Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms

Ab initio determination of the shape of membrane proteins in a nanodisc

New software, called Marbles, is introduced that employs SAXS intensities to predict the shape of membrane proteins embedded into membrane nanodiscs. To gain computational speed and efficient convergence, the strategy is based on a hybrid approach that allows one to account for the contribution of the nanodisc to the SAXS intensity through a semi-analytical model, while the embedded membrane protein is treated as a set of beads, similarly to as in well known ab initio methods. The reliability and flexibility of this approach is proved by benchmarking the code, implemented in C++ with a Python interface, on a toy model and two proteins with very different geometry and size.

DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes

Electron cryomicroscopy (cryo-EM), a 2017 Nobel prize-awarded technology, provides direct 3D maps of macromolecules and explains the shape and interactions of protein complexes such as SARS-CoV-2 viral proteins and human cell receptors. This understanding can be combined with detailed structural information gathered using other technologies to form the basis for modeling course of diseases and for designing therapeutic drugs. However, ab initio modeling of protein complex structure remains a challenging problem. Here, we present DeepTracer, a fully automated and robust tool that determines the all-atom structure of a protein complex based solely on its cryo-EM map and amino acid sequence, with improved accuracy and efficiency compared to previous methods. We also provide a web service for global access.

Information about macromolecular structure of protein complexes and related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully automated deep learning-based method for fast de novo multichain protein complex structure determination from high-resolution cryoelectron microscopy (cryo-EM) maps. We applied DeepTracer on a previously published set of 476 raw experimental cryo-EM maps and compared the results with a current state of the art method. The residue coverage increased by over 30% using DeepTracer, and the rmsd value improved from 1.29 Å to 1.18 Å. Additionally, we applied DeepTracer on a set of 62 coronavirus-related cryo-EM maps, among them 10 with no deposited structure available in EMDataResource. We observed an average residue match of 84% with the deposited structures and an average rmsd of 0.93 Å. Additional tests with related methods further exemplify DeepTracer’s competitive accuracy and efficiency of structure modeling. DeepTracer allows for exceptionally fast computations, making it possible to trace around 60,000 residues in 350 chains within only 2 h. The web service is globally accessible at https://deeptracer.uw.edu.

Optimization and Corroboration of the Regulatory Pathway of p42.3 Protein in the Pathogenesis of Gastric Carcinoma

AIMS

To optimize and verify the regulatory pathway of p42.3 in the pathogenesis of gastric carcinoma (GC) by intelligent algorithm.

METHODS

Bioinformatics methods were used to analyze the features of structural domain in p42.3 protein. Proteins with the same domains and similar functions to p42.3 were screened out for reference. The possible regulatory pathway of p42.3 was established by integrating the acting pathways of these proteins. Then, the similarity between the reference proteins and p42.3 protein was figured out by multiparameter weighted summation method. The calculation result was taken as the prior probability of the initial node in Bayesian network. Besides, the probability of occurrence in different pathways was calculated by conditional probability formula, and the one with the maximum probability was regarded as the most possible pathway of p42.3. Finally, molecular biological experiments were conducted to prove it.

RESULTS

In Bayesian network of p42.3, probability of the acting pathway "S100A11→RAGE→P38→MAPK→Microtubule-associated protein→Spindle protein→Centromere protein→Cell proliferation" was the biggest, and it was also validated by biological experiments.

CONCLUSIONS

The possibly important role of p42.3 in the occurrence of gastric carcinoma was verified by theoretical analysis and preliminary test, helping in studying the relationship between p42.3 and gastric carcinoma.

Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings

Within the past two decades, there has been an increase in the acquisition of residual dipolar couplings (RDC) for investigations of biomolecular structures. Their use however is still not as widely adopted as the traditional methods of structure determination by NMR, despite their potential for extending the limits in studies that examine both the structure and dynamics of biomolecules. This is in part due to the difficulties associated with the analysis of this information-rich data type. The software analysis tool REDCRAFT was previously introduced to address some of these challenges. Here we describe and evaluate a number of additional features that have been incorporated in order to extend its computational and analytical capabilities. REDCRAFT's more traditional enhancements integrate a modified steric collision term, as well as structural refinement in the rotamer space. Other, non-traditional improvements include: the filtering of viable structures based on relative order tensor estimates, decimation of the conformational space based on structural similarity, and forward/reverse folding of proteins. Utilizing REDCRAFT's newest features we demonstrate de-novo folding of proteins 1D3Z and 1P7E to within less than 1.6 Å of the corresponding X-ray structures, using as many as four RDCs per residue and as little as two RDCs per residue, in two alignment media. We also show the successful folding of a structure to less than 1.6 Å of the X-ray structure using {C(i-1)-N(i), N(i)-H(i), and C(i-1)-H(i)} RDCs in one alignment medium, and only {N(i)-H(i)} in the second alignment medium (a set of data which can be collected on deuterated samples). The program is available for download from our website at http://ifestos.cse.sc.edu .