Biomedical subjects

J R Cann

Publications and source records attributed to J R Cann.

At least 37 records · Page 2Linked to original sources

PubMed1991

Gel electrophoresis of reacting macromolecules. Rate-limited self-association.

Prompted by experimental sodium dodecyl sulfate-gradient polyacrylamide gel electrophoresis (PAGE) patterns of an oligomerizing 73-residue peptide, PAGE and gradient PAGE patterns were simulated numerically for two rate-limited, reversible self-associating systems, viz., monomer-dimer and monomer-dimer-tetramer interactions. A wide range of values for rate constants and other relevant parameters was examined. The cardinal result for interactions with half-times comparable to the time of electrophoresis is that the number of peaks in the pattern can exceed the number of interacting species. Since peaks of intermediate migration velocities are composed of interconverting monomer and oligomers, molecular weights corresponding to individual species cannot be assigned to them.

Computer Simulation↗

PubMed1991

Experimental and theoretical studies of rate constant evaluation for the solute-matrix interaction in affinity chromatography.

In an investigation of the problem of determining kinetic parameters for the interaction of a solute with immobilized ligand sites on an affinity matrix, a combination of experimental studies and numerical simulations of frontal chromatography of methyl orange on Sephadex G-25 has yielded a simpler method than existing procedures for characterizing solute-matrix kinetics. A significant change in approach has entailed the direct evaluation of the kinetic contribution to boundary spreading from the flow-rate dependence of boundary variance under conditions of concentration-independent chromatographic migration (linear kinetics). This kinetic contribution is then interpreted in terms of an experimentally more appropriate form of a quantitative relationship for diffusion-free chromatographic migration (H. W. Hethcote and C. DeLisi, 1982, J. Chromatogr. 240, 269-281). Finally, the results of numerical simulations of concentration-dependent chromatographic migration (Langmuir kinetics) have indicated that rate constants should also be determinable under these conditions by extrapolation of their apparent values obtained by the above procedure to infinite dilution.

Alcohol Dehydrogenase↗

PubMed1990

Analysis of the gel electrophoresis of looped protein-DNA complexes by computer simulation.

The theory of mass transport coupled to reversible interactions under chemical kinetic control forms the basis of a numerical model that has been applied to systems such as lac repressor-lac operator DNA, in which a protein binds in two different modes to linear DNA carrying two specific binding sites. Three complexes may be formed: (1) a linear 1:1 complex with one protein molecule bound to one site on the DNA molecule; (2) a 1:1 complex in which a single protein molecule is bound to both sites simultaneously, thereby inducing a large DNA loop; and (3) a 2:1 linear complex in which two protein molecules are bound in tandem, each occupying a single site. The computational model affords a quantitative numerical simulation of the observed gel electrophoretic patterns produced by titration of the DNA with protein and provides new insights into the shape and nature of the patterns. In particular, the patterns may represent unimodal or bimodal reaction zones. Nevertheless, analysis of the peaks in the patterns obtained at low DNA and high protein concentration provides essential information as to the stoichiometry of the complexes and satisfactory estimates of association constants. The theory thus provides the experimenter with guidelines for quantitative evaluation of the results of gel retardation assays of the particular system under investigation, once protein-induced DNA (or RNA) loops have been established by independent physical or chemical methods. It is suggested that these insights might also find application to systems involving the binding of two or three different proteins to DNA with loop formation.

Binding Sites↗

PubMed1990

Probing the role of proline in peptide hormones. NMR studies of bradykinin and related peptides.

The use of NMR methods to study conformational and dynamic aspects of the proline residues in the nonapeptide bradykinin is reviewed. NMR analyses involve considerations of bistable equilibria which include the cis/trans conformational heterogeneity of the imide bond, the cis'/trans' regions of conformational stability which characterize rotation about the C alpha-CO bond (dihedral angle psi), and the interconversion of the pyrrolidine ring of proline between puckered C gamma-endo and C gamma-exo conformations. These conformational features are all characterized by different kinetic behavior, are interdependent with peptide bond conformation, and exhibit sensitivity to amino acid substitutions. Thus, the substitution of Gly6 for Ser6 increases the fractional cis probability of the sixth peptide bond from 0.1 to 0.35. Substitutions of alpha-aminoisobutyric acid (AIB) residues for proline introduce conformational constraints analogous to those in cis' proline. Correlations of pyrrolidine ring conformation and dynamics with the cis/trans ratio of the imide bond have also been observed in model systems. Conformational and activity analyses of [AIB7]-bradykinin provided a stimulus for the development of the first bradykinin antagonist by Stewart and Vavrek (Vavrek RJ and Stewart JM, Competitive antagonists of bradykinin. Peptides 6: 161-164, 1985).

Aminoisobutyric Acids↗

PubMed1990

Evidence of neuropeptide bivalency in the interaction of substance P with cerebroside sulfate.

A precipitin effect has been observed with mixtures of cerebroside sulfate and the neuropeptide substnace P. This phenomenon is attributed to multivalency of the lipid due to its existence in micellar form, and to bivalency of substance P. One of those neuropeptide sites is almost certainly the basic residue(s) located at the N-terminal of substance P, whereas the hydrophobic residues at the C-terminus are suggested as candidates for the other site on the basis of turbidimetric, circular dichroic, and fluorometric studies. An intrinsic association constant of 3.6 x 10(4)M-1 has been obtained from the cerebroside sulfate concentration associated with maximal turbidity of mixtures containing a fixed concentration of the neuropeptide.

Binding Sites↗

PubMed1989

Phenomenological theory of gel electrophoresis of protein-nucleic acid complexes.

A phenomenological theory of gel electrophoresis is elaborated for protein-DNA complexes involving one, two, or three binding sites on the DNA molecule. The computed electrophoretic patterns simulate experimental patterns shown by both prokaryotic and eukaryotic systems. The mechanism whereby the electrophoretic protein-DNA ladder is generated upon titration of the operator with repressor is embodied in theory of mass transport coupled to reversible interactions under chemical kinetic control. In contrast to strong interactions (association constant greater than 10(12) M-1), patterns observed with weak complexes (K less than 10(10) M-1) could be simulated only by applying the cage effect, a model of which is formulated. Theoretical underpinning is provided for the electrophoretic estimation of equilibrium association constants, and requisite chemical kinetic conditions are elucidated for direct estimation of the rate constant for dissociation of the protein-DNA complex from gel patterns. The theory thus affords an experimenter with a means for determining the conditions required to render the gel retardation method a valid procedure for evaluating equilibrium constants and/or kinetic parameters for the particular protein-nucleic acid system under investigation. These several considerations apply not only to interactions of proteins with nucleic acids (DNA or RNA) but also to a wide range of macromolecular interactions involving peptides, drugs, and other ligands as well as large assemblies such as multienzyme complexes.

Animals↗

PubMed1989

A fluorometric study of the interaction of bradykinin with lipids.

The interaction of bradykinin (BK) with lipids has been followed by steady-state fluorescence measurements. Addition of either cerebroside sulfate (CS) or phosphatidylinositol (PI), solubilized with the nonionic surfactant C12E8, to BK or its analogue [Gly6]-BK enhances the relative fluorescence intensity of peptide emission at 288 nm. Fluorometric titration of the peptide with lipid has been used to quantitate the interactions in terms of stoichiometry and equilibrium constant. Job's method of continuous variation for the BK-CS interaction gave a stoichiometry of 1:2 for the complex. The value of the equilibrium constant, K, for the interaction of either BK or [Gly6]-BK with CS is 1.5.10(4) M-1. The BK-PI interaction is weaker; K = 5.0.10(3) M-1. Although electrostatic forces no doubt play a major role in these interactions, measurements on the model peptide Gly-Phe-Gly indicate that the phenylalanine residues of BK are disposed in the hydrophobic environment provided by the lipid-C12E8 mixed micelle. 13C-NMR measurements on [99% 13C alpha-Gly6]-BK show that there is no change in its cis/trans ratio upon interaction with CS. The increase in the relative fluorescence intensity of BK accompanying its cooperative interaction with sodium dodecyl sulfate (SDS) implicates the role of hydrophobic forces in this interaction as well. These results bear on the interpretation of the changes in circular dichroism (CD) of BK caused by SDS.

Amino Acid Sequence↗

PubMed1989

Boundary spreading in sedimentation velocity experiments on partially liganded aspartate transcarbamoylase. A ligand-mediated isomerization.

Transport theory for rapidly reversible interacting systems was used to analyze boundary spreading in sedimentation velocity experiments on partially liganded aspartate transcarbamoylase. In the presence of sub-stoichiometric amounts of a bisubstrate analog, N-(phosphonacetyl)-L-aspartate, which is bound with high affinity to the enzyme (Kd approximately 100 nM), broad boundaries were observed consistent with the presence of two conformational forms. The theoretical treatment showed that under these conditions, the interconversion between the compact (11.7 S) and swollen (11.3 S) forms of the enzyme appears uncoupled, due to the formation of a gradient of free ligand that is caused by the re-equilibration resulting from the differential sedimentation of the two enzyme forms. Sedimentation velocity patterns for such systems are interpretable in terms of two independent species. When, however, the enzyme is in the presence of a sub-saturating amount of the weakly bound ligand, succinate (Kd approximately 1 mM), the re-equilibration caused by the differential sedimentation does not perturb the large background of free ligand and form a gradient. Instead, the two different forms of the enzyme are in dynamic equilibrium, resulting in a boundary having average sedimentation and diffusion coefficients. The observed boundary spreading experiments with different ligands are satisfactorily interpreted in terms of a ligand-mediated isomerization of aspartate transcarbamoylase from a compact to a swollen conformation.

Aspartate Carbamoyltransferase↗

PubMed1989

A novel eye in 'eyeless' shrimp from hydrothermal vents of the Mid-Atlantic Ridge.

Rimicaris exoculata is a shrimp that swarms over high-temperature (350 degrees C) sulphide chimneys at Mid-Atlantic Ridge hydrothermal fields (3,600 m). This shrimp lacks an externally differentiated eye, having instead a pair of large organs within the cephalothorax immediately beneath the dorsal surface of the transparent carapace, connected by large nerve tracts to the supraesophageal ganglion. These organs contain a visual pigment with an absorption spectrum characteristic of rhodopsin. Ultrastructural evidence for degraded rhabdomeral material suggests the presence of photoreceptors. No image-forming optics are associated with the organs. We interpret these organs as being eyes adapted for detection of low-level illumination and suggest that they evolved in response to a source of radiation associated with the environment of hydrothermal vents.

Animals↗

PubMed1989

Numerical and experimental demonstrations of the need for caution in the use of zonal gel chromatography for characterizing ligand interactions with small acceptors.

Quantitative expressions are presented for the evaluation of equilibrium constants for interactions of the type A + B in equilibrium C from experiments entailing the application of a small zone of acceptor-ligand mixture to a column of gel preequilibrated with ligand solution [J.P. Hummel and W.J. Dreyer (1962) Biochim. Biophys. Acta 63, 530-532]. Only in the event that identical elution volumes pertain to acceptor and complex does the steady-state binding constant (Kss) obtained by that method equal the thermodynamic equilibrium constant (K). Simulated elution profiles are then generated with parameters relevant to gel chromatography of the ATP-Mg2+ system on Sephadex G-10 in order to demonstrate the practical importance of the need for distinction between Kss and K in situations where acceptor and complex do not comigrate. A study of the interaction between soybean trypsin inhibitor and cytochrome c by gel chromatography on Sephadex G-75 is then used to illustrate the feasibility of combining information from Hummel-Dreyer experiments with the theoretical expressions to characterize systems under the more general conditions that the elution volumes of A and C differ. A finding of considerable theoretical interest in relation to the simulation of mass migration behavior is the demonstration that a truncation error is the source of zonal spreading in the theoretical-plate model of chromatography. This truncation error is shown to be the source of spreading generated whenever solution of an abbreviated (diffusion-free) continuity equation involves substituting first differences for first derivatives in the differential equation describing mass transport.

Adenosine Triphosphate↗

PubMed1988

Small zone gel chromatography of interacting systems: theoretical and experimental evaluation of elution profiles for kinetically controlled macromolecule-ligand reactions.

A phenomenological theory of small zone gel chromatography is elaborated for kinetically controlled macromolecule-ligand interactions. Chromatography, direct binding experiments, and rate measurements are used for successful comparison of experimental behavior with theoretical elution profiles for the interaction of MAP-2 with two synthetic peptide fragments from the C-terminal moieties of alpha- and beta-tubulin subunits. The results of this study provide guidelines for interpretation of experimental small zone elution profiles of total ligand.

Acetic Anhydrides↗

PubMed1988

High-field NMR and circular dichroism solvent-dependent conformational studies of the bradykinin C-terminal tetrapeptide Ser-Pro-Phe-Arg.

The conformational properties of the tetrapeptide Ser1-Pro2-Phe3-Arg4, the C-terminal fragment of the nonapeptide hormone bradykinin, have been studied by circular dichroism and two-dimensional NMR techniques. Measurements of coupling constants, NH temperature dependence rates and nuclear Overhauser effects (performed with rotating frame nuclear Overhauser spectroscopy, ROESY) in H2O and CD3OH/D2O (80/20, v/v) reveal different conformations in the corresponding solvent. In aqueous solution the molecule exists in a random conformation or as an average of several conformations in rapid exchange. In CD3OH/D2O, however, the conformation is well-defined. The backbone of the peptide is extended, and the side-chains of Phe3 and Arg4 exhibit unusual rigidity for a peptide of this size. Evidently, the secondary structure is stabilized by a charge interaction between the guanidino group of Arg4 and the terminal carboxyl group, since experiments at various pH's show clearly that the definition of conformation decreases strongly upon protonation of the carboxyl function. A NH3+(Ser1)-COO-(Arg4) salt bridge, as well as any form of turn stabilized by hydrogen bonds can be ruled out with certainty.

Bradykinin↗

PubMed1987

Theory of electrophoresis of hybridizing enzymes with kinetic control: implications for population genetics of electrophoretic markers.

A phenomenological theory of zone electrophoresis has been formulated for reversible, kinetically controlled self-dimerization and hybridization of proteins. The computed electrophoretic patterns simulate many of the observed features of certain Drosophila enzymes. The patterns for rapid self-dimerization show a unimodal reaction zone over a wide range of rates of dissociation of the dimer, the migration velocity increasing with increasing rate of dissociation. Those for slow rates of both dimerization and dissociation are bimodal reaction zones exhibiting a peak composed largely of dimer and one largely of monomer separated by a low plateau. The nature of the pattern for hybridization of two dimerizing variants of a polymorphic protein is strikingly dependent upon the rates of reaction. For rapid association and very slow dissociation the pattern exhibits three zones corresponding to the two homodimers and the heterodimer. Very rapid rates of dissociation give two monomer zones. Intermediate rates of dissociation also give two zones, but here they are uncoupled reaction zones; each corresponds to an interconverting mixture of one of the homodimers and its monomer, the heterodimer having dissociated completely during early stages of electrophoresis. The transition from a three-zone pattern to this two-zone pattern has been examined in detail, and a mechanism is given. Practical implications are considered.

Animals↗

PubMed1987

Frontal gel chromatography of interacting systems: theoretical and experimental evaluation of the shapes of elution profiles for systems of the type A + B in equilibrium C.

A theoretical and experimental study has been made of the advancing elution profile in frontal gel chromatography of interacting systems for which the elution volume of the complex is smaller than that of the larger reactant. First, Gilbert-Jenkins theory is used to delineate the form of the elution profile from the magnitudes of the elution volumes and concentrations of reacting species. This procedure resulted in the detection of a misinterpretation of certain patterns obtained in a gel chromatographic study of the interaction between myoglobin and ovalbumin. Second, a numerical computational procedure, which incorporates both axial dispersion and concentration-dependence of species elution volumes, is used to establish the influence of these two factors on boundary shapes for such systems. Third, frontal gel chromatography on Sephadex G-75 is used to compare experimental behavior with theoretical profiles predicted for the electrostatic interaction between cytochrome c and soybean trypsin inhibitor (pH 6.8, I 0.01). Results of these experiments serve as a guide for future conduct of experiments aimed at characterization of biologically important, reversible complex formation between proteins and/or other macromolecules.

Chromatography, Gel↗

PubMed1987

A proton magnetic resonance and a circular dichroism study of the solvent dependent conformation of the synthetic tubulin fragment Ac tubulin, alpha (430-441) amide and its interaction with substance-P.

Proton magnetic resonance techniques were used to study the conformation of the synthetic tubulin fragment Ac-tubulin (430-441) amide in H2O and 80% CD3OH/20% D2O solutions, using water suppression techniques. Proton assignments are based on two-dimensional COSY experiments combined with one-dimensional spin decoupling. A comparison of the NH proton shifts between the two solvents, namely delta(CD3OH/H2O-H2O) shows a small solvent effect for the Lys1 to Val6 region of the molecule, whereas for Gly7 to Glu12 the solvent effect is much larger. The smaller effects in the region of Lys1 to Val6 may be due to some hydrogen bonding as these protons are shielded from the solvent. These conclusions are in agreement with the circular dichroism results in 80% methanol/20% water where the alpha helix is present to the extent of 30%, whereas the peptide is completely unstructured in water with some aggregation. The temperature dependence of the NH proton shifts was also carried out. In water these shifts are of the order of 7-9 X 10(-3) ppm/K indicating that most of the protons are not involved in hydrogen bonding. In CD3OH/H2O, these values range from about 4-6 X 10(-3) ppm/K, which are compatible with the presence of hydrogen bonds. Finally, binding studies were carried out between the tubulin peptide and the undecapeptide neutrotransmitter substance P. The largest shifts are for the Tyr3 NH proton of the tubulin fragment, whereas for substance P it is for the Lys3, Gln5 and Leu10 NH protons, indicating a change in conformation of both peptides on interaction.

Circular Dichroism↗

PubMed1987

CD-n.m.r. study of the solution conformation of bradykinin analogs containing alpha-aminoisobutyric acid.

The conformation in aqueous solution of several alpha-aminoisobutyric acid (AIB)-containing analogs of bradykinin (BK) has been probed by complementary CD and 1H n.m.r. measurements. The conclusion reached is that substitution of AIB for Pro2 and/or Pro3 in BK stabilizes a degree of beta-turn conformation in the N-terminal tetrapeptide moiety of the resulting analogs. Changing the solvent from water to DMSO or TFE further enhances the contribution of particular hydrogen bonded structures to the time-averaged conformation of these peptides. Bradykinin and [AIB7]-BK adopt similar hydrogen bonded conformations in TFE, apparently with a contribution from a beta-turn involving their common Arg1-Pro2-Pro3-Gly4 moiety. The contrasting biological activities of BK and its AIB-analogs are considered in terms of the conformational analogy between the AIB-residue and cis' Pro and the propensity for a beta-turn at the N-terminus of the peptide.

Amino Acid Sequence↗

PubMed1986

Characterization and structural aspects of the enhanced assembly of tubulin after removal of its carboxyl-terminal domain.

Limited subtilisin cleavage of tubulin results in formation of S-tubulin heterodimer and a 4-kDa carboxyl-terminal peptide fragment. This carboxyl-terminal domain constitutes an essential site for MAPs interaction and plays a role in modulating the interactions responsible for tubulin self-assembly into microtubules [Serrano et al. (1984) Proc. Natl Acad. Sci. USA 81, 5989; and Biochemistry 23, 4675]. In the present communication it is shown that addition of the 4-kDa peptide fragment from porcine tubulin to porcine S-tubulin in a molar ratio of about 2:1 does not affect the assembly of the latter. On the other hand, consistent with previous findings on the binding of the 4-kDa peptide by MAP-2, the peptide inhibited MAP-2-induced tubulin assembly (molar ratio of peptide to tubulin, about 2:1; peptide to MAP-2, about 30:1). Comparison of the amino acid composition of the 4-kDa peptide fragment and the C-terminal amino acid residues of S-tubulin with the amino acid sequence of tubulin indicated the subtilisin cleavage site on the tubulin molecule to be between residues Glu417 and Phe418 of the alpha-subunit sequence and between Glu407 and Phe408 of the beta-subunit sequence. The circular dichroism of the 4-kDa fragment in water as solvent is indicative of a molecule with an unordered structure, but when the solvent is changed to a water-trifluoroethanol mixture, the fragment becomes more highly structured. The critical concentration for S-tubulin assembly is not affected by MAPs nor by polylysine, but is decreased by either taxol of dimethylsulfoxide. S-tubulin, with its greater propensity for self-association, has a different conformation from tubulin as shown by a 50% decrease in alpha-helical content, a more hydrophobic environment of at least some of the tryptophan residues as judged from fluorimetry, and a greater compaction indicated by f/f0 = 1.3, as compared to 1.4 for tubulin. The latter point is supported by the observation that the value of the sedimentation coefficient, s20,w = 5.7 S, of the 92-kDa S-tubulin molecule is not significantly different from that of the 100-kDa tubulin, s20,w = 5.8S.

Amino Acids↗

PubMed1986

Interaction of substance P with tubulin.

Binding of the peptide neurotransmitter substance P to brain tubulin in vitro inhibits self-assembly of the protein into microtubules and disrupts preassembled microtubules. This cooperative inhibition of the maximum extent of self-assembly by substance P is explicable in terms of preferential binding to the protomer state as compared to the polymer state of tubulin. The inhibition is relieved by the microtubule-associated protein MAP2, which evidently acts in a mixed competitive-noncompetitive fashion. Substance P interacts directly with the isolated C-terminal 4-kDa peptide fragment of tubulin, which appears to contain the specific binding area for MAP2, but is without effect on the self-assembly of the larger (48-kDa) part of the tubulin molecule called S-tubulin. The results are consistent with the C-terminal fragment having a binding site for the cationic substance P as well as for MAP2. However, factors other than electrostatic interaction must be operative, since the sulfoxide of substance P, a derivative with oxidized methionine but similar electrostatic characteristics, is inactive in inhibiting the extent of microtubule assembly.

Animals↗