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J Torbet

Publications and source records attributed to J Torbet.

At least 19 recordsLinked to original sources
PubMed1996

Intercalation of small hydrophobic molecules in lipid bilayers containing cholesterol.

Partitioning of small hydrophobic molecules into lipid bilayers containing cholesterol has been studied using the 2XC diffractometer at the University of Missouri Research Reactor. Locations of the compounds were determined by Fourier difference methods with data from both deuterated and undeuterated compounds introduced into the bilayers from the vapor phase. Data fitting procedures were developed for determining how well the compounds were localized. The compounds were found to be localized in a narrow region at the center of the hydrophobic layer, between the two halves of the bilayer. The structures are therefore intercalated structures with the long axis of the molecules in the plane of the bilayer.

Cholesterol↗
PubMed1995

The thrombin activation pathway modulates the assembly, structure and lysis of human plasma clots in vitro.

Thrombin activation of the soluble plasma protein fibrinogen is vital for successful haemostasis. Thrombin is generated from prothrombin by the prothrombinase complex which also includes factor Xa, factor Va, Ca2+ and a procoagulant membrane surface. Factor X activation is catalysed in a complex including either factor VIIa and tissue factor, or factor IXa and factor VIIIa. Factor IXa can be generated either by the factor VIIa/tissue factor complex or by factor XIa which is in turn produced by the contact phase reactions in vitro. Once activated, fibrinogen develops into the fibrin polymeric matrix at the site of injury. It is not known to what extent the properties of this haemostatic plug are sensitive to the pathway leading up to thrombin generation. Here static human plasma is studied in vitro using magnetically induced birefringence. It is shown that the contact phase/factor XIa pathway gives rise to linear fibrin assembly process curves whereas the factor VIIa/ tissue factor activation of factor X provokes largely sigmoid assembly. The latter pathway also causes the formation of significantly thicker fibres even though assembly is more rapid. This result is the inverse of that anticipated from the study of simple model systems. Whilst the streptokinase activated lysis both types of clot exhibits similar biphasic kinetics, an exponential main phase followed by a sigmoidal tailing off, the data suggest that clots produced by the contact phase/factor XIa pathway are more recalcitrant to lysis. These results demonstrate that the profile of thrombin generation not only determines the kinetics of assembly but also influences the rate of lysis and structure of the haemostatic plug.

Birefringence↗
PubMed1992

A neutron solution scattering study of the structure of annexin-V and its binding to lipid vesicles.

Low-angle neutron solution scattering has been used to study the structure of annexin-V and its interaction with small single-bilayer vesicles consisting of phosphatidylserine and phosphatidylcholine at a 33:66 (mol:mol) ratio. There was no evidence for a change in the state of aggregation of annexin-V, which remained as a monomer in the presence of 3 mM-free calcium. The only difference between presence and absence of free calcium was the increase of the radius of gyration, from 19(+/- 0.4) A to 22(+/- 0.4) A in 2H2O buffer and from 19.7(+/- 1.2) A to 22.2(+/- 1.2) A in H2O buffer. The relative molecular weight, outer radius and average surface area per lipid of vesicles alone were respectively 2.5(+/- 0.5) x 10(6), 127 A and 90(+/- 19) A2. These parameters were not modified in the presence of free calcium, which testified to the absence of vesicle coalescence. The calcium-dependent binding of annexin-V was essentially interfacial and therefore did not alter significantly the structural characteristics of the vesicles. At saturation, 80(+/- 10) annexin-V molecules were bound per vesicle, the available area per molecule being 2500(+/- 300) A2 thus covering approximately 28 lipid head groups. The protein shell was approximately 35 A thick. The apparent dissociation constant was probably less than 1 nM. These data contribute to a more accurate definition of annexin-V as a possible probe of those cytodynamic events involving exposure of sequestered membrane aminophospholipids.

Annexin A5↗
PubMed1992

Solution behavior of DNA studied with magnetically induced birefringence.

Magnetically induced birefringence can provide useful information on the physical properties of nucleic acids in a variety of forms. The technique is particularly sensitive to structural changes. Difficulties arise with drawing precise structural conclusions principally because of doubts about the relative contributions of the form and intrinsic components to the optical anisotropy. Nevertheless results so far suggest that this might not be a severe limitation. The induced birefringence is very sensitive to cooperative behavior; consequently the transition from an isotropic to a liquid crystalline phase can be followed in detail. Finally the high degree of magnetic orientation often achieved with liquid crystals assists their study with other physical techniques.

Birefringence↗
PubMed1989

Supercoiled DNA is interwound in liquid crystalline solutions.

Two structures have been proposed for supercoiled DNA: it is idealized either as a toroidal ring or as a rod of two interwound duplex chains. The latter model is the most widely depicted but the evidence remains controversial. We have worked with monomers and dimers of two plasmids, pUC8 and pKS414, of similar size and natural superhelical density. pKS414 contains a bend promoting sequence whereas pUC8 does not. In concentrated solutions these plasmids form a partially ordered liquid crystalline phase which is found, using neutron diffraction, to consist of a hexagonally packed assembly of parallel rod-like particles. This shape strongly suggests an interwound conformation for which some structural parameters are deduced. The mass/unit length obtained by combining the area of the hexagonal lattice and the concentration is approximately 3.6 times that of linear DNA. This implies a shallow superhelical pitch angle approximately 36 degrees which, when combined with the known number of supercoil turns, yields the pitch approximately 360 A and radius approximately 80 A for the supercoil. Oriented X-ray fibre diffraction patterns at 92% relative humidity indicate a B type duplex structure. Nicked circular plasmids also form liquid crystals but their behaviour, as a function of concentration, differs from that of the superhelical plasmids.

Crystallization↗
PubMed1987

Neutron scattering determination of the binding of prothrombin to lipid vesicles.

Low-angle neutron scattering is used to study the binding of human prothrombin to small single-bilayer vesicles consisting of phosphatidylcholine and phosphatidylserine (1/1 w/w). The radius of gyration of prothrombin indicates that it is an elongated molecule. The vesicles alone were not observed to coalesce, and their molecular weight, outer radius, and average surface area per lipid were respectively (1.6 +/- 0.32) X 10(6), 114 +/- 4 A, and 110 +/- 18 A2. These values were independent of the presence of calcium and were not altered significantly by prothrombin, which binds reversibly to the vesicle outer surface with its long axis projecting approximately radially forming a 90-A thick protein shell. From the titration of the protein-vesicle interaction, the apparent dissociation constant of the binding of prothrombin to these vesicles is estimated to be 0.8 +/- 0.4 microM. At saturation, 57 +/- 7 prothrombin molecules bind, giving 25 +/- 6 lipid residues and an area of 2900 +/- 400 A2 per prothrombin molecule on the vesicle outer surface. This area is about twice that calculated from a prolate ellipsoid model for prothrombin. However, it is close to the maximum cross-sectional area of fragment 1, the lipid binding region of prothrombin, which is coin-shaped in the high-resolution X-ray structure [Park, C.H., & Tulinsky, A. (1986) Biochemistry 25, 3977-3982]. This similarity suggests that prothrombin binding could be sterically limited.

Humans↗
PubMed1987

Fibrin assembly after fibrinopeptide A release in model systems and human plasma studied with magnetic birefringence.

Magnetically induced birefringence was used to monitor fibrin polymerization after the release of the small negatively charged A fibrinopeptides from human fibrinogen by the action of the snake-venom-derived enzymes reptilase and ancrod. A range of conditions was investigated. Fibrin polymerization in solutions of purified fibrinogen shows a distinct break near the gelation point. On addition of Ca2+ or albumin the lag period is shortened, fibre thickness is increased and the break in assembly almost vanishes, probably because both of these additives promote lateral aggregation. There are minor differences in the kinetics, depending on the venom enzyme used. The kinetics of fibrin assembly in model systems containing either Ca2+ or albumin and in human plasma with a largely dormant coagulation cascade are very similar. Therefore in the latter condition there is no significant alteration in the assembly process due to interaction between fibrin or the venom enzymes and any of the plasma proteins. When the cascade is activated, the polymerization progress curves have a character that resembles a combination of the reactions observed when the venom enzymes and endogenously generated thrombin separately induce coagulation, except for a region near gelation where, paradoxically, polymerization appears to be slower on activation. The low-angle neutron-diffraction patterns from oriented gels made with thrombin or reptilase are identical. Therefore at low resolution the packing of the monomers within fibres is the same when fibrinopeptide A only or both fibrinopeptides A and B are removed.

Ancrod↗
PubMed1986

Fibrin assembly in human plasma and fibrinogen/albumin mixtures.

Magnetic birefringence is used to monitor the kinetics of thrombin-catalyzed fibrin polymerization in model systems of increasing complexity (i.e., fibrinogen solutions, fibrinogen/albumin mixtures, and plasma anticoagulated with citrate) and in plasma containing free calcium which is the physiological condition. The introduction of albumin into fibrinogen solutions shortens the lag period and enhances fiber thickness. The polymerization progress curves are sigmoidal at zero or low albumin concentrations, but at physiological and higher concentrations, they become hyperbola-like from the end of the lag period. High albumin concentration has thus induced a change in the assembly kinetics. The progress curves from plasma in which the cascade is dormant are also hyperbola-like although they round off more quickly because of antithrombin activity. In plasma containing free calcium, thrombin is endogenously produced, and the progress curves are nearly linear; hence, the assembly kinetics are very different from those of the model systems. The curves are not influenced by calcium-dependent cross-linking involving factor XIIIa. The progress curves are also linear when polymerization is induced with Russell's viper venom, which by directly activating factor X circumvents earlier steps in the cascade. This implies that linear polymerization is caused by events posterior to factor X activation and are thus likely to be largely dependent on the functioning of the prothrombinase complex. Addition of thrombin to plasma containing free calcium reduces the lag period. At low exogenous thrombin levels, the polymerization rate is increased, and the progress curves remain linear. However, at higher levels, the curves become more complicated and, paradoxically, full polymerization takes longer.(ABSTRACT TRUNCATED AT 250 WORDS)

Birefringence↗
PubMed1984

Orientation of skeletal muscle actin in strong magnetic fields.

Measurement of birefringence is used to follow actin filament and paracrystal formation in a strong magnetic field. Both F-actin and paracrystals orientate parallel to the field. This confirms that globular proteins arranged in filamentous assemblies can orientate in magnetic fields. This is consistent with the alpha-helical component of the actin subunits being approximately aligned along the actin filament.

Actins↗
PubMed1984

Magnetic alignment of collagen during self-assembly.

Magnetically induced birefringence is used to monitor the thermally induced self-assembly of collagen fibrils from a solution of molecules. The magnetic torque alone can, at best, only orient the fibrils into planes normal to the field direction. Nevertheless, the gels formed have a high degree of uniaxial alignment, probably due to the additional ordering effects of surface interactions. Thus magnetic orientation is potentially useful in the study of fibrillogenesis and in the production of highly oriented collagen gels.

Animals↗
PubMed1984

Fibrinogen and fibrin in strong magnetic fields. Complementary results and discussion.

When fibrin polymerizes in a strong magnetic field, it can be highly oriented. The structural diffraction study of the oriented polymer becomes thus possible. The magnetic birefringence can also be used to study the development of the polymer Fibrinogen in solution is weakly oriented in high magnetic fields. In this work we present complementary results and discussion. The validity of the comparison of the orientation parameters of fibrinogen and fibrin with those of other orientable known biological structures is discussed. The orientation of fibrin formed from fibrin monomer solution is compared to that of fibrin formed by the action of thrombin on fibrinogen. The conditions to obtain highly oriented fibrin gels suitable for three dimensional structure studies are also briefly discussed.

Animals↗
PubMed1983

Orientation of fibrin in strong magnetic fields.

Magnetic field orientation can be considered as a new valuable technique for the study of fibrin. Birefringence measurements during polymerization in the magnetic field enables a new approach to study the mode of association of fibrin monomers. Stable fully oriented clots can be obtained for investigation of the three-dimensional and the secondary structures of the fibrin fiber. Such experiments could be useful to assess the structure of other biopolymers diamagnetically anisotropic.

Animals↗
PubMed1983

Internal structural anisotropy of spherical viruses studied with magnetic birefringence.

Six so called spherical viruses (four plant and two animal) are shown to exhibit magnetically induced birefringence in solution. They must therefore be magnetically and optically anisotropic. This is attributed to static structural anisotropy of the interiors as neither natural shape nor field-induced deformations are likely causes. Thus at least part of these virus cores have a symmetry differing from that of their capsids. An estimate of the average orientation of the RNA bases is given for the plant viruses: turnip yellow mosaic, bromegrass mosaic, tomato bushy stunt and turnip crinkle. The packing geometry of the nucleic acid/protein cores of adenovirus and probably influenza virus are anisotropic but to an extent that cannot be quantified.

Adenoviridae↗
PubMed1983

Fibrinogen and fibrin structure and fibrin formation measured by using magnetic orientation.

Accurate birefringence measurements show that fibrinogen orients to a small degree in high magnetic fields. This effect can be explained as due to the molecule having about 30% (by weight) alpha-helix oriented relatively parallel to the long axis. Birefringence measurements on fully oriented fibrin suggest that aligned alpha-helical content is less than that estimated for fibrinogen. But because of limitations in the analysis this difference must be viewed with caution. Highly oriented fibrin results when polymerization takes place slowly in a strong magnetic field. Low-angle neutron diffraction patterns from oriented fibrin made in the presence of EDTA, made in the presence of calcium, or stabilized with factor XIIIa are very similar, showing that the packing of the molecules within the fibers is the same or very similar in these different preparations. The induced magnetic birefringence was used to follow fibrin formation under conditions in which thrombin was rate limiting. The fiber network formed by approximately the gelation point constitutes a kind of matrix or frame that is largely built upon during the remaining approximately 85% of the reaction. After gelation the reaction is pseudo-first order.

Animals↗
PubMed1982

The structure of the cell wall of Staphylococcus aureus studied with neutron scattering and magnetic birefringence.

The cell wall complex was extracted from Staphylococcus aureus and characterized in suspension by means of small-angle neutron scattering and magnetically induced birefringence. The neutron scattering measurements show that the complex has a thickness of approximately 420 A, a mass per unit area of 93 +/- 11 daltons/A2 and is approximately 75% water by volume. The neutron scattering density is higher near the surface than in the interior in accordance with a trilamellar structure. The magnetically induced birefringence measurements demonstrate that a high degree of magnetic orientation is possible due to the anisotropic nature of the wall complex structure.

Cell Wall↗
PubMed1981

Small-angle neutron scattering studies of the conformation of myeloma protein MOPC315 and its Fab fragment, and the interaction with a monovalent dinitrophenyl hapten.

The first small-angle scattering study of an immunoglobulin A is reported. Neutron measurements have been made to determine conformational parameters of the mouse myeloma protein MOPC315 and to relate these to previous immunoglobulin G results. Use of the contrast method shows that the MOPC315 IgA molecule is not simply globular, that it has a dry volume of 220.0 +/- 4.5 nm3 corresponding to a mass density of 1.275 +/- 0.025 g cm-3 and that its full and cross-sectional radii of gyration, corrected for concentration dependence, are 7.97 +/- 0.07 nm, 2.40 +/- 0.08 nm and 1.33 +/- 0.07 nm respectively. Similar study of its Fab fragment gives a dry molecular volume of 69.0 +/- 0.7 nm3, a mass density of 1.285 +/- 0.015 g cm-3 and uncorrected radii of gyration that are consistent with those of the parent and support an overall "T" or "Y" conformation in solution. Addition to saturation of a small monovalent dinitrophenyl hapten leaves the dry volume of the whole molecule unaltered, but may slightly lower one or more of its radii of gyration. The significance of this finding is discussed. Comparative studies with rabbit anti-dinitrophenyl immunoglobulin G antibody suggest a different initial conformation but similar consequences of hapten binding, which, if real, are probably unrelated to classical complement fixation.

Amino Acid Sequence↗
PubMed1981

Oriented fibrin gels formed by polymerization in strong magnetic fields.

Fibrinogen is a soluble plasma protein which, after cleavage by the specific proteolytic enzyme thrombin, polymerizes to form the filamentous fibrin network during blood clotting (see refs 1 and 2 for reviews). Fibrinogen has a molecular weight of 340,000 and is composed of two identical halves, each containing three peptide chains designated A alpha, B beta and gamma. Fibrin monomers are produced by thrombin which releases the small negatively charged fibrinopeptides A and B. The overall shape of the fibrinogen molecule has not been unequivocally established. The trinodular, elongated (approximately 450 A long) structure proposed by Hall and Slayter is the most widely accepted model and it has obtained additional support from recent work. Fibrin monomers are also about 450 A long and in fibres they probably have a half-staggered arrangement along the axis. The fibres are an assembly of protofibrils whose structure and packing are not reliably known. We report here that highly oriented fibrin gels are formed when polymerization takes place slowly in a strong magnetic field. It is shown that the protofibrils pack into a three-dimensional crystalline lattice. We introduce magnetically induced birefringence as a potential tool for studying polymerization and briefly speculate on the applications of strong magnetic fields.

Biopolymers↗