Protein and Peptide Letters - Volume 14, Issue 9, 2007

Lipoprotein (a) (Lp (a)) may be pro-thrombotic in humans due to its apolipoprotein (a) (apo(a))-mediated decreases in fibrinolysis. Such decreased fibrinolysis arises putatively from interference with plasminogen conversion to plasmin due to the considerable homology between apolipoprotein (a) and plasminogen. However, in vitro, most studies have shown that human Lp (a) decreases agonist-stimulated platelet aggregation while in vivo it appears to decrease aggregation as implied by increased bleeding times with higher blood serum concentrations of Lp(a). Lp (a) binding to platelets mediated by apo (a) increases platelet intracellular c-AMP levels in resting platelets, and decreases platelet production of thromboxane A2 and fibrinogen binding to platelets all of which reduce platelet aggregation. One, though not the only, explanation of these conflicting data may be that Lp(a) self-regulates its interference with fibrinolysis by reducing platelet aggregation and platelet binding of fibrinogen and hence the degree of requirement for fibrinolysis. However, it is concluded more in vivo work needs to be done to fully understand whether, if at all, Lp(a) in varying concentrations and isoforms, favours reduced platelet aggregation or fibrinolysis.

Polypeptides constituting the same functional enzyme in cells of different origins have small sequence similarities among themselves. Amino acid analysis reveals that each glycosyl hydrolase sub-family polypeptides conserves an average hydrophobicity value for total constituent apolar amino acids. The value may be a measure of the driving force present in the polypeptide for designed primary collapse for three-dimensional active site formation.

Leucocytes accumulate at sites of inflammation and microbial infection in response to locally produced chemotactic factors. N-formylpeptides produced by Gram negative bacteria were among the first chemotactic factors structurally defined which signal through G protein-coupled formylpeptide receptor (FPR) and FPR-like 1 (FPRL1) expressed by phagocytic leukocytes in human and in mouse homogogues mFPR and mFPR2. During the past few years, a number of pathogen- and host-derived agonists/antagonists for FPR, FPRL1 and another FPR variant FPR-like 2 (FPRL2) have been identified. Activation of formylpeptide receptors (FPRs) in phagocytic leukocytes by agonists results in increased cell chemotaxis, phagocytosis, and release of pro-inflammatory mediators. Peptide agonists for FPRs have also been shown to possess immune adjuvant activity when injected in mice. In addition, FPR aberrantly expressed on highly malignant human glioblastoma cells promotes tumor cell migration, proliferation and production of vascular endothelial growth factor in response to agonists released by necrotic tumor cells. Therefore, formylpeptide receptor ligands, by interacting with FPRs, play important roles in host defense and in the rapid progression of human glioblastoma.

This article is concerned with a study of the role of ice in the synthesis of oligopeptides containing L- or Denantiomeric excess (ee) from racemic alanine. With this aim, the oligomerization of DL-alanine-N-carboxyanhydride was investigated by keeping this activated derivative in liquid (+22°C) or frozen (-20°C) aqueous solutions for 30 days. The aqueous solution of the peptide mixtures were gel-filtered and the aliquots of the fractions were completely hydrolyzed to alanine monomers. These monomers were then derivatized with 1-fluoro-2,4-dinitrophenyl-5-L-alanine amide (Marfey's reagent) and analyzed by RP-HPLC to reveal the occasional enantiomeric excess of L- or D-Ala. The mass spectrometry of the gel-filtered fractions pointed to open-chain peptide mixtures together with a slight amount of cyclic ones, where the residue numbers ranged between 5-8. Our studies indicated that an enantiomeric excess of L- or D-Ala appeared in some oligopeptide fractions. Their excesses were significantly larger in the frozen than liquid solution. Speculations are made as concerns the implications of our findings in the events of prebiotic chemistry.

A Bowman-Birk type trypsin-chymotrypsin inhibitor was isolated from seeds of the legume green lentil (Lens culinaris) by means of affinity chromatography on Affi-gel blue gel, ion exchange chromatography on Q-Sepharose, ion exchange chromatography by fast protein liquid chromatography (FPLC) on Mono Q and Mono S, and gel filtration by FPLC on Superdex 75. The trypsin-chymotrypsin inhibitor was bound on the first three types of chromatographic media. It appeared as a single 16-kDa peak in gel filtration and a single 16-kDa band in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The trypsin inhibitory activity of the inhibitor was sensitive to the reducing agent dithiothreitol. It was completely abrogated after treatment with 10 mM dithiothreitol for 20 minutes. The protease inhibitor did not exert any inhibitory effect on hepatoma (Hep G2) and breast cancer (MCF 7) cell lines. There was no suppressive action on several fungal species including Botrytis cinerea, Fusarium oxysporum and Mycosphaerella arachidicola. It slightly inhibited the activity of HIV-1 reverse transcriptase, with an IC50 of 30 mM.

New putative antigenic peptides corresponding to the N- and C-terminal of the E2 envelope protein of GBVC/ HGV were synthesized using solid-phase chemistry. The antigens were obtained in linear and chimeric forms with the main aim of improving the sensitivity of the enzyme immunoassays. Furthermore, CD and FTIR have been used in conjunction to characterize their conformational changes showing that the chimeric peptide presents a more ordered secondary structure than its parent peptides.

Analysis of amino acid sequences can provide useful insights into the tertiary structures of proteins and their biological functions. One of the critical problems in amino acid analysis is how to establish a digital coding system to better reflect the properties of amino acids and their degeneracy. Based on the hydrophobic index, a one-to-one relationship has been established between the amino acid sequence and the digital signal process. Such a “bridge” will make it possible to apply all the existing powerful methods in the signal processing area to analysis of the amino acid sequences.

For the preparation of the complex of IGF-II and IGFBP-6, a co-expression vector containing two copies of human IGF-II and IGFBP-6 expression cassette was constructed with alcohol oxidase (AOX1) promoter and secretion signal sequence of %-factor, and transformed to Pichia pastoris yeast. Through a purification procedure involving anionexchange chromatography and gel filtration, a complex of IGF-II with IGFBP-6 was obtained. An additional C-terminal sequence of IGFBP-6 (CS-BP6) was found to be bound to this complex. Dynamic light scattering showed that this complex was very stable and homogenous in solution. Western blotting based on non-reducing Tricine-SDS-PAGE indicated that IGF-II expression coupled with IGFBP-6 might significantly avoid the mispairing of disulfide bonds compared with the IGF-II expressed alone.

An efficient preparation of Periplaneta americana nymphae allergen, Cr PI (54 kDa) is described. It was expressed as a GST-tag fusion protein in Escherichia coli, strain BL21 (DE3). Expression of recombinant Cr PI (rCr PI), denaturation/ renaturation of the inclusion bodies and the effects of protein and L-arginine concentration on inclusion body aggregation were optimized. The fusion protein was purified by affinity chromatography and size exclusion chromatography, and Cr PI fusion protein was purified to >95%. rCr PI bound strongly to IgE in the sera of individuals with cockroach allergies as shown by western blot and ELISA. Highly refolded and purified recombinant protein was obtained, providing a basis for the large-scale preparation of Cr PI allergen.

Effects of plant lectins on sea urchin (Lytechinus variegatus) fertilization and a partial characterization of lectin-binding involved in the process were evaluated. IC50 doses for inhibition of fertilization varied from 4.1 to 135.5 μg/ml when the lectins were pre-incubated with sperms and from 0.7 to 33.4 μg/ml when pre-incubated with eggs. Such effects were reversed when the lectins were heat inactivated. FITC-labeled lectins bound egg surfaces while their denatured forms did not. Glucose/mannose specific lectins bound weaker to eggs when pre-incubated with the glycoprotein bovine lactotransferrin. None of the glycoproteins assayed diminished FITC patterns of the Gal/GalNAc binding lectins. Pre-incubation of Glucose/mannose binding lectins with eggs did not alter binding of Gal/GalNAc lectins. Lectins with distinct competencies for binding monosaccharide and glycoconjugates were able to inhibit sea urchin fertilization.

Preservation of non-covalent interactions in biopolymer mass spectrometry offers new approaches to binding analysis. Recent work from our laboratory is reviewed here and discussed with reference to recent literature in the field. Three issues are considered in particular: hydrophobically stabilized complexes, pH-dependent transitions, and linked protein- ligand and protein-protein binding equilibria.

Major histocompatibility complex (MHC) molecules bind short peptides resulting from intracellular processing of foreign and self proteins, and present them on the cell surface for recognition by T-cell receptors. We propose a new robust approach to quantitatively model the binding affinities of MHC molecules by quantitative structure-activity relationships (QSAR) that use the physical-chemical amino acid descriptors E1-E5. These QSAR models are robust, sequencebased, and can be used as a fast and reliable filter to predict the MHC binding affinity for large protein databases.

A series of new peptidomimetics based on the tripeptide sequence Z-Leu-Phe-Gln-OH were synthesized, with ten of these including the α-nitrogen atom of the N-terminal amino acid incorporated into the pyrrole cycle. The synthesized compounds were tested for antiviral activity by agar-diffusion plaque inhibition test against Coxsackievirus B1 replication in FL cell. Four of the products were observed to possess an antiviral activity, which was proven to be significant for one product. N- terminal pyrrole moiety and C-terminal free carboxyl function are available in all active compounds. On the other hand, their corresponding -OBzl and -OBut esters are inactive.

Wild type of bovine thrombin has been crystallized in a ligand-free form by the hanging drop vapor diffusion method with polyethylene glycol 4000 and 2-propanol. The crystals belong to space group P43212 with unit cell parameters of a = b = 87.7 Å, c = 195.9 Å. X-ray diffraction data were collected to 2.8 Å resolution.

Bifunctional pyrimidine deaminase/reductase (RibD) plays an important role during riboflavin biosynthesis in many microorganisms. The 40.4 kDa RibD from Shigella flexneri 2a has been cloned, expressed, purified and characterized. Three Crystals of RibD have been obtained by the hanging-drop technique at 291 K using PEG 20k or NaCl as precipitant. The RibD crystal using PEG 20k as precipitant diffracted to 2.5Å.

The technique of fluorescence (or Forster) resonance energy transfer (FRET) is widely used to observe bimolecular interaction in living cells. Cyan and yellow fluorescent proteins are the most widely used pair in FRET analysis. CyPet and YPet are two newly optimized fluorescent proteins that have much better dynamic range and sensitivity than CFP/YFP pair, although the crystallographic structure and the mechanism of better fluorescent characteristics of CyPet are still unknown. We have expressed the cyan fluorescent protein CyPet using pT7 prokaryocyte expression system in Escherichia coli strain Rosetta (DE3) pLysS by auto-induction. After purification, the recombinant CyPet protein was crystallized by hanging drop vapor diffusion technique and could diffract to 2.55Å resolution. The data showed that the orthorhombic CyPet crystal was in space group P212121 with unit cell parameters (51.55, 61.53, 63.36) and contained one molecule in one asymmetric unit.