The case for post-predictional modifications in the AlphaFold Protein Structure Database.

@article{Bagdonas2021TheCF,
  title={The case for post-predictional modifications in the AlphaFold Protein Structure Database.},
  author={Haroldas Bagdonas and Carl A. Fogarty and Elisa Fadda and Jon Agirre},
  journal={Nature structural \& molecular biology},
  year={2021}
}

Designing drugs when there is low data availability: one-shot learning and other approaches to face the issues of a long-term concern.

TLDR
approaches that may help provide solutions to generate or obtain enough relevant data or improve/accelerate existing methods within the last five years were reviewed.

Glycoinformatics in the Artificial Intelligence Era.

TLDR
The historical development of the application of various AI methods in the broader field of glycoinformatics is discussed, with a particular focus on shining a light on challenges in glyco-data handling, contextualized by lessons learnt from related disciplines.

Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology

TLDR
This work identifies and classifies transmembrane ABC protein structures using PFAM search and aims to determine their conformational states based on special geometric measures, conftors, and performs AF2-Multimer predictions for human ABC half transporters functioning as dimers.

Multifaceted Computational Modeling in Glycoscience.

TLDR
The Review leads the reader through the detailed presentations of the applications of computational modeling of carbohydrates and complex glycans, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins.

Assessment of AlphaFold2 for Human Proteins via Residue Solvent Exposure

TLDR
Using solvent exposure as a metric, the performance of AF2 for human proteins is quantified and estimates of the expected agreement as a function of ligand presence, multimer/monomer status, local residue solvent exposure, pLDDT, and amino acid type are provided.

Thirty years of molecular dynamics simulations on posttranslational modifications of proteins

TLDR
In this Perspective, the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs are covered and results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization are distinguished.

Glycoproteomics

Whole-proteome structures shed new light on posttranslational modifications

TLDR
In this issue of PLOS Biology, Bludau and colleagues add a functional context to models by combining them with readily available proteomics results.

The structural context of posttranslational modifications at a proteome-wide scale

TLDR
This analysis uncovers global patterns of PTM occurrence across folded and intrinsically disordered regions and determines the structural context of these PTMs, which can help to distinguish regulatory PTMs from those marking improperly folded proteins.

A database of calculated solution parameters for the AlphaFold predicted protein structures

Recent spectacular advances by AI programs in 3D structure predictions from protein sequences have revolutionized the field in terms of accuracy and speed. The resulting “folding frenzy” has already

References

SHOWING 1-10 OF 13 REFERENCES

Highly accurate protein structure prediction for the human proteome

TLDR
This work dramatically expands structural coverage by applying the state-of-the-art machine learning method, AlphaFold, at scale to almost the entire human proteome, covering 58% of residues with a confident prediction, of which a subset have very high confidence.

Highly accurate protein structure prediction with AlphaFold

TLDR
This work validated an entirely redesigned version of the neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14)15, demonstrating accuracy competitive with experiment in a majority of cases and greatly outperforming other methods.

Oligomannose N-Glycans 3D Architecture and Its Response to the FcγRIIIa Structural Landscape

TLDR
The results show that the protein’s structural constraints shift the oligomannoses conformational ensemble to promote conformers that satisfy the steric requirements and hydrogen bonding networks demanded by the protein's surface landscape, finding that theprotein does not actively distort the N-glycans into structures not populated in the unlinked forms in solution.

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein

TLDR
An essential structural role of N-glycans at sites N165 and N234 in modulating the conformational dynamics of the spike’s receptor binding domain (RBD) is revealed, which reduces binding to ACE2 as a result of the RBD conformational shift toward the “down” state.

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

TLDR
This work will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve the validation of 3D glycoprotein structures.

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

TLDR
The stalk domain of S contains three hinges, giving the head unexpected orientational freedom and it is proposed that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat.

Structural glycobiology in the age of electron cryo-microscopy.

TLDR
This review will focus on the new software developments that have been introduced in the past two years, and their impact on the field of structural glycobiology in terms of published structures.

Privateer: software for the conformational validation of carbohydrate structures

TLDR
Privateer is a new software package aimed at the detection and prevention of conformational, regiochemical and stereochemical anomalies in cyclic monosaccharide structures, and identifies incorrect regiochemistry and stereochemistry and unlikely conformations.

Myristoylation: An Important Protein Modification in the Immune Response

TLDR
The hitherto unappreciated implication of myristoylation during myelopoiesis, innate immune response, lymphopOiesis for T cells, and the formation of the immunological synapse is discussed.