Small-world view of the amino acids that play a key role in protein folding.
We use geometrical considerations to provide a different perspective on the fact that a few selected amino acids, the so-called "key residues," act as nucleation centers for protein folding. By constructing graphs corresponding to protein structures we show that they have the "small-world" feature of having a limited set of vertices with large connectivity. These vertices correspond to the key residues that play the role of "hubs" in the network of interactions that stabilize the structure of the transition state.
Oxford Centre for Molecular Sciences, Central Chemistry Laboratory, South Parks Road, OX1 3QH Oxford, United Kingdom.
M
M
Vendruscolo
N V
NV
Dokholyan
E
E
Paci
M
M
Karplus
D000596:Amino Acids / Q000737:chemistry*; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D008958:Models, Molecular; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins