On the structure of Hg2I3+ in dimethylsulfoxide and aqueous solution. An X-ray scattering and raman spectroscopic study

Dimethylsulfoxide and aqueous solutions of mercury(II) in large excess over iodide have been investigated by X-ray scattering techniques supported by Raman spectroscopic measurements. The composition of the solutions has been selected to ensure that the cationic complex Hg₂I³⁺ is the predominant iodide species. The structure parameters of the solvated Hg₂I³⁺ ion have been refined by a least- squares procedure on the scattering data, using known structural parameters for the additional molecular entities present. The Hg₂I³⁺ entity is more or less identical in DMSO and water. The HgI bond distance is 2.613(12) and 2.632(5) Å and the HgHg distance is 3.66(5) and 3.70(1) Å in DMSO and water, respectively. This yields a HgIHg angle of 89° in both solvents. The mercury(II) atom in this complex is most probably solvated in a tetrahedral fashion by three DMSO or H₂O molecules. The structure of Hg₂I³⁺ is discussed in the light of recent results for the Ag₄I³⁺ complex in solution and relevant crystal structures.     

The structure of silver(I) iodide and bromide,and the silver(I) solvate in tetrahydrothiophene solution: An X-ray scattering and raman spectroscopic study

Structures of silver(I) iodide and bromide, and the solvated silver(I) ion are determined in tetrahydrothiophene solution with Large Angle X-ray Scattering (LAXS) technique. In a silver(I) perchlorate tetrahydrothiophene solution, silver(I) is solvated by four tetrahydrothiophene molecules in a regular tetrahedron. The main peak in the radial distribution function corresponds to four AgS distances at 2.526(7) Å. An SS distance at 2.65(2) Å in the solvent bulk is also included in the main peak. This shows that an internal structure exists in the tetrahydrothiophene bulk. Silver(I) iodide and bromide are tetrameric complexes with a stella quadrangula configuration, in saturated solution. The distances in the [AgI(SC₄H₈)]₄ complex are AgI 2.799(4); AgAg, 3.072(6) and II, 4.638(19) Å and in the [AgBr(SC₄H₈)]₄ complex they are AgBr, 2.592(3); AgAg, 2.866(5) and BrBr, 4.25(4) Å. The AgI bond distances in the [AgI(SC₄H₈)]₄ complex is shorter in solution than in the solid solvate. This is because bulk tetrahydrothiophene is a markedly weaker donor than free tetrahydrothiophene due to the sulfursulfur interactions in the bulk, shown to be around 2.65 Å. Raman spectroscopic studies on silver(I) and copper(I) iodide and silver(I) chloride tetrahydrothiophene solutions show that the polymetric structures predominate in concentrated solution and that they disintegrate upon dilution.     

Concanavalin A stimulation modifies the lipid and protein structure or rabbit thymocyte plasma membranes. A laser raman study.

(1) We have compared the laser Raman spectra of isolated plasma membranes from resting rabbit thymocytes and cells mitogenically stimulated with concanavalin A. (2) Major alterations in the CH stretching, CH deformation and CC stretching regions indicate a different lipid architecture in the membranes from activated cells. (3) Spectral changes in the Amide I and II regions, by reference to the spectra of model compounds indicate greater protein amidation in the membranes from stimulated cells.     

Conformational analysis of dipeptides in aqueous solution. II. Molecular structure of glycine and alanine dipeptides by depolarized rayleigh scattering and laser Raman spectroscopy

A new approach to the experimental conformational analysis of peptides in aqueous solution is presented and discussed. The basic idea is to combine laser Raman spectroscopy and depolarized Rayleigh scattering in order to interpret scattering properties of the dissolved molecule in terms of both local and global structure. We outline a simple method (anisotropic perturbation treatment) appropriate for solving conformational problems in large molecules by studying together slightly perturbed homologous compounds. This method is applied to the study of the molecular structure of simple glycine and alanine dipeptides. The preferred conformation for such molecules is the seven-membered chelated ring (C₇) additionally stabilized by two intermolecular hydrogen bonds involving one molecule of water.     

The structure of glutaraldehyde in aqueous solution determined by ultraviolet absorption and light scattering.

The structure of glutaraldehyde (GA) in aqueous solutions has been the subject of much debate. Since there were fundamental problems in the experiments in the preceding studies, in this article, the structure of GA was investigated with uv absorption and light scattering to avoid those problems. It was discovered that 70% glutaraldehyde solution contains a large quantity of polymeric species with cyclic hemiacetal structure. On dilution, the polymerized glutaraldehyde slowly converted to monomers. In dilute solution, glutaraldehyde is almost monomeric at pH 3-8, the major portion taking the cyclic hemiacetal structure. The structure of GA in 20% solution is similar to that in more dilute solution. alpha, beta-Unsaturated structure does not exist in aqueous solution regardless of the concentration of glutaraldehyde.     

Studies of calmodulin structure: laser raman spectroscopy of biomolecules

The structure of bovine brain calmodulin was probed by using laser Raman spectroscopy to elucidate cation-induced conformational changes in the protein. Local changes, most likely reflecting metal binding but not rearrangement of the peptide backbone, were observed in the presence of calcium or magnesium. A conformational change involving the peptide backbone and secondary structure content of calmodulin was observed only in the presence of calcium. The calcium-induced conformational change in the peptide backbone involves increased alpha helix and beta sheet. This was the only major calcium-specific change observed in the Raman spectrum, which suggests that the flexibility of the backbone conformation may play a critical role in the physiological activity of calmodulin.     

Infrared absorption and raman scattering of sulfate groups of heparin and related glycosaminoglycans in aqueous solution

The i.r. spectra for aqueous solutions of sulfated glycosaminoglycans and model compounds in the transmittance “window” region of the solvent (1400-950 cm^?1) are dominated by the strong and complex absorption centered at ～1230 cm^?1 and associated with the antisymmetric stretching vibrations of the SO groups. Primary and secondary O-sulfate groups absorb at somewhat higher frequencies (1260-1200 cm^?1) than N-sulfates (～1185 cm^?1). Each sulfate band lends itself to quantitative applications, especially within a given class of sulfated polysaccharide. Laser-Raman spectra of heparin and model compounds have been obtained in aqueous solution and in the solid state. The most-prominent Raman peak (at ～1060 cm^?1) is attributable to the symmetrical vibration of the SO groups, with N-sulfates emitting at somewhat lower frequencies (～1040 cm^?1) than O-sulfates. The Raman pattern in the 950-800 cm^?1 region (currently used in the i.r. for distinguishing between types of sulfate groups) also involves vibrations that are not localized only in the COS bonds.     

The solution structure and activation of visual arrestin studied by small-angle X-ray scattering.

Visual arrestin is converted from a 'basal' state to an 'activated' state by interaction with the phosphorylated C-terminus of photoactivated rhodopsin (R*), but the conformational changes in arrestin that lead to activation are unknown. Small-angle X-ray scattering (SAXS) was used to investigate the solution structure of arrestin and characterize changes attendant upon activation. Wild-type arrestin forms dimers with a dissociation constant of 60 micro m. Small conformational changes, consistent with local movements of loops or the mobile N- or C-termini of arrestin, were observed in the presence of a phosphopeptide corresponding to the C-terminus of rhodopsin, and with an R175Q mutant. Because both the phosphopeptide and the R175Q mutation promote binding to unphosphorylated R*, we conclude that arrestin is activated by subtle conformational changes. Most of the arrestin will be in a dimeric state in vivo. Using the arrestin structure as a guide [Hirsch, J.A., Schubert, C., Gurevich, V.V. & Sigler, P.B. (1999) Cell 97, 257-269], we have identified a model for the arrestin dimer that is consistent with our SAXS data. In this model, dimerization is mediated by the C-terminal domain of arrestin, leaving the N-terminal domains free for interaction with phosphorylated R*.     

Characterization of protein fold by wide-angle X-ray solution scattering

Wide-angle X-ray solution scattering (WAXS) patterns contain substantial information about the three-dimensional structure of a protein. Although WAXS data have far less information than is required for determination of a full three-dimensional structure, the actual amount of information contained in a WAXS pattern has not been carefully quantified. Here we carry out an analysis of the amount of information that can be extracted from a WAXS pattern and demonstrate that it is adequate to estimate the secondary-structure content of a protein and to strongly limit its possible tertiary structures. WAXS patterns computed from the atomic coordinates of a set of 498 protein domains representing all of known fold space were used as the basis for constructing a multidimensional space of all corresponding WAXS patterns (‘WAXS space’). Within WAXS space, each scattering pattern is represented by a single vector. A principal components analysis was carried out to identify those directions in WAXS space that provide the greatest discrimination among patterns. The number of dimensions that provide significant discrimination among protein folds agrees well with the number of independent parameters estimated from a naïve Shannon sampling theorem approach. Estimates of the relative abundances of secondary structures were made using training/test sets derived from this data set. The average error in the estimate of α-helical content was 11%, and of β-sheet content was 9%. The distribution of proteins that are members of the four structure classes, α, β, α/β and α+β, are well separated in WAXS space when data extending to a spacing of 2.2 Å are used. Quantification of the information embedded within a WAXS pattern indicates that these data can be used as a powerful constraint in homology modeling of protein structures.     

Complexes of RecA protein in solution. A study by small angle neutron scattering

RecA complexes on DNA and self-polymers were analysed by small-angle neutron scattering in solution. By Guinier analysis at small angles and by model analysis of a subsidiary peak at wider angles, we find that the filaments fall into two groups: the DNA complex in the presence of ATP gamma S, an open helix with pitch 95 A, a cross-sectional radius of gyration of 33 A and a mass per length of about six RecA units per turn, which corresponds to the state of active enzyme; and the compact form (bound to single-stranded DNA in the absence of ATP, or binding ATP gamma S in the absence of DNA, or just the protein on its own), a helical structure with pitch 70 A, cross-sectional radius of gyration 40 A and mass per length about five RecA units per turn, which corresponds to the conditions of inactive enzyme. The results are discussed in the perspective of unifying previous conflicting structural results obtained by electron microscopy.     

Oligomeric domain structure of human complement factor H by X-ray and neutron solution scattering.

Factor H is a regulatory component of the complement system. It has a monomer Mr of 150,000. Primary structure analysis shows that the polypeptide is divided into 20 homologous regions, each 60 amino acid residues long. These are independently folding domains and are termed "short consensus repeats" (SCRs) or "complement control protein" (CCP) repeats. High-flux synchrotron X-ray and neutron scattering studies were performed in order to define its solution structure in conditions close to physiological. The Mr of factor H was determined as 250,000-320,000 to show that factor H is dimeric. This structure is maintained at concentrations between 1 and 11 mg/mL in the pH range 5-9. Zn2+ ions are an inhibitor of C3b cleavage by factor I, a reaction in which factor H acts as a cofactor. Additions of Zn2+ to factor H caused it to form oligomers containing 4-10 monomers. The radius of gyration RG of native factor H by X-rays or by neutrons in 0% or 100% 2H2O buffers is not measurable but is greater than 12.5 nm. Two cross-sectional radii of gyration RXS-1 and RXS-2 were determined as 3.0-3.1 and 1.8 nm, respectively. Analyses of the cross-sectional intensities show that factor H is composed of two distinct subunits. The RXS-1 corresponds to the cross-sectional properties of both subunits and exhibits an unusual radiation dependence on the X-ray flux. Since RXS-2 is close to the corresponding RXS of C4b binding protein (91% of which is formed from SCR/CCP domains), it is inferred that the SCR/CCP domains of factor H and C4b binding protein have similar solution structures. The use of hydrodynamic spheres to reproduce literature sedimentation coefficients of 5.5-5.6 S showed that these were compatible with a V-shaped arrangement of two rods (36 spheres each, length 87 +/- 5 nm) joined at an angle of 5 degrees. The use of a similar arrangement of 244 spheres arranged in two rods (length 77 nm) to fit the experimental X-ray and neutron scattering curves showed that the two rods are joined at an angle of 5 degrees. This model corresponds to an actual RG of 21-23 nm. The separation between each SCR/CCP in factor H is close to 4 nm. In the solution structure of factor H, the SCR/CCP domains are in a highly extended conformation.     

Refined solution structure of human profilin I.

Profilin is a ubiquitous eukaryotic protein that binds to both cytosolic actin and the phospholipid phosphatidylinositol-4,5-bisphosphate. These dual competitive binding capabilities of profilin suggest that profilin serves as a link between the phosphatidyl inositol cycle and actin polymerization, and thus profilin may be an essential component in the signaling pathway leading to cytoskeletal rearrangement. The refined three-dimensional solution structure of human profilin I has been determined using multidimensional heteronuclear NMR spectroscopy. Twenty structures were selected to represent the solution conformational ensemble. This ensemble of structures has root-mean-square distance deviations from the mean structure of 0.58 A for the backbone atoms and 0.98 A for all non-hydrogen atoms. Comparison of the solution structure of human profilin to the crystal structure of bovine profilin reveals that, although profilin adopts essentially identical conformations in both states, the solution structure is more compact than the crystal structure. Interestingly, the regions that show the most structural diversity are located at or near the actin-binding site of profilin. We suggest that structural differences are reflective of dynamical properties of profilin that facilitate favorable interactions with actin. The global folding pattern of human profilin also closely resembles that of Acanthamoeba profilin I, reflective of the 22% sequence identity and approximately 45% sequence similarity between these two proteins.     

Rigidity of protein structure revealed by incoherent neutron scattering

The rigidity and flexibility of a protein is reflected in its structural dynamics. Studies on protein dynamics often focus on flexibility and softness; this review focuses on protein structural rigidity. The extent of rigidity can be assessed experimentally with incoherent neutron scattering; a method that is complementary to molecular dynamics simulation. This experimental technique can provide information about protein dynamics in timescales of pico- to nanoseconds and at spatial scales of nanometers; these dynamics can help quantify the rigidity of a protein by indices such as force constant, Boson peak, dynamical transition, and dynamical heterogeneity. These indicators also reflect the rigidity of a protein's secondary and tertiary structures. In addition, the indices reveal how rigidity is influenced by different environmental parameters, such as hydration, temperature, pressure, and protein-protein interactions. Hydration affects both rigidity and softness more than other environmental factors. Interestingly, hydration affects harmonic and anharmonic motions in opposite ways. This difference is probably due to the protein's dynamic coupling with water molecules via hydrogen bonding.