A general method for the evaluation of diffusion constants,dilute-solution viscoelasticity,and the complex dielectric constant of a rigid macromolecule with an arbitrary configuration. II

As a continuation of a previous paper [Biopolymers 16 , (1977)], in which we described a general method for the evaluation of the diffusion constants of a rigid macromolecule with an arbitrary configuration, this paper presents a theory for evaluating the relaxational behavior of the molecule in solution. The diffusion equation of a molecule subjected to hydrodynamic or electric forces is solved and both a complex viscosity and a complex dielectric constant are obtained by assuming that the molecule is composed of Tokes spheres and, in the dielectric property, the molecule possesses a fixed charge distribution. The viscoelasticity of a rigid rod is calculated and compared with the analytical results.     

Rotational dynamics of erythrocyte spectrin

The rotational diffusion of erythrocyte spectrin has been measured using time-resolved phosphorescence anisotropy. The anisotropy of the spectrin dimer decays to zero with a time constant of 3 microseconds at 21 degrees C. The results are compared with the correlation times predicted for the anisotropy decay of an equivalent sphere and rigid rod. The data indicate that the ribbon-like spectrin molecule possesses considerable torsional and segmental flexibility. These motions are restricted, but not abolished, when spectrin is reconstituted into cross-linked cytoskeletal protein networks, or bound to spectrin-actin depleted erythrocyte membrane vesicles.     

Dynamic light scattering as a probe of superhelical DNA-intercalating agent interaction

Polarized dynamic light-scattering measurements on superhelical pBR322-plasmid DNA solutions in 0.2M NaCl, 2 mM NaPi, pH 7.0, 2 mM EDTA result in a translational diffusion coefficient D = (3.77 ± 0.10) × 10^?8 cm²/s for the native molecule. Modeling the DNA, in the simplest approximation, as a 10 × 440-nm effective hydrodynamic rigid rod yields a good fit to the apparent diffusion coefficient angular-dependence data up to 70°; the model fails at higher angles, probably due to the effects of flexibility or branching of the rod. Diffusion coefficient titration experiments with a platinum complex intercalating agent (PtTS) result in a titratable superhelix density of σ = ?0.079 ± 0.008 under our experimental conditions, corresponding to about 34 superhelical turns in the native DNA. The DNA contour length predicted by our two independent results, the rod dimensions and the number of superhelical turns, is in excellent agreement with the contour length calculated from the number of base pairs, supporting the hydrodynamic approximation of an effective rodlike structure for this small DNA molecule in solution.     

Molecular structure and physical properties of type IV collagen in solution

The physical properties of intact type IV collagen from the mouse EHS sarcoma were studied in acid solution using laser light scattering and viscometry. The experimentally observed values of molecular weight, translational diffusion coefficient, particle scattering factor at 175.5° and a wavelength of 633 nm and intrinsic viscosity at 22°C were 532000, 0.66 × 10⁻⁷cm²s⁻¹, 0.492 and 74.7 ml/g respectively. Plots of $\text{Kc/}\text{R}{}_0$ versus collagen concentration were linear with a slope of approximately 0, indicating that under the conditions studied, type IV collagen molecules do not form supra-molecular aggregates. Experimentally determined translational diffusion coefficients closely approximated the calculated value for a rod-like molecule 424 nm long and 1.5 nm in diameter. Based on this observation, it is concluded that the type IV collagen molecule translates like a bent rigid rod similar to the interstitial collagens. However, the low intrinsic viscosity and larger value of the particle scattering factor for type IV collagen molecules in comparison with the interstitial collagens indicate that type IV collagen is considerably more flexible. Physical measurements on molecules in solution are consistent with a model of the type IV molecule containing numerous flexible bends with bend angles less than 125°. It is concluded that the type IV collagen molecule behaves like a worm-like rod in solution.     

Hydrodynamic resistance and diffusion coefficients of a freely hinged rod

The seven-dimensional hydrodynamic resistance and diffusion tensors are evaluated for a rod which is freely hinged at its center and immersed in a viscous fluid. The hydrodynamic resistance tensor is first determined at the hinge, then transformed to other points and inverted to obtain the diffusion tensor. Hydrodynamic interactions between rod halves are neglected, which is asymptotically correct for long rods. In the long-rod limit, the diffusion coefficient characterizing translations over macroscopic distances is decreased by 3–6% from that for a rigid straight rod of same total length, while the average end-over-end rotational diffusion coefficient for each rod half is increased 4.67 times.     

Quasielastic light-scattering studies on human fibrinogen and fibrin. I. Fibrinogen

A quasielastic light-scattering system has been constructed to study human fibrinogen. The first phase of the investigation was an attempt to clarify the shape of the firbinogen molecule using diffusion methods. The translational diffusion coefficient was measured as 2.04 ± 0.09 × 10^?7 cm² sec^?1. Aggregation is suggested as the reason for a lower value previously obtained using this technique. Diffusion indicated the molecule was rigid and did not dissociate at low concentration, low ionic strength, or 37°C. Thermal denaturation was observed at 40°C. At 3°C, a second thermal instability was discovered.     

Molecular configuration of compost's humic acid by viscometric studies

Summary The macromolecular configuration of humic acid sample obtained from Farm Yard Manure was investigated by viscometric measurements at varying sample concentrations and in presence of a neutral electrolyte. The humic acid molecule behaved like a linear flexible colloid at lower sample concentrations and rigid rod like or sphereo-colloid polyelectrolyte at higher sample concentrations. The polymeric behaviour was alsos shown in the presence of high amount of neutral electrolyte. An analysis of the data for particle weight, volume and axial ratio showed the molecular configuration as rod like.     

Heat-induced Denaturation of Myosin Total Rod

The myosin total rod, which consists of smaller segments of light meromyosin and heavy meromyosin subfragment-2 (HMM S–2), prepared by limited papain digestion of rabbit myosin, was purified by Sepharose-2B column chromatography. The purified total rod was more homogeneous than any previously reported, and the sodium dodecyl sulfate (SDS) gel electrophoretic method yielded a molecular weight of 22?23 × 10⁴ (11?11.5 × 10⁴ × 2).

Transition temperatures of this purified myosin total rod obtained from the melting profile during heating were 47.5 and 55°C. The results of ORD and CD measurements showed almost full reversibility upon cooling after thermal treatment. However, the results obtained from difference spectra and fluorescence spectra showed incomplete reversibility with hysteresis.

This ostensible dichotomy concerning the structural thermostability of the rod portion of myosin molecule may mean that although ORD and CD studies show almost full reversibility of the helix-coil transition, local irreversible conformational changes, involving aromatic amino acid residues take place. This fact suggests that the renahired α-rope of the myosin total rod can exhibit different properties than the native molecule under conditions where no discernible loss in helix content occurs.     

Studies on the myosin molecule from smooth muscle

The myosin molecule was extracted from the smooth muscle parts of horse esophagus and purified by ammonium sulfate fractionation. The schlieren pattern of the sedimentation velocity run showed a very sharp single peak of.5.9. S (s_20,w). Molecular weight of the protein was measured by means of the Archibald and sedimentation equilibrium methods, both in 0.5M KCI buffered by 1/150 M phosphate at pH 7.5 and at 5°C. The values obtained were 6.25 × 10⁵ and 5.81 × 10⁵respectively, for the two methods. The second virial coefficients were 1.1 × 10⁴ and 1.2 × 10^?4 ml/g. Denatured smooth muscle myosin was prepared in a solution of 5M guanidine HC1 containing 0.4 M KC1 and 0.2 M β-mercaptoet hanol buffered at p^H 8.0. The weight-average molecular weight of the denatured smooth muscle myosin was 2.24 × 10⁵ and the second virial coefficient was 7.6 × 10^?4 ml/g. The values described above are in good agreement with those reported for rabbit skeletal myosin with ammonium sulfate fractionation. The molecular dimension of the molecule is estimated as the value for an axial ratio of 100, assuming a rigid rod molecular model for this molecule, both the thermodynamical and hydrodynamical treatment being in a good agreement with this estimation.     

A kinetic study of -acetohydroxy acid isomeroreductase from Salmonella typhimurium

The kinetic mechanism of α-acetohydroxy acid isomeroreductase from Salmonella typhimurium has been investigated by initial velocity kinetic and product inhibition studies. The results of the initial velocity studies are consistent with a sequential reaction. The product inhibition studies suggest an ordered reaction with NADPH and the acetohydroxy acid adding in that order, and dihydroxy acid release before NADP release.NADPH binding has been studied both by fluorimetric techniques and difference spectroscopy. From these investigations it has been calculated that 4 moles of NADPH bind per mole of enzyme; the first molecule of NADPH binds with a dissociation constant of 1.7 × 10^?6m, the subsequent 3 moles of NADPH bind with a constant of 6 × 10^?6m. Biphasic kinetics have been demonstrated at a wide range of NADPH concentrations. The occurrence of biphasic kinetics and two separate binding constants are discussed in terms of negative cooperativity.     

Activation parameters for directly determined first order rate constants for outer sphere electron transfer reactions,and crystal structure of a pertinent pentaammine of CoIII

The outer sphere reductions of Co(NH₃)₅B³⁺ by Fe(CN)₅A³⁻ have been studied. The observed pseudo first order rate constants (Co complex in excess) obey the dependence k_obs=K_osk_et[Co]/(1 +K_os[Co]), as expected for outer sphere electron transfer reactions. Values of the fundamental electron transfer rate constants k_et have been determined, along with the equilibrium constant K_os for a range of reactions in which A and B are pyridyl ligands of different sizes. The first order electron transfer rate constants vary in a manner that is consistcnt with adiabatic electron transfer. The outer sphere ion pairing equilibrium constants K_os have been calculated: K_os=8.6 ± 0.1 × 10² M⁻¹ when A and B=pyridine; K_os=1.07 ± 0.09 × 10³ M⁻¹ where A=pyridine, B=1-phenyl-3-(4-pyridyl)propane; K_os=1.86 ± 0.11 × 10³ M⁻¹ when A=4,4′-bipyridine, B=pyridine; K_os=1.27 ± 0.08 × 10³ M⁻¹ when A=4,4′-bipyridine, B=4-phenylpyridine. Distances of closest approach between the metal centers in the reactive ion pairs are compared, and it is concluded that there is a common mechanism, in which the ammonia side of the cobalt complex approaches the cyano side of the iron complex in each reactive ion pair.The distance of closest approach between the two metal centers (a) was calculated from the experimental values for the ion pairing equilibrium constant K_os at 25 °C: 5.2 Å when A=4,4′-bipyridine, B=pyridine; 5.4 Å when A=4,4′-bipyridine, B=4-phenylpyridine; 5.5 Å when A=pyridine, B=1-phenyl-3-(4-pyridyl)propane; 5.7 Å when A=B=pyridine. These relatively short metal-metal distances, when compared to the X-ray structure of the compound [Co(NH₃)₅(4-phenylpyridine)]₂[S₂O₆]₃· 4H₂O, do not support an ion pair orientation in which the two substituted pyridine ligands A and B are oriented toward each other. [P2₁/c,a=7.399(3), b=22.355(10), c=13.776(4) Å, β=92.02(3)°, R=0.070.] The crystallographic results show that if the two pseudo-octahedral coordination spheres are oriented in the reactive ion pair so that an ammonia face of the cobalt complex is at hydrogen bonding distance from a cyano face on the iron complex, the metal-metal distance is 5.3 Å, a distance which is in agreement with the kinetic results.     

Noncompetitive Amine Uptake Inhibition by the New Antidepressant Pridefine

Abstract: Pridefine (AHR-1118) is a pyrrolidine derivative with clinically established antidepressant efficacy. Previous work from this laboratory indicates that pridefine is a reuptake blocker of catecholamines and serotonin with weak releasing activity. This study characterized the mode of amine uptake inhibition by pridefine as noncompetitive. The uptake experiments were performed utilizing ouabain instead of zero-degree controls to differentiate between the passive and active components of uptake. Furthermore, the passive component was resolved into diffusion and binding of substrate. Correction was made for the effects of ouabain on binding. Kinetic constants determined from Lineweaver-Burk plots were: K_m= 3 × 10^?7 M for NE, K_m= 9 × 10^?8 M for DA, and K_m= 3 × 10^?8 M for 5-HT. Dixon analyses of uptake at various pridefine concentrations indicated noncompetitive inhibition with K_i= 2.5 × 10^?6 M for NE uptake, K_i= 2.0 × 10^?6 M for DA uptake, and K_i= 1 × 10^?5 M for 5-HT uptake. These constants compare well with IC₅₀ values for the same transmitters: NE, IC₅₀= 2.4 × 10^?6 M; DA, IC₅₀= 2.8 × 10^?6 M; 5-HT, IC₅₀= 1.0 × 10^?5 M. The in vitro results indicate that pridefine is relatively specific as a catecholamine uptake blocker. It differs from tricyclic antidepressants which are reportedly competitive inhibitors of monoamine uptake. The possible mechanisms by which pridefine acts as a noncompetitive inhibitor are discussed.     

NMR relaxation processes of 31P in macromolecules

³¹P-Nmr relaxation parameters (spin-lattice relaxation time, linewidth, and nuclear Overhauser effect) were obtained at three different frequencies for poly(U) and a well-defined (145 ± 3 base-pair) fragment of DNA in solution. Data sets for the two samples were analyzed by theories which included relaxation by the mechanisms of ³¹P chemical shift anisotropy as well as by ¹H-³¹P dipole–dipole interaction. Neither data set could be satisfactorily described by a single correlation time. A model of a rigid rotor most nearly fits the data for the DNA molecule. Parameters obtained from the least-square fit indicate (1) that the DNA undergoes anisotropic reorientation with a correlation time τ₀ = 6.5 × 10^?7 sec for the end-to-end motion, (2) the ratio of diffusion constants D_∥/D_⊥ is 91, and (3) that the linewidth is due to chemical shift dispersion to the extent of 0.5 ppm. Some deviations of the calculated from the observed values suggested that significant torsional and bending motions may also take place for this DNA. Another model which contains isotropic motion but with a broad distribution of correlation times was required to fit the data for poly(U). A log ? χ² distribution function of correlation times [Scheafer, J. (1973) Macromolecules 6 , 881–888] described well the motion of poly(U) with the average correlation time τ = 3.3 × 10^?9 sec and a distribution parameter p = 14.     

Binding of 4-methylumbelliferyl-galactosides to peanut agglutinin

The binding of 4-methylumbelliferyl-α-D-galactopyranoside, -β-D-galactopyranoside and -D-Galβ(1→3)DGalNac to peanut agglutinin was studied by fluorescence. Peanut agglutinin quenched the fluorescence intensity of 4-methylumbelliferyl-α-D-galactopyranoside but enhanced that of the two 4-methylumbelliferyl-β-galactosides. For α-D-galactopyranoside, the association constants measured at 4 and 25°C were 3.4 × 10³ and 1.7 × 10³ M^?1 respectively, and for D-Galβ(1→3)DGalNac, 1.5 × 10⁵ and 3.3 × 10⁴ M^?1. The binding enthalpies estimated from these values are consistent with the existence of extended sugar binding sites in the peanut agglutinin molecule.     

Low Values of the Scheraga–Mandelkern β parameter for proteins. An explanation based on porous sphere hydrodynamics

Several globular proteins have values of the Scheraga–Mandelkern β parameter significantly below the theoretical minimum value, β₀ = 2.112 × 10⁶, for an impermeable sphere. Using the Felderhof–Deutch generalization of the Debye–Bueche–Brinkman theory of hydrodynamics of porous spheres, we have shown that values of β slightly below this supposed minimum are theoretically expected. A porous sphere of uniform density has a minimum β of 2.084 × 10⁶ at a Debye shielding ratio of 6.5, corresponding, for example, to a sphere radius of 11 Å and an inverse hydrodynamic shielding length of 0.6 Å^?1, values not far from those of small proteins. A two-layer porous sphere model gives similar results. Although this is the first theoretical explanation of values of β below β₀, the theory is incomplete since β values as low as 2.03 × 10⁶ are observed.     

Electric birefringence study of rabbit skeletal myosin subfragments HMM, LMM, and rod in solution.

Electric birefringence measurements and depolarized light scattering experiments were performed with HMM, LMM, and rod, the three fragments of myosin, under conditions (0.3 M KCl, 0.02 M PO4, pH 7.3) the medium currently used for biochemical assays of myosin in its native state as well as of its subfragments. The comparison of myosin and rod relaxation times (17.2 and 22.8 microseconds, respectively) suggests that the average bend angle in the tail is sharper in intact myosin (90 degrees) whereas rod, when detached from the heads, is a more elongated species with an average bend angle of 120-135 degrees. The LMM relaxation time (6.4 microseconds) is consistent with a rigid linear stick model of length 78 nm. Flexibility in myosin tail is thus confirmed as located in the HMM-LMM hinge. LMM and rod did not exhibit any significant variation of their apparent relaxation times with concentration and the decay curves were best fitted by a single exponential, evidence that the concentration of parallel staggered dimers was negligible in the concentration range studied here (0-7 g/l). This observation lends support to previous results obtained with myosin. Respective HMM, LMM, and rod molecular weights and homogeneity as evaluated by SDS-PAGE analysis were correlated to the Kerr constants of their solutions. Large variations in LMM Kerr constants could be related to the loss of a COOH-terminal peptide on prolonged chymotryptic digestion. Electric birefringence combined with depolarized light scattering is presented as a potential method for net charge distribution studies.     

Heparin binding to antithrombin III: Variation in binding sites and affinity

Heparin fractions of different molecular weights and anticoagulant activities were prepared by chromatography on protamine-Sepharose, and the association constants and stoichiometry for binding to antithrombin III were determined by measurement of enhancement of tryptophan fluorescence. A 7,900 molecular weight heparin preparation bound to antithrombin III with a stoichiometry of close to 2:1, whereas 14,300 and 21,600 molecular weight fractions bound at approximately 1:1 with the protein. Apparent association constants were 0.66 × 10⁶ M^?1 for the low molecular weight preparation and 2.89 × 10⁶ M^?1 for the high molecular weight material. Maximal fluorescence enhancement was greater with the higher molecular weight heparin. These results suggest a model of heparin-antithrombin III binding in which two sites on antithrombin III can accommodate one large heparin molecule with high affinity or two smaller molecules with low affinity.     

Thermodynamic and kinetic parameters of ion condensation to polynucleotides: Outer sphere complex formed by Mg++ ions

The coupling of ion binding to the single strand helix—coil transition in poly (A) and poly(C) is used to obtain information about both processes by ion titration and field-jump relaxation methods. Characterisation of the field-jump relaxation in poly(C) at various concentrations of monovalent ions leads to the evaluation of a stability constant K = 71 M^?1 for the ion binding to the polymer. The rate constant of helix formation is found to be 1.3 × 10⁷ s^?1, whereas the dissociation rate is 1.0 × 10⁶ s^?1. Similar data are presented for poly (A) and poly (dA).The interaction of Mg⁺⁺ and Ca⁺⁺ with poly (A) and poly (C) is measured by a titration method using the polymer absorbance for the indication of binding. The data can be represented by a model with independent binding “sites”. The stability constants increase with decreasing salt concentration from 2.7 × 10⁴ M^?1 at medium ionic strengths up to 2.7 × 10⁷ M^?1 at low ionic strength. The number of ions bound per nucleotide residue is in the range 0.2 to 0.3. Relaxation time constants associated with Mg⁺⁺ binding are characterised over a broad range of Mg⁺⁺ concentrations from 5 μM to 500 μM. The observed concentration dependence supports the conclusion on the number of binding places inferred from equilibrium titrations. The rate of Mg⁺⁺ and Ca⁺⁺ association to the polymer is close to the limit of diffusion control (k_R = 1 × 10¹⁰ to 2 × 10¹⁰ M^?1 s^?1). This high rate demonstrates that Mg⁺⁺ and Ca⁺⁺ ions do not form inner-sphere complexes with the polynucleotides. Apparently the distance between two adjacent phosphates is too large for a simultaneous site binding of Mg⁺⁺ or Ca⁺⁺, and inner sphere complexation at a single phosphate seems to be too weak. The data support the view that the ions like Mg⁺⁺ and Ca⁺⁺ surround the polynucleotides in the form of a mobile ion cloud without site binding.     

Studies on the conformational state of the chromophore group (11-cis-retinal) in rhodopsin by computer molecular simulation methods

The molecular dynamics of the rhodopsin chromophore (11-cis-retinal) has been followed over a 3-ns path, whereby 3 × 10⁶ discrete conformational states of the molecule were recorded. It is shown that within a short time, 0.3–0.4 ns from the start of simulation, the retinal β-ionone ring rotates about the C6–C7 bond through ～60° relative to the initial configuration, and the whole chromophore becomes twisted. The results of ab initio quantum chemical calculations indicate that for the final conformation of the chromophore center (t = 3 ns) the rhodopsin absorption maximum is shifted by 10 nm toward longer wavelengths as compared with the initial state (t = 0). In other words, the energy of transition of such a system into the excited singlet state S1 upon photon capture will be lower than that for the molecule where the β-ionone ring of the chromophore is coplanar to its polyene chain.     

Flexibility of smooth and skeletal tropomyosins

The rotational relaxation times of nonpolymerizable skeletal and smooth muscle tropomyosin were measured by analysis of the decay of the zero-field birefringence at different temperatures and salt concentrations. Skeletal tropomyosin in solution is equally well modeled as a rigid rod or as a semiflexible rod with a persistence length of 150 nm. Smooth muscle tropomyosin does not fit the rigid rod model but is well approximated by a semiflexible rod model with a persistence length of 55 nm. The results indicate that smooth muscle tropomyosin is either a more flexible molecule than skeletal muscle tropomyosin or is a curved structure with an end-to-end length shorter than the coiled-coil contour length. Smooth muscle tropomyosin controls the actomyosin ATPase differently from skeletal muscle tropomyosin and it had been suggested that the reason is because it is more rigid; clearly, another explanation must be sought.