Wide‐angle X‐ray solution scattering (WAXS) patterns contain substantial information about the structure and dynamics of a protein. Solution scattering from a
The breathing motions of proteins are thought to play a critical role in function. However, current techniques to study key collective motions are limited to spectroscopy and computation. We present a high-resolution experimental approach based on the total scattering from protein crystals at room temperature (TS/RT-MX) that captures both structure and collective motions. To reveal the scattering signal from protein motions, we present a general workflow that enables robust subtraction of lattice disorder. The workflow introduces two methods: GOODVIBES, a detailed and refinable lattice disorder model based on the rigid-body vibrations of a crystalline elastic network; and DISCOBALL, an independent method of validation that estimates the displacement covariance between proteins in the lattice in real space. Here, we demonstrate the robustness of this workflow and further demonstrate how it can be interfaced with MD simulations towards obtaining high-resolution insight into functionally important protein motions.
more » « less- NSF-PAR ID:
- 10400076
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Nature Communications
- Volume:
- 14
- Issue:
- 1
- ISSN:
- 2041-1723
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract rigid protein can be predicted from atomic coordinate sets to within experimental error. However, structural fluctuations of proteins in solution can lead to significant changes in the observed intensities. The magnitude and form of these changes contain information about the nature and spatial extent of structural fluctuations in the protein. Molecular dynamics (MD) simulations based on a crystal structure and selected force field generate models for protein internal motions, and here we demonstrate that they can be used to predict the impact of structural fluctuations on solution scattering data. In cases where the observed and calculated intensities correspond, we can conclude that the X‐ray scattering provides direct experimental validation of the structural and MD results. In cases where calculated and observed intensities are at odds, the inconsistencies can be used to determine the origins of these discrepancies. They may be because of overestimates or underestimates of structural fluctuations in MD simulations, under‐sampling of the structural ensemble in the simulations, errors in the structural model, or a mismatch between the experimental conditions and the parameters used in carrying out the MD simulation. -
more » « less
Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput.
Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software (
https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were severalBacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics.Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
-
more » « less
Abstract Protein regions which are intrinsically disordered, exist as an ensemble of rapidly interconverting structures. Cooling proteins to cryogenic temperatures for dynamic nuclear polarization (DNP) magic angle spinning (MAS) NMR studies suspends most of the motions, resulting in peaks that are broad but not featureless. To demonstrate that detailed conformational restraints can be retrieved from the peak shapes of frozen proteins alone, we developed and used a simulation framework to assign peak features to conformers in the ensemble. We validated our simulations by comparing them to spectra of α‐synuclein acquired under different experimental conditions. Our assignments of peaks to discrete dihedral angle populations suggest that structural constraints are attainable under cryogenic conditions. The ability to infer ensemble populations from peak shapes has important implications for DNP MAS NMR studies of proteins with regions of disorder in living cells because chemical shifts are the most accessible measured parameter.
-
more » « less
Abstract Nickel‐rich layered materials LiNi1‐x‐yMnxCoyO2are promising candidates for high‐energy‐density lithium‐ion battery cathodes. Unfortunately, they suffer from capacity fading upon cycling, especially with high‐voltage charging. It is critical to have a mechanistic understanding of such fade. Herein, synchrotron‐based techniques (including scattering, spectroscopy, and microcopy) and finite element analysis are utilized to understand the LiNi0.6Mn0.2Co0.2O2material from structural, chemical, morphological, and mechanical points of view. The lattice structural changes are shown to be relatively reversible during cycling, even when 4.9 V charging is applied. However, local disorder and strain are induced by high‐voltage charging. Nano‐resolution 3D transmission X‐ray microscopy data analyzed by machine learning methodology reveal that high‐voltage charging induced significant oxidation state inhomogeneities in the cycled particles. Regions at the surface have a rock salt–type structure with lower oxidation state and build up the impedance, while regions with higher oxidization state are scattered in the bulk and are likely deactivated during cycling. In addition, the development of micro‐cracks is highly dependent on the pristine state morphology and cycling conditions. Hollow particles seem to be more robust against stress‐induced cracks than the solid ones, suggesting that morphology engineering can be effective in mitigating the crack problem in these materials.
-
more » « less
Abstract The correlation between lattice chemistry and cation migration in high‐entropy Li+conductors is not fully understood due to challenges in characterizing anion disorder. To address this issue, argyrodite family of Li+conductors, which enables structural engineering of the anion lattice, is investigated. Specifically, new argyrodites, Li5.3PS4.3Cl1.7−
x Brx (0 ≤x ≤ 1.7), with varying anion entropy are synthesized and X‐ray diffraction, neutron scattering, and multinuclear high‐resolution solid‐state nuclear magnetic resonance (NMR) are used to determine the resulting structures. Ion and lattice dynamics are determined using variable‐temperature multinuclear NMR relaxometry and maximum entropy method analysis of neutron scattering, aided by constrained ab initio molecular dynamics calculations. 15 atomic configurations of anion arrangements are identified, producing a wide range of local lattice dynamics. High entropy in the lattice structure, composition, and dynamics stabilize otherwise metastable Li‐deficient structures and flatten the energy landscape for cation migration. This resulted in the highest room‐temperature ionic conductivity of 26 mS cm−1and a low activation energy of 0.155 eV realized in Li5.3PS4.3Cl0.7Br, where anion disorder is maximized. This study sheds light on the complex structure–property relationships of high‐entropy superionic conductors, highlighting the significance of heterogeneity in lattice dynamics.
