Assessment of protein-protein interfaces in cryo-EM derived assemblies

Structures of macromolecular assemblies derived from cryo-EM maps often contain errors that become more abundant with decreasing resolution. Despite efforts in the cryo-EM community to develop metrics for map and atomistic model validation, thus far, no specific scoring metrics have been applied systematically to assess the interface between the assembly subunits. Here, we comprehensively assessed protein–protein interfaces in macromolecular assemblies derived by cryo-EM. To this end, we developed Protein Interface-score (PI-score), a density-independent machine learning-based metric, trained using the features of protein–protein interfaces in crystal structures. We evaluated 5873 interfaces in 1053 PDB-deposited cryo-EM models (including SARS-CoV-2 complexes), as well as the models submitted to CASP13 cryo-EM targets and the EM model challenge. We further inspected the interfaces associated with low-scores and found that some of those, especially in intermediate-to-low resolution (worse than 4 Å) structures, were not captured by density-based assessment scores. A combined score incorporating PI-score and fit-to-density score showed discriminatory power, allowing our method to provide a powerful complementary assessment tool for the ever-increasing number of complexes solved by cryo-EM

MODIFICATION OF THE ORGANO-POLYMERIC ANIONITES SURFACE WITH XYLENOL ORANGE BY SORPTION

In this paper, the peculiarities of xylenol orange sorption removal with the help of organopolymeric anion exchangers AB-17-8 and Granion AWA-G1 in the static mode are studied. The state of the matrix and the surface of the organopolymeric anion exchanger granion AWA-G1 was characterized by the IR and Raman spectroscopy. It was established that at pH 5 and 9 the maximum sorption removal (90-95%) of xylenol orange by organopolymeric anion exchanger Granion AWA-G1 lasts for 60 minutes. On the basis of the obtained sorption isotherms and the calculated thermodynamic characteristics, it was concluded that the formation of the adsorption layer occurs spontaneously by a mixed mechanism. The initial process of adsorption layer formation due to chemisorption mechanism. Below, at high concentration of xylenol orange the sorption mechanism changes to the physical nature. It was shown that with changes in temperature and pH, the type of isotherms changes from L3 to H4, which indicates a high affinity of the adsorbate to the adsorbent surface. The obtained sorption isotherms are satisfactorily described by the Langmuir adsorption model. It was shown that the increase in temperature is accompanied by an increase in the amount of sorbed xylenol orange, which is due to the acceleration of the process of reorientation of sorbate molecules to the vertical. In the study of xylenol orange desorption from the Granion AWA-G1 anionite surface, it was found that distilled water and 1M solutions of sulphuric acid slightly desorb xylenol orange (Sdes ≤ 25%), in contrast, the desorption of xylenol orange with 1 M sodium hydroxide solutions reaches Sdes ~ 65%. Thus, the organopolymeric anion exchanger granion AWA-G1 modified with xylenol orange is resistant to water and acid desorption and can subsequently be used as a solid-phase reagent

MODIFICATION OF THE ORGANO-POLYMERIC ANIONITES SURFACE WITH XYLENOL ORANGE BY SORPTION

In this paper, the peculiarities of xylenol orange sorption removal with the help of organopolymeric anion exchangers AB-17-8 and Granion AWA-G1 in the static mode are studied. The state of the matrix and the surface of the organopolymeric anion exchanger granion AWA-G1 was characterized by the IR and Raman spectroscopy. It was established that at pH 5 and 9 the maximum sorption removal (90-95%) of xylenol orange by organopolymeric anion exchanger Granion AWA-G1 lasts for 60 minutes. On the basis of the obtained sorption isotherms and the calculated thermodynamic characteristics, it was concluded that the formation of the adsorption layer occurs spontaneously by a mixed mechanism. The initial process of adsorption layer formation due to chemisorption mechanism. Below, at high concentration of xylenol orange the sorption mechanism changes to the physical nature. It was shown that with changes in temperature and pH, the type of isotherms changes from L3 to H4, which indicates a high affinity of the adsorbate to the adsorbent surface. The obtained sorption isotherms are satisfactorily described by the Langmuir adsorption model. It was shown that the increase in temperature is accompanied by an increase in the amount of sorbed xylenol orange, which is due to the acceleration of the process of reorientation of sorbate molecules to the vertical. In the study of xylenol orange desorption from the Granion AWA-G1 anionite surface, it was found that distilled water and 1M solutions of sulphuric acid slightly desorb xylenol orange (Sdes ≤ 25%), in contrast, the desorption of xylenol orange with 1 M sodium hydroxide solutions reaches Sdes ~ 65%. Thus, the organopolymeric anion exchanger granion AWA-G1 modified with xylenol orange is resistant to water and acid desorption and can subsequently be used as a solid-phase reagent

Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences.

Small angle X-ray scattering (SAXS) measures comprehensive distance information on a protein's structure, which can constrain and guide computational structure prediction algorithms. Here, we evaluate structure predictions of 11 monomeric and oligomeric proteins for which SAXS data were collected and provided to predictors in the 13th round of the Critical Assessment of protein Structure Prediction (CASP13). The category for SAXS-assisted predictions made gains in certain areas for CASP13 compared to CASP12. Improvements included higher quality data with size exclusion chromatography-SAXS (SEC-SAXS) and better selection of targets and communication of results by CASP organizers. In several cases, we can track improvements in model accuracy with use of SAXS data. For hard multimeric targets where regular folding algorithms were unsuccessful, SAXS data helped predictors to build models better resembling the global shape of the target. For most models, however, no significant improvement in model accuracy at the domain level was registered from use of SAXS data, when rigorously comparing SAXS-assisted models to the best regular server predictions. To promote future progress in this category, we identify successes, challenges, and opportunities for improved strategies in prediction, assessment, and communication of SAXS data to predictors. An important observation is that, for many targets, SAXS data were inconsistent with crystal structures, suggesting that these proteins adopt different conformation(s) in solution. This CASP13 result, if representative of PDB structures and future CASP targets, may have substantive implications for the structure training databases used for machine learning, CASP, and use of prediction models for biology

Time Resolved XUV Absorption Spectroscopy and Magnetic Circular Dichroism at the Ni M 2,M 3 Edges

Ultrashort optical pulses can trigger a variety of non equilibrium processes in magnetic thin films affecting electrons and spins on femtosecond timescales. In order to probe the charge and magnetic degrees of freedom simultaneously, we developed an X ray streaking technique that has the advantage of providing a jitter free picture of absorption cross section changes. In this paper, we present an experiment based on this approach, which we performed using five photon probing energies at the Ni M2,3 edges. This allowed us to retrieve the absorption and magnetic circular dichroism time traces, yielding detailed information on transient modifications of electron and spin populations close to the Fermi level. Our findings suggest that the observed absorption and magnetic circular dichroism dynamics both depend on the extreme ultraviolet XUV probing wavelength, and can be described, at least qualitatively, by assuming ultrafast energy shifts of the electronic and magnetic elemental absorption resonances, as reported in recent work. However, our analysis also hints at more complex changes, highlighting the need for further experimental and theoretical studies in order to gain a thorough understanding of the interplay of electronic and spin degrees of freedom in optically excited magnetic thin film