Protein and Peptide Letters - Volume 9, Issue 3, 2002

SH3 domains are small but important domains in cell-signaling and function through protein-protein interactions. Their promiscuous nature in binding to polyproline peptides makes them much more important because many SH3 domains from different proteins bind to different proteins having polyproline template on their surface. Very subtle changes in the sequence of SH3 domains and the binding peptides determine the specificity of the peptide binding. Recent observation that SH3 domains bind to non- proline peptides makes the scenario of peptide binding involving SH3 domains complicated. If domain swapped dimerization as observed in Eps8-SH3 domain also binds different peptides, it proves the versatility of the SH3 domains in binding to peptides in various ways. An overview of the promiscuity of SH3 domains has been discussed.

It is suggested that the interactions between the hydrophobic C-H groups of carbohydrate residues and the p-electron systems of aromatic amino-acid residues play an important role in the ligand-recognition function of carbohydrate-binding proteins. This review focuses on our recent structural and functional studies of human lysozyme and hevein-domain type lectins (wheat-germ agglutinin and Ac-AMP2) aimed at understanding how CH / π interactions are involved in the actual binding events.

The acute-phase response consists in a large number of behavioural, physiologic, biochemical, and nutritional changes involving many organ systems distant from the site, or sites, of inflammation. One of the most investigated, but still not well understood, characteristic of the acute phase is the up-regulation, or downregulation, of many plasma proteins, known as the acute-phase proteins. The changes in the concentrations of these positive acute-phase proteins and negative acute-phase proteins are due to changes in their liver production. Their increase may vary from 25 percent to 1000 fold, as in the case of C-reactive protein and serum amyloid A. This review summarises the recent advances that have been acquired on the acute-phase proteins, in particular their function in pathologies such as infections or inflammatory lesions.

Removal of some commonly used protecting groups in peptide synthesis by catalytic transfer hydrogenation employing hydrazinium monoformate and 10%Pd on carbon is described. This method is equally competitive with other methods in deblocking most of the commonly used protecting groups in peptide synthesis. tert-Butyl derived and base labile protecting groups were completely stable under these conditions. This is more effective than hydrazine or formic acid.

We have characterized the interaction between S-(carbamoylmethyl)-papain and chicken cystatin by means of fluorescence titration at acidic pH. The calculated binding constant was 32 x 10 6, which is less than the tight affinity at pH 7.4 (∼7 x 10 10). Results have been discussed in terms of the burial of Trp-104 of cystatin and the possible role of the charge of the carbamoylmethyl moiety.

We report the physical-chemical characterization of the major alcohol-soluble proteins present in seeds of pearl millet (Pennisetum glaucum) by SDS-PAGE, bidimensional gel electrophoresis, MALDI-TOF / MS and RP-HPLC. We demonstrate the presence of three major prolamins, called A-, B- and C-pennisetin with mass values around 27, 22 and 12 kDa, respectively. We present partial amino acid sequences of these major proteins, which should allow the posterior isolation of the respective genes.

Three peptide fragments selected from the NS-1 region of hepatitis C-viral polyprotein(Leu-Ile-Asn-Thr-Asn-Ala-Ser-Trp-His-Ala-Asn-Arg-Thr-Ala-Leu-Ser-Asn- Asp-Ser-Lys-Leu-Asn-Thr-Gly-Ala-NH2, Leu-lle-Asn-Thr-Asn-Ala-Ser-Trp-His-Ala-Asn-Arg-Thr-Ala-NH2 and Leu-Asn-Cys(Acm)-Asn-Asp-Ser-Leu-Asn-Thr-Ala-NH2) [1] have been synthesized on PS-BDODMA resin. The synthetic capability of the resin PS-BDODMA resin was compared with Merrifield resin. The peptides were synthesized by the stepwise fluoren-9-yl methoxycarbonyl (Fmoc) solid-phase method. The synthesized peptides were purified by HPLC and the identity of the peptides was established by mass spectrum and amino acid analysis. The synthesis of these peptides illustrates the application of the PS-BDODMA resin for the synthesis of long chain peptides in high yield and homogeneity compared to the Merrifield resin.

In this work, we report the crystallization of ovocleidin-17, the major protein of the avian eggshell calcified layer and the preliminary X-ray characterization of this soluble protein which is implied into the CaCO3 formation of the eggshell in avians. Crystals belong to one of the trigonal space group P3 with cell dimensions a= b= 59.53 Å and c = 83.33 Å, and α=β= 90 and γ =120 . Crystals diffract up to 3.0 Å.

A humanized version of the apoptosis-inducing mouse anti-human Fas monoclonal antibody, HFE7A, is under further development for the treatment of autoimmune diseases such as rheumatoid arthritis. We have crystallized the antigen-binding fragment (Fab) of the humanized HFE7A. The crystals belong to the orthorhombic space group P2 1 2 1 2 1 with cell dimensions a = 54.4 Å, b = 82.7 Å, c = 104.9 Å and contain one Fab molecule in the asymmetric unit. X-ray diffraction data were collected to 2.8 Å resolution.

A new member of class II chitinase from Phaseolus vulgaris was purified and crystallized. Diffraction data to 2.7Å resolution have been collected and the preliminary crystallographic studies have been completed. The space group is P1 with unit cell parameters of a=36.32Å, b=46.24Å, c=70.36Å, α =97.9 , β=103.8 and γ =110.5 . Molecular replacement and initial refinement statistics indicate there are two chitinase molecules in the crystallographic asymmetric unit.

Trichosanthin (TCS) is a type I ribosome-inactivating protein (RIP) which possesses rRNA N-glycosidase activity. TCS has various pharmacological properties. It is possible to reduce the antigenicity of TCS by deleting up to seven C-terminal residues of TCS (TCS-C7) with minimal effect on its activity [1]. TCS-C7 has been crystallized and the crystal diffracted to 1.8 Å. It belongs to space group P21, with unit-cell parameters a=71.6Å, b=74.4Å, c=87.6Å, β=97.0°. It is given that there are four molecules per asymmetric unit.