1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins.

The three-dimensional structure of the Sorghum bicolor seed protein gamma-thionin SIalpha1 has been determined by 2D 1H nuclear magnetic resonance (NMR) spectroscopy. The secondary structure of this 47-residue antifungal protein with four disulphide bridges consists of a three-stranded antiparallel sheet and one helix. The helix is tethered to the sheet by two disulphide bridges which link two successive turns of the helix to alternate residues i, i+2 in one strand. Possible binding sites for antifungal activity are discussed. The same fold has been observed previously in several scorpion toxins.

Design, synthesis and structure of a zinc finger with an artificial beta-turn.

We have incorporated a bicyclic beta-turn mimetic (BTD; beta-turn dipeptide) into a zinc finger, creating a zinc finger with an artificial beta-turn. The designed peptide chelates zinc and has the same fold as the unmodified native zinc finger (finger 3 of the human YY1 protein). A combination of 1H NMR and structure calculations reveals that, in solution, this zinc finger has a fold similar to the known wild-type crystal structure and to other zinc fingers containing the consensus sequence X3-Cys-X4-Cys-X12-His-X3-His-X. The peptide was designed with BTD between the chelating cysteine residues, with BTD forming a type II' beta-turn linking the two strands of a distorted anti-parallel beta-sheet. The C-terminal portion of the peptide forms a helix with zinc co-ordinating histidine residues on successive turns of the helix. This work represents a step towards developing methods by which parts of a target protein may be replaced by peptide mimetics.

Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage.

Knottins are a group of small, disulphide-bonded proteins that bind with high specificity to their target molecules. These proteins appear to use different faces of the protein for their interactions with different targets. Here, we attempted to create knottins with novel binding activities based on the cellulose-binding domain of the fungal enzyme cellobiohydrolase I. Variation was introduced to the face of the protein that binds cellulose. Seven residues, which are located in two regions of the polypeptide chain and form a patch of about 400 A2 on the protein surface, were simultaneously varied by random mutation of the gene. The repertoire was cloned for display on filamentous bacteriophage (5.5 x 10(8) clones), and selected for binding to cellulose or to one of three enzymes (alpha-amylase, alkaline phosphatase and beta-glucuronidase). We thereby isolated variant knottins against cellulose (differing in sequence from the parent knottin) and also against alkaline phosphatase. The binding to (glycosylated) alkaline phosphatase was highly specific with an affinity of about 10 microM, required the presence of disulphide bonds and was mediated through protein (rather than carbohydrate) contacts. Knottin scaffolds therefore appear to be a promising architecture for the creation of small folded proteins with binding activities, with the potential for improvement of binding affinities by mutation, or of using other faces of the protein to provide greater structural diversity in the primary repertoire.

Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1).

Structural studies of Ib-AMP1, a small antimicrobial peptide derived from the seeds of Impatiens balsamina have been performed using circular dichroism (CD) and two-dimensional proton nuclear magnetic resonance (1H NMR). This 20-residue peptide is highly basic with five arginine residues and contains four cysteines which form two intramolecular disulfide bonds. CD results reveal that the peptide may include a beta-turn but do not show evidence for either helical or beta-sheet structure over a range of temperature and pH. Structural information from NMR was obtained in the form of proton-proton internuclear distances inferred from NOEs and dihedral angle restraints from spin-spin coupling constants, which were used for distance geometry calculations. Owing to the difficulty in obtaining the correct disulfide connectivities by chemical methods, three separate calculations were performed; with no disulfides and with the two possible alternate disulfide connectivities. Results from distance geometry calculations reveal that although the peptide is small, the cysteines constrain part of it to adopt a well-defined main chain conformation. From residue 6 to 20, the backbone is well defined, whilst the N-terminal region, residues 1-5, has very few constraints and appears to be very flexible. In the defined core region, there are three beta-turns at residues 9-12, 10-13, and 12-15. The side chains show no strong interactions in the NMR spectra and are therefore thought to adopt multiple conformations. Superposition of the structures generated shows that the peptide has two hydrophilic patches which are at opposite ends of the molecule separated by a large hydrophobic patch. Little is known about the mode of action of this protein, but it is thought to interact with a membrane-bound receptor, and possible sites of interaction are discussed. The structures determined are compared with those of the alpha-conotoxins, which are also highly basic proteins with similar disulfide connectivities.

Prognostic significance of tumor angiogenesis in advanced breast carcinoma: an Indian experience.

Angiogenesis is essential for tumor growth and metastasis. In the present study we investigated the prognostic significance of microvessels (MV) density using immunohisto-localization of factor VIII antigen in 51 breast cancer patients. We counted microvessels per 200x field in the most active areas of neovascularization by staining factor VIII related antigen and graded MV density and correlated with stage, LN involvement and histologic grade. Patients who subsequently developed metastases had significantly high MV counts than patients without metastatic disease (p < 0.001). Patients who subsequently died of the disease had significantly high mean microvessels counts than patients who remained alive at the end of 5 years (p < 0.001). As density of factor VIII antigen staining increased the survival decreased (p < 0.001). All the patients having > 25 MV per 200x field had tumor recurrence faster as compared with patients having < 25 MV (p < 0.02). Thus, the MV count correlates with the prediction for metastasis and poor survival. Such an indicator would be useful in selection of a subgroup of patients with breast cancer who are at high risk for having occult metastasis at presentation and subsequently would benefit from aggressive therapy.

Observation of albumin resonances in proton nuclear magnetic resonance spectra of human blood plasma: N-terminal assignments aided by use of modified recombinant albumin.

Two-dimensional total shift correlation spectroscopy (TOCSY) and double-quantum-filtered phase-sensitive homonuclear shift-correlated spectroscopy (DQF-COSY) 1H NMR spectra are used to assign peaks for about one sixth of the amino acids residues of isolated human serum albumin (67 kDa) to amino acid types. Sequential assignments are presented for 1H NMR resonances of the N-terminal residues Asp1, Ala2 and His3 of human serum albumin (HSA). These are based on pH-dependent chemical shifts reflecting the titrating N-terminal NH2 and the His3 imidazole ring, in addition to DQF-COSY and TOCSY experiments. Studies of variant recombinant human albumin with Asp1 deleted, rHA(2-585), aided the assignments. The structural nature of the N-and C-termini of HSA are discussed and pKa values of 7.9 and 6.3 were determined for the N-terminal amino group and His3 imidazole ring, respectively. About 20 spin systems for albumin, including those for the N-terminal amino acids, were assigned in 1H NMR spectra of blood plasma buy comparison with isolated albumin. Resonances for lipids within lipoproteins and also several low molecular mass components can also be assigned in 2D TOCSY 1H NMR spectra of plasma.

Oxalate- and Ga(3+)-induced structural changes in human serum transferrin and its recombinant N-lobe. 1H NMR detection of preferential C-lobe Ga3+ binding.

(1) The binding of the synergistic anion oxalate and Ga3+ to human serum transferrin (HTF, 80 kDa) and its recombinant N-lobe (HTF/2N, 40 kDa) has been studied by one- and two-dimensional 1H NMR spectroscopy, at 310 K, pH*7.25. (2) Specific protein resonances are sensitive to oxalate binding (fast exchange on the NMR time scale) and allowed determination of the apparent binding constant for oxalate binding to the N-lobe (log K 4.04). (3) Slow exchange between apo-HTF and Ga-loaded HTF or HTF/2N was observed. Binding of Ga3+ appeared to be accompanied by small changes in the orientations of residues in hydrophobic pockets in the interdomain hinge region close to the metal binding site. (4) Under the conditions used, preferential binding of Ga3+ (added as Ga(NTA)2) to the C-lobe of HTF was observed. Binding to the C-lobe markedly perturbed resonances in the glycan N-acetyl region of the spectrum, suggesting that metal binding is communicated to the surface of the protein. This could be important in receptor recognition of metallotransferrins. (5) The displacement of Ga3+ from Ga-ox-HTF with Fe3+ was studied, and the paramagnetic broadening effects allowed identification of resonances from groups close to Fe3+. The passage of Fe3+ from the exterior to the interior of the protein was followed by 1H NMR spectroscopy, and the half-life for Ga(3+)-Fe3+ exchange was determined to be 4.3 h (310 K).

Aldehydes from metal ion- and lipoxygenase-induced lipid peroxidation: detection by 1H-n.m.r. spectroscopy.

The modification of lipoproteins by reactive aldehydes formed via lipid peroxidation is thought to be a key process in the pathogenesis of atherosclerosis. We show that 1H-n.m.r. spectroscopy can readily be used to detect a variety of different aldehydes resulting from peroxidation of liposomes induced by Fenton's reagent or lipoxygenase, and aldehydes arising from copper-induced reactions of low-density lipoprotein. There is a clear contrast between the major aldehydic products arising from metal-ion- and lipoxygenase-induced reactions.