Protein and Peptide Letters - Volume 16, Issue 1, 2009

Type II transmembrane serine proteases (TTSPs) are involved in important physiological processes, such as pro-hormone processing, cellular signaling, host immune defense, and cancer development. The diversity of functions is reflected by the multidomain architecture of these proteases, which are composed of a variety of functional domains in addition to the catalytic domain. Recently, we identified rat DESC4, a member of the HAT/DESC1-like subfamily of TTSPs. Intriguingly, DESC4 gene expression is confined to few tissues including gustatory papillae. In the current publication we present the purification of the catalytic domain of recombinant rat DESC4. Subsequently, the catalytic domain was subjected to a refolding procedure. During refolding we observed endogenous catalytic activity leading to smaller fragments, which were analyzed by peptide sequencing. The identified cleavage-sites are typical for trypsin-like serine proteases. For further analyses a homology-based model of the DESC4 catalytic domain was generated enabling us to investigate protease-substrate interaction in more detail.

A biosurfactant-producing strain was isolated from the production water of an oil-field and was identified as Bacillus subtilis HOB2 by 16S rRNA gene sequencing. The production of biosurfactant by Bacillus subtilis HOB2 has been investigated using different carbon and nitrogen sources, under thermophilic and mesophilic conditions. The strain was able to grow and to produce surfactant, reducing the surface tension of medium to 27 mN/m on sucrose, and 28 mN/m on glucose after 24 h of cultivation. The strain was able to produce the maximum amount of biosurfactant when ammonium ions were used as nitrogen source. The surface-active compound was stable during exposure to elevate temperature (100°C), high salinity (25% NaCl) and a wide range of pH values (5.0-11.0). The biosurfactant was capable of forming a promising emulsification index (E24= 68%) with kerosene. The kinetic studies revealed that biosurfactant production is a cell growth-associated process. Preliminary chemical characterization revealed that the surfactant has a lipopeptide composition similar to surfactin as confirmed by TLC and IR analysis. Properties and characteristics of the biosurfactant produced by Bacillus subtilis HOB2 suggesting potential commercial applications, such as enhanced oil recovery, bioremediation of soil and marine environments, and food industries.

The prion protein is a cell surface glycoprotein that is converted to a protease resistant abnormal isoform during the course of prion disease. The normal isoform of this protein has been shown to be an antioxidant that aids the survival of neurones. The abnormal isoform is associated with both the transmissible agent of prion diseases and is also toxic. Recent studies have shown that there are multiple end states in terms of aggregation of the protein. Both soluble oligomers and insoluble fibrils can form from the abnormal isoform. Although fibrils are characteristic of the disease, the most infectious prions are associated with oligomers. Neurotoxicity can be associated with fibrils but mostly appears to be due to small aggregates. For many years fibrils were believed to be central to the disease process but currently evidence supports the notion that fibrils represent a ‘bulk’ form of abnormal protein, which is largely inert, but carried along a small active component. This review will examine what is known about the mechanisms behind prion protein aggregation, and the relevance of each form for the disease.

Protein secondary structure carries information about local structural arrangements. Significant majority of successful methods for predicting the secondary structure is based on multiple sequence alignment. However, the multiple alignment fails to achieve accurate results when a protein sequence is characterized by low homology. To this end, we propose a novel method for prediction of secondary structure content through comprehensive sequence representation. The method is featured by employing a support vector machine (SVM) regressing system and adopting a different pseudo amino acid composition (PseAAC), which can partially take into account the sequence-order effects to represent protein samples. It was shown by both the self-consistency test and the independent-dataset test that the trained SVM has remarkable power in grasping the relationship between the PseAAC and the content of protein secondary structural elements, including α-helix, 310-helix, π-helix, β-strand, β-bridge, turn, bend and the rest random coil. Results prior to or competitive with the popular methods have been obtained, which indicate that the present method may at least serve as an alternative to the existing predictors in this area.

ROS, including .OH, is now recognized as the hallmark of inflammation and damage to the anti-proteinase barrier has been implicated in a number of pathophysiological conditions. We have previously shown that O2 .- and H2O2/HOCl are physiologically relevant inactivators of α2M, a key anti-proteinase. Here, we show that .OH disrupted caprine α2M structure and antiproteolytic potential in vitro, suggesting that its function could be compromised via oxidative modification.

Aminopeptidase A (PepA) is a metalloexopeptidase found in Vibrio cholerae .It functions as a transcriptional repressor in regulatory cascade that controls virulence gene expression in V. cholerae. It is involved in protein degradation and in the metabolism of biologically active peptides. We proposed a 3D model of PepA based upon the crystal structure of PepA from Escherichia coli (E. coli) with an intention to evaluate the active site of the enzyme and to predict the properties of this enzyme, study of its 3D structure will help in understanding its role in DNA binding.

Propofol (2,6-diisopropylphenol) is a hypnotic intravenous agent with in vivo antioxidant properties. This study was undertaken to examine the in vitro effect of propofol on lactoperoxidase (LPO; E.C. 1.11.1.7) obtained from bovine milk. Lactoperoxidase was purified with three purification steps: Amberlite CG-50 resin, CM-Sephadex C-50 ionexchange chromatography and Sephadex G-100 gel filtration chromatography, respectively. Lactoperoxidase was purified with a yield of 21.6%, a specific activity of 34 EU/mg proteins and 14.7-fold purification. One enzyme unit is defined as the oxidation of 1 μmol ABTS per min under the assay condition (25oC, pH: 6.0). To determine enzyme purity, sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) was performed and single band was observed. The effect of propofol on lactoperoxidase were determined using 2,2'-azino-bis (3-ethylbenzthiazoline-6 sulfonic acid) diammonium salt (ABTS) as a chromogenic substrate. The IC50 value of propofol was found as 15.97 μM. Also, Ki constant for propofol was 3.72 μM and propofol was found as competitive inhibitor.

As the most widely utilized technique to determine the 3-dimensional structure of protein molecules, X-ray crystallography can provide structure of the highest resolution among the developed techniques. The resolution obtained via X-ray crystallography is known to be influenced by many factors, such as the crystal quality, diffraction techniques, and X-ray sources, etc. In this paper, the authors found that the protein sequence could also be one of the factors. We extracted information of the resolution and the sequence of proteins from the Protein Data Bank (PDB), classified the proteins into different clusters according to the sequence similarity, and statistically analyzed the relationship between the sequence similarity and the best resolution obtained. The results showed that there was a pronounced correlation between the sequence similarity and the obtained resolution. These results indicate that protein structure itself is one variable that may affect resolution when X-ray crystallography is used.

Proteins may form undesirable aggregates during the process of folding. Increasing evidence suggests that amyloid fibrils may arise from partially folded precursor molecules. We have previously demonstrated that hen egg white lysozyme [HEWL] exists as molten globule at pH 12.7. Here, we report that lysozyme at pH 7.0 and 11.0 are nearly stable to the addition of up to 45% t-butanol, but treatment of the alkali-induced molten globule form of HEWL [AMGL] with 20% t-butanol caused the formation of amyloid-like fibrils as evidenced by enhanced Thioflavin T binding and DLS measurements.

Until now it was impossible to obtain atomic structure of intrinsically disordered protein (IDP) tau and/or its assembly in Alzheimer's paired helical filaments as neither of them could have been prepared in the form amenable to Xray or NMR techniques. Using IDP tau property to attain regular tertiary structure after binding events during selfassembly or when complexed with its target we propose monoclonal antibodies as surrogate tau protein binding partners to form complexes and crystals for structure solution by X-ray technique.

We studied expression of HPV 58 long and short L1 proteins in primary mouse keratinocyte (KC) cultures by transient transfection of the L1 expression constructs. Following transient transfection, long and short L1 open reading frames (ORFs) were transcribed continuously for 9 days; however, no significant difference was detected between the long and short L1 mRNA levels measured by quantitative RT-PCR. Western blot analysis showed that both long and short L1 proteins were continuously detected in L1-transfected KCs for 9 days post-transfection and the significantly increased signals of the L1 proteins over time were associated with KC differentiation. Moreover, L1 protein was more abundant in KCs transfected with the short L1 ORF than the long L1 ORF. In vitro translation of the L1 mRNAs indicated further that the short L1 mRNA had significantly higher translation efficiency than the long L1 mRNA in cell-free lysate system. The L1 proteins expressed from the two L1 mRNAs in KCs were similarly stable. Thus, approximate 40% lower level of expression of the L1 protein in KCs transfected with the long L1 ORF was probably due to a stem-loop structure with high ΔG value downstream the first AUG codon in its mRNA secondary structure. This stem-loop structure might prevent efficient binding of the ribosome to mRNA and therefore reduced translation.

Glutathione transferases, GSTs, are detoxification proteins that are found in most organisms. The acGSTE3-3 had the ability to conjugate 4-hydroxynonenal, a cytotoxic lipid peroxidation product. Although other Epsilon GSTs showed roles in insecticide metabolism, the acGSTE3-3 appeared to have a major role in detoxifying lipid peroxidation products conferring protection against oxidative damage.

A new antifungal peptide designated as pomegranin, with an N-terminal sequence resembling that of rice disease resistance NB-S-LRR-like protein, was isolated from fresh pomegranate peels by ion exchange chromatography on DEAE-cellulose, affinity chromatography on Affi-gel blue gel, and gel filtration by fast protein liquid chromatography on Superdex 75. Pomegranin was unadsorbed on DEAE-cellulose but adsorbed on Affi-gel blue gel. It exhibited a molecular mass of 11 kDa in both gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It inhibited mycelial growth in the fungi Botrytis cinerea and Fusarium oxysporum with an IC50 of 2 μM and 6.1 μM, respectively. It was devoid of hemagglutinating, ribonuclease, deoxyribonuclease and protease inhibitory activities.

Both stereoisomer of hydroxyethylamine (HEA) and hydroxyethylsulfide (HES) transition-state isostere inhibitors of BACE-1 were synthesized. The syn-HEA epimer resulted always more active than the anti stereoisomer independently from the P1 and the P1' substituents. On the contrary, the anti epimer of the HES isostere resulted more active than the syn stereoisomer. The change of stereopreference was studied by molecular modelling.

Here, we show for the first time that non-fibrillar and spherical aggregates produced from PrP-(23-98) in the presence of NADPH plus copper ions are toxic to cultured cells and induce apoptotic signals. It is also confirmed that endogenous cellular PrP isoform is not required for toxicity to occur.

The plasma form of the human enzyme platelet activating factor acetylhydrolase (PAF-AH) has been crystallized, and X-ray diffraction data were collected at a synchrotron source to a resolution of 1.47 Å. The crystals belong to space group C2, with unit cell parameters of a = 116.18, b = 83.06, c = 96.71 Å, and β = 115.09° and two molecules in the asymmetric unit. PAF-AH functions as a general anti-inflammatory scavenger by reducing the levels of the signaling molecule PAF. Additionally, the LDL bound enzyme has been linked to atherosclerosis due to its hydrolytic activities of pro-inflammatory agents, such as sn-2 oxidatively fragmented phospholipids.

Nudix hydrolases are a family of proteins that contains the Nudix signature of the characteristic amino-acid sequence Gx5Ex5[UA]xREx2EExGU, where x represents any amino acid and U usually a bulky hydrophobic amino acid, such as Leu, Val, or Ile. They ubiquitously exist in more than 200 species. YmfB, a novel Nudix hydrolase found in Escherichia coli, is a nonspecific nucleoside tri- and di-phosphatase, which atypically releases inorganic orthophosphate from triphosphates instead of pyrophosphate. In this study, YmfB was cloned, overexpressed, and crystallized. Two different crystals, one belonging to an orthorhombic space group C2221 and the other a monoclinic space group P21, diffracted to 2.7 Å and 2.6 Å resolution, and had unit cell parameters of a = 68.7 Å, b = 283.1 Å, c = 70.4 Å and a = 69.1 Å, b = 70.3 Å, c = 145.6 Å, β = 103.3°, respectively. For the C2221 space group, four or five monomers exist in the asymmetric unit, with a corresponding Vm of 2.48 or 1.99 Å3 Da-1 and a solvent content of 50.5 or 38.2%. For the P21 space group, eight or nine monomers exist in the asymmetric unit, with a corresponding Vm of 2.49 or 2.21 Å3 Da-1 and a solvent content of 50.7 or 44.5%.