Ion solvation and water structure in potassium halide aqueous solutions

The structure of water and the nature of ionic hydration is explored in aqueous solutions of potassium fluoride, chloride, bromide and iodide over a range of concentrations up to 4.8 ion pairs per 100 water molecules, using the combined techniques of neutron diffraction with hydrogen isotope substitution. The diffraction data are interpreted using the method of empirical potential structure refinement, which attempts to build a three-dimensional model of the scattering system consistent with the diffraction data. The water structure is strongly perturbed in the first hydration shells of both anion and cation, but is found to be only mildly perturbed outside of this region, with the largest effects occurring with the smallest anion and highest concentrations. For the potassium ion there are strong orientational correlations in the first hydration shell, with the water molecules lying with their dipole moments pointing almost directly away from the cation on average, but with an angular spread of approximately +/-60 degrees which is mildly dependent on the anion type present. For all the anions the water molecules in the first shell are strongly oriented with one O-H vector pointing directly towards the anion on average, with an angular spread of approximately +/-10 degrees for F(-), increasing to approximately +/-22 degrees for I(-). For both anions and cations the second hydration shell is much more disordered than the first, but there is a weak pattern of orientational correlation which becomes more pronounced with the larger anions. There is some evidence that the fluoride ion structures water significantly in its first hydration shell, but not beyond. The findings throw further light on recent findings that the orientational relaxation time for water outside the first shell of dissolved ions is the same as in the bulk liquid.     

Analytical ultracentrifugation combined with X-ray and neutron scattering: Experiment and modelling

Analytical ultracentrifugation and solution scattering provide different multi-parameter structural and compositional information on proteins. The joint application of the two methods supplements high resolution structural studies by crystallography and NMR. We summarise the procedures required to obtain equivalent ultracentrifugation and X-ray and neutron scattering data. The constrained modelling of ultracentrifugation and scattering data is important to confirm the experimental data analysis and yields families of best-fit molecular models for comparison with crystallography and NMR structures. This modelling of ultracentrifugation and scattering data is described in terms of starting models, their conformational randomisation in trial-and-error fits, and the identification of the final best-fit models. Seven applications of these methods are described to illustrate the current state-of-the-art. These include the determination of antibody solution structures (the human IgG4 subclass, and oligomeric forms of human IgA and its secretory component), the solution structures of the complement proteins of innate immunity (Factor H and C3/C3u) and their interactions with macromolecular ligands (C-reactive protein), and anionic polysaccharides (heparin). Complementary features of joint ultracentrifugation and scattering experiments facilitate an improved understanding of crystal structures (illustrated for C3/C3u, C-reactive protein and heparin). If a large protein or its complex cannot be crystallised, the joint ultracentrifugation-scattering approach provides a means to obtain an overall macromolecular structure.     

Synchrotron radiation wide-angle X-ray scattering studies of glycinin solutions

X-ray scattering studies of glycinin solutions have been extended to higher scattering angles of 2θ 0.15 rad. Reproducible, high quality data in the angular range 0.38–6.29 nm⁻¹ have been obtained. Scattering curves show features hitherto unreported that reveal details not only of overall shape and size of the protein but also its internal structure. Analysis suggests that currently accepted models for this protein based on the assumptions of equal-sized, touching spheres are inadequate to describe experimental observations.     

Hydration structure in natural DNA observed by thermal neutron scattering

Films of highly oriented Na- and LiDNA showing the typical X-ray diffraction patterns for the A-,B-, and C-conformation have been investigated by elastic and quasielastic neutron scattering. Information concerning the question of the DNA-water interaction has been obtained by varying the parameters H₂O/D₂O contrast, humidity, and temperature. Main observations are: A coexistence of one- and three-dimensionally correlated DNA which shifts towards the one-dimensionally correlated C-conformation for high humidity; a coexistence of A-, B-, and C-conformation for NaDNA with a similar humidity dependence; a factor of two increase between the average degree of localization of water hydrogens compared with DNA hydrogens at 75% r.h. for NaDNA; a strong water contribution to layer peaks which are close to the susceptibility maximum of water; a strong temperature dependence of the axial repeat distance for C-DNA; broad quasielastic spectra around the inverse of this distance. The observations are interpreted in terms of a competition between finite three-dimensional correlation and an optimized spatial resonance of nearly one-dimensionally correlated DNA with the correlation of bulk water. The observations are compatible with the concept of water spine formation (Dickerson 1983). The interpretation emphasizes the dynamic character of this mechanism in the region of nearly one-dimensionally correlated DNA.     

Solution scattering studies of dimeric and tetrameric spectrin

The structure of spectrin dimers and tetramers in solution has been examined by light, low-angle X-ray and neutron scattering. The results show a good correspondence between the solution dimensions of these molecules and their appearance in the electron microscope after shadowing. The scattering profiles are not compatible with an extended rod-like character, but reflect the presence of a considerable degree of bending. The radii of gyration of the dimer and tetramer were determined to be 170 and 375 Å and the cross-section radii of gyration 14 and 12.3 Å. respectively. Both are thus long. thin. rather bent molecules, and the tetramer is twice the length of the dimer.     

Water structure around dipeptides in aqueous solutions

The bulk water structure around small peptide fragments-glycyl-L: -alanine, glycyl-L: -proline and L: -alanyl-L: -proline-has been determined by a combination of neutron diffraction with isotopic substitution and empirical potential structural refinement techniques. The addition of each of the dipeptides to water gives rise to decreased water-water coordination in the surrounding water solvent. Additionally, both the O(w)-O(w) radial distribution functions and the water-water spatial density functions in all of the solutions indicate an electrostrictive effect in the second water coordination shell of the bulk water network. This effect is not observed in similar experiments on the amino acid L: -proline alone in solution, which is one component of two of the peptides measured here.     

Contrast variation studies of clathrin coated vesicles by small-angle neutron scattering

Structural information on clathrin coated vesicles has been obtained by small angle neutron scattering using contrast variation. A characteristic peak in the neutron scattering profile, which is apparent in 75 % D₂O, as well as in H₂O, disappears when contrast matching the protein component of the coated vesicles in 42% D₂O. Neutron, as well as dynamic, light scattering give a coated vesicle size of about 900 Å in H₂O and D₂O, but for neutron scattering the diameter decreases when matching out the protein coat of the clathrin coated vesicles. From the match point for the clathrin coated vesicles it is demonstrated that the clathrin cages do contain internal membrane. The mass of 34 MD and composition of 75% protein and 25% lipid found from the analysis of the small-angle scattering data are both in good agreement with the values reported in the literature. Electron microscopy gives an average outer diameter of 880 Å for the coated vesicles and an average diameter of 460 Å for the vesicle itself. Offprint requests to: Correspondence to: R. Bauer     

Solution structure of the chicken skeletal muscle troponin complex via small-angle neutron and X-ray scattering

Troponin is a Ca2+-sensitive switch that regulates the contraction of vertebrate striated muscle by participating in a series of conformational events within the actin-based thin filament. Troponin is a heterotrimeric complex consisting of a Ca2+-binding subunit (TnC), an inhibitory subunit (TnI), and a tropomyosin-binding subunit (TnT). Ternary troponin complexes have been produced by assembling recombinant chicken skeletal muscle TnC, TnI and the C-terminal portion of TnT known as TnT2. A full set of small-angle neutron scattering data has been collected from TnC-TnI-TnT2 ternary complexes, in which all possible combinations of the subunits have been deuterated, in both the +Ca2+ and -Ca2+ states. Small-angle X-ray scattering data were also collected from the same troponin TnC-TnI-TnT2 complex. Guinier analysis shows that the complex is monomeric in solution and that there is a large change in the radius of gyration of TnI when it goes from the +Ca2+ to the -Ca2+ state. Starting with a model based on the human cardiac troponin crystal structure, a rigid-body Monte Carlo optimization procedure was used to yield models of chicken skeletal muscle troponin, in solution, in the presence and in the absence of regulatory calcium. The optimization was carried out simultaneously against all of the scattering data sets. The optimized models show significant differences when compared to the cardiac troponin crystal structure in the +Ca2+ state and provide a structural model for the switch between +Ca2+ and -Ca2+ states. A key feature is that TnC adopts a dumbbell conformation in both the +Ca2+ and -Ca2+ states. More importantly, the data for the -Ca2+ state suggest a long extension of the troponin IT arm, consisting mainly of TnI. Thus, the troponin complex undergoes a large structural change triggered by Ca2+ binding.     

Small angle neutron scattering studies of HbA in concentrated solutions.

Differential cross-sections for neutrons scattered by normal human hemoglobin have been determined over the range of concentrations from 2 to approximately 35 weight percent. Data are compared with structure factors calculated from models of monodisperse hard spheres interacting through a screened Coulomb potential. Good agreement is noted when the volume fraction eta is adjusted during multivariate fitting of data, but the fitted value of eta is always lower than expected from the known Hb concentration of the samples. Calculations of cross-sections for polydisperse scatterers suggest that the samples may contain oligomers of the fundamental tetrameric Hb molecule.     

Small-angle X-ray scattering studies of the structure of nucleosome core histone complexes in solution

The nucleosome core histone complex in solution at 2 M NaCl and pH 7 has a radius of gyration R_s, of 3.48 nm and a maximum dimension, L, of 12 nm. Its shape is disc-like with a mean thickness of 3 nm. The radius of gyration determined by us is of the same value as the radius of gyration of the complex in intact core particles (Braddock) et al., Biopolymers 1981, 20, 327). Thus, we conclude that the basic histone tails of the protein complex project about 2 nm from its central part.     

Comparison of the three-dimensional molecular models of bovine submicellar caseins with small-angle X-ray scattering. Influence of protein hydration

To test the applicability of two energy-minimized, three-dimensional structures of the bovine casein submicelle, theoretical small-angle X-ray scattering curves in the presence and absence of water were compared to experimental data. The published method simulates molecular dynamics of proteins in solution by employing adjustable Debye-Waller temperature factors (B factors) for the protein, for the solvent, and for protein-bound water. The programs were first tested upon bovine pancreatic trypsin inhibitor beginning with its known X-ray crystal structure. To approximate the degree of protein hydration previously determined by NMR relaxation experiments (0.01 g water/g protein), 120 water molecules were docked into the large void of the-casein portion of the structure for both the symmetric and asymmetric casein submicelle models. To approximate hydrodynamic hydration (0.244 g water/g protein), 2703 water molecules were added to each of the above structures using the droplet algorithm in the Sybyl molecular modeling package. All structures were then energy-minimized and their solvation energies calculated. Theoretical small-angle X-ray scattering curves were calculated for all unhydrated and hydrated structures and compared with experimentally determined scattering profiles for submicellar casein. Best results were achieved with the 120-bound-water structure for both the symmetric and asymmetric submicelle models. Comparison of results for the protein submicelle models with those for the theoretical and literature values of bovine pancreatic trypsin inhibitor demonstrates the applicability of the methodology.Reference to a brand or firm name does not constitute endorsement by the U.S. Department of Agriculture over others of a similar nature not mentioned.     

Small-angle X-ray scattering studies of giant haemoglobin from the annelid Tylorrhynchus heterochaetus

The extracellular haemoglobin of the polychaete Tylorrhynchus heterochaetus was studied in solution by small-angle X-ray scattering. The following molecular parameters were determined: radius of gyration 10.8±0.2 nm and a maximum intraparticular distance of 29.5±0.5 nm. Models which fit well the experimental data and reflect also the biochemical structure especially the known number of polypeptide chains are presented.     

The effect of organic cryosolvents on actin structure: studies by small angle X-ray scattering

Small-angle X-ray scattering was used to probe the structure of actin in the presence of cryosolvents: 1,2-propanediol, glycerol, or a mixture of both solvents. In media devoid of polymerizing salts, a radius of gyration of 23 Å is measured, as expected from the literature. In the presence of 1,2-propanediol alone, the scattering pattern begins to exhibit the characteristic slope of elongated objects with a non-negligible thickness, such as actin filaments polymerized in 40 mM KCl and 1 mM MgCl₂. However, only short fragments (radius of gyration 40 Å) are generated. We infer that in a medium of low ionic strength containing 15% 1,2-propanediol, actin assumes a structure closer to that of filamentous actin. 1,2-propanediol apparently induces nucleation of oligomers, as with polymerizing salts, but no propagation occurs. Glycerol and/or propanediol induce no alteration in the structure of individual salt-polymerized actin filaments. Aggregation occurs with propanediol, even in the presence of glycerol. Glycerol alone has no such effect. No shortening is detected within the scale covered, with either solvent, although 1,2-propanediol is known to shorten actin filaments. We suggest that in the absence of salts, 1,2-propanediol induces a conformational change in monomeric actin that is necessary for nucleation. This could correlate with a conformational change of actin protomers within microfilaments observed in the presence of 1,2-propanediol by other authors using different techniques.Abbreviations SAXS small-angle X-ray scattering - G-actin globular monomeric actin - F-actin filamentous polymerized actin Correspondence to: E. Pajot-Augy     

X-ray, neutron and NMR studies of the catalytic mechanism of aspartic proteinases

Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing non-hydrolysable analogues of the scissile peptide bond. Until recent years, the positions of protons on the catalytic aspartates and the ligand in these complexes had not been determined with certainty due to the inadequate resolution of these analyses. There has been much interest in locating the catalytic protons at the active site of aspartic proteinases since this has major implications for detailed understanding of the mechanism of action and the design of improved transition state mimics for therapeutic applications. In this review we discuss the results of studies which have shed light on the locations of protons at the catalytic centre. The first direct determination of the proton positions stemmed from neutron diffraction data collected from crystals of the fungal aspartic proteinase endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex at a resolution of 2.1 A provided evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. Atomic resolution X-ray studies of inhibitor complexes have corroborated this finding. A similar study of the native enzyme established that it, unexpectedly, has a dipeptide bound at the catalytic site which is consistent with classical reports of inhibition by short peptides and the ability of pepsins to catalyse transpeptidation reactions. Studies by NMR have confirmed the findings of low-barrier and single-well hydrogen bonds in the complexes with transition state analogues.     

Amylose conformation in aqueous solution: a small-angle X-ray scattering study

An investigation of the small-angle X-ray scattering properties of aqueous solutions of an amylose derivative has been carried out. Experiments have been conducted in stable and fairly concentrated polymer solutions (up to 3.2%) by using a slightly substituted carboxymethylamylose having a degree of substitution of 0.08. Scattering intensities display a maximum in the low angle range which prevents extrapolation of the angular dependence to zero angle. Data obtained in the range of scattering vector 0.01<η<0.1Å^?1 yield 8 Å as the radius of gyration of the chain cross-section and 140 dalton Å^?1 as the mass per unit length. These results are analysed in terms of the current model of amylose solution conformation and compared with the theoretical calculations of the Debye scattering function of the isolated chain.     

Fast compaction of alpha-lactalbumin during folding studied by stopped-flow X-ray scattering

To monitor the fast compaction process during protein folding, we have used a stopped-flow small-angle X-ray scattering technique combined with a two-dimensional charge-coupled device-based X-ray detector that makes it possible to improve the signal-to-noise ratio of data dramatically, and measured the kinetic refolding reaction of alpha-lactalbumin. The results clearly show that the radius of gyration and the overall shape of the kinetic folding intermediate of alpha-lactalbumin are the same as those of the molten globule state observed at equilibrium. Thus, the identity between the kinetic folding intermediate and the equilibrium molten globule state is firmly established. The present results also suggest that the folding intermediate is more hydrated than the native state and that the hydrated water molecules are dehydrated when specific side-chain packing is formed during the change from the molten globule to the native state.     

Dynamics of hydration water in deuterated purple membranes explored by neutron scattering

The function and dynamics of proteins depend on their direct environment, and much evidence has pointed to a strong coupling between water and protein motions. Recently however, neutron scattering measurements on deuterated and natural-abundance purple membrane (PM), hydrated in H(2)O and D(2)O, respectively, revealed that membrane and water motions on the ns-ps time scale are not directly coupled below 260 K (Wood et al. in Proc Natl Acad Sci USA 104:18049-18054, 2007). In the initial study, samples with a high level of hydration were measured. Here, we have measured the dynamics of PM and water separately, at a low-hydration level corresponding to the first layer of hydration water only. As in the case of the higher hydration samples previously studied, the dynamics of PM and water display different temperature dependencies, with a transition in the hydration water at 200 K not triggering a transition in the membrane at the same temperature. Furthermore, neutron diffraction experiments were carried out to monitor the lamellar spacing of a flash-cooled deuterated PM stack hydrated in H(2)O as a function of temperature. At 200 K, a sudden decrease in lamellar spacing indicated the onset of long-range translational water diffusion in the second hydration layer as has already been observed on flash-cooled natural-abundance PM stacks hydrated in D(2)O (Weik et al. in J Mol Biol 275:632-634, 2005), excluding thus a notable isotope effect. Our results reinforce the notion that membrane-protein dynamics may be less strongly coupled to hydration water motions than the dynamics of soluble proteins.     

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.     

Solution structure determination of monomeric human IgA2 by X-ray and neutron scattering, analytical ultracentrifugation and constrained modelling: a comparison with monomeric human IgA1

Immunoglobulin A (IgA), the most abundant human immunoglobulin, mediates immune protection at mucosal surfaces as well as in plasma. It exists as two subclasses IgA1 and IgA2, and IgA2 is found in at least two allotypic forms, IgA2m(1) or IgA2m(2). Compared to IgA1, IgA2 has a much shorter hinge region, which joins the two Fab and one Fc fragments. In order to assess its solution structure, monomeric recombinant IgA2m(1) was studied by X-ray and neutron scattering. Its Guinier X-ray radius of gyration R(G) is 5.18 nm and its neutron R(G) is 5.03 nm, both of which are significantly smaller than those for monomeric IgA1 at 6.1-6.2 nm. The distance distribution function P(r)for IgA2m(1) showed a broad peak with a subpeak and gave a maximum dimension of 17 nm, in contrast to the P(r) curve for IgA1, which showed two distinct peaks and a maximum dimension of 21 nm. The sedimentation coefficients of IgA1 and IgA2m(1) were 6.2S and 6.4S, respectively. These data show that the solution structure of IgA2m(1) is significantly more compact than IgA1. The complete monomeric IgA2m(1) structure was modelled using molecular dynamics to generate random IgA2 hinge structures, to which homology models for the Fab and Fc fragments were connected to generate 10,000 full models. A total of 104 compact best-fit IgA2m(1) models gave good curve fits. These best-fit models were modified by linking the two Fab light chains with a disulphide bridge that is found in IgA2m(1), and subjecting these to energy refinement to optimise this linkage. The averaged solution structure of the arrangement of the Fab and Fc fragments in IgA2m(1) was found to be predominantly T-shaped and flexible, but also included Y-shaped structures. The IgA2 models show full steric access to the two FcalphaRI-binding sites at the Calpha2-Calpha3 interdomain region in the Fc fragment. Since previous scattering modelling had shown that IgA1 also possessed a flexible T-shaped solution structure, such a T-shape may be common to both IgA1 and IgA2. The final models suggest that the combination of the more compact IgA2m(1) and the more extended IgA1 structures will enable human IgA to access a broader range of antigens than either acting alone. The hinges of both IgA subclasses appear to show reduced flexibility when compared to their equivalents in IgG, and this may be important for maintaining an extended IgA structure.