The Protein Folding Network
- 1 September 2004
- journal article
- Published by Elsevier BV in Journal of Molecular Biology
- Vol. 342 (1), 299-306
- https://doi.org/10.1016/j.jmb.2004.06.063
Abstract
The conformation space of a 20 residue antiparallel β-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Snapshots saved along the trajectory are grouped according to secondary structure into nodes of the network and the transitions between them are links. The conformation space network describes the significant free energy minima and their dynamic connectivity without requiring arbitrarily chosen reaction coordinates. As previously found for the Internet and the World-Wide Web as well as for social and biological networks, the conformation space network is scale-free and contains highly connected hubs like the native state which is the most populated free energy basin. Furthermore, the native basin exhibits a hierarchical organization, which is not found for a random heteropolymer lacking a predominant free-energy minimum. The network topology is used to identify conformations in the folding transition state (TS) ensemble, and provides a basis for understanding the heterogeneity of the TS and denatured state ensemble as well as the existence of multiple pathways.This publication has 40 references indexed in Scilit:
- Fast protein folding on downhill energy landscapeProtein Science, 2003
- Small-world view of the amino acids that play a key role in protein foldingPhysical Review E, 2002
- Small-world networks and the conformation space of a short lattice polymer chainEurophysics Letters, 2001
- Role of native topology investigated by multiple unfolding simulations of four SH3 domainsJournal of Molecular Biology, 2001
- Free Energy Surface of the Helical Peptide Y(MEARA)6The Journal of Physical Chemistry B, 2000
- Local Interactions Drive the Formation of Nonnative Structure in the Denatured State of Human α-Lactalbumin: A High Resolution Structural Characterization of a Peptide Model in Aqueous Solution,Biochemistry, 1999
- "New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding SimulationsScience, 1997
- MOLMOL: A program for display and analysis of macromolecular structuresJournal of Molecular Graphics, 1996
- Intermediates and barrier crossing in a random energy model (with applications to protein folding)The Journal of Physical Chemistry, 1989
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry, 1983