operon of the Escherichia coli Read More

Restrictocin, a member of the fungal ribotoxin family, specifically cleaves a single phosphodiester bond in the 28S rRNA and potently inhibits eukaryotic protein synthesis. The long loops in restrictocin molecule have been shown structurally to be involved in target RNA recognition. In this study we have investigated the role of some putative substrate- interacting residues in loops L2 and L4, spanning residues 36-48 and 99- Read More

Messenger RNA (mRNA) decay utilizes both exoribonucleolytic and endoribonucleolytic enzymes where the latter are generally more prone to be transcript-specific. An erythroid-enriched endoribonuclease, ErEN, can destabilize the α -globin mRNA through directing a site-specific cleavage within the 3' untranslated region (3' UTR) both in vitro and in vivo. ErEN activity is sequence- and/or local structure-specific as the minim Read More

Endonuclease tRNase Z catalyzes the generation of the mature 3' end of tRNA precursors through specific endonucleolytic cleavage. The enzyme has been characterized from organisms representative of all domains of life as well as from organelles, and the crystal structure of three bacterial enzymes has been determined. This review presents an overview of its properties and what is known about its structure, substrate reco Read More

Recently, two sequence-specific cleavage sites were found in the ceiE7 gene of the cea-cei-cel polycistronic transcript from the ColE7 operon. The crystal structure of the ColE7 immunity protein (ImE7) suggested that a novel ribonuclease active site is created at the interface of the dimeric structure of the protein. Frame shift mutation of the ceiE7 gene and mutation of histidine residues at the putative active site of the dime Read More

The present review is aimed at giving a general overview of our results in the field of designing and synthesizing simple peptide-like molecules that mimic structural and functional aspects of natural ribonucleases, as well as designing oligonucleotide-based artificial ribonucleases.

Previously we characterized an acetyl-esterase from Escherichia coli, formally Aes, from a thermodynamic point of view in comparative studies with thermophilic homologs. Since the enzyme appeared unusually resistant to the thermal denaturation we analysed the kinetic behaviour with respect to the temperature. The enzyme displays a surprising optimal temperature at 65 °C, showing a specific activity of 250 U/mg usin Read More

Lipid-induced α -helix folding, which occurs in many lipid surface-binding proteins and peptides such as apo- lipoproteins and synucleins, has been proposed to provide an energy source for protein-lipid interactions. We propose that in a system comprised of a phospholipid surface and a small polypeptide that is unfolded in solution and binds reversibly to lipid surface, helical folding involves expenditure of free energy as compa Read More

While beta-propeller phytases (BPPs) from Gram-positive bacteria do not carry disulfide bonding, their counterparts from Gram-negative bacteria contain cysteine residues that may form disulfide bonds. By molecular modeling, two amino acid residues of B. subtilis 168 phytase (168PhyA), Ser-161 and Leu-212, were mutated to cysteine residues. Although the double cysteine mutant was secreted from B. subtilis at an expressio Read More

In this paper, we propose the adoption of the bounded support vector machine (BSVM) to predict the B-factors of residues based on a number of distinctive properties of residues. Due to the ability of multi-class classification of the BSVM, we can elaborately distinguish our targets and obtain relatively higher accuracy.

In a continuation of our attempt to predict mutations in proteins from influenza A virus, this study attempted to answer the question of whether distinguishing between arginine, leucine and serine can improve the predictability as these residues are governed by different probabilistic mechanism translating from RNA codons to amino acids. In this study, we made the prediction based on the mutation relation among 2 Read More

In this study, effects of some antibiotics, namely, ofloxacin, cefepime, cefazolin, and ampicillin on the in vitro enzyme activity of 6-phosphogluconate dehydrogenase have been investigated. For this purpose, 6-phosphogluconate dehydrogenase was purified from chicken liver 535-fold with a yield of 18% by using ammonium sulphate precipitation, 2',5'-ADP Sepharose 4B affinity chromatography, and Sephadex Read More

As the knowledge of protein signal peptides can be used to reprogram cells in a desired way for gene therapy, signal peptides have become a crucial tool for researchers to design new drugs for targeting a particular organelle to correct a specific defect. To effectively use such a technique, however, we have to develop an automated method for fast and accurately predicting signal peptides and their cleavage sites, particula Read More

Transgelin was solubly expressed in E. coli. Crystals of transgelin have been grown at 291K using sodium formate or PEG-4000 as precipitants. X-ray diffraction by the crystal extends to 2.3 Å resolution. The crystal belongs to the space group P21, with the unit cell parameters a=39.3, b=61.9, c=56.0 Å and β =90.2 .