Protein and Peptide Letters - Volume 13, Issue 1, 2006

Modulation by pardaxin of the phase transitions of dimyristoyl phosphatidylcholine, 1-stearoyl-2-oleoyl phosphatidylcholine or 1-stearoyl-2-oleoyl phosphatidylglycerol in the presence or absence of cholesterol was studied by differential scanning calorimetry. The transition enthalpy of each of the phospholipids was lowered by pardaxin and there was a small decrease in the transition temperature. Addition of cholesterol and pardaxin to dimyristoyl phosphatidylcholine resulted in a very marked lowering of the transition temperature. Although the peptide broadens the transition of the pure phospholipids, it sharpens the transition of mixtures of the phospholipids with cholesterol. This and the observation that pardaxin also causes the formation of crystallites of anhydrous cholesterol, suggest that the peptide promotes redistribution of cholesterol in the membrane.

O-acetylserine sulfhydrylase (OASS) catalyzes the last step in the cysteine biosynthetic pathway in enteric bacteria and plants. The overall pathway involves the substitution of the β-acetoxy group of O-acetyl-L-serine with inorganic bisulfide. Two isozymes are present in S. typhimurium, the A- and B-isozymes, expressed under aerobic and anaerobic conditions, respectively. No crystal structure is presently available for the B-isozyme. Kinetic data indicate the catalytic mechanism of OASS-B is ping-pong, as found for the A-isozyme, but kinetic parameters and substrate specificity differ. In order to estimate whether structural differences may be responsible for the kinetic differences, a homology model was built using the structure of OASS-A as the template for the OASS-B model. The β- subunit of tryptophan synthase and cystathionine β-synthase were used for comparison. Differences between the OASS-A structure and the homology model for OASS-B are discussed.

Plastocyanin was purified from the gymnosperm Ginkgo biloba L., and its complete amino acid sequence was determined. The protein was shown to contain Phe-83 instead of Tyr-83 conserved in other land plant plastocyanins. This is the first report of the characterization and complete amino acid sequence of a gymnosperm plastocyanin.

Urocortin (UCN), an endogenous cardioprotective peptide, has been reported to activate several ion channels but its effects on the cardiac KATP channels are unknown. In this paper, we showed that adult rat cardiac myocytes had small KATP currents that could be increased 20-fold by pinacidil. UCN also concentration-dependently activated the KATP current and this effect was influenced by ATP and PKA inhibitor peptide, Rp-cAMPS.

The representation system for protein conformation has a crucial effect on the speed of various protein-related simulations, including ab initio protein structure prediction and protein-protein docking simulation. Usually, the finer a representation system, the longer is the computational time required to employ the representation system in simulations. On the other hand, very coarse lattice systems cannot be directly applied to the simulation problems with real proteins. We report a new, fragment library-based protein conformation representation system, prepared by clustering amino acid conformations from 154 proteins. This system was composed of 64 most representative fragments per each amino acid, and based on the unified residue approach in which two spheres per amino acid were used. It could represent the conformation of the 82 proteins in an independent test set with the mean and standard deviation RMSD of 1.01 and 0.09 Å, respectively, based on the position of alpha carbons and the centers of mass of sidechains.

The conformational changes in the thermal denaturation of bovine pancreatic ribonuclease A was followed with infrared spectra and analyzed by second derivative and two-dimensional correlation techniques. By analyzing the sequential events in each transition stage, the results were consistent with a step-wise thermal denaturation mechanism in which the structural adjustment of the N-terminal and the opening of the central structure of the protein come before the main unfolding process. Non-native turns were found to form along with the unfolding of the native structures. The central region that is composed of some β-sheet and α-helical structures was found to be the most stable part that might form the residual structure at high temperatures.

PP5715 is a putative tumor suppressor gene that encodes a protein of 199 amino acids. Expression of PP5715 in E. coli was mainly as inclusion bodies. The recombinant protein was purified by a NTA-Ni2+ affinity column, refolded by dialysis, and shown to suppress growth of two human hepatocellular carcinoma cell lines using the MTT assay or the clonogenic assays. Computer analysis and fusion expression of PP5175 and GFP showed that PP5715 may be a secretory protein. It may bind to receptors on the membrane surface and thus induce regulation of cell growth. These preliminary results suggest that protein PP5715 may be a new tumor suppressor with growth inhibition effects on hepatocellular carcinoma cells.

The secondary structure of a new type of recombinant RGD-hirudin, which has the activities of anti-thrombin and anti-platelet aggregation, has been studied by Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy and circular dichroism (CD) methods. The distribution of various secondary structure elements was determined using only a very small amount of sample protein. It was found that the recombinant RGD-hirudin contains about 26% extended chain, 21% β-turn and 53% unordered structure, leaving no α-helix. The results showed that the regular secondary structure of recombinant RGD-hirudin is increased compared with wild-type hirudin. The RGD segment that is located at the end of a long arm of a β-sheet is thought to play an important role in the additional function of anti-platelet aggregation. Throughout the experiments, FT-IR, Raman spectroscopy and CD generated mutually reinforcing results.

We investigated the in vitro antibiotic activity of the 19-amino acid antimicrobial peptide HP (2-20), derived from the N-terminus of Helicobacter pylori Ribosomal Protein L1 (RPL1), against antibiotic susceptible and resistant pathogens from a patient with gallstones. HP (2-20) was active against antibiotic-susceptible and antibiotic-resistant clinical isolates of pathogens from a patient with gallstones, but this peptide showed no hemolytic activity against normal human erythrocytes. HP (2-20) acted synergistically with ciprofloxacin against pathogenic bacteria. Fluorescence activated flow cytometry revealed that the effect of HP (2-20) was dependent on energy and salt concentration. In addition, scanning electron microscopy showed that HP (2-20) caused significant morphological alterations to the cell surface of pathogens. Using 16S rDNA sequences, we found that isolates from bile were 100% homologous to Pseudomonas aeruginosa. These findings suggest that HP (2-20) may be useful clinically as an antibiotic against acquired pathogens from patients with gallstones and against pathogens resistant to other antibiotics.

The full-length and four alternatively spliced variant mRNA transcripts of rat TERT were identified. One of the variant, rTERTb, was predominantly expressed during brain development in accordance with the decrease in telomerase activity. The rTERTb mRNA encoded an inactive truncated protein. Alternative splicing of TERT may be important during brain development.

We tested two alternative oxidation strategies to produce conotoxins α-GI and μ-PIIIA. The peptides were either reversibly immobilized on a solid support and then oxidized, or the immobilized disulfide reagent (CLEAR-OX™) was used to oxidize the peptides. Both strategies appeared more efficient at higher peptide concentrations, consistent with pseudo-dilution effects.

Shrimp High Density Lipoprotein-β-Glucan Binding Protein (HDL/BGBP) has been studied by its role in nutrition and innate defense. Although the mechanisms of lipid loading are still unknown, HDL-BGBP binds and aggregates phospholipids vesicles in vitro. To gain insights into the HDL-BGBP mechanism of interaction with membranes, we have used fluorescence spectroscopy and electron microscopy. Data show that HDL-BGBP does not induce membrane fusion, leakage nor lipid exchange, although microstructural changes are clearly observed. This work supports a model where protein aggregation leads to liposome clustering. Such interaction may be a critical factor for the activation of the shrimp blood cell in vivo.

There is evidence that the P2X1 receptor subunit is involved in apoptosis, platelet aggregation, and smooth muscle contraction. The conformation of the membrane-embedded, ligand-gated mouse P2X1 glycoprotein, a monovalent-bivalent cation channel-forming receptor, is predicted. The first step is based on secondary structure prediction. The secondary structure is converted into a three-dimensional geometry. Then, the secondary and tertiary structures are optimized by using the quantum chemistry RHF/3-21G minimal basic set and the all-atom molecular mechanics AMBER96 force field. The fold of the membrane-embedded protein is simulated by a suitable dielectric. The structure is refined using a conjugate gradient minimizer (Fletcher-Reeves modification of the Polak- Ribiere method). Although the mouse P2X1 receptor subunit is more complex (388 amino acids) than the KcsA protein (160 amino acids), the overall folds are similar. The geometry optimized P2X1 receptor subunit is freely available for academic researchers on e-mail request (PDB format).

The present work reports the characterization of Fastuosain, a novel cysteine protease of 25kDa, purified from the unripe fruits of Bromelia fastuosa, a wild South American Bromeliaceae. Proteolytic activity, measured using casein and synthetic substrates, was dependent on the presence of thiol reagents, having maximum activity at pH 7.0. The present work reports cDNA cloning of Fastuosain; cDNA was amplified by PCR using specific primers. The product was 1096pb long. Mature fastuosain has 217 residues, and with the proregion has a total length of 324 residues. Its primary sequence showed high homology with ananain(74%), stem bromelain (66%) and papain (44%).

It has been reported that the cooperative binding of calcium ions indicated a local conformational change of the human cytosolic phospholipase A 2 (cPLA2) C2 domain (Nalefski et al., (1997) Biochemistry 36, 12011-12018). However its structural evidence is less known (Malmberg et al., (2003) Biochemistry 42, 13227-13240). In this letter, life-time decay and fluorescence quenching techniques were employed to compare the calcium-induced conformational changes. The life-time decay parameters and fluorescence quenching constant changes were small between the apo- and holo-C2 domains when tryptophan residue was excited at 295 nm. In contrast, the quenching constant change was large, from 0.52 M-1 for the apo-C2 to 8.8 M-1 for the holo-C2 domain, when tyrosine residues were excited at 284 nm. Our results provide new information on amino acid side chain orientation change at calcium binding loop 3, which is necessary for Ca2+ binding regulated membrane targeting of human cytosolic phospholipase A2.

Capillary-channeled polymer (C-CP) fibers are demonstrated as a potential stationary phase for liquid chromatography separation of protein mixtures. Separation of a synthetic mixture of four proteins is accomplished within a 45-second window using a conventional revered-phase (RP) gradient, at a mobile phase flow rate of 7 mL/min (10,200 mm/min).

In this study, we used the distribution rank, which has been developed by us over the past several years, to quantify 134 mutations in the human hemoglobin α-chain in order to gain an insight into the general pattern in mutations. The results suggest that the pattern presented by distribution rank can approximately estimate the positions that are sensitive to mutations in human hemoglobin α-chain.