BioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software is designed for biological SAXS data and enables creation and plotting of one-dimensional scattering profiles from twodimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and advanced analysis such as calculation of inverse Fourier transforms and envelopes. It also allows easy processing of inline size-exclusion chromatography coupled SAXS data and data deconvolution using the evolving factor analysis method. It provides an alternative to closed-source programs such as Primus and ScÅ tter for primary data analysis. Because it can calibrate, mask and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.

Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.DOI: http://dx.doi.org/10.7554/eLife.07574.001

Diffuse reflectance infrared (IR) spectroscopy performed over a wide temperature range (35-298 K) is used to study the dynamics of H(2) adsorbed within the isostructural metal-organic frameworks M(2)L (M = Mg, Mn, Co, Ni and Zn; L = 2,5-dioxidobenzene-1,4-dicarboxylate) referred to as MOF-74 and CPO-27. Spectra collected at H(2) concentrations ranging from 0.1 to 3.0 H(2) per metal cation reveal that strongly red-shifted vibrational modes arise from isolated H(2) bound to the available metal coordination site. The red shift of the bands associated with this site correlate with reported isosteric enthalpies of adsorption (at small surface coverage), which in turn depend on the identity of M. In contrast, the bands assigned to H(2) adsorbed at positions >3 Å from the metal site exhibit only minor differences among the five materials. Our results are consistent with previous models based on neutron diffraction data and independent IR studies, but they do not support a recently proposed adsorption mechanism that invokes strong H(2)···H(2) interactions (Nijem et al. J. Am. Chem. Soc.2010, 132, 14834-14848). Room temperature IR spectra comparable to those on which the recently proposed adsorption mechanism was based were only reproduced after contaminating the adsorbent with ambient air. Our interpretation that the uncontaminated spectral features result from stepwise adsorption at discrete framework sites is reinforced by systematic red shifts of adsorbed H(2) isotopologues and consistencies among overtone bands that are well-described by the Buckingham model of molecular interactions in vibrational spectroscopy.

Small angle x-ray scattering (SAXS) is a versatile and widely used technique for obtaining low-resolution structures of macromolecules and complexes. SAXS experiments measure molecules in solution, without the need for labeling or crystallization. However, radiation damage currently limits the application of SAXS to molecules that can be produced in microgram quantities; for typical proteins, 10-20 μL of solution at 1 mg/mL is required to accumulate adequate signal before irreversible x-ray damage is observed. Here, we show that cryocooled proteins and nucleic acids can withstand doses at least two orders of magnitude larger than room temperature samples. We demonstrate accurate T = 100 K particle envelope reconstructions from sample volumes as small as 15 nL, a factor of 1000 smaller than in current practice. Cryo-SAXS will thus enable structure determination of difficult-to-express proteins and biologically important, highly radiation-sensitive proteins including light-activated switches and metalloenzymes.

Compartmentalization by liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mechanism underlying the organization of biomolecules in space and time. Here, we combine rapid-mixing time-resolved small-angle X-ray scattering (SAXS) approaches to characterize the assembly kinetics of a prototypical prion-like domain with equilibrium techniques that characterize its phase boundaries and the size distribution of clusters prior to phase separation. We find two kinetic regimes on the micro- to millisecond timescale that are distinguished by the size distribution of clusters. At the nanoscale, small complexes are formed with low affinity. After initial unfavorable complex assembly, additional monomers are added with higher affinity. At the mesoscale, assembly resembles classical homogeneous nucleation. Careful multi-pronged characterization is required for the understanding of condensate assembly mechanisms and will promote understanding of how the kinetics of biological phase separation is encoded in biomolecules.

A series of studies that provide a consistent and illuminating picture of global radiation damage to protein crystals, especially at temperatures above ∼200 K, are described. The radiation sensitivity shows a transition near 200 K, above which it appears to be limited by solvent-coupled diffusive processes. Consistent with this interpretation, a component of global damage proceeds on timescales of several minutes at 180 K, decreasing to seconds near room temperature. As a result, data collection times of order 1 s allow up to half of global damage to be outrun at 260 K. Much larger damage reductions near room temperature should be feasible using larger dose rates delivered using microfocused beams, enabling a significant expansion of structural studies of proteins under more nearly native conditions.

Diffuse reflectance infrared spectroscopy is used to measure the quantum dynamics of molecular hydrogen adsorbed in the microporous material MOF-5. Low-temperature spectra reveal at least three distinct binding sites. The induced redshifts in the vibrational mode frequencies allow the estimation of site-specific binding energies ranging from 2.5 to 4 kJ/mol. Splittings in the rovibrational sidebands are consistent with the existing theories and indicate that H 2 is relatively freely rotating even at temperatures as low as 10 K. Ortho to para conversion of the adsorbed H 2 is observed to occur over the course of several hours. A translational sideband of 84 cm −1 arises from the center-of-mass motion of H 2 at the primary adsorption site and indicates that the zero-point energy is a substantial fraction of the binding energy of this site.

Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations of the technique, such as minimum required sample volume, and of experimental design, such as sample flow cells, are necessary because the biological samples are sensitive to damage from the X-rays. Radiation damage typically manifests as aggregation of the sample, which makes the collected data unreliable. However, there has been little systematic investigation of the most effective methods to reduce damage rates, and results from previous damage studies are not easily compared with results from other beamlines. Here a methodology is provided for quantifying radiation damage in SAXS to provide consistent results between different experiments, experimenters and beamlines. These methods are demonstrated on radiation damage data collected from lysozyme, glucose isomerase and xylanase, and it is found that no single metric is sufficient to describe radiation damage in SAXS for all samples. The radius of gyration, molecular weight and integrated SAXS profile intensity constitute a minimal set of parameters that capture all types of observed behavior. Radiation sensitivities derived from these parameters show a large protein dependence, varying by up to six orders of magnitude between the different proteins tested. This work should enable consistent reporting of radiation damage effects, allowing more systematic studies of the most effective minimization strategies.