Isolation and identification of a snake venom metalloproteinase inhibitor from California ground squirrel (Spermophilus beecheyi) blood sera.

California ground squirrels (Spermophilus beecheyi) show blood-based defenses to a variety of toxins in the venom of the Northern Pacific rattlesnake (Crotalus oreganus oreganus). In this study we demonstrate the presence of an effective snake venom metalloproteinase inhibitor (SVMPI) in S. beecheyi. The blood sera of California ground squirrels were effective at reducing the metalloproteinase activity of Northern Pacific (C. o. oreganus) and prairie rattlesnake (Crotalus viridis viridis) venoms by over 75%, significantly more than its ability to reduce the activity of western diamondback rattlesnake venom. We used anion exchange and affinity chromatography to isolate this protein from the blood sera of S. beecheyi. This SVMPI had a molecular mass of 108.3 kDa and a pI of 5.1. The IC(50) of this inhibitor against whole venom from C. o. oreganus was determined to be 3.14 × 10(-8) M. Subsequent LC MS/MS analysis of a CNBr/tryptic digest of the inhibitor yielded multiple internal peptide sequences. These sequences showed homology to three other known mammalian plasma proteins: inter-α trypsin inhibitor, and two hibernation-associated proteins, HP25 and HP27. The presence of SVMPI in S. beecheyi blood sera is consistent with the resistance of these animals to venom-induced hemorrhage and tissue damage, and consistent with the protective factors conferring venom resistance in other mammals. However, the variety of SVMPI identified to date from mammalian taxa suggests that different species have converged on neutralization of venom metalloproteinase activity as a key step in venom neutralization.

A rapid and sensitive fluorometric method for the quantitative analysis of snake venom metalloproteases and their inhibitors.

Metalloproteases are responsible for the hemorrhagic effects of many snake venoms and contribute to other pathways that lead to local tissue damage. Methods that quantify snake venom metalloproteases (SVMP) are therefore valuable tools in research on the clinical, physiological, and biochemical effects of envenomation. Comparative analysis of individual, population, and species differences requires screening of large numbers of samples and treatments, and therefore require a method of quantifying SVMP activity that is simple, rapid, and sensitive. This paper demonstrates the properties of a new fluorometric assay of SVMP activity that can provide a measure of metalloprotease activity in 1 h. The assay is reliable, with variation among replicates sufficiently small to reliably detect differences in between species (F(19,60) = 2924, p < 0.001), even for those venoms with low overall activity. It is also sensitive enough to detect differences among venoms using <2 ng of whole venom protein. We provide an example use of this assay to detect the presence of natural SVMP inhibitors in minute samples of blood plasma from rock squirrels (S. variegatus), a natural prey species for North American rattlesnakes. We propose this assay is a useful addition to the set of tools used to characterize venoms, as well as high-throughput screening of natural or synthetic inhibitors, or other novel therapeutic agents against SVMP effects.

Redesigning nucleic acids.

A research program has applied the tools of synthetic organic chemistry to systematically modify the structure of DNA and RNA oligonucleotides to learn more about the chemical principles underlying their ability to store and transmit genetic information. Oligonucleotides (as opposed to nucleosides) have long been overlooked by synthetic organic chemists as targets for structural modification. Synthetic chemistry has now yielded oligonucleotides with 12 replicatable letters, modified backbones, and new insight into why Nature chose the oligonucleotide structures that she did.

Synthesis of oligodeoxynucleotides containing 2-thiopyrimidine residues--a new protection scheme.

A method is described for the incorporation of 2'-deoxy-2-thiouridine (dS2U) and 2'-deoxy-2-thiothymidine (dS2T) into oligodeoxynucleotides at predetermined positions. This requires N3 or O4-acylation of dS2U and dS2T with toluoyl chloride. These base-protected thiopyrimidines are completely stable toward the aqueous iodine oxidation reagent used in the phosphoramidite DNA synthesis method. The toluoyl protecting group is removed during the standard post-synthetic ammonia treatment. This novel protection strategy allows dS2U and dS2T to be efficiently incorporated into oligodeoxynucleotides at predetermined sites without the usual problem of desulfurization and decomposition. Several 14-mers containing the Eco-RI recognition site (dGGCGGAAXXCCGCC and dGGCGGAAXXCGCGG, where X represents dT, dS2U or dS2T) have been synthesized and characterized by base composition, thermal denaturation, CD spectroscopy and endonuclease substrate activity.

Stabilization of beta-ribbon structures in peptides using disulfide bonds.

The effect of a disulfide crosslink between two peptide chains on the stability of beta-ribbon secondary structures formed by these peptides has been investigated. Based on structural principles, we hypothesized that introduction of an unstrained disulfide crosslink at appropriate locations on two peptide chains should have a stabilizing effect on the beta-ribbon structure formed by these two peptide chains. To test this hypothesis, we designed and synthesized two sets of 9-residue peptides incorporating cysteine in one and (S)-alpha-amino-epsilon-mercaptohexanoic acid in the other. Comparison of the CD data clearly show that the dimer containing a disulfide bond between the longer sidechains of (S)-alpha-amino-epsilon-mercaptohexanoic acid shows dramatically higher beta-ribbon character as compared to the dimer with cystine disulfide bond, thus validating our structural hypothesis.

Stabilization of alpha-helical structures in short peptides via end capping.

The alpha-helix-stabilizing effect of different amino acid residues at the helical termini of short peptides in aqueous solution has been determined. Several dodecapeptides containing alanine, asparagine, aspartate, glutamine, glutamate, and serine at the amino terminus and arginine, lysine, and alanine at the carboxyl terminus were synthesized, and the alpha-helical content of each peptide was measured by using circular dichroism spectroscopy. The trend in alpha-helix-inducing ability of these amino acids was found to be as follows: aspartate > asparagine > serine > glutamate > glutamine > alanine at the amino terminus and arginine > lysine > alanine at the carboxyl terminus. Our results agree with the Presta and Rose hypothesis [Presta, L. G. & Rose, G. D. (1988) Science 240, 1632-1641] on the role of end capping in helix stabilization.

The ribonuclease from an extinct bovid ruminant.

The sequence of the ribonuclease from the ancestor of swamp buffalo, river buffalo, and ox, corresponding approximately to Pachyportax latidens, an extinct ruminant known from the fossil record, has been reconstructed using the rule of 'maximum parsimony'. This protein and two sequences that may have been intermediates in the evolution of modern ribonuclease have been constructed in the laboratory by site-directed mutagenesis, and their properties examined.

6-Fluorocholesterol as a growth factor for the yeast mutant GL7.

6-Fluorocholesterol supports the growth of the sterol-requiring yeast mutant GL7 albeit less efficiently than cholesterol or ergosterol. When the fluoro analogue is combined with very much smaller amounts of cholesterol, the growth response to the sterol pair is synergistic, i.e., greater than additive. On further addition of trace amounts of ergosterol to the 6-fluorocholesterol-cholesterol pair, an additional synergistic growth response is observed. On 6-fluorocholesterol alone, the growth rate of the yeast mutant is slow initially, but after several transfers of such cells to the same media containing the fluoro analogue, growth improves substantially. When incorporated into artificial membranes, cholesterol and its 6-fluoro analogue have essentially identical effects on membrane fluidity as judged from microviscosity measurements. The contrasting responses of artificial membranes and whole cells to the 6-fluoro analogue of cholesterol might be due to sterol-protein interactions in natural membranes.

Expression of bovine pancreatic ribonuclease A in Escherichia coli.

A synthetic gene for bovine pancreatic ribonuclease A (RNase A) has been expressed in Escherichia coli as a fusion protein with beta-galactosidase linked by the tetrapeptide Ile-Glu-Gly-Arg. RNase A was cleaved from the fusion using factor Xa, and the resulting product purified and reconstituted. The isolated RNase A was chromatographically, catalytically, and immunologically identical with authentic RNase A. This work argues that the method suggested by Nagai and Thogersen [Nagai, K. & Thogersen, H. C. (1984) Nature (Lond.) 309, 810-812] for releasing fusion proteins is quite general, even when applied to particularly complicated expression problem. The procedure here makes RNase A available for the first time as a model for studying structure-function relationships in proteins using site-directed mutagenesis.

Total synthesis and cloning of a gene coding for the ribonuclease S protein.

A gene for ribonuclease S protein, has been chemically synthesized and cloned. The gene is designed to have 25 specific restriction endonuclease sites spaced at short intervals, permitting its structure to be rapidly modified. This flexibility facilitates tests of hypotheses relating the primary structure of the enzyme to its physical and catalytic behavior.