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.     

Contrast-Matched Small-Angle X-ray Scattering from a Heavy-Atom-Labeled Protein in Structure Determination: Application to a Lead-Substituted Calmodulin-Peptide Complex

The information content in 1-D solution X-ray scattering profiles is generally restricted to low-resolution shape and size information that, on its own, cannot lead to unique 3-D structures of biological macromolecules comparable to all-atom models derived from X-ray crystallography or NMR spectroscopy. Here we show that contrast-matched X-ray scattering data collected on a protein incorporating specific heavy-atom labels in 65% aqueous sucrose buffer can dramatically enhance the power of conventional small- and wide-angle X-ray scattering (SAXS/WAXS) measurements. Under contrast-matching conditions the protein is effectively invisible and the main contribution to the X-ray scattering intensity arises from the heavy atoms, allowing direct extraction of pairwise distances between them. In combination with conventional aqueous SAXS/WAXS data, supplemented by NMR-derived residual dipolar couplings (RDCs) measured in a weakly aligning medium, we show that it is possible to position protein domains relative to one another within a precision of 1 ?. We demonstrate this approach with respect to the determination of domain positions in a complex between calmodulin, in which the four Ca(2+) ions have been substituted by Pb(2+), and a target peptide. The uniqueness of the resulting solution is established by an exhaustive search over all models compatible with the experimental data, and could not have been achieved using aqueous SAXS and RDC data alone. Moreover, we show that the correct structural solution can be recovered using only contrast-matched SAXS and aqueous SAXS/WAXS data.     

Proton Transverse Relaxation as a Sensitive Probe for Structure Determination in Solid Proteins

Solid‐state nuclear magnetic resonance (NMR) spectroscopy has been successfully applied to elucidate the atomic‐resolution structures of insoluble proteins. The major bottleneck is the difficulty to obtain valuable long‐distance structural information. Here, we propose the use of distance restraints as long as 32 Å, obtained from the quantification of transverse proton relaxation induced by a methanethiosulfonate spin label (MTSL). Combined with dipolar proton–proton distance restraints, this method allows us to obtain protein structures with excellent precision from single spin‐labeled 1 mg protein samples using fast magic angle spinning.     

X-ray study of microstructure of slightly plasticized poly-(vinylchloride) (PVC)

Small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS) as well as transmission electron microscopy (TEM) techniques have been applied to investigate the microstructure of a number of commercial poly-(vinylchloride) (PVC) samples, stretched 200% and annealed for 1 h at 110 °C. From SAXS analysis, the microstructure is described as an ensemble of quasi-spherical particles one-dimensionally ordered (in the fiber axis direction) and with large distance fluctuations in the equatorial plane. The superstructure is described as fibrillar or nematic-like. TEM micrographs confirm the SAXS data.SAXS meridional patterns present 001 and 003 reflections of Ca-stearate added as stabilizer to the samples, while WAXS profiles do not show any crystalline reflection of Castearate.An interaction of Ca-stearate molecules with PVC chains is postulated, which could partially account for the phenomenon called antiplasticization of PVC.     

Structural and morphological studies on the deformation behavior of polypropylene/multi‐walled carbon nanotubes nanocomposites prepared through ultrasound‐assisted melt extrusion process

Structural and morphological behavior under stress–strain of polypropylene/multi‐walled carbon nanotubes (PP/MWCNTs) nanocomposites prepared through ultrasound‐assisted melt extrusion process was studied by means of optical microscopy, scanning electron microscopy, transmission electron microscopy, Raman spectroscopy, small angle X‐ray scattering (SAXS), and wide angle X‐ray scattering (WAXS). A high ductile behavior was observed in the PP/MWCNT nanocomposites with low concentration of MWCNTs. This was related to an energy‐dissipating mechanism, achieved by the formation of an ordered PP‐CNTs interphase zone and crystal oriented structure in the undeformed samples. Different strain‐induced‐phase transformations were observed by ex situ SAXS/WAXS, characterizing the different stages of structure development during the deformation of PP and PP/MWCNTs nanocomposites. The high concentration of CNTs reduced the strain behavior of PP due to the agglomeration of nanoparticles. A structural pathway relating the deformation‐induced phase transitions and the dissipation energy mechanism in the PP/MWCNTs nanocomposites at low concentration of nanoparticles was proposed. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 475–491     

Compound formation and solvent (dis)ordering in syndiotactic polystyrene/benzylmethacrylate systems

In-situ small- and wide-angle X-ray scattering (SAXS and WAXS) experiments combined with Raman spectroscopy have been performed to study the phase behaviour of syndiotactic polystyrene (sPS) and benzylmethacrylate (BzMA). In the quenched gels, sPS adopts a helical conformation which is stabilised by the solvent molecules, in fact compound formation occurs. From the combined experimental data it was concluded that two different structural modifications exist within the solvent-included helical δ-phase, respectively the δ' phase in which the solvent molecules are intercalated and ordered between the phenyl rings of sPS and a δ” phase where this solvent ordering is lost.     

Thermodynamic, structural, and nanomechanical properties of a fluorous biphasic material

The dynamics of the amphiphilic semifluorinated F(CF2)12(CH2)12H (F12H12) alkane that undergoes two condensed phase transitions have been investigated by Brillouin light spectroscopy, shear rheometry, small- (SAXS) and wide-angle (WAXS) X-ray scattering, and thermodynamic PVT measurements. The solid (I)-solid (II) transition (Ts) is marked by a stronger temperature dependence of the sound velocity in phase II and by a 2 orders of magnitude drop of the shear modulus. Between the Ts and the melting transition (Tm), the presence of two phonons implies a coexistence of solid (II) and amorphous (liquid) regions in the submicrometer range at thermal equilibrium as revealed by the SAXS pattern of a single reflection superimposed on a very broad amorphous halo. This intriguing finding of a transient, very slow (over 10 h) solid/liquid coexistence within phase II is rationalized by a two-stage mechanism for melting of the smectic phase (II) of F12H12. A refinement of the known packing motifs for the two solid-state structures is proposed.     

Initial characterization of the primary photochemistry of AppA, a blue-light-using flavin adenine dinucleotide-domain containing transcriptional antirepressor protein from Rhodobacter sphaeroides: a key role for reversible intramolecular proton transfer from the flavin adenine dinucleotide chromophore to a conserved tyrosine?

The flavin adenine dinucleotide (FAD)-containing photoreceptor protein AppA (in which the FAD is bound to a novel so-called BLUF domain) from the purple nonsulfur bacterium Rhodobacter sphaeroides was previously shown to be photoactive by the formation of a slightly redshifted long-lived intermediate that is thought to be the signaling state. In this study, we provide further characterization of the primary photochemistry of this photoreceptor protein using UV-Vis and Fourier-transform infrared spectroscopy, pH measurements and site-directed mutagenesis. Available evidence indicates that the FAD chromophore of AppA may be protonated in the receptor state, and that it becomes exposed to solvent in the signaling state. Furthermore, experimental data lead to the suggestion that intramolecular proton transfer (that may involve [anionic] Tyr-17) forms the basis for the stabilization of the signaling state.     

Microfibril diameter in celery collenchyma cellulose: X-ray scattering and NMR evidence

Cellulose isolated from celery collenchyma is typical of the low-crystallinity celluloses that can be isolated from primary cell-walls of higher plants, except that it is oriented with high uniformity. The diameter of the microfibrils of celery collenchyma cellulose was estimated by three separate approaches: ¹³C NMR measurement of the ratio of surface to interior chains; estimation of the dimensions of the crystalline lattice from wide angle X-ray scattering (WAXS) measurements using the Scherrer equation; and the observation that microfibrils of this form of cellulose have the unusual property of packing into an irregular array from which small angle X-ray scattering (SAXS) shows features of both form and interference functions. The interference function contributing to the SAXS pattern implied a mean microfibril centre-to-centre distance of 3.6 nm, providing an upper limit for the diameter. However modelling of the scattering pattern from an irregular array of microfibrils showed that the observed scattering curve could be matched at a range of diameters down to 2.4 nm, with the intervening space more or less sparsely occupied by hemicellulose chains. The lateral extent of the crystalline lattice normal to the 200 plane was estimated as a minimum of 2.4 nm by WAXS through the Scherrer equation, and a diameter of 2.6 nm was implied by the surface: volume ratio determined by ¹³C NMR. The WAXS and NMR measurements both depended on the assumption that the surface chains were positioned within an extension of the crystalline lattice. The reliability of this assumption is uncertain. If the surface chains deviated from the lattice, both the WAXS and the NMR data would imply larger microfibril diameters within the range consistent with the SAXS pattern. The evidence presented is therefore all consistent with microfibril diameters from about 2.4 to 3.6 nm, larger than has previously been suggested for primary-wall cellulose. Some degree of aggregation may have occurred during the isolation of the cellulose, but the larger microfibril diameters within the range proposed are a consequence of the novel interpretation of the experimental data from WAXS and NMR and are consistent with previously published data if these are similarly interpreted.     

Structural characterization of proteins with an attached ATCUN motif by paramagnetic relaxation enhancement NMR spectroscopy

The use of a short, three-residue Cu(2+)-binding sequence, the ATCUN motif, is presented as an approach for extracting long-range distance restraints from relaxation enhancement NMR spectroscopy. The ATCUN motif is prepended to the N-termini of proteins and binds Cu(2+) with a very high affinity. Relaxation rates of amide protons in ATCUN-tagged protein in the presence and absence of Cu(2+) can be converted into distance restraints and used for structure refinement by using a new routine, PMAG, that has been written for the structure calculation program CNS. The utility of the approach is demonstrated with an application to ATCUN-tagged ubiquitin. Excellent agreement between measured relaxation rates and those calculated on the basis of the X-ray structure of the protein have been obtained.     

MLCT state structure and dynamics of a copper(I) diimine complex characterized by pump-probe X-ray and laser spectroscopies and DFT calculations

The molecular structure and dynamics of the photoexcited metal-to-ligand-charge-transfer (MLCT) state of [Cu(I)(dmp)(2)](+), where dmp is 2,9-dimethyl-1,10-phenanthroline, in acetonitrile have been investigated by time-domain pump-probe X-ray absorption spectroscopy, femtosecond optical transient spectroscopy, and density functional theory (DFT). The time resolution for the excited state structural determination was 100 ps, provided by single X-ray pulses from a third generation synchrotron source. The copper ion in the thermally equilibrated MLCT state has the same oxidation state as the corresponding copper(II) complex in the ground state and was found to be penta-coordinate with an average nearest neighbor Cu-N distance 0.04 A shorter than that of the ground state [Cu(I)(dmp)(2)](+). The results confirm the previously proposed "exciplex" structure of the MLCT state in Lewis basic solvents. The evolution from the photoexcited Franck-Condon MLCT state to the thermally equilibrated MLCT state was followed by femtosecond optical transient spectroscopy, revealing three time constants of 500-700 fs, 10-20 ps, and 1.6-1.7 ns, likely related to the kinetics for the formation of the triplet MLCT state, structural relaxation, and the MLCT excited-state decay to the ground state, respectively. DFT calculations are used to interpret the spectral shift on structural relaxation and to predict the geometries of the ground state, the tetracoordinate excited state, and the exciplex. The DFT calculations also indicate that the amount of charge transferred from copper to the dmp ligand upon photoexcitation is similar to the charge difference at the copper center between the ground-state copper(I) and copper(II) complexes.     

Investigation by combined solid‐state NMR and SAXS methods of the morphology and domain size in polystyrene‐b‐polyethylene oxide‐b‐polystyrene triblock copolymers

The microphase structure of a series of polystyrene‐b‐polyethylene oxide‐b‐polystyrene (SEOS) triblock copolymers with different compositions and molecular weights has been studied by solid‐state NMR, DSC, wide and small angle X‐ray scattering (WAXS and SAXS). WAXS and DSC measurements were used to detect the presence of crystalline domains of polyethylene‐oxide (PEO) blocks at room temperature as a function of the copolymer chemical composition. Furthermore, DSC experiments allowed the determination of the melting temperatures of the crystalline part of the PEO blocks. SAXS measurements, performed above and below the melting temperature of the PEO blocks, revealed the formation of periodic structures, but the absence or the weakness of high order reflections peaks did not allow a clear assessment of the morphological structure of the copolymers. This information was inferred by combining the results obtained by SAXS and ¹H NMR spin diffusion experiments, which also provided an estimation of the size of the dispersed phases of the nanostructured copolymers. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 55–64, 2010     

Evaluation of new organosolv dissolving pulps. Part II: Structure and NMMO processability of the pulps

The supermolecular structure of dissolving pulps produced from hardwood by the organosolv processes Acetosolv, Formacell, and Milox was characterized by physical methods (TEM, WAXS, SAXS, NMR) and compared with conventional Sulfite and standard commercial dissolving pulps. The suitability of the pulps for the NMMO technology was tested by spinning fibres and blowing films, whose structural and mechanical properties have also been determined. With TEM it was shown that the TCF-bleached organosolv pulps have only the primary (Formacell), the primary and S1 (Milox), or mainly the S1 (Acetosolv) layers exposed to the surface, whereas Sulfite pulping exposes the S2 cell wall layer. Especially for Milox and Acetosolv Eucalyptus wood pulps, a reduced degree of crystallinity was found, both with WAXS and NMR. The SAXS results indicate a lower pore intersection length for the new pulps as compared to conventional pulps. Unbleached organosolv pulps show a lower crystallinity, very low pore intersection lengths, and an average crystallite shape different from their bleached counterparts. The dissolution behaviour in NMMO and the processability of the bleached organosolv pulps was satisfactory so far. Fibres and films could be produced with structural and mechanical properties comparable with conventional Sulfite and standard commercial dissolving pulp products. However, unbleached organosolv pulps did not meet the requirements of the NMMO process.     

In situ SAXS investigation of dibromomethane adsorption in ordered mesoporous silica

A SAXS/WAXS apparatus with the aid of a specially designed sample cell capable for performing both SAXS and WAXS experiments was used for adsorption studies in nanoporous materials. The applicability of the instrument for structural investigations and its ability for adsorption experiments because of the advanced sample environment were demonstrated by carrying out in situ SAXS measurements during gas physisorption. SAXS profiles of ordered mesoporous silica were measured at selected equilibrium points alongside a dibromomethane (CH₂Br₂) adsorption isotherm at 293 K. SBA-15 was the adsorbent of choice because it consists of a regular 2D hexagonal array of cylindrical mesopores that gives rise to Bragg reflections in the small-angle regime. CH₂Br₂ was selected as a contrast-matching fluid because it has almost the same electron density as silica. We obtained high-quality data comparable to those resulting from experiments performed in synchrotron light sources which produce intense beams of x-rays and support advanced instrumentation for high-resolution diffraction and SAXS studies. The Bragg peaks of the pore lattice are clearly visible for the evacuated sample and at the early stages of the adsorption process. The intensity decrease and the elimination of the Bragg peaks for the saturated sample suggest that an almost perfect contrast matching was achieved. A model has been used for monitoring the fluid condensation and evaporation regime in SBA-15 by taking into account both the Bragg scattering and the diffuse scattering for spatially random pore filling. The results show the absence of spatial correlations between filled pores suggesting random pore filling.     

A Two-Armed Probe for In-Cell DEER Measurements on Proteins**

The application of double electron-electron resonance (DEER) with site-directed spin labeling (SDSL) to measure distances in proteins and protein complexes in living cells puts rigorous restraints on the spin-label. The linkage and paramagnetic centers need to resist the reducing conditions of the cell. Rigid attachment of the probe to the protein improves precision of the measured distances. Here, three two-armed Gd^III complexes, Gd^III-CLaNP13a/b/c were synthesized. Rather than the disulfide linkage of most other CLaNP molecules, a thioether linkage was used to avoid reductive dissociation of the linker. The doubly Gd^III labeled N55C/V57C/K147C/T151C variants of T4Lysozyme were measured by 95 GHz DEER. The constructs were measured in vitro, in cell lysate and in Dictyostelium discoideum cells. Measured distances were 4.5 nm, consistent with results from paramagnetic NMR. A narrow distance distribution and typical modulation depth, also in cell, indicate complete and durable labeling and probe rigidity due to the dual attachment sites.     

Micro‐phase‐separation behavior of amphiphilic polyurethanes involving poly(ethylene oxide) and poly(tetramethylene oxide)

The temperature dependence of thermal, morphological, and rheological properties of amphiphilic polyurethanes was examined with differential scanning calorimetry (DSC), wide‐angle X‐ray scattering (WAXS), small‐angle X‐ray scattering (SAXS), rheological measurements, and Fourier transform infrared spectroscopy. Multiblock (MPU) and triblock (TPU) polyurethanes were synthesized with two crystallizable segments—poly(ethylene oxide) (PEO) as a hydrophilic block and poly(tetramethylene oxide) (PTMO) as a hydrophobic block. DSC and WAXS measurements demonstrated that the microphase of MPUs in the solid state is dominantly affected by the PEO crystalline phase. However, high‐order peaks were not observed in the SAXS measurements because the crystallization of the PEO segments in MPUs was retarded by poor sequence regularity. The microphase in the melt state was induced by the hydrogen bonding between the N? H group of hexamethylene diisocyanate linkers and the ether oxygen of PEO or PTMO blocks. As the temperature increased, the smaller micro‐phase‐separated domains were merged into the larger domains, and the liquidlike ordering was eventually disrupted because of the weakening hydrogen bonding. However, the fully homogeneous state of an MPU with a molar ratio of 5/5 PEO/PTMO (MPU55) was not confirmed even at much higher temperatures with both SAXS and rheological measurements. However, the SAXS patterns of TPU showed weak but broad second‐order peaks below the melting temperature of the PEO block. Compared with MPU55, the ordering of the TPU crystalline lamellar stacks was enhanced because of the high sequence regularity and the low hydrogen‐bonding density. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2365–2374, 2003     

Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex

Nuclear magnetic resonance (NMR) spectroscopy provides a range of powerful techniques for determining the structures and the dynamics of proteins. The high-resolution determination of the structures of protein-protein complexes, however, is still a challenging problem for this approach, since it can normally provide only a limited amount of structural information at protein-protein interfaces. We present here the determination using NMR chemical shifts of the structure (PDB code 2K5X) of the cytotoxic endonuclease domain from bacterial toxin colicin (E9) in complex with its cognate immunity protein (Im9). In order to achieve this result, we introduce the CamDock method, which combines a flexible docking procedure with a refinement that exploits the structural information provided by chemical shifts. The results that we report thus indicate that chemical shifts can be used as structural restraints for the determination of the conformations of protein complexes that are difficult to obtain by more standard NMR approaches.     

Excited state dynamics and fragmentation channels of the protonated dipeptide H2N-Leu-Trp-COOH

The excited state dynamics of the isolated and protonated peptide H(2)N-Leu-Trp-COOH are analyzed by fs pump-probe spectroscopy. The peptides are brought into the gas phase by electrospray ionization, and fs pump-probe excitation is detected by fragment ion formation. The pump laser addressed the excited pipi* state of the indole chromophore of the amino acid tryptophan. The subsequent excited state dynamics agreed with a biexponential decay with time constants of 500 fs and 10 ps. This is considerably shorter than the lifetime of neutral tryptophan in solution and in proteins, but similar to isolated, protonated tryptophan. Several models are discussed to explain the experimental results but the detailed quenching mechanism remains unresolved.