Protein and Peptide Letters - Volume 15, Issue 7, 2008

Protein hydration plays a crucial role in almost all aspects of biomolecular processes. In this research, we studied the hydration/dehydration-induced infrared amide I band-shift by using poly-L-lysine and bovine pancreas ribonuclease A as model polypeptides. It was found that a 1-4 cm-1 shift could be clearly distinguished for all regular secondary structures during protein thermal unfolding. This shift was proven to be due to backbone hydration but not from experimental error, temperature effect or possible incomplete hydrogen/deuterium exchange of the samples. Moreover, we also found that protein aggregation was closely associated with the backbone hydration/dehydration status of proteins. In conditions favoring aggregation, a significant shift to a higher wavenumber of the band from the intermolecular β-sheet structures in aggregates was observed. The present study suggested that the changes of the amounts of regular secondary structures could be monitored by the intensity changes, while the changes of the hydration status could be monitored by the shift of the infrared bands.

This study investigated the effects of Photorhabdus temperata infection on the activities of digestive enzymes of the sugarcane stalk borer Diatraea saccharalis. Non-infected D. saccharalis larvae present a major α-amylase, several proteinases, three sucrose hydrolases and two α-glucosidases in their midgut. Analysis of these hydrolases by electrophoresis and “in gel” assays showed that the activities of all enzymes decreased following infection, with an initial decline observed 12 h after infection. The activities of α-glucosidases decreased by 50% twelve hours after infection, whereas, at this time, the α-galactosidase activities decreased by 70%. Interestingly, the animals died 48 h after infection, but approximately 5% of all the enzymes tested remained active in the midgut following host death. At this time, most of the cultivable native intestinal bacteria had died.

Glycation, a non-enzymatic reaction between glucose and protein is the primary cause of diabetic complications. Albumin, the most abundant plasma protein undergoes glycation both in vivo and in vitro. The influence of albumin on glycation of less abundant proteins has not been addressed. For the first time, we show that albumin competitively inhibits the glycation of less abundant proteins. This study suggests that at least in the initial stages of diabetes, albumin may protect other proteins from glycation.

The observation in 1979 that opioid receptors interact, led to the design of bivalent ligands in an attempt to improve selectivity and affinity towards the different subtypes (i.e. μ, δ and κ). Dimers of monovalent “parent” opioid structures have been evaluated and include: (a) endogenous (e.g. enkephalins) or exogenous (e.g. dermorphin) peptide dimer analogues (b) mixed peptidic-non-peptidic bivalent ligands and (c) dual non-peptidic dimers. Chimeric structures, using an opioid pharmacophore in combination with a non-opioid pharmacophore, have also been prepared. The common aim in all these studies is to improve the pharmacological profile of potential analgesics to minimize common opioid-induced side-effects, such as physical dependence and tolerance. Here we present a brief overview of efforts to develop bivalent opioid ligands for use in pain-related research.

The nervous and the immune systems can exchange information through opioid peptides. Furthermore, some opioid peptides can function as endogenous messengers of the immune system, and participate in an important part in the regulation of the various components of the immune response. Since the capacity of immunocytes to release and respond to opioid neuropeptide messengers is not restricted to mammalian organisms, recent studies have indicated that invertebrate models have been particularly useful to understand the mechanisms of the immune response. Moreover, the immunocytes of molluscs resemble cells of the vertebrate monocyte/macrophage lineage and are activated by similar substances, which control the main immune responses, i.e. phagocytosis, chemotaxis, and cytotoxicity. Recently, Mytilus edulis has been the subject of recent studies to determine whether the relationship between the immune and nervous systems seen in vertebrates also exists in invertebrates. The focus of this review is to describe how the opioid peptides participate in immune processes in molluscs.

In order to explore the possibility of preparing a high-efficiency aquaporin-based biofilter, an efficient approach for expression of membrane-bound Aquaporin Z (AqpZ) in E. coli was proposed. The AqpZ gene was amplified by means of PCR, and two expression vectors (pET28-AqpZ and pET32-AqpZ) were constructed. The channel protein of interest was synthesized in E. coli BL21(DE3)/pET32-AqpZ as an insoluble fusion protein linked with trxA. However, with BL21(DE3)/pET28-AqpZ, significant amount of AqpZ fused only with 6-His (6-His-AqpZ) could be expressed, correctly folded and targeted into the membrane. Under the optimized culture conditions, the highest expression level (9.05 mg/l) of membrane-bound 6-His-AqpZ was achieved with BL21(DE3)/pET28-AqpZ, and an additional amount (2.35 mg/l) was expressed concomitantly as the inclusion body form. This expression result was 3.5 times higher than that in the previous studies.

Although the yeast Saccharomyces cerevisiae is the best exemplified single-celled eukaryote, the vast number of protein-protein interactions of integral membrane proteins of Saccharomyces cerevisiae have not been characterized by experiments. Here, based on the kernel method of Greedy Kernel Principal Component analysis plus Linear Discriminant Analysis, we identify 300 protein-protein interactions involving 189 membrane proteins and get the outcome of a highly connected protein-protein interactions network. Furthermore, we study the global topological features of integral membrane proteins network of Saccharomyces cerevisiae. These results give the comprehensive description of protein-protein interactions of integral membrane proteins and reveal global topological and robustness of the interactome network at a system level. This work represents an important step towards a comprehensive understanding of yeast protein interactions.

A family of 4kDa neurotoxic peptides was purified from venoms of Phoneutria spiders. All have six cysteine residues, and low similarity with other neurotoxins. Three toxins caused moderate inhibition of L-type Ca2+ channels. The structure of toxin PRTx27C3 was modeled and compared with toxin ADO1. The importance of four residues is suggested.

SCO6571 protein from Streptomyces coelicolor A3(2) was overexpressed and purified using Rhodococcus erythropolis as an expressing host. Crystals of selenomethionine-substituted SCO6571 have been obtained by vapor diffusion method. SCO6571 crystals diffract to 2.3 Å and were found to belong to the orthorhombic space group P212121 with unit cell parameters a = 84.5, b = 171.6, c = 184.8 Å. Six molecules in the asymmetric unit give a crystal volume per protein mass (VM) of 2.97 Å3 Da-1 and solvent content of 58.6 %. The structure was solved by the single wavelength anomalous diffraction (SAD) method. SCO6571 is a TIM-barrel fold protein that assembles into a hexameric molecule with D3 symmetry.

The IR-spectroscopic and structural elucidation of tetrapeptide glycyl-L-prolyl-glycyl-glycine and its hydrogensquarate was performed by employing linear-polarized IR-spectroscopy of oriented colloid suspensions in nematic host as well as mass spectrometry. Quantum-chemical ab initio calculations were carried out in order to evaluate both the electronic structure and optical properties of the compound studied.

To investigate properties of yellow lupine cytosolic cyclophilin, an expression vector pET15CYP was constructed. The CyP cDNA (GenBank accession no.Y16088) reveals an open reading frame of 172 amino acids with the conserved tryptophan residue at position 128 and an insertion of seven amino acids spanning positions 48-54. Yellow lupine cyclophilin, purified after expression in E. coli cells, exhibits peptidyl-prolyl cis/trans isomerase activity when assayed with a synthetic oligopeptide. We have demonstrated that the recombinant cyclophilin is able to interact with nucleic acids, both single and double stranded DNA fragments as well as RNA.

Miliin, a new thiol-dependent serine protease purified from the latex of Euphorbia milii possesses a molecular weight of 79 kDa, an isoelectric point of 4.3 and is optimally active at 60 °C in the pH range of and 7.5-11.0. Activity tests indicate that milliin is a thiol-dependent serine protease.

After several studies on prediction of mutation, we examine the effect of three sampling strategies, the sampling based on years, the sampling based on number of mutations, and the sampling based on the unpredictable portion of amino-acid pairs, on the prediction performance in H5N1 hemagglutinins. The results show that the sampling strategy does play an important role in prediction, which should be taken into account when predicting the next generation of mutations in proteins from influenza A virus.

The successful prediction of protein subcellular localization directly from protein primary sequence is useful to protein function prediction and drug discovery. In this paper, by using the concept of pseudo amino acid composition (PseAAC), the mycobacterial proteins are studied and predicted by support vector machine (SVM) and increment of diversity combined with modified Mahalanobis Discriminant (IDQD). The results of jackknife cross-validation for 450 nonredundant proteins show that the overall predicted successful rates of SVM and IDQD are 82.2% and 79.1%, respectively. Compared with other existing methods, SVM combined with PseAAC display higher accuracies.

In order to prevent atherosclerosis, a chimeric enzyme vaccine of AnsB-TTP-PADRE-CETPC was successfully constructed, expressed and purified to immunize New Zealand white rabbits for inducing high titers of anti-CETP antibodies to improve lipid abnormality. The protein was expressed as soluble protein in Escherichia coli and purified by anion exchange column and Sephadex G-100 size-exclusion chromatography. After immunizing rabbits with the purified protein, high titer anti-CETP antibodies were induced and lasted more than nineteen weeks in vivo; High density lipoprotein cholesterol (HDL-C) content in the serum was elevated to 61% while decreased low density lipoprotein cholesterol (LDL-C) to 37.2% compared with control rabbits in the presence of Al(OH)3.

ORFans are orphan open reading frames. The numbers of ORFans are steadfastly increasing despite of the genome database increment. Characterizing ORFans is essential to fully understanding the diversity of the structure and function of proteins in nature. In this study, MPN423 from Mycoplasma pneumoniae has been cloned, expressed, purified, and crystallized. MPN423 is an orthologous ORFan whose only known homologue in the whole genome database is MG296 from M. genitalium. X-ray diffraction data were collected to 2.7 Å from the crystal of a selenomethionine substitute MPN423. The crystal belongs to the primitive monoclinic space group P21, with unit-cell parameters of a = 50.5 Å, b = 89.2 Å, c = 50.6 Å, and β = 102.9°. A preliminary electron density map shows five α-helical segments per MPN423 molecule. A full structure determination is under way to provide helpful information to general questions about orthologous ORFan products.