Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data

Determination of the 3D structures of multidomain proteins by solution NMR methods presents a number of unique challenges related to their larger molecular size and the usual scarcity of constraints at the interdomain interface, often resulting in a decrease in structural accuracy. In this respect, experimental information from small-angle scattering of X-ray radiation in solution (SAXS) presents a suitable complement to the NMR data, as it provides an independent constraint on the overall molecular shape. A computational procedure is described that allows incorporation of such SAXS data into the mainstream high-resolution macromolecular structure refinement. The method is illustrated for a two-domain 177-amino-acid protein, gammaS crystallin, using an experimental SAXS data set fitted at resolutions from approximately 200 A to approximately 30 A. Inclusion of these data during structure refinement decreases the backbone coordinate root-mean-square difference between the derived model and the high-resolution crystal structure of a 54% homologous gammaB crystallin from 1.96 +/- 0.07 A to 1.31 +/- 0.04 A. Combining SAXS data with NMR restraints can be accomplished at a moderate computational expense and is expected to become useful for multidomain proteins, multimeric assemblies, and tight macromolecular complexes.     

Protein structural dynamics of photoactive yellow protein in solution revealed by pump-probe X-ray solution scattering

Photoreceptor proteins play crucial roles in receiving light stimuli that give rise to the responses required for biological function. However, structural characterization of conformational transition of the photoreceptors has been elusive in their native aqueous environment, even for a prototype photoreceptor, photoactive yellow protein (PYP). We employ pump-probe X-ray solution scattering to probe the structural changes that occur during the photocycle of PYP in a wide time range from 3.16 μs to 300 ms. By the analysis of both kinetics and structures of the intermediates, the structural progression of the protein in the solution phase is vividly visualized. We identify four structurally distinct intermediates and their associated five time constants and reconstructed the molecular shapes of the four intermediates from time-independent, species-associated difference scattering curves. The reconstructed structures of the intermediates show the large conformational changes such as the protrusion of N-terminus, which is restricted in the crystalline phase due to the crystal contact and thus could not be clearly observed by X-ray crystallography. The protrusion of the N-terminus and the protein volume gradually increase with the progress of the photocycle and becomes maximal in the final intermediate, which is proposed to be the signaling state. The data not only reveal that a common kinetic mechanism is applicable to both the crystalline and the solution phases, but also provide direct evidence for how the sample environment influences structural dynamics and the reaction rates of the PYP photocycle.     

Mineral–water interfacial structures revealed by synchrotron X-ray scattering

Chemical reactions occurring at the mineral–water interface are controlled by an interfacial layer, nanometers thick, whose properties may deviate from those of the respective bulk mineral and water phases. The molecular-scale structure of this interfacial layer, however, is poorly constrained, and correlations between macroscopic phenomena and molecular-scale processes remain speculative. The application of high-resolution X-ray scattering techniques has begun to provide substantial new insights into the molecular-scale structure of the mineral–water interface. In this review, we describe the characteristics of synchrotron-based X-ray scattering techniques that make them uniquely powerful probes of mineral–water interfacial structures and discuss the new insights that have been derived from their application. In particular, we focus on efforts to understand the structure and distribution of interfacial water as well as their dependence on substrate properties for major mineral classes including oxides, carbonates, sulfates, phosphates, silicates, halides and chromates. We compare these X-ray scattering results with those from other structural and spectroscopic techniques and integrate these to provide a conceptual framework upon which to base an understanding of the systematic variation of mineral–water interfacial structures.     

Analysis of small-angle scattering data from colloids and polymer solutions: modeling and least-squares fitting

Analysis and modeling of small-angle scattering data from systems consisting of colloidal particles or polymers in solution are discussed. The analysis requires application of least-squares methods, and the basic principles of linear and non-linear leastsquares methods are summarized with emphasis on applications in the analysis of small-angle scattering data. These include indirect Fourier transformation, square-root deconvolution, size distribution determinations, and modeling. The inclusion of corrections for instrumental smearing effects is also discussed. The most common analytical expressions for model form factors and structure factors are summarized. An example of analysis of small-angle neutron and X-ray scattering data from block copolymer micelles is given.     

Small-angle X-ray scattering and structural modeling of full-length: cellobiohydrolase I from Trichoderma harzianum

Cellobiohydrolases hydrolyze cellulose releasing cellobiose units. They are very important for a number of biotechnological applications, such as, for example, production of cellulosic ethanol and cotton fiber processing. The Trichoderma cellobiohydrolase I (CBH1 or Cel7A) is an industrially important exocellulase. It exhibits a typical two domain architecture, with a small C-terminal cellulose-binding domain and a large N-terminal catalytic core domain, connected by an O-glycosylated linker peptide. The mechanism by which the linker mediates the concerted action of the two domains remains a conundrum. Here, we probe the protein shape and domain organization of the CBH1 of Trichoderma harzianum (ThCel7A) by small angle X-ray scattering (SAXS) and structural modeling. Our SAXS data shows that ThCel7A linker is partially-extended in solution. Structural modeling suggests that this linker conformation is stabilized by inter- and intra-molecular interactions involving the linker peptide and its O-glycosylations.     

Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles

With the advent of powerful synchrotron sources, solution X-ray scattering is being increasingly used to get basic information about the structure of polypeptides. The solution scattering technique essentially provides one-dimensional data, which are then interpreted in terms of a three-dimensional structure through model building. Here we calculate wide-angle solution scattering patterns for an ensemble of simulated unfolded structures of villin headpiece, which differ from the native structure by rmsd = 8.8 +/- 1.0 A and have only negligible amounts of native secondary structure. We show that the wide-angle solution scattering pattern of such an ensemble shares significant similarity with the one based on the experimental NMR structures of the molecule. Our results suggest that solution scattering in the wide-angle limit, by itself, provides very little information about the secondary structure content of a polypeptide or its side-chain packing.     

Direct observation of cooperative protein structural dynamics of homodimeric hemoglobin from 100 ps to 10 ms with pump-probe X-ray solution scattering

Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps to 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I(1), I(2), and I(3)) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme-heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I(1) intermediate is generated within 100 ps and transforms to the R-like I(2) intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I(3) intermediate is formed via subunit rotation, a decrease in the heme-heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 μs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I(3) intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme-heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics.     

Mn(II) staircase structures stitched by water clusters to a 3D metal-organic open framework: X-ray structural and magnetic studies

4-Hydroxypyridine-2,6-dicarboxylic acid (chelidamic acid, cdaH2) reacts with Mn(OAc)2 x 4H2O to form a 1D staircase structure with dimeric Mn(II) units connected by water clusters to form a 3D framework, {[Mn2(cda)2 x 4H2O] x 4H2O}n, 1, in aqueous pyridine at room temperature. The compound crystallizes in the triclinic space group P1 with a = 9.495(3), b =10.733(5), c = 11.065(4) A, alpha = 87.42(5), beta = 74.14(5), gamma = 80.07(2) degrees, U = 1068.5(9) A3, Z = 2, rho(calcd) = 1.915 g cm(-3), T = 100 K, mu = 1.28 mm(-1), R1 = 0.0453 (I > 2sigma(I)), wR2 = 0.1046, GOOF = 1.282. Upon removal of the water molecules by heating, the 3D structure breaks down. Thermogravimetric analysis, infrared, X-ray powder diffraction studies, and X-ray crystallography were performed to characterize this compound. Since the coordination polymer has diaqua-bridged Mn(II) centers, it was subjected to variable-temperature magnetic studies.     

A structural development of an organogel explored by synchrotron time-resolved small-angle X-ray scattering

We investigated the gelation process of 12-hydroxystearic acid (12-HSA)/dodecane gel (turbid gel), 12-HSA/xylene and 12-HSA/toluene gels (transparent gels) by using time-resolved synchrotron small-angle X-ray scattering technique. The fibers were developed via nucleation and growth mechanism, and the induction period was longer at higher temperatures. After the induction period, the fiber growth can be divided into two regimes. In the first stage, the scattering intensity increased with time without appearance of any crystalline peak, and in the second stage (001) peak appeared due to crystalline nucleation. In the former regime, the fibers grew with increasing the cross-sectional size, while in the latter regime, they grew with keeping it almost constant, i.e., with keeping the fiber thickness constant. The fiber thickness for the turbid gel (radius of the gyration R _c of ～100 Å) was thicker than that for the transparent gel (R _c of ～82 Å). The fractal dimensions of the fibrillar aggregates for the turbid gels (2.0–2.3) at various temperatures were larger than those for the transparent gels (1.4–1.6), suggesting that the structure of the former gels is more branching or more compact in comparison with the latter.     

Investigation of structural changes in semi-crystalline polymers during deformation by synchrotron X-ray scattering

The mechanical behavior of polymer materials is strongly dependent on polymer structure and morphology of the material. The latter is determined mainly by processing and thermal history. Temperature-dependent on-line X-ray scattering during deformation enables the investigation of deformation processes, fatigue and failure of polymers. As an example, investigations on polypropylene are presented. By on-line X-ray scattering with synchrotron radiation, a time resolution in the order of seconds and a spatial resolution in the order of microns can be achieved. The characterization of the crystalline and amorphous phases as well as the study of cavitation processes were performed by simultaneous SAXS and WAXS. The results of scattering experiments are complemented by DSC measurements and SEM investigations. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1574–1586, 2010     

Studies of electrode structures and dynamics using coherent X-ray scattering and imaging

1. Download : Download high-res image (191KB)
2. Download : Download full-size image

     

X-ray scattering intensities of water at extreme pressure and temperature

We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure using the ab initio density functional theory (DFT). Our calculations span the molecular liquid, ice VII, and superionic solid phases, including the recently predicted symmetrically hydrogen bonded region. We compute simulated spectra for ice VII and superionic water. We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We show that our modified atomic form factors allow for a nearly exact comparison with the total x-ray scattering intensities calculated from DFT. Finally, we analyze the effect of their new form factors have on the determination of the oxygen-oxygen radial distribution function from experiment.     

Arsenate incorporation in gypsum probed by neutron, X-ray scattering and density functional theory modeling

The ability of gypsum, a common sulfate mineral, to host arsenic atoms in its crystalline structure, is demonstrated through experimental structural studies of the solid solutions formed upon synthetic coprecipitation of gypsum (CaSO4 x 2 H2O) and arsenic. Neutron and X-ray diffraction methods show an enlargement of the gypsum unit cell proportional to the concentration of arsenic in the solids and to the pH solution value. The substitution of sulfate ions (SO4(2-)) by arsenate ions is shown to be more likely under alkaline conditions, where the HAsO4(2-) species predominates. A theoretical Density Functional Theory model of the arsenic-doped gypsum structure reproduces the experimental volume expansion. Extended X-ray Absorption Fine Structure (EXAFS) measurements of the local structure around the arsenic atom in the coprecipitated solids confirm solid state substitution and allow some refinement of the local structure, corroborating the theoretical structure found in the simulations. The charge redistribution within the structure upon substitutions of either the protonated or the unprotonated arsenate species studied by means of Mulliken Population Analyses demonstrates an increase in the covalency in the interaction between Ca(2+) and AsO4(3-), whereas the interaction between Ca(2+) and HAsO4(2-) remains predominantly ionic.     

On the interpretation of small-angle X-ray scattering during water adsorption by carbon adsorbents

Two models accounting for the changes of shape of the small-angle X-ray scattering (SAXS) curves during water adsorption by carbon adsorbents are discussed. The first model is based on the assumption of partial filling of the pore space; the second one presumes micropore swelling during water adsorption. Analysis of the results allows one to conclude that the first model is valid. This conclusion is in agreement with adsorption investigation data.Deseased 1993.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1220–1223, July, 1993.     

A comparative study of immunoglobulin IgM and rheumatoid factor IgMRF in solution by small-angle X-ray scattering

The shapes of rheumatoid factor molecules calculated from X-ray small-angle solution scattering data suggest that the peripheral Fab regions of rheumatoid factor in solution are more flocculent because of a higher flexibility of Fab domains.     

Analysis of small-angle scattering data from micelles and microemulsions: free-form approaches and model fitting

The free-form methods for analyzing small-angle scattering data have, during the last years, found more widespread use for micelles and microemulsions. Recent developments have made them applicable also to systems with size polydispersity and particle correlations, however, model fitting still constitutes a very important and partly complementary analysis tool.     

Quantification of RNA in bacteriophage MS2-like viruses in solution by small-angle X-ray scattering

Recombinant forms of bacteriophage MS2 virus particles, wild-type MS2 and MS2 capsids have been examined in solution using small-angle X-ray scattering (SAXS). SAXS was used to determine the overall size of the virus particles and to quantify the amount of encapsulated viral RNA. These studies show that analysis of natural and recombinant forms of MS2 virus by SAXS can be used as both a quantitative measure of nucleic acid content in situ and diagnostic indicator of sample integrity.