Corpus ID: 236428357

How sticky are our proteins? Quantifying hydrophobicity of the human proteome

@inproceedings{Gils2021HowSA,
  title={How sticky are our proteins? Quantifying hydrophobicity of the human proteome},
  author={Juami Hermine Mariama van Gils and Dea Gogishvili and J. A. van Eck and Robbin Bouwmeester and Erik van Dijk and Sanne Abeln},
  year={2021}
}
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some ’sticky’ hydrophobic residues to the solvent. These residues can play an important functional role, for example in protein-protein and membrane interactions. Here, we investigate how hydrophobic protein surfaces are by providing three measures for surface hydrophobicity: the total hydrophobic… Expand

Figures and Tables from this paper

References

SHOWING 1-10 OF 64 REFERENCES
Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins.
TLDR
It is shown that knowledge-based pair-potentials, which include explicitly calculated energy terms between the solvent and each amino acid, enable the simulation of proteins that are much less aggregation-prone in the folded state. Expand
Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of Proteins
TLDR
The ability to predict surface accessibility of hydrophobic residues directly from the sequence is of great help in choosing the sites of chemical modification or specific mutations and in the studies of protein stability and molecular interactions. Expand
Morphology of protein-protein interfaces.
TLDR
A visual survey of 136 homodimeric proteins from the Brookhaven Protein Data Bank, with images that highlight the major structural features of each protein-protein interaction surface, finds that the archetypal protein interface, with a defined hydrophobic core, is present in only a minority of the surveyed homod racer proteins. Expand
The nature of the accessible and buried surfaces in proteins.
  • C. Chothia
  • Chemistry, Medicine
  • Journal of molecular biology
  • 1976
TLDR
The accessible surface areas have been calculated for the individual residues in 12 proteins, and for the extended chains, the secondary structures and tertiary structure of six proteins and it is shown that the accessible surface area of folded proteins is simply proportional to the two-thirds power of their molecular weight. Expand
Surface and inside volumes in globular proteins
TLDR
The study of the accessibility to solvent of amino acid residues in several proteins confirmed the early observation that polar residues are found mostly on the surface and non-polar residues mostly inside globular protein structures, but the accessibility shows systematic variations with the molecular weight. Expand
A role for surface hydrophobicity in protein‐protein recognition
TLDR
Results suggest that surface hydrophobicity can be used to identify regions of a protein's surface most likely to interact with a binding ligand, and may be useful for identifying small sets of well‐defined loci for possible ligand attachment. Expand
Dominant forces in protein folding.
  • K. Dill
  • Chemistry, Medicine
  • Biochemistry
  • 1990
TLDR
The present review aims to provide a reassessment of the factors important for folding in light of current knowledge, including contributions to the free energy of folding arising from electrostatics, hydrogen-bonding and van der Waals interactions, intrinsic propensities, and hydrophobic interactions. Expand
A method for detecting hydrophobic patches on protein surfaces
TLDR
Its potential as a tool in the study of protein‐protein interactions and substrate recognition is demonstrated by applying the method to myoglobin, Leu/Ile/Val‐binding protein, lipase, lysozyme, azurin, triose phosphate isomerase, carbonic anhydrase, and phosphoglycerate kinase. Expand
Disordered Flanks Prevent Peptide Aggregation
TLDR
The work provides insights into a mechanism that prevents the aggregation of signalling peptides, distinct from the general mechanism of protein folding, and provides a testable hypothesis to explain the abundance of disordered regions in proteins. Expand
Hydrophobic patches on protein subunit interfaces: Characteristics and prediction
TLDR
Hydrophobic patches, defined as clusters of neighboring apolar atoms deemed accessible on a given protein surface, have been investigated on protein subunit interfaces and should prove useful for subunit design and engineering as well as for prediction of subunit interface regions. Expand
...
1
2
3
4
5
...