• Corpus ID: 978353

Why aren't the small worlds of protein contact networks smaller

@article{Khor2011WhyAT,
  title={Why aren't the small worlds of protein contact networks smaller},
  author={Susan Khor},
  journal={ArXiv},
  year={2011},
  volume={abs/1101.2229}
}
  • S. Khor
  • Published 11 January 2011
  • Computer Science
  • ArXiv
Computer experiments are performed to investigate why protein contact networks (networks induced by spatial contacts between amino acid residues of a protein) do not have shorter average shortest path lengths in spite of their importance to protein folding. We find that shorter average inter-nodal distances is no guarantee of finding a global optimum more easily. Results from the experiments also led to observations which parallel an existing view that neither short-range nor long-range… 
1 Citations

Figures and Tables from this paper

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review.

TLDR
It is proposed that disordered protein regions evolved to help other protein segments reach 'rarely visited' but functionally-related states and to show the role of disorder in 'spatial games' of amino acids.

References

SHOWING 1-10 OF 26 REFERENCES

Assortative mixing in Protein Contact Networks and protein folding kinetics

TLDR
The results indicate that the general topological parameters of these naturally evolved protein networks can effectively represent the structural and functional properties required for fast information transfer among the residues facilitating biochemical/kinetic functions, such as, allostery, stability and the rate of folding.

Small-world communication of residues and significance for protein dynamics.

Topological determinants of protein folding

TLDR
A macroscopic measure of the protein contact network topology, the average graph connectivity, is used by constructing graphs that are based on the geometry of protein conformations and it is found that the average connectivity is higher for conformations with a high folding probability than for those with ahigh probability to unfold.

Residues crucial for maintaining short paths in network communication mediate signaling in proteins

TLDR
It is proposed that centrally conserved residues, whose removal increases the characteristic path length in protein networks, may relate to the system fragility.

Uncovering network systems within protein structures.

Principles of protein folding — A perspective from simple exact models

TLDR
These studies suggest the possibility of creating “foldable” chain molecules other than proteins, and can account for the properties that characterize protein folding: two‐state cooperativity, secondary and tertiary structures, and multistage folding kinetics.

Polymer principles and protein folding

  • K. Dill
  • Computer Science
    Protein science : a publication of the Protein Society
  • 1999
TLDR
The emerging role of statistical mechanics and polymer theory in protein folding is surveyed, finding that in the polymer perspective, the folding code is more a solvation code than a code of local ØΨ propensities.

Collective dynamics of ‘small-world’ networks

TLDR
Simple models of networks that can be tuned through this middle ground: regular networks ‘rewired’ to introduce increasing amounts of disorder are explored, finding that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.

Reconstruction of 3D Structures From Protein Contact Maps

The prediction of the protein tertiary structure from solely its residue sequence (the so called Protein Folding Problem) is one of the most challenging problems in Structural Bioinformatics. We

Specificity and Stability in Topology of Protein Networks

TLDR
It is found that for both interaction and regulatory networks, links between highly connected proteins are systematically suppressed, whereas those between a highly connected and low-connected pairs of proteins are favored.