DNA,oligosaccharides, and mononucleotides stimulate oligomerization of human lactoferrin

Using small‐angle X‐ray scattering (SAXS), light scattering (LS), and soft laser ablation we have shown that lactoferrin (LF) in solution at neutral pH is oligomerized in the absence of salt or at physiological salt concentrations. The level of oligomerization depends on the concentration of LF, KCl or NaCl, and on the duration of the protein storage in solution. At the concentrations comparable with those in human milk (1 ÷ 6 mg/ml), the average radius of gyration (R_g) values of LF can attain 400 ÷ 480 Å´, while fresh solution of previously lyophylized LF demonstrate a lower average R_g (50 ÷ 100 Å´), and R_g value characterizing the LF monomer formed at 1 M NaCl is 26.7 Å´. The addition of oligonucleotides, oligosaccharides, or mononucleotides to LF in the presence or in the absence of KCl with different level of initial oligomerization accelerates the oligomerization rate and increases the R_g values up to ～600 ÷ 700 Å´, which correspond to associates containing ten or more protein molecules. During gel filtration on Sepharose 4B, high‐degree LF oligomers dissociate nearly completely forming different degraded complexes, but in some cases it is possible to reveal small amount of a decamer. A possible role for oligomerization of LF, a highly polyfunctional protein, for its different biological activities is discussed. Copyright © 2009 John Wiley & Sons, Ltd.     

DNA and oligosaccharides stimulate oligomerization of human milk lactoferrin

Lactoferrin (LF) is a Fe³⁺-transferring glycoprotein and is contained in human barrier fluids, blood, and milk. LF is an acute phase protein, is involved in nonspecific defense, and displays a unique set of biological functions. Small-angle X-ray scattering and light scattering experiments demonstrated that DNA and oligosaccharides added to LF with various levels of initial oligomerization increased the oligomerization rate. Almost complete dissociation into monomers was observed when 1 M NaCl was added to LF oligomers obtained in the presence of DNA, oligosaccharides, and nucleotides, previously identified as oligomerization effectors. LF complexes obtained with different oligomerization effectors differed in stability. Incubation with 50 mM MgCl₂ completely destructed LF complexes formed in the presence of ATP and oligosaccharides but only partly destructed AMP- and d(pT)₁₀-dependent complexes, which was followed by the formation of new complexes with a higher salt stability. A possible role of oligomerization in various LF functions is discussed.     

The effect of nucleotides on oligomeric state of human lactoferrin

A polyfunctional protein lactoferrin (LF) which is present in human barrier fluids, blood and milk and this protein of acute phase is responsible for nonspecific cells defense against microbial and viral infection and cancer diseases. Using the methods of small-angle X-ray scattering and light-scattering it was shown that LF in solution exists in oligomeric state. The level of LF oligomerization depends upon its concentration and time of keeping of no frozen neutral protein solutions. At the concentrations comparable with those in human milk (1-6 mg/ml) the average inertial radius values (Rg) of LF can reach 100-450 angstroms, while Rg for monomer LF form is 26.7 angstroms. LF was shown to complex with different nucleotides and hydrolyze them. The addition of ATP and AMP to LF demonstrating any level of oligomerization leads to increase of oligomerization processes and enhancement of the Rg values up to 600-700 angstroms According to different models of LF monomer association to its oligomeric forms (sphere, plate, cylinder) the oligomeric complexes demonstrate high Rg values which can contain from several tens up to several thousands of LF monomers. A possible role of LF oligomerization for different biological functions of the protein is discussed.     

On the subunit structure of crotoxin: hydrodynamic and shape properties of crotoxin, phospholipase A and crotapotin.

This paper reports physical-chemical properties of the subunit structure of crotoxin, phospholipase A and crotapotin. The native crotoxin has a sedimentation coefficient of 3S and a radius of gyration of R_g = 16.5 Å and a molecular weight of 30,900. Dissociation of the 3S particle results in two proteins of unequal size with sedimentation coefficients of 1.5 S (crotapotin) and 1S (phospholipase A). These dissociated species and the reconstituted complex were investigated by means of hydrodynamic methods including small angle X-ray scattering. The actual frictional ratios were obtained indicating that crotoxin is a sphere with a Stokes' radius of R_o = 22.5 Å and an axial ratio of 1:3, whereas phospholipase A, depending on the degree of association, has a radius of gyration of R_g = 32.4 Å and a high axial ratio of 1:14 for the monomer. Crotapotin has a radius of gyration of R_g = 12.4 Å, indicating an oblate ellipsoid of revolution of an axial ratio of 1:4. Evidently, the crotoxin complex consists of one highly asymmetric molecule (phospholipase A) and an oblate ellipsoid (crotapotin), which reconstitutes to a spherical 3S-particle (crotoxin).     

Small-angle neutron scattering study of bovine casein micelles and sub-micelles

Whole micelles and sub-micelles of cows' milk casein have been studied in solution by small-angle neutron scattering. Sub-micelles were found to have a mean molecular weight of approximately 3.0 × 10⁵ and a radius of gyration (R_g) in ²H₂O of 65 Å. R_g² appeared to decrease slightly with increasing reciprocal contrast (1/-?) whereas most globular proteins show the opposite behaviour. Estimated voluminosity (hydrated specific volume) of sub-micelles was 4.0 to 5.5 ml/g, which is much higher than values from electron microscopic measurements on whole micelles.Scattering from whole micelles showed an inflection at $\text{Q((}\text{4π sin θ)}\text{λ}\text{) = 0.035}\text{A}\text{?}{}^{\mathrm{?1}}$), which was attributed to inter-sub-micelle interference within the whole micelle.     

Small-angle X-ray characterization of the nucleoprotein complexes resulting from DNA-induced oligomerization of HIV-1 integrase

HIV-1 integrase (IN) catalyses integration of a DNA copy of the viral genome into the host genome. Specific interactions between retroviral IN and long terminal repeats (LTR) are required for this insertion. To characterize quantitatively the influence of the determinants of DNA substrate specificity on the oligomerization status of IN, we used the small-angle X-ray scattering (SAXS) technique. Under certain conditions in the absence of ODNs IN existed only as monomers. IN preincubation with specific ODNs led mainly to formation of dimers, the relative amount of which correlated well with the increase in the enzyme activity in the 3′-processing reaction. Under these conditions, tetramers were scarce. Non-specific ODNs stimulated formation of catalytically inactive dimers and tetramers. Complexes of monomeric, dimeric and tetrameric forms of IN with specific and non-specific ODNs had varying radii of gyration (R_g), suggesting that the specific sequence-dependent formation of IN tetramers can probably occur by dimerization of two dimers of different structure. From our data we can conclude that the DNA-induced oligomerization of HIV-1 IN is probably of importance to provide substrate specificity and to increase the enzyme activity.     

Crystal structure of zinc citrate

The crystal structure of zinc citrate [Zn(II) (C₆H₅O₇)₂·4NH₄⁺] shows isolated zinc ions octahedrally coordinated to two equivalent citrates via a central hydroxyl, central carboxyl, and one terminal carboxyl from each citrate. The clusters are linked through hydrogen bonds to ammonium ions in the lattice. The structure is distinctly different from that of other divalent cation triply ionized citrate complexes, which are polymeric. Crystal data : space group P2₁/C, a = 8.784(3) Å, b = 13.499(4) Å, c = 9.083(3) Å, β = 113.4°(1), V = 988(1) ų. Citrate has been identified as the low molecular weight ligand that complexes zinc in human milk; this may be of interest in relation to intestinal zinc absorption.     

New preparations and molecular structures of cis-MCl2(Ph2PCH2PPh2)2, M = Ru,Os and trans-RuCl2(Ph2PCH2PPh2)2

The title compounds were made by reacting bis(diphenylphosphino)methane (dppm) with reduced solutions of OsCl₆^4? and Ru₂OCl₁₀^4?. The crystal and molecular structures of these compounds have been determined form three-dimensional X-ray study. The cis-isomers crystallize with one CHCl₃ per molecule of the complex. All three compounds crystallize in the monoclinic space group P2₁/n with unit cell dimensions as follows: Cis-OsCl₂(dppm)₂·CHCl₃: a = 13.415(4) Å, b = 22.859(4) Å, c = 16.693(3) Å, β = 105.77(3)°, V = 4926(3) ų, Z = 4. cis-RuCl₂(dppm)₂·CHCl₃: a = 13.442(3) Å, b = 22.833(7) Å, c = 16.750(4) Å, β = 105.53(2)°, V = 4953(3) ų, Z = 4. trans-RuCl₂(dppm)₂: a = 11.368(7) Å, b = 10.656(6) Å, c = 18.832(12) Å; β = 103.90(6)°, V = 2213(7) ų; Z = 2. The structures were refined to R = 0.044 (R_w = 0.055) for cis-OsCl₂(dppm)₂·CHCl₃; R = 0.065 (R_w = 0.079) for cis-RuCl₂(dppm)₂·CHCl₃ and R = 0.028 (R_w = 0.038) for trans-RuCl₂(dppm)₂. The complexes are six coordinate with stable four-membered chelate rings. The PMP angle in the chelate rings is ca. 71° in each case.     

Small-angle X-ray scattering of D-Ribulose-1,5-diphosphate carboxylase from Dasycladus clavaeformis roth (Ag.) in solution

D-Ribulose-1,5-diphosphate carboxylase from $\text{Dasycladus}$ was purified, and the gross dimensions were obtained by means of small-angle X-ray scattering measurements in solution. Dissolved single crystals of this enzyme (called “fraction I protein”) gave the same hydrodynamic parameters as the purified form. The molecular weight was found to be 535,000, and a radius of gyration of R_g = 45.5 Å was determined. The experimental scattering curves revealed a geometrical particle of D-Ribulose-1,5-diphosphate carboxylase with gross dimensions of that of a hollow sphere with outer radius of 56 Å and inner radius of 12 Å. Determinations of the diffusion coefficients lead to the conclusion that the enzyme has a spherical shape of almost uniform density.     

An Extended Guinier Analysis for Intrinsically Disordered Proteins

Guinier analysis allows model-free determination of the radius of gyration (R_g) of a biomolecule from X-ray or neutron scattering data, in the limit of very small scattering angles. Its range of validity is well understood for globular proteins, but is known to be more restricted for unfolded or intrinsically disordered proteins (IDPs). We have used ensembles of disordered structures from molecular dynamics simulations to investigate which structural properties cause deviations from the Guinier approximation at small scattering angles. We find that the deviation from the Guinier approximation is correlated with the polymer scaling exponent ν describing the unfolded ensemble. We therefore introduce an empirical, ν-dependent, higher-order correction term, to augment the standard Guinier analysis. We test the new fitting scheme using all-atom simulation data for several IDPs and experimental data for both an IDP and a destabilized mutant of a folded protein. In all cases tested, we achieve an accuracy of the inferred R_g within ～ 3% of the true R_g. The method is straightforward to implement and extends the range of validity to a maximum qR_g of ～ 2 versus ～ 1.1 for Guinier analysis. Compared with the Guinier or Debye approaches, our method allows data from wider angles with lower noise to be used to analyze scattering data accurately. In addition to R_g, our fitting scheme also yields estimates of the scaling exponent ν in excellent agreement with the reference ν determined from the underlying molecular ensemble.     

Vancomycin forms ligand-mediated supramolecular complexes

The emergence of resistance to vancomycin and related glycopeptide antibiotics is spurring efforts to develop new antimicrobial therapeutics. High-resolution structural information about antibiotic-ligand recognition should prove valuable in the rational design of improved drugs. We have determined the X-ray crystal structure of the complex of vancomycin with N-acetyl-d-Ala-d-Ala, a mimic of the natural muramyl peptide target, and refined this structure at a resolution of 1.3 Å to R and R_free values of 0.172 and 0.195, respectively. The crystal asymmetric unit contains three back-back vancomycin dimers; two of these dimers participate in ligand-mediated face-face interactions that produce an infinite chain of molecules running throughout the crystal. The third dimer packs against the side of a face-face interface in a tight “side-side” interaction that involves both polar contacts and burial of hydrophobic surface. The trimer of dimers found in the asymmetric unit is essentially identical to complexes seen in three other crystal structures of glycopeptide antibiotics complexed with peptide ligands. These four structures are derived from crystals belonging to different space groups, suggesting that the trimer of dimers may not be simply a crystal packing artifact and prompting us to ask if ligand-mediated oligomerization could be observed in solution. Using size-exclusion chromatography, dynamic light scattering, and small-angle X-ray scattering, we demonstrate that vancomycin forms discrete supramolecular complexes in the presence of tripeptide ligands. Size estimates for these complexes are consistent with assemblies containing four to six vancomycin monomers.     

Light scattering and viscosity study of heat aggregation of insulin

Aggregation behavior and hydrodynamic parameters of insulin have been determined from static and dynamic light scattering experiments and intrinsic viscosity measurements carried out at pH 4.0, 7.5, and 9.0 in the temperature range 20–40°C in aqueous solutions. The protein aggregated extensively at elevated temperatures in the acidic solutions. Intermolecular interactions were found to be attractive and to increase with temperature. The measured intrinsic viscosity [η], diffusion coefficient D₀, molecular weight M, and radius of gyration R_g exhibited the universal behavior: M[η] = (2.4 ± 02) × 10⁻²⁷ (R_e,η/R_e,D)³(D_0η/T)⁻³ and (D₀√n)₋₁ ≃ (√6 πη₀ζβ/k_BT) [1 + 0.201)(v/β³)√n], where n is the number of segments in the polypeptide. The effective hydrodynamic radii deduced from [η], (R_e, η) and the same deduced from D₀, (R_e,D) showed a constant ratio, (R_e,η/R_e,D = 1.1 ± 0.1). R_e,D/R_g = ξ was found to be (0.76 ± 0.07). From the known solvent viscosity η₀, the segment length β was deduced to be (10 ± 1) Å. The excluded volume was deduced to be (5 Å)³ regardless of pH. The Flory-Huggins interaction parameter was found to be χ = 0.45 ± 0.04, independent of pH and temperature. © 1998 John Wiley & Sons, Inc. Biopoly 45: 1–8, 1998     

Small-angle x-ray scattering study of lysine transfer RNA ligase from yeast

The scattered X-ray intensities from dilute solutions of lysine transfer RNA ligase, in 0.1 m-phosphate buffer at pH 7.0, have been measured at 21 °. The radius of gyration R (37.5 Å), the molecular weight M (114,000), and the volume V (295,000 ų) were determined.A comparison between the scattering curves obtained from the enzyme and the theoretical scattering curves of different triaxial bodies shows that the shape of the molecule can be represented by an oblate ellipsoid with the semiaxes A = 62.7, B = 50.1 and $\text{C = 23.5}\text{A}\text{?}$.     

Neutron scattering studies of escherichia coli tyrosyl-trna synthetase and of its interaction with trna tyr

Small-angle neutron scattering studies of Escherichia coli tyrosyl-tRNA synthetase indicate that in solution this enzyme is a dimer of M_r, 91 (±6) × 10³ with a radius of gyration R_G of 37.8 ± 1.1 Å.The increase in the scattering mass of the enzyme upon binding tRNA^Tyr has been followed in 20 mm-imidazole · HCl (pH 7.6), 10 mm-MgCl₂, 0.1 mm-EDTA, 10 mm-2-mercaptoethanol, 150 mm-KCl. A stoichiometry of one bound tRNA per dimeric enzyme molecule was found. The R_G of the complex is equal to 41 ± 1 Å. Titration experiments in 74% ²H₂O, close to the matching point of tRNA, show an R_G of 38.5 ± 1 Å for the enzyme moiety in the complex. From these values, a minimum distance of 49 Å between the centre of mass of the bound tRNA and that of the enzyme was calculated.In low ionic strength conditions (20 mm-imidazole-HCl (pH 7.6), 10 mm-MgCl₂, 0.1 mm-EDTA, 10 mm-2-mercaptoethanol) and at limiting tRNA concentrations with respect to the enzyme, titrations of the enzyme by tRNA^Tyr are characterized by the appearance of aggregates, with a maximum scattered intensity at a stoichiometry of one tRNA per two enzyme molecules. At this point, the measured M_r and R_G values are compatible with a compact 1:2, tRNA: enzyme complex. This complex forms with a remarkably high stability constant: (enzyme:tRNA:enzyme)/(enzyme:tRNA)(enzyme) of 0.1 to 0.3(× 10⁶) m^?1 (at 20 °C). Upon addition of more tRNA, the complex dissociates in favour of the 1:1, enzyme:tRNA complex, which has a higher stability constant (1 to 3 (× 10⁶) m^?1).     

Preparation,crystal and molecular structure of aquadichlorobis(ethylpyridine)-oxovanadium

The compound VOCl₂·2(3-Etpy)·H₂O (Etpy = ethylpyridine) was prepared by slow hydrolysis of the toluene suspension obtained from the reaction of VCl₄ with 3-ethylpyridine The crystal was found to be monoclinic C2/c, Z = 4, ϱ(calc.) = 1.426 × 10³ kg m⁻³, a = 13.281(5), b = 13.989(7), c = 9.277(8) Å, V = 1723(2) ų β = 90.53(5)°.Final full matrix least-square refinement with anisotropic thermal parameters for all non-hydrogen atoms gave R = 0.039, R_w = 0.042, R_g = 0.053. The vanadium atom is hexacoordinate with the pyridine ligands in mutually trans positions in the plane containing the Cl atoms. The O vanadyl atom is in an axial position trans to the coordinated H₂O molecule, and the OVO line is a binary axis for the molecule.     

Very stable high molecular mass multiprotein complex with DNase and amylase activities in human milk

For breastfed infants, human milk is more than a source of nutrients; it furnishes a wide array of proteins, peptides, antibodies, and other components promoting neonatal growth and protecting infants from viral and bacterial infection. It has been proposed that most biological processes are performed by protein complexes. Therefore, identification and characterization of human milk components including protein complexes is important for understanding the function of milk. Using gel filtration, we have purified a stable high molecular mass (~1000 kDa) multiprotein complex (SPC) from 15 preparations of human milk. Light scattering and gel filtration showed that the SPC was stable in the presence of high concentrations of NaCl and MgCl₂ but dissociated efficiently under the conditions that destroy immunocomplexes (2 M MgCl₂, 0.5 M NaCl, and 10 mM DTT). Such a stable complex is unlikely to be a casual associate of different proteins. The relative content of the individual SPCs varied from 6% to 25% of the total milk protein. According to electrophoretic and mass spectrometry analysis, all 15 SPCs contained lactoferrin (LF) and α‐lactalbumin as major proteins, whereas human milk albumin and β‐casein were present in moderate or minor amounts; a different content of IgGs and sIgAs was observed. All SPCs efficiently hydrolyzed Plasmid supercoiled DNA and maltoheptaose. Some freshly prepared SPC preparations contained not only intact LF but also small amounts of its fragments, which appeared in all SPCs during their prolonged storage; the fragments, similar to intact LF, possessed DNase and amylase activities. LF is found in human epithelial secretions, barrier body fluids, and in the secondary granules of leukocytes. LF is a protein of the acute phase response and nonspecific defense against different types of microbial and viral infections. Therefore, LF complexes with other proteins may be important for its functions not only in human milk. Copyright © 2014 John Wiley & Sons, Ltd.     

Formation and characterisitcs of hepatic dexamethasone-receptor complexes of different molecular weight

The dexamethasone-binding receptor protein in rat liver cytosol has a Stokes radius of 61 Å and a sedimentation coefficient of 4.0 S. In contrast, cell nuclei labelled with [³H]dexamethasone in vivo or in vitro (reconstitution experiments with [³H]dexamethasone-labelled cytosol and isolated unlabelled nuclei) contain a high-salt-extractable dexamethasone-receptor complex with a Stokes radius of 30–36 Å and a sedimentation coefficient of 3.2 S. Exposure of liver homogenate or 1000 × g homogenate supernatant to low ionic strenght during preparation of cytosol resulted in conversion of the 61 Å to a 36 Å complex very similar to the intranuclear form of dexamethasone receptor. 61 → 36 Å complex-verting activity was present in both the 100 × g ?10 000 × g sediment of liver homogenate, from which it could be extracted by hypotonic media, and in the liver cell nuclei, from which it could be extracted by hypertonic media. Mild digestion of the 61 Å dexamethasone-receptor complex with trypsin also gave rise to a complex with a Stokes radius of 36 Å. Reconstitution experiments with isolated liver cell nuclei indicated that both the 61 Å and 36 Å dexamethasone-receptor complexes were taken up by the nuclei; reextraction of the nuclei incubated with the 61 Å complex revealed that this form had been converted to the 30–36 Å complex.Further digestion of teh 61 and 36 Å [³H]dexamethasone-receptor complexes with hypotonic extract of the 1000 × g ?10 000 × g sediment of liver homogenate or with trypsin resulted in formation of a third complex with a Stokes radius of 19 Å and a sedimentation coefficient of 2.5 S. The approximate molecular weights of the 61, 36 and 19 Å dexamethasone-receptor complexes were calculated as 102 000, 46 00 and 19 000, respectively, and the frictional ratios of the molecules as 1. 84, 1. 38 amd 1.00, respectively.It is concluded that the nuclear 30–36 Å dexamethasone-receptor complex is formed from the cytosol 61 Å complex by proteolytic digestion and that this latter protein contains at least two sites with a relatively high sensitivity to protelytic cleavage.     

Monomeric molybdenum(V) complexes. 4. The structure of tetraphenylarsonium oxodichloro(N-2-oxophenylsalicylideniminato)molybdate(V), [Ph4As] [MoOCl2(SalphO)]

The structure of [Ph₄As] [MoOCl₂(SalphO)], where SalphO is N-2-oxophenylsalicylideniminate dianion, has been determined by X-ray crystallography. The complex crystallizes in the monoclinic space group P2₁/n with a = 11.829(2), b = 16.149(3), c = 17.410(3) Å, β = 97.485(15)° and Z = 4. The calculated and observed densities and 1.566 and 1.573(10) g cm^?3, respectively. Block-diagonal least-squares refinement of the structure using 4722 independent reflections with I ? 3σ(I) converged at R = 0.0345 and R_w = 0.0484. The crystal contains [Ph₄As]⁺ cations and [MoOCl₂(SalphO)]^? anions. The Mo atom in the anion is in a distorted octahedral coordination environment. A planar terdentate Schiff base ligand occupies meridional positions with the N atom trans to the terminal oxo group (O_t). Two Cl atoms are cis to the O_t atom. The Mo atom is displaced by 0.33 Å from the equatorial plane toward the O_t atom. The MoO_t distance is 1.673(3) Å. The MoN bond trans to the O_t atom is 2.298(4) Å. The two MoCl bond lengths are 2.371(1) and 2.408(1) Å. The difference of 0.037 Å is significant (30 σ). Preparations of the title complex and the related complexes are also described.     

Structural,infrared and Mössbauer studies of octahedral cis-dichlorobis(diketonate)tin(IV) complexes having anti-tumour activity

Two complexes, SnCl₂(bzac)₂ [Hbzac = benzoylacetone] and SnCl₂(bzbz)₂ [Hbzbz = dibenzoylmethane], have been prepared and characterised by analytical, infrared and Mössbauer studies. In addition, the X-ray crystal structure of SnCl₂(bzbz)₂ has been determined. The crystals are orthorhombic, space group Pbca with cell parameters a=18.767(9), b=17.611(8), c=16.563(8) Å. A total of 2116 reflections with I/σ(I)⩾3 gave R=3.0%. The tin is coordinated to two cis-chlorine and four oxygen atoms from the dibenzoylmethanato ligands in an approximately octahedral arrangement. The bond distances in the tin coordination sphere are SnCl 2.335(2) and 2.344(2) Å and SnO 2.062(4), 2.074(4), 2.063(4) and 2.063(4) Å and the ClSnCl angle is 95.1(1)°. The results of anti-tumour tests on these complexes are given and attempts are made to correlate the anti-tumour activity of SnCl₂(bzbz)₂ with its structure.