The factor V HR2 haplotype: prevalence and association of the A4070G and A6755G polymorphisms.

Recently, a polymorphism was identified in exon 25 of the factor V gene that is possibly a functional candidate for the HR2 haplotype. This haplotype is characterized by a single base substitution named R2 (A4070G) in the B domain of the protein. A mutation (A6755G; 2194Asp-->Gly) located near the C terminus has been hypothesized to influence protein folding and glycosylation, and might be responsible for the shift in factor V isoform (FV1 / FV2) ratio. This study investigated the prevalence of these two factor V HR2 haplotype polymorphisms in a cohort of normal blood donors, patients with osteoarthritis and women with complications during pregnancy, and in families of factor V Leiden individuals. A high allele frequency for the two polymorphisms was found in the blood donor group (6.2% R2, 5.6% A6755G). No significant difference in allele frequency was observed in the clinical groups (obstetric complications and osteoarthritis, 4.1-4.9% for the two polymorphisms) when compared with that of healthy blood donors. We confirm that the factor V A6755G polymorphism shows strong linkage to the R2 allele, although it is not exclusively inherited with the exon 13 A4070G variant and can occur independently.

Multiple analysis of three common genetic alterations associated with thrombophilia.

We have previously reported the use of a novel mini-sequencing protocol for detection of the factor V Leiden variant, the first nucleotide change (FNC) technology. This technology is based on a single nucleotide extension of a primer, which is hybridized immediately adjacent to the site of mutation. The extended nucleotide that carries a reporter molecule (fluorescein) has the power to discriminate the genotype at the site of mutation. More recently, the prothrombin 20210 and thermolabile methylene tetrahydrofolate reductase (MTHFR) 677 variants have been identified as possible risk factors associated with thrombophilia. This study describes the use of the FNC technology in a combined assay to detect factor V, prothrombin and MTHFR variants in a population of Australian blood donors, and describes the objective numerical methodology used to determine genotype cut-off values for each genetic variation. Using FNC to test 500 normal blood donors, the incidence of Factor V Leiden was 3.6% (all heterozygous), that of prothrombin 20210 was 2.8% (all heterozygous) and that of MTHFR was 10% (homozygous). The combined FNC technology offers a simple, rapid, automatable DNA-based test for the detection of these three important mutations that are associated with familial thrombophilia.

DNA technology for the detection of common genetic variants that predispose to thrombophilia.

With the identification of common single locus point mutations as risk factors for thrombophilia, many DNA testing methodologies have been described for detecting these variations. Traditionally, functional or immunological testing methods have been used to investigate quantitative anticoagulant deficiencies. However, with the emergence of the genetic variations, factor V Leiden, prothrombin 20210 and, to a lesser extent, the methylene tetrahydrofolate reductase (MTHFR677) and factor V HR2 haplotype, traditional testing methodologies have proved to be less useful and instead DNA technology is more commonly employed in diagnostics. This review considers many of the DNA techniques that have proved to be useful in the detection of common genetic variants that predispose to thrombophilia. Techniques involving gel analysis are used to detect the presence or absence of restriction sites, electrophoretic mobility shifts, as in single strand conformation polymorphism or denaturing gradient gel electrophoresis, and product formation in allele-specific amplification. Such techniques may be sensitive, but are unwielding and often need to be validated objectively. In order to overcome some of the limitations of gel analysis, especially when dealing with larger sample numbers, many alternative detection formats, such as closed tube systems, microplates and microarrays (minisequencing, real-time polymerase chain reaction, and oligonucleotide ligation assays) have been developed. In addition, many of the emerging technologies take advantage of colourimetric or fluorescence detection (including energy transfer) that allows qualitative and quantitative interpretation of results. With the large variety of DNA technologies available, the choice of methodology will depend on several factors including cost and the need for speed, simplicity and robustness.

Specificity of coenzyme analogues and fragments in promoting or impeding the refolding of clostridial glutamate dehydrogenase.

NAD+ facilitates high-yield reactivation of clostridial glutamate dehydrogenase (GDH) after unfolding in urea. The specificity of this effect has been explored by using analogues and fragments of NAD+. The adenine portion, unlike the nicotinamide portion, is important for reactivation. Alteration in the nicotinamide portion, in acetylpyridine adenine dinucleotide, has little effect, whereas loss of the 6-NH2 substitution on the adenine ring, in 6-deamino NAD, diminishes the effectiveness of the nucleotide in promoting refolding. Also ADP-ribose, lacking nicotinamide, promotes reactivation whereas NMN-phosphoribose, lacking the adenine, does not. Of the smaller fragments, those containing an adenosine moiety, and especially those with one or more phosphate groups, impede the refolding ability of NAD+, and are able to bind to the folding intermediate though unable to facilitate refolding. These results are interpreted in terms of the known 3D structure for clostridial glutamate dehydrogenase. It is assumed that the refolding intermediate has a more or less fully formed NAD+-binding domain but a partially disordered substrate-binding domain and linking region. Binding of NAD+ or ADP-ribose appears to impose new structural constraints that result in completion of the correct folding of the second domain, allowing association of enzyme molecules to form the native hexamer.

Computer modelling of the receptor-binding domains of VEGF and PIGF.

Models of the platelet-derived growth factor (PDGF)-like domains of vascular endothelial growth factor (VEGF) and placenta growth factor (PIGF) were built based on their homology to PDGF. These domains contain most of the determinants for receptor binding. The sequences of these proteins exhibit limited but significant homology to that of platelet-derived growth factor (PDGF), a member of the cystine knot growth factor family. The eight cysteine residues that are involved in intra- and interchain disulphide bonds are conserved. Two high affinity receptors for VEGF have been identified, only one of which binds PIGF. The models presented here are consistent with results that show that VEGF receptor binding is mediated by charged residues in the loops. A comparison of the models suggests that the difference in receptor-binding specificity between VEGF and PIGF may be due to differences in the distribution of positively charged residues and the exposure of hydrophobic residues in the loops.

Partial identification of the epitope on D-dimer for monoclonal antibody, DD-3B6/22.

This study provides new information about the recognition site on fibrin for DD-3B6/22, a monoclonal antibody used in the diagnosis of thrombotic disease and proposed as a delivery agent for radioisotopes to visualize thrombi in situ. Preliminary chemical modification and proteolytic digestion of D-dimer revealed key residues in the interaction of D-dimer with its diagnostic antibody DD-3B6/22. Following the initial survey, thermolysin was used to produce digestion fragments for more specific sequence analysis. The gamma-polypeptide chain of D-dimer was confirmed as a recognition site for the antibody, with the residues S86RK88 being implicated in binding, and a second, novel site of antibody interaction was identified on the alpha-polypeptide as D105NTYNR110. Based on evidence from this study and from a previous investigation of the DD-3B6/22 binding site on D-dimer (Devine and Greenberg), a model for the DD-3B6/22 binding site is proposed to comprise regions from parts, at or near the N-terminus, of at least two different subunits: one region on the alpha-polypeptide chain of one D monomer and another region on the gamma-polypeptide chain of an adjacent D monomer. The model is discussed in the context of the predicted secondary and tertiary structure of D-dimer.

Use of first nucleotide change technology to determine the frequency of factor V Leiden in a population of Australian blood donors.

Activated protein C resistance (APCR), the most common risk factor for venous thrombosis, is the result of a G to A base substitution at nucleotide 1691 (R506Q) in the factor V gene. Current techniques to detect the factor V Leiden mutation, such as determination of restriction length polymorphisms, do not have the capacity to screen large numbers of samples in a rapid, cost-effective test. The aim of this study was to apply the first nucleotide change (FNC) technology, to the detection of the factor V Leiden mutation. After preliminary amplification of genomic DNA by polymerase chain reaction (PCR), an allele-specific primer was hybridised to the PCR product and extended using fluorescent terminating dideoxynucleotides which were detected by colorimetric assay. Using this ELISA-based assay, the prevalence of the factor V Leiden mutation was determined in an Australian blood donor population (n = 500). A total of 18 heterozygotes were identified (3.6%) and all of these were confirmed with conventional MnlI restriction digest. No homozygotes for the variant allele were detected. We conclude from this study that the frequency of 3.6% is compatible with others published for Caucasian populations. In addition, the FNC technology shows promise as the basis for a rapid, automated DNA based test for factor V Leiden.

Variable immunoreactivity of D-dimer preparations for monoclonal antibody DD-3B6/22.

The monoclonal antibody DD-3B6/22, which is specific for crosslinked fibrin breakdown products, is used clinically in the diagnosis and monitoring of certain thrombotic conditions and has potential as a delivery agent for in vivo clot localisation. Laboratory preparations of D-dimer are used as reference standards in DD-3B6/22 assay systems. In this study, four D-dimer preparations, produced using a standardised method, were presented to the monoclonal antibody, DD-3B6/22 in different antigenic formats and immunoreactivity was assessed using a variety of methods. The results show a variability in reactivity of the D-dimer samples to DD-3B6/22; one preparation (QUT2) was immunoreactive only when immobilised on a surface and not when in solution. The implications of variable immunorecognition of target antigens are discussed with regard to diagnostic standards and in vivo clot localisation.

Visual reading method for detection of bacterial tannase.

Tannase activity of bacteria capable of degrading tannin-protein complexes was determined by a newly developed visual reading method. The method is based on two phenomena: (i) the ability of tannase to hydrolyze methyl gallate to release free gallic acid and (ii) the green to brown coloration of gallic acid after prolonged exposure to oxygen in an alkaline condition. The method has been successfully used to detect the presence of tannase in the cultures of bacteria capable of degrading tannin-protein complexes.

Ciguatoxin-protein association in skeletal muscle of Spanish mackerel (Scomberomorus commersoni).

A study of soluble protein from skeletal muscle of Scomberomorus commersoni was undertaken to elucidate aspects of ciguatoxin (CTX) bioaccumulation in marine teleosts. Skeletal muscle tissue samples from toxic and non-toxic specimens were subjected to fractionation, centrifugation, (NH4)2SO4 precipitation and Sephacryl S-200 chromatography of soluble proteins. Toxicity associated with various fractions was assessed by mouse bioassay, and toxic and non-toxic soluble protein fractions were compared using SDS-PAGE. CTX eluted from Sephacryl S-200 with soluble proteins of apparent mol. wt between 35,500 and 59,500. The toxic eluate contained 1.4% of total sample protein and 15% of total sample toxicity, with an associated 7.2-fold increase in specific activity. SDS-PAGE comparisons show two protein bands in the 37,400 and 40,600 mol. wt range which appeared in toxic soluble protein fractions, but were not detectable in control (non-toxic) samples. These findings are interpreted as being consistent with the association of CTX with at least one monomeric soluble protein of 37,000 to 40,600 mol. wt from toxic S. commersoni skeletal muscle.

Different calcium dependence of the capping and cutting activities of villin.

The concentration of ionized calcium required for the capping of barbed filament ends by villin is about 4 orders of magnitude lower than that required for the cutting activity of villin. Capping was 50% complete at about 10-30 nM Ca2+, a level expected in resting cells, whereas the cutting rate was half-maximal at about 200 microM, making it possible to completely separate filament capping from filament cutting. Analysis of capping in terms of coupled equilibria between calcium binding to villin and calcium-villin binding to the barbed ends of actin filaments gives a value of 10(16)-10(17) M-2 for the product of the two binding constants. By comparison the binding constant reported for the rapidly exchanging calcium sites on villin is 2 X 10(5) M-1 and that for binding of calcium-saturated villin to barbed ends has a minimum value of 10(11) M-1 giving a product of 2 X 10(16) M-1. The close similarity of the two sets of values suggests that capping is regulated by the rapidly exchanging calcium sites on villin. In terms of coupled equilibria the calcium requirement for filament capping decreases with increasing concentrations of free villin. The scant information on the mechanism of cutting allows only an estimate of the maximal value for the calcium-binding constant of the site regulating cutting which is about 2-5 X 10(3) M-1. Cutting is followed by rapid capping of the newly released barbed ends.

Removal of tropomyosin overlap and the co-operative response to increasing calcium concentrations of the acto-subfragment-1 ATPase.

The co-operative response of regulated actomyosin ATPase to increasing concentrations of calcium has been attributed to nearest-neighbor interactions, presumably between troponin-tropomyosin complexes. The degree of co-operativity was not decreased after the carboxy-terminal 11 amino acid residues had been removed from tropomyosin by carboxypeptidase A. This indicates that the interactions between neighboring troponin-tropomyosin complexes do not occur through the overlapping tropomyosin ends.

Calcium dependence of villin-induced actin depolymerization.

"Cutting" of actin filaments by villin was evaluated from the time course of filament depolymerization. Depolymerization was initiated by diluting polymerized actin, labeled with a fluorescent probe on either lysine-374 or cysteine-375, to a concentration well below the critical into a medium containing free villin and various concentrations of calcium (in addition to potassium and magnesium). It was observed that at high calcium concentrations (200 microM) the time course of depolymerization could not be described by the single exponential that defines it at low calcium and low villin levels. Instead, at high calcium, the exponent increased with time and the rate of depolymerization became greater than that of controls in the absence of villin. This contrasts with the inhibition of depolymerization by villin at low calcium. The latter inhibition is a consequence of the capping of the barbed filament end by villin as are the inhibition of filament elongation and the elevation of the critical concentration. Evidence is presented that the effects of villin at high calcium are the result of cutting of the actin filaments by villin. It thus appears that different calcium binding sites control capping and cutting and that the calcium binding sites regulating cutting have a much lower affinity for calcium than the sites regulating capping of the barbed filament ends.

Effect of villin on the kinetics of actin polymerization.

The effect of villin on the critical concentration of actin and on the kinetics of its polymerization has been measured. In the presence of villin and 10 microM calcium, the critical concentration of actin increased from 0.2 to 0.9 microM. This effect of villin on the critical concentration was shown to be the result of its well-documented ability to block the "barbed" end of actin filaments, i.e., the "high-affinity end" of a polymer with a different monomer binding constant at each end. Thus, below 0.8 microM actin polymerization was prevented when the ratio of villin to actin was about 1 in 1000. Furthermore, the effect of villin was saturable; i.e., the critical concentration remained constant with increasing villin concentration once the maximal change had been obtained. In addition, fragmentation of actin filaments previously capped with villin, producing uncapped filaments, caused a rapid, transient fall of the monomer concentration. With the disappearance of the uncapped filaments the actin monomer concentration returned to that measured before fragmentation. The binding constant of villin to the barbed end of the actin filament was calculated to be greater than 10(11) M-1. The rate constants of elongation and of depolymerization at each end of an actin filament were measured. The depolymerization rate constant from the barbed end was about 10 times greater under conditions leading to complete depolymerization than under steady-state conditions. We discuss a possible explanation for the finding and its implication for possible regulatory mechanisms.