Stopped-flow fluorescence kinetics of bovine alpha 2-antiplasmin inhibition of bovine midiplasmin

A novel microfluidic mixer based on dual-hydrodynamic focusing for interrogating the kinetics of DNA-protein interaction

Kinetic measurement of biomacromolecular interaction plays a significant role in revealing the underlying mechanisms of cellular activities. Due to the small diffusion coefficient of biomacromolecules, it is difficult to resolve the rapid kinetic process with traditional analytical methods such as stopped-flow or laminar mixers. Here, we demonstrated a unique continuous-flow laminar mixer based on microfluidic dual-hydrodynamic focusing to characterize the kinetics of DNA-protein interactions. The time window of this mixer for kinetics observation could cover from sub-milliseconds to seconds, which made it possible to capture the folding process with a wide dynamic range. Moreover, the sample consumption was remarkably reduced to <0.55 μL min⁻¹, over 1000-fold saving in comparison to those reported previously. We further interrogated the interaction kinetics of G-quadruplex and the single-stranded DNA binding protein, indicating that this novel micromixer would be a useful approach for analyzing the interaction kinetics of biomacromolecules.

A rapid microfluidic mixer for high-viscosity fluids to track ultrafast early folding kinetics of G-quadruplex under molecular crowding conditions

Tracking the folding kinetics of macromolecules under molecular crowding conditions represents a tremendous challenge due to the high viscosity of the solution. In this paper, we report a unique T-type microfluidic mixer with seven consecutive ω-shaped baffles for fast mixing of high-viscosity fluids. Numerical simulations and experimental characterizations proved that the micromixer could achieve a mixing time of 579.4 μs for solutions with viscosities about 33.6 times that of pure water. Over a 1000-fold improvement in mixing dead time was accomplished in comparison to those reported previously. We further used this highly efficient micromixer to track the early folding kinetics of human telomere G-quadruplex under molecular crowding conditions. Results indicated an exponential process in the initial folding phase of G-quadruplex, and the G-quadruplex formed a more compact structure under higher degrees of molecular crowding conditions.

Effects of extracellular DNA on plasminogen activation and fibrinolysis

The increased levels of extracellular DNA found in a number of disorders involving dysregulation of the fibrinolytic system may affect interactions between fibrinolytic enzymes and inhibitors. Double-stranded (ds) DNA and oligonucleotides bind tissue-(tPA) and urokinase (uPA)-type plasminogen activators, plasmin, and plasminogen with submicromolar affinity. The binding of enzymes to DNA was detected by EMSA, steady-state, and stopped-flow fluorimetry. The interaction of dsDNA/oligonucleotides with tPA and uPA includes a fast bimolecular step, followed by two monomolecular steps, likely indicating slow conformational changes in the enzyme. DNA (0.1-5.0 μg/ml), but not RNA, potentiates the activation of Glu- and Lys-plasminogen by tPA and uPA by 480- and 70-fold and 10.7- and 17-fold, respectively, via a template mechanism similar to that known for fibrin. However, unlike fibrin, dsDNA/oligonucleotides moderately affect the reaction between plasmin and α(2)-antiplasmin and accelerate the inactivation of tPA and two chain uPA by plasminogen activator inhibitor-1 (PAI-1), which is potentiated by vitronectin. dsDNA (0.1-1.0 μg/ml) does not affect the rate of fibrinolysis by plasmin but increases by 4-5-fold the rate of fibrinolysis by Glu-plasminogen/plasminogen activator. The presence of α(2)-antiplasmin abolishes the potentiation of fibrinolysis by dsDNA. At higher concentrations (1.0-20 μg/ml), dsDNA competes for plasmin with fibrin and decreases the rate of fibrinolysis. dsDNA/oligonucleotides incorporated into a fibrin film also inhibit fibrinolysis. Thus, extracellular DNA at physiological concentrations may potentiate fibrinolysis by stimulating fibrin-independent plasminogen activation. Conversely, DNA could inhibit fibrinolysis by increasing the susceptibility of fibrinolytic enzymes to serpins.

Ensembles of uncertain mathematical models can identify network response to therapeutic interventions

The role of mechanistic modeling and systems biology in molecular medicine remains unclear. In this study, we explored whether uncertain models could be used to understand how a network responds to a therapeutic intervention. As a proof of concept, we modeled and analyzed the response of the human coagulation cascade to recombinant factor VIIa (rFVIIa) and prothrombin (fII) addition in normal and hemophilic plasma. An ensemble of parametrically uncertain human coagulation models was developed (N = 437). Each model described the time evolution of 193 proteins and protein complexes interconnected by 301 interactions under quiescent flow. The 467 unknown model parameters were estimated, using multiobjective optimization, from published in vitro coagulation studies. The model ensemble was validated using published in vitro thrombin measurements and thrombin measurements taken from coronary artery disease patients. Sensitivity analysis was then used to rank-order the importance of model parameters as a function of experimental or physiological conditions. A novel strategy for the systematic comparison of ranks identified a family of fX/FXa and fII/FIIa interactions that became more sensitive with decreasing fVIII/fIX. The fragility of these interactions was preserved following the addition of exogenous rFVIIa and fII. This suggested that exogenous rFVIIa did not alter the qualitative operation of the cascade. Rather, exogenous rFVIIa and fII took advantage of existing fluid and interfacial fX/FXa and fII/FIIa sensitivity to restore normal coagulation in low fVIII/fIX conditions. The proposed rFVIIa mechanism of action was consistent with experimental literature not used in model training. Thus, we demonstrated that an ensemble of uncertain models could unravel key facets of the mechanism of action of a focused intervention. Whereas the current study was limited to coagulation, perhaps the general strategy used could be extended to other molecular networks relevant to human health.

Molecular cloning and functional expression of rabbit alpha2-antiplasmin

The rabbit is frequently employed in small animal models of in-vivo coagulation and fibrinolysis, but the degree to which its plasma proteins resemble their human counterparts is incompletely known. Our aims were: to determine the nucleotide sequence of a full-length rabbit liver alpha(2)-antiplasmin (alpha(2)AP) cDNA; compare it with its human, murine, and bovine counterparts; and express it in functional form. Partial cDNAs encoding 5' and 3' portions of the alpha(2)AP mRNA were obtained by reverse transcriptase (RT)-polymerase chain reaction (PCR), using rabbit liver RNA and 'guessmer' oligonucleotides based on known sequences. This information was employed to design additional oligonucleotides for RT-PCR and rapid amplification of cDNA ends (RACE) procedures yielding overlapping clones corresponding to the entire rabbit alpha(2)AP mRNA sequence. Mature alpha(2)AP was expressed as a hexahistidine-tagged recombinant protein in Escherichia coli, purified by nickel-chelate affinity and ion exchange chromatography, and its reaction with plasmin and soluble fibrin assessed electrophoretically and compared with an analogous recombinant human alpha(2)AP. The consensus rabbit alpha(2)AP cDNA is 2,157 bp long, and encodes a 464-residue mature sequence and a 27-amino-acid presequence. The mature protein is 82% identical to its human counterpart, and its recombinant form produced denaturation-resistant complexes with both plasmin and fibrin. The region of greatest sequence divergence lies within the C-terminal extension of alpha(2)AP, unique in the serpin family of proteins to which alpha(2)AP belongs. The highly conserved nature of rabbit alpha(2)AP reinforces its role as a vital antifibrinolytic protein and supports fibrinolytic investigations in models employing this small animal.

Tissue-mimicking liquid for use in exposimetry

OBJECTIVE

Current determinations of diagnostic ultrasound exposure parameters (eg, peak rarefactional pressure and pulse intensity integral) are intended to correspond to propagation through soft tissue with a propagation speed of 1540 m/s and attenuation of 0.3 dB x cm(-1) x MHz(-1). These current measurements are made in water, which has very little attenuation, and a linear derating factor is applied to approximate 0.3 dB x cm(-1) x MHz(-1) attenuation. The fact that propagation through water as well as through soft tissue involves nonlinear propagation is not directly addressed. A better way to determine exposure parameters would be to use a liquid that has the desired tissue-mimicking properties, including a value of the nonlinearity parameter B/A representative of soft tissue. To be of practical use in the laboratory, the ultrasonic properties of this liquid must remain stable and spatially uniform for many months or years without need for periodic mixing by the user.

METHODS

Fifty-two samples of fat-free milk that was concentrated to one third of its original volume by ultrafiltration were created. Each sample was preserved by a different method. The speed of sound, attenuation, and nonlinearity parameter B/A of each sample were periodically monitored by narrowband through-transmission techniques.

RESULTS

Six of the 52 samples remained liquid and retained acceptably stable acoustic properties over 22 months of storage at room temperature.

CONCLUSIONS

Fat-free milk, concentrated via ultrafiltration and preserved in 1 of 6 different methods, has been found to be a stable tissue-mimicking liquid with acoustic properties appropriate for use in exposimetry.

Influence of soluble fibrin on reaction kinetics of plasmin type 1 and type 2 with alpha2-antiplasmin

This study investigates, by slow binding kinetics methods, reaction kinetics of both plasmin types 1 and 2 with alpha -antiplasmin in the presence of increasing concentrations of either epsilon-amino-caproic acid (EACA) or soluble fibrin. All curves of plasmin-alpha -antiplasmin interaction followed the same pattern, indicating reversible slow binding inhibition with an initial loose complex and a following tight complex. Without soluble fibrin or EACA, differences between plasmin types 1 and 2 could be seen in the initial loose complex formation. The presence of increasing concentrations of EACA slowed down the first step of the reaction (without any effect on the second step), resulting in increasing values for K. Plasmin type 1 demonstrated a steep slope of K at an EACA concentration of 1 mmol/l. In plasmin type 2, the increase of K started at higher EACA concentrations. The value for K at a high EACA concentration (100 mmol/l) was the same for both plasmin types. In contrast to EACA, increasing concentrations of soluble fibrin slowed down both reaction steps. At high concentrations of soluble fibrin, the inhibitory effect of alpha -antiplasmin was almost completely abolished. Our data demonstrate that the effect of soluble fibrin and the lysine analogue EACA on plasmin-antiplasmin reactions are different and that the use of lysine analogues does not mimic fibrin in laboratory analyses of plasmin inhibition. In addition, our data indicate theoretical differences between plasmin type 1 and plasmin type 2, when used for local thrombolytic therapy.(2) (2) (i initial) (i initial) (i initial) (i initial) (2)

The structural puzzle of how serpin serine proteinase inhibitors work

Serine proteinase cleavage of proteins is essential to a wide variety of biological processes and is primarily regulated by protein inhibitors. Many inhibitors are conformationally rigid simulations of optimal serine proteinase substrates, which makes them highly efficient competitive inhibitors of target proteinases. In contrast, members of the serpin family of serine proteinase inhibitors display extensive flexibility and polymorphism, particularly in their reactive site segments and in beta-sheet secondary structure, which can take up and expel strands. Reactive site and beta-sheet polymorphism appear to be coupled in the serpins and may account for the extreme stability of serpin-proteinase complexes through the insertion of the reactive site strand into a beta-sheet. These unusual properties may have opened an adaptive pathway of proteinase regulation that was unavailable to the conformationally rigid proteinase inhibitors.

Reaction of human alpha2-antiplasmin and plasmin stopped-flow fluorescence kinetics

The interaction of human plasmin with human alpha2-antiplasmin was measured in the presence and absence of lysine-binding ligands using the corresponding active site fluorescence changes. The stopped-flow method allows for direct determination of reliable values of the second order rate constant for the fast association step of plasmin and alpha2-antiplasmin in the absence of another interacting compound, e.g. a plasmin substrate. At pH 7.4, 25 degrees C, k1 = 2.2 x 10(7) M(-1)s(-1) was obtained. Substantial reductions in k1 were seen in the presence of trans-4-(aminomethyl)cyclohexane-1-carboxylic acid at concentrations corresponding to lysine-binding site interactions at kringle 4 of plasmin; at saturation the rate constant is reduced 20-fold, whereas the effect of saturation of kringle 1 is only a 2-fold reduction. It is thus found that the interaction of alpha2-antiplasmin with the lysine-binding site of kringle 1 is of little importance compared with that of kringle 4 in regulating the inhibition reaction of plasmin with alpha2-antiplasmin. Similar results were recently obtained for the bovine plasmin-bovine alpha2-antiplasmin reaction (Christensen et al. (1995) Biochem. J. 305, 97-102).

Stabilization of plasmin by lysine derivatives

Plasmin is a serine protease with trypsin-like specificity and is activated from plasminogen by several plasminogen activators. Since plasmin has lysine binding site in its heavy chain, lysine derivatives react with plasmin and then modify its activity. The effects of lysine derivatives such as epsilon-aminocaproic acid (EACA) and tranexamic acid on bovine plasmin activity were investigated. In the absence of lysine derivatives, the bovine plasmin activity which was evaluated as the amidolytic activity was reduced in a time- or temperature-dependent manner. However, the bovine plasmin activity became stable upon adding EACA or tranexamic acid. When plasmin was incubated at 4 degrees C for 1, 3 or 5 days without lysine derivatives, the plasmin activity decreased to 43.9%, 19.9% and 11.9% of the initial activity, respectively. On the other hand, when plasmin was incubated at 37 degrees C for 1, 3 or 5 days with tranexamic acid, its activity remained at 110%, 95.6% and 85.9%, respectively. After bovine plasmin had been incubated for 5 days at 4 degrees C in the absence of tranexamic acid, the plasmin activity declined to less than 20%. However, when bovine plasmin had been incubated for 5 days at 37 degrees C in the presence of tranexamic acid, the residual plasmin activity was more than 80%. A similar effect of EACA on bovine plasmin was observed, but it was weaker than that of tranexamic acid. Reversed-phase HPLC followed by SDS-PAGE demonstrated that bovine plasmin was degraded into several fragments. Amino acid sequencing of these fragments revealed that the Lys77-Arg78 or Arg78-Ile79, Arg342-Met343 and Arg557-Ile558 peptide bonds in the bovine plasmin molecule were cleft, respectively. Only the fragment consisting of the amino acid region from Met343 to the C-terminal amino acid, Asn786, exhibited amidolytic activity. In proportion to inactivation of the bovine plasmin, this fragment disappeared. The above findings suggest that lysine derivatives react with bovine plasmin and then stabilize the activity of plasmin by preventing the degradation of active fragment (Met343-Asn786).

Sialic acid content of plasminogen 2 glycoforms as a regulator of fibrinolytic activity. Isolation, carbohydrate analysis, and kinetic characterization of six glycoforms of plasminogen

Six glycoforms of plasminogen 2 were isolated using a combination of lectin affinity chromatography and chromatofocussing, and the sialic acid content of each glycoform was determined. The kinetics of activation of each glycoform by tissue-type plasminogen activator were analyzed on a fibrin surface and in solution. The second-order rate constant (measured on a fibrin surface) decreased from 1.65 x 10(6) M-1 s-1 to 3.77 x 10(4) M-1 s-1 as the sialic acid content of the glycoforms increased from 1.3 mol/mol of protein to 13.65 mol/mol of protein. A similar correlation was noted for activation in solution. Each glycoform was converted to plasmin, and the inhibition constants for the reaction between alpha 2-antiplasmin and plasmin glycoforms were determined. All overall Ki values, reflecting the final essentially irreversible complex, were in the picomolar range. Sialic acid does not affect inhibition of plasmin by alpha 2-antiplasmin; however, hypersialylated plasmin does not appear to have a kringle-dependent component to inhibition.