Protein and Peptide Letters - Volume 19, Issue 11, 2012

Protein structure information is very useful for the confirmation of protein function. The protein structural class can provide information for protein 3D structure analysis, causing the conformation of the protein overall folding type plays a significant part in molecular biology. In this paper, we focus on the prediction of protein structural class which was based on new feature representation. We extract features from the Chou-F Read More

Yeast tRNA-thiouridine modification protein 1 (Tum1) plays essential role in the sulfur transfer process of Urm1 system, which in turn is involved in many important cellular processes. In the rhodanese-like domain (RLD), conserved cysteine residue is proved to be the centre of active site of sulfurtransferases and crucial for the substrate recognition. In this report, we describe the crystal structure of Tum1 protein at 1.90 A re Read More

A novel α-helical antimicrobial peptide G6 rich in Val/Arg residues has been screened previously. In this study, we further evaluated the biochemical stability, interaction with whole bacteria, and in vivo therapeutic or prophylactic role of the peptide in Salmonella typhimurium-infected mice. The results showed that G6 exhibited strong resistance to pH, heat, and salts. But G6 lost the antimicrobial activity when treated with proteol Read More

Rheumatoid arthritis (RA) is a chronic disease with an autoimmunological background. RA is mostly characterized by systemic inflammation and injuries of synovial joints. There is a hypothesis that bacterial infections may be connected with development of the disease. It has been suggested that molecular mimicry between bacterial and human antigens may be one of possible mechanisms of RA development. One of potentia Read More

Bacterial lipoproteins play critical roles in various physiological processes including the maintenance of pathogenicity and numbers of them are being considered as potential candidates for generating novel vaccines. In this work, we put forth an algorithm to identify and predict ligand-binding sites in bacterial lipoproteins. The method uses three types of pocket descriptors, namely fpocket descriptors, 3D Zernike descriptors an Read More

Machine learning is a kind of reliable technology for automated subcellular localization of viral proteins within a host cell or virus-infected cell. One challenge is that the viral protein samples are not only with multiple location sites, but also class-imbalanced. The imbalanced dataset often decreases the prediction performance. In order to accomplish this challenge, this paper proposes a novel approach named imbalance-w Read More

Transcription factors (TF) are proteins that control the first step of gene expression, the transcription of DNA into RNA sequences. The mechanism of transcriptional regulatory can be much better understood if the category of transcription factors is known. We developed a new method for predicting the classification of transcription factors by incorporating their binding site properties into a novel mode of Chou's pseudo ami Read More

β-N-acetyl-D-glucosaminidase (NAGase) is a major member in chitinolytic enzymes system, which plays an important role in the hatching and molting processes of marine organism. The effects of guanidinium chloride (GuHCl) on the activity of NAGase from green crab (Scylla serrata) were investigated in this study. In results, GuHCl causes reversible inactivation of the enzyme at below 0.8 M concentrations, and the IC50 is e Read More

The NAD+-requiring enzymes of the aldehyde dehydrogenase (ALDH) family contain a glycine motif, GX1– 2GXXG, which is reminiscent of the fingerprint region of the Rossman fold, a conserved structural motif of the classical nicotinamide nucleotide-binding proteins. In this research, the role of three glycine residues situated within the putative NAD+-binding motif (211-GPGSSAG) together with Gly233 and Gly238 of Bacill Read More

The gap between known protein sequences and structures is increasing rapidly and experimental methods alone will not be able to fill in this gap. Therefore it is necessary to use computational methods to predict protein structures. Template based modeling methods could be used for sequences, which have detectable relationship with sequences of one or more experimentally determined protein structures. For predict Read More

Pectin methylesterase (PME) (3.1.1.11) is the pectin degrading enzyme which catalyses the hydrolysis of pectin methylester group, resulting in de-esterification. PME is widely distributed in plants, fungi, yeast and bacteria. In the present study, PME was extracted from tomato by using 8.8% NaCl (4°C). The crude enzyme precipitated with 60% ammonium sulphate resulted in 1.02 fold purification of the enzyme. The purificati Read More

Short antimicrobial peptides were designed and synthesized by C-terminal truncation and residue substitution of avian β-defensin-4. The biological activity of these peptides was examined to elucidate the quantitative structureactivity relationships and find a lead peptide for the development of a novel antimicrobial peptide. The results showed that the truncation of the avian β-defensin-4 eliminated the hemolysis of the peptide. Read More

Nucleotide phosphorylation is a key step towards DNA replication and during viral infections the maintenance of the nucleotide triphosphates pool is required. Deoxythymidine triphosphate (dTTP) is the unique nucleotide that is produced either by de novo or salvage pathways. Thymidine monophosphate kinase (TMK) is the enzyme that phosphorylates deoxythymidine monophosphate (dTMP) using adenosine triphosphate Read More

ThyX, a flavin-dependent thymidylate synthase that is involved in the synthesis of dTMP from dUMP, is a promising target for the development of novel antibacterial drugs that aimed at blocking the biosynthesis of dTMP, one of the building blocks of DNA. This enzyme has been recently identified in some dsDNA viruses and pathogenic bacteria, including the gastric pathogen Helicobacter pylori. It shares neither sequence Read More

A microwave assisted peptide synthesis in water using nanosized Fmoc-amino acids was developed. 5, 7, and 10 mer peptides (Leu-enkephalinamide, dermorphinamide, and a typical difficult sequence, ACP (65-74) peptide) were successfully synthesized in water according to Fmoc chemistry using water-dispersible nanoparticles with microwave irradiation.