Ultrasonic absorption in aqueous solution of lysozyme.

The titration curve of ultrasonic absorption at 2.82 MHz in aqueous solutions of lysozyme measured by Zana and Lang [J. Phys. Chem., 74 , 2734 (1970)] is theoretically analyzed. The maxima at pH 3 and pH 11 are describable with proton-transfer reactions of dissociable carboxyl and amino groups by assuming that volume changes due to the reactions are 2.3 and 5.2 cm³/mole, respectively, which are appreciably smaller than those of simple amino acids. The remaining, pH-independent excess absorption over solvent is measured at frequencies ranging from 3 to 150 MHz. The absorption is ascribed to the internal loss of protein. The complex compressibility β′_p ? iβ″_p of lysozyme molecule is evaluated as β′_p = 7.2 × 10^?12 cm²/dyne and β″_P = 4.3 × 10^?14 cm²/dyne from the increments over solvent in absorption as well as in sound velocity.     

Further quasi-classical trajectory studies on the C++ H2O reaction

Further trajectory studies on the C⁺ + H₂O reaction have been performed using a potential energy surface described through a finite element method in its p version. In former trajectory studies [Y. Ishikawa, T. Ikegami and R.C. Binning Jr., Direct ab initio molecular dynamics study of C⁺+H₂O: angular distribution of products and distribution of product kinetic energies, Chem. Phys. Lett. 370 (2003), pp. 490–495; J.R. Flores, Quasichemical trajectories on a finite element density functional potential energy surface: the C⁺+H₂O reaction revisited, J. Chem. Phys. 125 (2006), 164309], tunnelling was not taken into account. The present results together with the analysis of the electronic excited states [J.R. Flores and A.B. González, The role of the excited electronic states in the C⁺+H₂O reaction, J. Chem. Phys. 128 (2008), 144310] are useful to interpret the mechanism of the title reaction, which has been the subject of crossed beam experiments [D.M. Sonnenfroh, R.A. Curtiss and J.M. Farrar, Collision complex formation in the reaction of C⁺ with H₂O, J. Chem. Phys. 83 (1985), pp. 3958–3964] and can be considered a prototypical ion–molecule reaction.     

Impact of lyoprotectors on protein-protein separation in the solid state: Neutron- and X-ray-scattering investigation

BackgroundPolyhydroxycompounds (PHC) are used as lyoprotectors to minimize aggregation of pharmaceutical proteins during freeze-drying and storage.MethodsLysozyme/PHC mixtures with 1:1 and 1:3 (w/w) ratios are freeze-dried from either H₂O or D₂O solutions. Disaccharides (sucrose and trehalose), monosaccharide (glucose), and sugar alcohol (sorbitol) are used in the study. Small-angle neutron and X-ray scattering (SANS and SAXS) are applied to study protein-protein interaction in the freeze-dried samples.ResultsProtein interaction peak in the freeze-dried mixtures has been detected by both SANS (D₂O-based samples only) and SAXS (both D₂O- and H₂O-based). In the 1:1 mixtures, protein separation distances are similar (center-of-mass distance of approx. 31 Å) between all lyoprotectors studied. Mixtures with a higher content of the disaccharides (1:3 ratio) have a higher separation distance of approx 40 Å. The higher separation could reduce protein-protein contacts and therefore be associated with less favourable aggregation conditions. In the 1:3 mixtures with glucose and sorbitol, complex SANS and SAXS/WAXS patterns are observed. The pattern for the glucose sample indicate two populations of lysozyme molecules, while the origin of multiple SAXS peaks in the lysozyme/sorbitol 1:3 mixture is uncertain.ConclusionsProtein-protein separation distance is determined predominantly by the lyoprotector/protein weight ratio.General significanceUse of SANS and SAXS improves understanding of mechanisms of protein stabilization by sugars in freeze-dried formulations, and provide a tool to verify hypothesis on relationship between protein/protein separation and aggregation propensity in the dried state.     

Interaction of Amino Acids with Transition Metal Ions in Solution (I) Solution Structure of l-Lysine with Co(II) and Cu(II) Ions as Studied by Nuclear Magnetic Resonance Spectroscopy

Interaction of l-lysine with Co(II) and Cu(II) ions has been studied using ¹H- and ¹³C-NMR and solution absorption spectrometry. In l-lysine-Co²⁺ solution in D₂O (100: 1 in concentration), coordination interaction of the α-amino and carboxyl groups with Co²⁺ occurs from the neutral to alkaline pD region, whereas no interaction of the ?-amino group was observed throughout the whole pD region. On the other hand, in l-lysine-Cu²⁺ solution, the ?-amino group also takes part in complexation in the higher pD region (pD≧10). Structural changes in complexation of l-lysine with the divalent cations along with pD variations in aqueous solution are discussed. Dissociation constants of the three functional groups were obtained by ¹H-NMR chemical shifts; pKa₁ = 2.2, pKa₂ = 9.5 and pKa₃ = 11.2.     

Comparison of Poisson-Boltzmann and condensation model expression for the colligative properties of cylindrical polyions

Closed-form expression have been derived for the polyelectrolyte contribution to the colligative properties of solutions containing rodlike polyions in the presence of excess added salt. The derivations are based on: the conventional Poisson-Boltzmann equation for cylindrical symmetry; the thermodynamics of the cell model developed by Marcus [J. Chem. Phys. 23 , 1057–1068 (1955)]; and an equation derived from the cylindrical Poisson-Boltzmann cell model by Anderson and Record [Biophys. Chem. 11 , 353–360 (1980)]. Subject to the inherent limitations of the Poisson-Boltzmann approximation [Fixman (1979) J. Chem. Phys. 70 , 4995–5005], the resulting expressions are nevertheless applicable outside the “limit of infinite dilution.” They conform over a range of salt concentrations to the limiting laws deduced by Manning from the hypothesis of counterion condensation [J. Chem. Phys. 51 , 924–933 (1969)]. This hypothesis is found to be compatible with the Poisson-Boltzmann cell model but is not required in the derivation of the thermodynamic coefficients presented here. It is demonstrated that the magnitude of the polyion axial charge density plays a critical role in determining the low-salt limiting forms of the colligative properties obtained from the Poisson-Boltzmann equation, in close analogy with Manning's model.     

SANS studies of concentrated protein solutions. I. Bovine serum albumin

Small-angle neutron scattering (SANS) was used to examine concentrated bovine serum albumin solutions of up to 20% protein w/v. At higher protein concentrations, scattering data show distinct features that can be ascribed to strong intermolecular interactions. Differential scattering cross-sections are fitted to a theoretical model of interparticle potential consisting of a hard core plus an exponentially decaying “tail.” For moderate ionic strength (0.03M K Acetate, pH 5.9), the intermolecular interaction agrees with the double-layer repulsive part of the well-known DLVO (Derjaguin, Landau, Verwey, Overbeek) theory for interacting colloidal particles. We thus demonstrate that it is possible to determine size parameters and the surface charge of protein molecules in dense solutions. At high salt concentrations (≥0.2M NaCl) data can be fitted by the same potential model, although interpretation in terms of DLVO theory is not possible. Even in this case, however, “effective” molecular size and potential parameters can be determined.     

Effects of alcohol/water mixtures on the structure and reactivity of cytochrome c

The oxidation reaction of ferrocytochrome c (produced in situ by pulse radiolysis) by Fe(CN)^3?₆, was used to probe the effect of alcohol/water mixtures on the reactivity of the protein. Reduced cytochrome c is oxidized in a biphasic process. The relative contribution of each phase depended on: pH, alcohol concentration and temperature. pK_a values were derived from the kinetic data. These pK_a values were identical with the spectroscopic pK_a values determined under similar conditions by monitoring the 695 nm absorption band of the oxidized protein. The two phases of oxidation were therefore related to the oxidation of a relaxed and a nonrelaxed conformer of reduced cytochrome c produced in situ. A shift in the pK_a of ferricytochrome c and a retardation of the redox reactions of both the reduced and the oxidized protein were observed at low alcohol concentrations (up to 5 mol %). These low alcohol concentrations are known to affect the structure of water (Yaacobi, M. and Ben-Naim, A. (1973) J. Sol. Chem. 5, 425?443; Ben-Naim, A. (1967) J. Phys. Chem. 71, 4002?4007 and Ben-Naim, A. and Baer, S. (1964) Trans. Faraday Soc. 60, 1736?1741) but have only minor effects on the protein. Accordingly, the kinetic results are interpreted on the basis of involvement of water molecules in the reaction complex of cytochrome c with its redox substrates.     

Structure of Lennard–Jones fluid near large spherical particles: further test of the “universality” of adjustable parameter in perturbation density functional theory

Grand canonical Monte Carlo simulation is used to study the density profiles of Lennard–Jones (LJ) fluid next to a large hard sphere (mimicking a colloidal particle) of various sizes. The LJ fluid in the inhomogeneous system thus maintains equilibrium with the bulk LJ fluid. The chosen density and potential parameters for the bulk fluid correspond to the conditions situated at “dangerous” regions of the phase diagram, i.e. near the critical temperature or close to the gas–liquid coexistence curve. The aim of present extensive simulations is to provide exact data for the broad range of the bulk parameters against which the “universality” of adjustable parameter associated with a perturbation density functional approximation (DFA) can be tested. Here the term “universality” means independence of this parameter on the particular external field responsible for the generation of a non-uniform density profile of the fluid. It is shown that the “universality” of this parameter associated with a third order+second order perturbation DFA holds also in the present case of a large spherical particle as a source of external potential, similarly as established in previous studies dealing with other interaction potential and other external fields [J. Chem. Phys., 122, 064503 (2005); J. Chem. Phys., 123 124708 (2005)]. This DFA can be used as input into a recently proposed framework for the calculation of interparticle potential of mean force (PMF).     

Speciation of phytate ion in aqueous solution. Non covalent interactions with biogenic polyamines

Abstract

The noncovalent interactions of phytate (Phy^6-) with biogenic amines were studied potentiometrically in aqueous solution, at t= 25°C. Several species are formed in the different H+-Phy^6--amine (A) systems, which have the general formula A_p(Phy)H_q^(12-q)-, with p ≤ 3 and 6 ≤ q ≤ 10. The stability of these species is strictly dependent on the charges involved in the formation equilibria. For the equilibrium pH_iAⁱ⁺ + H_j(Phy)⁽¹²-^j)- = A_p(Phy)H_q(^12q)-, (q = pi + j)we found the relationship logK= aζ (ζ is the charge product of reactants), where a= 0.35(0.03, valid for all the amines; this roughly indicates an average free energy contribution per bond -ΔG⁰ = 4.0 ± 0.2 kJ mol^-1. A slightly more sophisticated equation is also proposed for predicting the stability of these species. Owing to the quite high (partially protonated) phytate charge, the stability of A_p(Phy)H_q^(12-q)- species is quite high, making phytate a strong amine sequestering agent in a wide pH range.     

Hydroxyl group as a substituent with varying electronic properties: Effect of strength of H-bonding on charge density changes in Ph–OH…F<Superscript>−</Superscript> complexes

Due to gradual and controlled changes of interatomic distances between heavy atoms in OH…F⁻ of C₆H₅OH…F⁻ systems it was possible to study the electronic structure evolution. Computation at B3LYP/6-311+G(d,p) level of theory was performed for this purpose. Changes in charges at atoms and characteristics at bond critical points (BCPs) of the H-bond region and also in distant parts of the systems were investigated by means of natural bond orbitals (NBO) and atoms in molecules (AIM) analyses. It is shown that at the border line between partially covalent and non-covalent H-bonding (Espinosa et al. in J Chem Phys 117:5529, 2002; Grabowski et al. in J Phys Chem B 110:6444, 2006) with the H…F interatomic distance ∼1.8 Ǻ the hydrogen atom has the most positive charge. In addition, the change in the atomic charge values in the interacting region affects the phenyl ring properties. The decrease of the sum of atomic charges as well as of the aromaticity was noticed when the OH….F distance is shortened.     

Thermodynamics of polyelectrolyte solutions. An empirical extension of the manning theory to finite salt concentrations

The range of application of the Manning theory of polyelectrolyte solutions (J. Chem. Phys., 51 , 924 (1969)) is extended to finite concentrations of simple electrolyte by the empirical superposition of excess free energies arising from (i) interactions between mobile ions and polyions and (ii) mutual interactions between mobile ions. A comparison of published results with the modified theory shows excellent agreement over a wide range of concentrations. Results for a polyelectrolyte of low charge density suggest that the effective inter-charge spacing may be less than that of the fully extended polyion.     

Age,growth and mortality of common two‐banded seabream,Diplodus vulgaris (Geoffroy Saint‐Hilaire, 1817), in the eastern Adriatic Sea (Croatian coast)

Age, growth and mortality were analysed for the common two‐banded seabream, Diplodus vulgaris, collected in the eastern Adriatic (Croatian coast) from commercial fishery catches by ‘tramata’ fishing (2005–2006) to obtain growth estimation. The oldest female was estimated to be age 11, the oldest male age 10 years. The von Bertalanffy growth parameters estimated by reading scales were: L_∞ = 48.60 cm (SE = 1.101), K = 0.112 (SE = 0.005) and t₀ = ?2.366 (SE = 0.060) for all specimens; L_∞ = 51.96 cm (SE = 2.153), K = 0.095 (SE = 0.007) and t₀ = ?2.837 (SE = 0.120) for females and L_∞ = 56.25 cm (SE = 2.662), K = 0.084 (SE = 0.067) and t₀ = ?2.920 (SE = 0.117) for males. The overall sex ratio was 1.22 : 1 in favour of males. Total mortality, corresponding to the slope of the descending limb of the catch curve, was Z = 0.81 per year for females and Z = 0.85 per year for males. Exploitation ratios were E = 0.68 for females and E = 0.73 for males.     

Small angle neutron scattering from lysozyme solutions in unsaturated and supersaturated states (SANS from lysozyme solutions)

Small angle neutron scattering (SANS) method was used to study lysozyme solutions, with particular interest in an understanding of the crystallization process at the initial stage. It is found that (1) in the unsaturated solution, the protein molecules aggregate with a continuous increase in size when NaCl concentration is increased, and (2) in the supersaturated solution, an irreversible change, superimposed on the former process, occurs when the supersaturation is realized. These facts indicate the usefulness of SANS in detecting changes of protein molecules in solution on the nanometer scale. The reliability of the SANS results are indicated by (1) comparing them with those of small angle X-ray scattering (SAXS), and (2) comparing the effect of D(2)O and H(2)O as solvent. Since the interparticle interaction is essential in the crystallization process and a simple Guinier plot analysis is not allowed, a more rigorous framework of analyzing data with interference function is developed, through which both average interparticle distance and particle size are estimated.     

Periosteal versus true cross‐sectional geometry: A comparison along humeral,femoral, and tibial diaphyses

Cross‐sectional geometric (CSG) properties of human long bone diaphyses are typically calculated from both periosteal and endosteal contours. Though quantification of both is desirable, periosteal contours alone have provided accurate predictions of CSG properties at the midshaft in previous studies. The relationship between CSG properties calculated from external contours and “true” (endosteal and periosteal) CSG properties, however, has yet to be examined along the whole diaphysis. Cross‐sectional computed tomography scans were taken from 21 locations along humeral, femoral, and tibial diaphyses in 20 adults from a late prehistoric central Illinois Valley cemetery. Mechanical properties calculated from images with (a) artificially filled medullary cavities (“solid”) and (b) true unaltered cross‐sections were compared at each section location using least squares regression. Results indicate that, in this sample, polar second moments of area (J), polar section moduli (Z_p), and cross‐sectional shape (I_max/I_min) calculated from periosteal contours correspond strongly with those calculated from cross‐sections that include the medullary cavity. Correlations are high throughout most of the humeral diaphysis and throughout large portions of femoral and tibial diaphyses (R² = 0.855–0.998, all P < 0.001, %SEE ≤ 8.0, %PE ≤ 5.0), the major exception being the proximal quarter of the tibial diaphysis for J and Z_p. The main source of error was identified as variation in %CA. Results reveal that CSG properties quantified from periosteal contours provide comparable results to (and are likely to detect the same differences among individuals as) true CSG properties along large portions of long bone diaphyses. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

Improving protein template recognition by using small-angle x-ray scattering profiles

Small-angle x-ray scattering (SAXS) is able to extract low-resolution protein shape information without requiring a specific crystal formation. However, it has found little use in atomic-level protein structure determination due to the uncertainty of residue-level structural assignment. We developed a new algorithm, SAXSTER, to couple the raw SAXS data with protein-fold-recognition algorithms and thus improve template-based protein-structure predictions. We designed nine different matching scoring functions of template and experimental SAXS profiles. The logarithm of the integrated correlation score showed the best template recognition ability and had the highest correlation with the true template modeling (TM)-score of the target structures. We tested the method in large-scale protein-fold-recognition experiments and achieved significant improvements in prioritizing the best template structures. When SAXSTER was applied to the proteins of asymmetric SAXS profile distributions, the average TM-score of the top-ranking templates increased by 18% after homologous templates were excluded, which corresponds to a p-value < 10⁻⁹ in Student's t-test. These data demonstrate a promising use of SAXS data to facilitate computational protein structure modeling, which is expected to work most efficiently for proteins of irregular global shape and/or multiple-domain protein complexes.     

Markov branching processes with varying growth rates

A branching processZ(t) which behaves as Markov branching processesZ ₁(t) andZ ₂(t) during the free and dead times of a counter process is considered. Expression forE[Z(t)] is given.     

CD-monitored redox titration of the Rieske Fe-S protein of Rhodobacter sphaeroides: pH dependence of the midpoint potential in isolated bc1 complex and in membranes

The redox potential of the Rieske Fe-S protein has been investigated using circular dichroism (CD)-spectroscopy. The CD features characteristic of the purified bc₁ complex and membranes of Rhodobacter sphaeroides were found in the region between 450 and 550 nm. The difference between reduced and oxidized CD-spectra shows a negative band at about 500 nm with a half of width 30 nm that corresponds to the specific dichroic absorption of the reduced Rieske protein (Fee, J.A. et al. (1984) J. Biol. Chem. 259, 124–133; Degli Esposti, M. et al. (1987) Biochem. J. 241, 285–290; Rich, P.R. and Wiggins, T.E. (1992) Biochem. Soc. Trans. 20, 241S). It was found that the redox potential at pH 7.0 for the Rieske center in the isolated bc₁ complex and in chromatophore membranes from the R-26 strain of Rb. sphaeroides is 300±5 mV. In chromatophores from the BC17C strain of Rb. sphaeroides, the E_m value measured for the Rieske iron-sulfur protein (ISP) was higher (315±5 mV), but the presence of carotenoids made measurement less accurate. The E_m varied with pH in the range above pH 7, and the pH dependence was well fit either by one pK at 7.5 in the range of titration, or by two pK values, pK₁=7.6 and pK₂=9.8. Similar titrations and pK values were found for the Rieske Fe-S protein in the isolated bc₁ complex and membranes from the R-26 strain of Rb. sphaeroides. The results are discussed in the context of the mechanism of quinol oxidation by the bc₁ complex, and the role of the iron sulfur protein in formation of a reaction complex at the Q_o-site.     

Transgene-coded chimeric proteins as reporters of intracellular proteolysis: Starvation-induced catabolism of a lacZ fusion protein in muscle cells of Caenorhabditis elegans

The product of an integrated transgene provides a convenient and cell-specific reporter of intracellular protein catabolism in 103 muscle cells of the nematode Caenorhabditis elegans. The transgene is an in-frame fusion of a 5′-region of the C. elegans unc-54 (muscle myosin heavy-chain) gene to the lacZ gene of Escherichia coli [Fire and Waterston (1989): EMBO J 8:3419–3428], encoding a 146-kDa fusion polypeptide that forms active β-galactosidase tetramers. The protein is stable in vivo in well-fed animals, but upon removal of the food source it is inactivated exponentially (t_1/2 = 17 h) following an initial lag of 8 h. The same rate constant (but no lag) is observed in animals starved in the presence of cycloheximide, implying that inactivation is catalyzed by pre-existing proteases. Both the 146-kDa fusion polypeptide (t_1/2 = 13 h) and a major 116-kDa intermediate (t_1/2 = 7 h) undergo exponential physical degradation after a lag of 8 h. Degradation is thus paradoxically faster than inactivation, and a number of characteristic immunoreactive degradation intermediates, some less than one-third the size of the parent polypeptide, are found in affinity-purified (active) protein. Some of these intermediates are conjugated to ubiquitin. We infer that the initial proteolytic cleavages occur in the cytosol, possibly by a ubiquitin-mediated proteolytic pathway and do not necessarily inactivate the fusion protein tetramer. J. Cell. Biochem. 67:143–153, 1997. © 1997 Wiley-Liss, Inc.     

Effect of a molecular dipole on the ionic strength dependence of a biomolecular rate constant. Identification of the site of reaction.

A theory is proposed for determining the location of a reaction site on a protein of known tertiary structure with an asymmetric charge distribution by an analysis of the effect of ionic strength on the rate of reaction of the protein with a small ion, using equations of Brønsted (J. N. Brønsted, 1922, Z. Phys, Chem. 102:169-207), Debye and Hückel (P. Debye and E. Hückel, 1923, Phys. Z. 24:185-206), and Kirkwood (J. G. Kirkwood, 1934, J. Chem. Phys. 2:351-361). The theory is based on the fact that the dipole moment of the transition complex differs from that of the protein, which will be reflected in the ionic strength dependence of the reaction. The location of the small ion with respect to the dipole axis of the protein can be calculated from this difference. For protein-protein reactions, an a priori assumption has to be made about the orientation of one of the reaction partners, since many different orientations of the reactants with respect to each other result in dipole moments of the same magnitude.