Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions
Abstract
:1. Introduction
2. Results and Discussion
2.1. The Majority of Instances in the ELM Database Bind Ligands and Are from Human
2.2. Accessibility and Lack of Secondary Structure Influence SLiM Functionality More than Disorder
2.3. SLiMs from Viruses Are Less Disordered
2.4. Most SLiMs Lack Secondary Structure
2.5. Disordered or Flexible?
2.5.1. SLiMs Are Found in Flexible Regions
2.5.2. A Comparison of Viral and Bacterial Motifs with Their Corresponding Eukaryotic Motifs
2.5.3. To Fold or Not to Fold: A Tale of Two Motifs
Are MOD_N-GLC_1 Instances Indeed Predominantly Ordered in Viruses or Is This Perhaps Due to Insufficient Data?
LIG_Rb_LxCxE_1 Is Less Disordered in Viruses
3. Conclusions
4. Methods
4.1. The ELM Dataset
4.2. Sequence-Based Structural Predictions
4.2.1. Intrinsic Disorder Prediction
4.2.2. Relative Solvent Accessibility and Secondary Structure Predictions
4.3. Phylogenetic Tree Analysis
4.4. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
PPI | Protein-protein interactions |
ELM | Eukaryotic Linear Motifs |
SLiMs | Short Linear Motifs |
IDR | Intrinsically Disordered protein Region |
IDP | Intrinsically Disordered Protein |
MIDS | Mean IUPRED2A Disorder Score |
MCCS | Mean Coil Confidence Score |
mMIDS | mean MIDS |
mMCCS | mean MCCS |
LIG | Ligand binding motifs |
MOD | Post-translational modification motifs |
TRG | Targeting motifs |
DOC | Docking motifs |
CLV | Cleavage sites motifs |
DEG | Degradation motifs |
WNV | West Nile Virus |
Rb | Retinoblastoma protein |
DSSP | Dictionary of Secondary Structure of Proteins |
PDB | Protein Data Bank |
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Elkhaligy, H.; Balbin, C.A.; Siltberg-Liberles, J. Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions. Pathogens 2022, 11, 583. https://doi.org/10.3390/pathogens11050583
Elkhaligy H, Balbin CA, Siltberg-Liberles J. Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions. Pathogens. 2022; 11(5):583. https://doi.org/10.3390/pathogens11050583
Chicago/Turabian StyleElkhaligy, Heidy, Christian A. Balbin, and Jessica Siltberg-Liberles. 2022. "Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions" Pathogens 11, no. 5: 583. https://doi.org/10.3390/pathogens11050583