Neutron scattering studies of chromatosomes

Neutron scattering data establish that the radius of gyration of the DNA in chicken erythrocyte chromatosome particles is significantly higher, by about 0.3 nm, than the radius of gyration of the DNA in the core particle. Corresponding information of the radius of gyration of the protein component in the chromatosomes (3.75 nm) indicated an enlargement, compared to the radius of gyration of the octamer of histone proteins both in core particles and in the histone octamer stabilised in 2 M NaCl (3.25 nm). From the latter data, we could calculate the distance in the chromatosome between the centre of mass of the linker histone and the histone octamer as 5.5 nm. These results impose severe limitations for the organisation of the 22 bp extra DNA and the possible location of H1/H5 in the chromatosome, implying that the H1/H5 is close to the centre turn of the core particle DNA.     

A Neutron Scattering Study of the Ternary Complex EF-Tu•GTP-valy1-tRNAVal 1A

Abstract

The complex formation between elongation factor Tu (EF-Tu), GTP, and valyl-tRNA^Val _1A has been investigated in a hepes buffer of “pH” 7.4 and 0.2 M ionic strength using the small-angle neutron scattering method at concentrations of D₂O where EF-Tu (42% D₂O) and tRNA (71% D₂O) are successively matched by the solvents. The results indicate that EF-Tu undergoes a conformational change and contracts as a result of the complex formation, since the radius of gyration decreases by 15% from 2.82 to 2.39 nm. tRNA^Val _1A, on the other hand, seems to mainly retain its conformation within the complex, since the radii of gyration for the free (after correction for interparticular scattering) and complexed form are essentially the same. 2.38 and 2.47 nm, respectively.     

Neutron scattering studies of subcomponent C1q of first component C1 of human complement and its association with subunit C1r2C1s2 within C1

Neutron scattering studies are reported on subcomponent C1q of component C1 of human complement, and on C1, the complex of C1q with subunit C1r₂C1s₂. For C1q, the molecular weight was determined as 460,000. The radius of gyration at infinite contrast R_c is 12.8 nm. The R_c values for the proteolytically cleaved forms of C1q, namely the heads and the stalks, are 1.5 to 2 nm and 11 nm, respectively, and thus the axis-to-arm angle of C1q is estimated at 45 °. Neutron data for subunit C1r₂C1s₂ are published elsewhere. The neutron data on C1 lead to an R_c value of 12.6 nm for proenzymic C1 and a molecular weight of 820,000. The wideangle scattering curve of C1q exhibits a minimum at Q = 0.28 nm^?1 and a maximum at 0.39 nm^?1; on the addition of C1r₂C1s₂, this minimum disappears. The neutron data on C1 indicate that C1q and C1r₂C1s₂ have complexed with a large conformational change in one or both parts. No conformational changes can be detected on the activation of C1 by this method.     

Chromatin fiber dimensions and nucleosome orientation: a neutron scattering investigation.

Chromatin fibers were studied in solutions of mM monovalent salt by small angle neutron scattering. The variation of the cross section radius of gyration with H2O/D2O contrast shows that DNA is at much larger average radial distances from the fiber axis than histone. Consequently, the coils of DNA in a core particle must be approximately parallel to the fiber direction. The radii of gyration suggest that the maximum diameter of chromatin and nucleosomes is approximately 14 nm and that the DNA id distributed in two radial layers. The concentration dependence of the scattering maxima near 14 nm spacings furnishes independent support for a 14 nm external diameter and can be interpreted by a double DNA layer configuration.     

Syntheses, structures, and photoluminescent properties of four d metal-quinolinato coordination polymers with similar rod-like SBUs

Four M^II quinolinato complexes, [Zn₂(quin)₂(H₂O)₃]_n (1), [Zn(quin)(H₂O)₂]_n (2), [Zn(quin)(H₂O)]_n (3) and [Cd(quin)]_n (4) (H₂quin = 2,3-pyridinedicarboxylic acid or quinolinic acid), have been hydrothermally synthesized and structurally characterized. X-ray diffraction analyses reveal that all of these four complexes are constructed from similar rod-like SBUs, [M(quin)]_n (M = Zn or Cd). Complexes 1 and 2 have similar 1-D box-like chains but different packing structures; complex 3 has a 2-D grid-like network and complex 4 has an unusual 2-D bilayer structure. Due to the different structural features, these complexes exhibit different photoluminescent emissions: complex 1 at 439 nm (λ_ex = 345 nm), complex 2 at 428 nm (λ_ex = 360 nm), complex 3 at 508 nm (λ_ex = 304 nm) and complex 4 at 500 nm (λ_ex = 324 nm).     

Hyperacetylation of core histones does not cause unfolding of nucleosomes. Neutron scatter data accords with disc shape of the nucleosome

Recent studies report that the frictional resistance of partially acetylated core particles increases when the number of acetyl groups/particle exceeds 10 (Bode, J., Gomez-Lira, M. M. & Schr?ter, H. (1983) Eur. J. Biochem. 130, 437-445). This was attributed to an opening of the core particle though other explanations, e.g. unwinding of the DNA ends were also suggested. Another possible explanation is that release of the core histone N-terminal domains by acetylation increased the frictional resistance of the particle. Neutron scatter studies have been performed on core particles acetylated to different levels up to 2.4 acetates/H4 molecule. Up to this level of acetylation the neutron scatter data show no evidence for unfolding of the core particle. The fundamental scatter functions for the envelope shape and internal structure are identical to those obtained previously for bulk core particles. The structure that gave the best fit to these fundamental scatter functions was a flat disc of diameter 11-11.5 nm and of thickness 5.5-6 nm with 1.7 +/- 0.2 turns of DNA coiled with a pitch of 3.0 nm around a core of the histone octamer. The data analysis emphasizes the changes in pair distance distribution functions at relatively low contrasts, particularly when the protein is contrast matched and DNA dominates the scatter. Under these conditions there is no evidence for the unwinding of long DNA ends in the hyperacetylated core particles. The distance distribution functions go to zero between 11.5 and 12 nm which gives the maximum chord length in a particle of dimension, 11 nm X 5.5 nm. The distance distribution function for the histone octamer contains 85% of the vectors within the 7.0-nm diameter of the histone core. 15% of the histone vectors lie between 7.0 and 12.0 nm, and these are attributed to the N-terminal domains of the core histones which extend out from the central histone core. Histone vectors extending beyond 7.0 nm are necessary to account for the measured radius of gyration of the histone core of 3.3 nm. A similar value of 3.2 nm is calculated for the recent ellipsoidal shape of 11.0 X 6.5 X 6.5 nm from the crystal structure of the octamer. However, the nucleosome model based on this structure is globular, roughly 11 nm in diameter, which does not accord with the flat disc shape core particle obtained from detailed neutron scatter data nor with the cross-section radii of gyration of the histone and DNA found previously for extended chromatin in solution.     

Interactions of yeast valyl-tRNA synthetase with RNAs and conformational changes of the enzyme.

Different conformations have been identified for the enzyme valyl-tRNA synthetase from yeast inside its complex with one tRNA molecule by neutron scattering. One form is identical to that of the free enzyme in solution; the other form is more contracted, having a radius of gyration which is smaller by 10% and a specific volume which is smaller by 1%. The contracted conformation has been found for the complexes with tRNA^Val and tRNA^Asp in phosphate buffer (pH 6.3) provided the ionic strength is lower than about 150 mm. In higher ionic strength (up to about 500 mm) the enzyme still forms a complex with tRNA^Val but its conformation remains that of the free protein in solution. In the complex with tRNA₃^Leu, the enzyme conformation is that of the free state even at the lowest ionic strength examined (that of the phosphate buffer, 60 mm). The free enzyme is an elongated molecule of radius of gyration 40 Å (a compact protein of the same molecular weight would have a radius of gyration of 30 Å).The positioning within the complex of tRNA^Val, on the one hand, and tRNA₃^Leu, on the other, is very different. The first tRNA is intimately associated with the enzyme, lying predominantly closer to the centre of mass of the complex than the protein. In the complex with tRNA₃^Leu, the tRNA lies further away from the centre of mass of the complex than the protein.Small concentrations of tRNA^Val, tRNA^Asp, tRNA₃^Leu or Escherichia coli 5 S ribosomal RNA cause the enzyme to aggregate into dimers, trimers and higher aggregates provided the ionic strength of the buffer is below 150 mm. In higher ionic strength or for [RNA]: [enzyme] > 1 the aggregates are dissociated to yield the one-to-one RNA-enzyme complex.     

Antico-operative binding of initiator transfer RNAMet to methionyl-transfer RNA synthetase from Escherichia coli: neutron scattering studies.

The interaction of methionyl-tRNA synthetase with initiator tRNA^Met has been investigated by neutron scattering. On the basis of parallel fluorescence measurements, two types of titrations have been performed. (1) In the presence of 10 mm-MgCl₂, a condition which insures antico-operative binding of two tRNA molecules to the enzyme dimer. (2) With saturating amounts of 5′-AMP and l-methioninol, in the presence of 50 mm-MgCl₂, conditions which allow two transfer RNA molecules to bind the dimer with very similar affinities.Varying the solvent density (²H₂O fraction) in the samples has allowed the identification by neutron scattering of changes in the radius of gyration and in the degree of dissociation of the enzyme dimer upon tRNA binding. In buffer containing 10 mm-MgCl₂, at each contrast studied, the binding process involves two steps. Firstly, one tRNA^met_f molecule binds easily to one dimeric enzyme molecule with an associated decrease of the radius of gyration of the enzyme moiety. The centre of mass of this tRNA lies very close to the centre of mass of the protomer with which it associates. Then, at higher tRNA concentration, a second tRNA molecule binds to the enzyme. However, the affinity of this second site is very much weaker. With the binding of the second tRNA, the radius of gyration of the enzyme moiety increases markedly. Concomitant limited dissociation of the dimer is suggested by the experimental data. These observations combined with the fact that, in 50 mm-MgCl₂ both the increased radius of gyration and the partial dissociation of the enzyme are accomplished in the absence of tRNA and remain unaffected upon binding one or two tRNA, confirm that the hindrance to binding a second tRNA in 10 mm-MgCl₂ arises from the constrained conformation of the one tRNA-enzyme complex.     

Solution structure of deglycosylated human IgG1 shows the role of CH2 glycans in its conformation

The human immunoglobulin G (IgG) class is the most prevalent antibody in serum, with the IgG1 subclass being the most abundant. IgG1 is composed of two Fab regions connected to a Fc region through a 15-residue hinge peptide. Two glycan chains are conserved in the Fc region in IgG; however, their importance for the structure of intact IgG1 has remained unclear. Here, we subjected glycosylated and deglycosylated monoclonal human IgG1 (designated as A33) to a comparative multidisciplinary structural study of both forms. After deglycosylation using peptide:N-glycosidase F, analytical ultracentrifugation showed that IgG1 remained monomeric and the sedimentation coefficients s⁰_20,w of IgG1 decreased from 6.45 S by 0.16–0.27 S. This change was attributed to the reduction in mass after glycan removal. X-ray and neutron scattering revealed changes in the Guinier structural parameters after deglycosylation. Although the radius of gyration (R_G) was unchanged, the cross-sectional radius of gyration (R_XS-1) increased by 0.1 nm, and the commonly occurring distance peak M2 of the distance distribution curve P(r) increased by 0.4 nm. These changes revealed that the Fab-Fc separation in IgG1 was perturbed after deglycosylation. To explain these changes, atomistic scattering modeling based on Monte Carlo simulations resulted in 123,284 and 119,191 trial structures for glycosylated and deglycosylated IgG1 respectively. From these, 100 x-ray and neutron best-fit models were determined. For these, principal component analyses identified five groups of structural conformations that were different for glycosylated and deglycosylated IgG1. The Fc region in glycosylated IgG1 showed a restricted range of conformations relative to the Fab regions, whereas the Fc region in deglycosylated IgG1 showed a broader conformational spectrum. These more variable Fc conformations account for the loss of binding to the Fcγ receptor in deglycosylated IgG1.     

A new blue luminescent dichlorido-bridged dinuclear copper(II) complex with DNA binding and cytotoxic activities: Synthesis, structure and DFT studies

A blue luminescent dichlorido-bridged dinuclear copper(II) (S = 1/2) complex, [Cu^II₂(HL)₂(μ-Cl)₂]·2H₂O, 1a was synthesized with the 1:1 reaction of the acyclic tridentate salicylaldehyde 2-pyridyl hydrazone ligand, HL, 1. The complex 1a displays multiple bands in the visible region (400-470 nm). The association constant (K_ass, UV-Vis) was found to be 1.186 × 10⁴ for 1a at 298 K. The copper(II)-copper(III) oxidation potential lies near 0.32 V versus Ag/AgCl electrode. On excitation at 390 nm, the ligand 1 strongly emits at 444 nm due to an intraligand ¹(π-π^∗) transition. Upon complexation with copper(II) the emission peak is slightly red shifted (λ_ex 390 nm, λ_em 450 nm, F/F₀ 0.81) with little quenching. Molecular structure of 1a (Cu···Cu 3.523 Å) has been determined by single crystal X-ray diffraction studies. DFT and TDDFT calculations strongly support the spectral behavior of the ligand and the complex. The complex 1a exhibits a strong interaction towards DNA as revealed from the K_b (intrinsic binding constant) 2.05 × 10⁴ M⁻¹ and K_sv (Stern-Volmer quenching constant) 2.47 values. The complex exhibits cytotoxic effect and the LD₅₀ value for HeLa cells was calculated as 5.44 μM at which the cell cycle was arrested at G₂/M phase.     

Synthesis of two configurational isomers of a 14-membered tetraaza macrocycle bearing N-CH2CH2CONH2 pendent arms and their copper(II) complexes: Crystal structures of the complexes

Two isomers of 1,8-bis(N-carbamoylethyl)-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane (L²) bearing two N-CH₂CH₂CONH₂ groups, C-meso-L² and C-racemic-L², have been prepared and characterized. Each isomer reacts with Cu(II) ion to form a five-coordinate complex, [Cu(C-meso-L²)](ClO₄)₂ (1) or [Cu(C-racemic-L²)](ClO₄)₂ (2), in which only one pendent amide group is coordinated to the metal ion. The crystal structure of 1 · CH₃CN shows that the complex possesses trans-III-type N-configuration and has a slightly distorted square-pyramidal coordination geometry with a relatively long axial Cu-O (N-CH₂CH₂CONH₂) bond (2.207(3) Å). On the other hand, 2 exhibits trans-V configuration and has a slightly distorted trigonal bipyramidal coordination geometry with a very short equatorial Cu-O (N-CH₂CH₂CONH₂) bond (2.007(3) Å); the Cu-O distance is distinctly shorter than the Cu-N distances (2.062(4)-2.090(4) Å). The complex 1 exhibits a d-d transition band at approximately 565 nm, whereas the band for 2 is observed at approximately 770 nm.     

Synthesis, crystal structure and properties of dinuclear iron(III) complexes containing terminally coordinated phenolate/H2O/OH groups as models for purple acid phosphatases: efficient hydrolytic DNA cleavage

We present here the syntheses of two dinuclear iron(III) complexes with the polydentate N,O-donor ligand H₂BPClNOL (N-(2-hydroxybenzyl)-N-(2-pyridylmethyl)[(3-chloro)(2- hydroxy)]propylamine). The reaction between Fe^III(ClO₄)₃ · 9H₂O, the title ligand and two equivalents of NaOAc · 3H₂O resulted in the complex . When the synthesis was performed with a lesser amount of NaOAc · 3H₂O (half equivalent), the complex without bridging acetate, was obtained. The complexes were characterized by X-ray structural analysis, magnetochemistry, Mössbauer and UV-Vis spectroscopies, and electrochemistry. Complex 2 was also characterized in solution through potentiometric titration. Both complexes crystallize in the monoclinic system. Complex 2 has one water molecule coordinated to each iron centre. Their pK_a values are 5.00 and 7.03 for the first protonation/deprotonation equilibrium of each coordinated water molecule. The UV-Vis and electrochemical techniques showed that the absence of an acetate bridge in 2 results in a significant difference in the Lewis acidity of both iron centres, when compared with 1. The lack of an acetate bridge in 2 also results in changes in the anti-ferromagnetic coupling as revealed by magnetic measurements. Complex 2 is an interesting structural model for the active site of iron containing PAPs, since it has an Fe(-alkoxo)₂Fe core with an Fe^III?Fe^III distance of 3.122(1) Å, containing phenolate and water molecules coordinated to the iron centres and is soluble in aqueous solutions. Furthermore, the UV-Vis properties of 2 are similar to those of PAPs, since the complex absorbs at 580 nm in the oxidized form (550-570 nm for PAPs) and at 499 nm in the mixed-valence form (505-510 nm for PAPs) as revealed through spectroelectrochemical studies. Finally, complex 2 successfully promoted the hydrolytic cleavage of plasmid DNA under aerobic and anaerobic conditions, producing single and double DNA strand breaks at biological pH values.     

Preparation,structure and properties of dicyano silver complexes of the M(en)3Ag2(CN)4 and M(en)2Ag2(CN)4 type

Complexes of the M(en)₃Ag₂(CN)₄ (M = Ni, Zn, Cd) and M(en)₂Ag₂(CN)₄ (M = Ni, Cu, Zn, Cd) type were prepared and identified by elemental analysis, infrared spectroscopy, measurement of magnetic susceptibility, and X-ray powder diffractometry. The crystal structures of Ni(en)₃Ag₂(CN)₄ (I) and Zn(en)₂Ag₂(CN)₄ (II) were determined by the method of monocrystal structure analysis. Complex I crystallizes in the space group C2/c, a = 1.2639(5), b = 1.3739(4), c = 1.2494(4) nm, β = 113.25(4)°, D_m = 1.86(1), D_c = 1.86 gcm⁻³ Z = 4, R = 0.0429. The crystal structure of I consists of complex cations [Ni(en)₃]²⁺ and complex anions [Ag(CN)₂]⁻. Complex II crystallizes in the space group I2/m, a = 0.9150(3), b = 1.3308(4), c = 0.6442(2) nm, β = 95.80(3)°, D_m = 2.14(1), D_c = 2.15 gcm⁻³, Z = 2, R = 0.0334. Its crystal structure consists of infinite, positively charged chains of the [-NCAgCNZn- (en)₂]_nⁿ⁺ type and isolated [Ag(CN)₂]⁻ anions. The atoms of Ag are positioned parallely to the z axis and the AgAg distance is equal to 0.3221(2) nm.     

Cyclam cored luminescent dendrimers as ligands for Co(II), Ni(II) and Cu(II) ions

We have investigated the photophysical properties of two dendrimers containing a cyclam core decorated with 4 naphthyl units (G0), 12 dimethoxybenzene and 16 naphthyl units (G2). These dendrimers show fluorescence bands that can be assigned to naphthyl localized excited states (λ_max = 337 nm), naphthyl-amine exciplexes (λ_max = 470 nm) and, for G2, naphthyl excimers (λ_max ca. 400 nm). Cyclam is a very good ligand for transition metal ions and we have investigated complex formation between these dendritic ligands and Ni(II), Co(II) and Cu(II), added as nitrate salts. This process can be monitored by the strong changes, both in shape and intensity, observed in the emission spectra of these dendrimers. Complexation with Cu(II) causes not only changes in the relative intensities of the fluorescence bands, but also the appearance of a new absorption band in the near UV spectral region. An analysis of the titration curves has allowed us to obtain clear evidence for the formation of not only 1:1 species, but also 1:2 metal to ligand species. G2 shows a clear preference, compared to G0, in forming complexes with a 1:2 metal-to-ligand stoichiometry, although it possesses very bulky dendrons appended to the cyclam central unit.     

Low-angle neutron scattering from chromatin subunit particles.

Monomer chromatin particles containing 140 base pairs of DNA and eight histone molecules have been studied by neutron scattering. From measurements in various H2O/D2O mixtures, radii of gyration and the average scattering density of the particle were determined. The radius of gyration under conditions when scattering from the DNA dominates is 50A, and when scattering from the protein dominates, 30A. Consequently the core of the particle is largely occupied by the histones while the outer shell consists of DNA together with some of the histone.     

A low resolution model for the chromatin core particle by neutron scattering

Neutron scattering studies have been applied to chromatin core particles in solution, using the contrast variation technique. On the basis of the contrast dependance of the radius of gyration and the radial distribution function it is shown that the core particle consists of a core containing most of the histone around which is wound the DNA helix,following a path with a mean radius of 4.5 nm,in association with a small proportion of the histones. Separation of the shape from the internal structure, followed by model calculations shows that the overall shape of the particle is that of a flat cylinder with dimensions ca. 11x11x6 nm. Further details of the precise folding of the DNA cannot be deduced from the data, but detailed model calculations support concurrent results from crystallographic studies(25).Images     

Small-angle X-ray studies of Lumbricus terrestris haemoglobin

Small-angle X-ray scattering of Lumbricus terrestris haemoglobin was measured in dilute solutions in 0.1 M Tris HCl buffer, pH 7.0. The following molecular parameters were determined: radius of gyration 11.2 nm, volume 7700 nm³, maximum diameter 29 nm, molecular weight 3.95 × 10⁶. The experimental scattering curve was compared with the scattering curves and distance distribution functions calculated for various models. The overall shape of the haemoglobin could be approximated by a hollow cylinder with the following dimensions: outer radius 13.5 nm, inner radius 5.4 nm, height 16.0 nm. The best fit was obtained with a model which consists of 12 large subunits arranged in two superimposed hexagonal rings with a number of smaller subunits between the large subunits and in the centre of the molecule.     

Studies of rheniumtricarbonyl complexes of tripodal pyridyl-based ligands

The reaction of N-benzoyl and N-acetyl tris(pyridin-2-yl)methylamine 1b and 1c (LH = tpmbaH and tpmaaH) with [Re(CO)₅Br] has been investigated and shown to proceed via the initial formation of a cationic rheniumtricarbonyl complex [(LH)Re(CO)₃]Br in which coordination of the ligand occurs via the three pyridine rings. For tpmbaH 1b, but not tpmaaH 1c, this initial complex 2b readily undergoes the loss of HBr to give a neutral octahedral complex 4b [(L)Re(CO)₃] where coordination occurs via two of the pyridine rings and the deprotonated amide nitrogen. The ¹H NMR spectrum of the latter complex 4b is very unusual in that at room temperature the signals for the 3-H protons on the coordinated pyridine rings are not visible due to extreme broadening of these resonances. Comparison with the analogous complex 7 from N-benzoyl bis(pyridin-2-yl)methylamine 6b (bpmbaH) confirms that this is due to rotation of the uncoordinated pyridine ring. The structure of the cationic complex 3d [(LH)Re(CO)₃]Br formed from N-benzyl tris(pyridin-2-yl)methylamine 1d (bz-tpmaH) is also discussed. The crystal structures of complexes [(tpmba)Re(CO)₃] 4b, [(bz-tpmaH)Re(CO)₃]Br 3d and [(bpmba)Re(CO)₃] 7 have been determined. In all complexes the coordination geometry around Re is distorted octahedral with a fac-{Re(CO)₃}⁺ core.     

Properties of aqueous solutions of lentinan in the absence and presence of zwitterionic surfactants

Morphological and conformational transitions of lentinan (LT), a β-glucan extracted from Shiitake mushrooms (Lentinula edodes), were investigated at different concentrations of aqueous NaOH, using Small Angle X-ray Scattering (SAXS) technique. At low NaOH_(aq) concentration LT chains are self-associated and adopt the triple helix form where as at higher NaOH concentrations the polymer chains undergo a transition to random coil chains. Also, the presence of fractal dimensions was observed through analysis of the exponential decay of the scattering intensity as a function of the scattering angle. In addition, the lateral radius of gyration was determined for LT in different concentrations of NaOH solution, indicating a rigid triple helix present as a small rod-like structure. Interactions of LT with two zwitterionic surfactants were investigated by surface tension, fluorescence, and static light scattering measurements. Experimental data showed that the formation of LT–(surfactant) complexes occurred through a cooperative process.