A systematic structural comparison of all solved small proteins (4-6 kDa) reveals the weight of disulfide bonds in proteins' foldability
Moreira, M. H.; Almeida, F. C. L.; Domitrovic, T.; Palhano, F. L.
Show abstract
Defensins are small proteins, usually ranging from 4 to 6 kDa, amphipathic, disulfide-rich, and with a small or even absent hydrophobic core. Since a hydrophobic core is generally found in globular proteins that fold in an aqueous solvent, the peculiar fold of defensins can challenge tertiary protein structure predictors. We performed a PDB-wide survey of small proteins (4-6 kDa) to understand the similarities of defensins with other small disulfide-rich proteins. We found no differences when we compared defensins with non-defensins regarding the proportion and exposition to the solvent of apolar, polar, and charged residues. Then we divided all small proteins (4-6 kDa) deposited in PDB into two groups, one group with at least one disulfide bond (bonded, defensins included) and another group without any disulfide bond (unbonded). The group of bonded proteins presented apolar residues more exposed to the solvent than the unbonded group. The ab initio algorithm for tertiary protein structure prediction Robetta was more accurate to predict unbonded than bonded proteins. Our work highlights one more layer of complexity for the tertiary protein prediction structure: small disulfide-rich proteins ability to fold even with a poor hydrophobic core.
Matching journals
The top 8 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Navigating the Unstructured by Evaluating AlphaFold's Efficacy in Predicting Missing Residues and Structural Disorder in Proteins 95%
- Using AlphaFold to predict the impact of single mutations on protein stability and function 95%
- A Dimer between Monomers and Hexamers - Oligomeric Variations in Glucosamine 6-Phosphate Deaminase Family 95%
Similar papers in this journal
Similar papers in this journal
- Signal Peptide of Human Serum Albumin (residues 1-18) Forms Amyloid-like Aggregates 94%
- Predictive Models and Impact of Interfacial Contacts and Amino Acids on Protein-protein Binding Affinity 94%
- Designing BH3-mimetic Peptide Inhibitors for the Viral Bcl-2 Homologs A179L and BHRF1: Importance of long-range electrostatic interactions 93%
Similar papers in this journal
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.