Premium
Substructural cooperativity and parallel versus sequential events during protein unfolding
Author(s) -
Reich Lothar,
Weikl Thomas R.
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20966
Subject(s) - cooperativity , protein folding , degree (music) , folding (dsp implementation) , funnel , statistical physics , energy landscape , molecular dynamics , closure (psychology) , chemistry , physics , crystallography , computational chemistry , thermodynamics , acoustics , electrical engineering , engineering , economics , market economy , biochemistry , organic chemistry
According to the “old view,” proteins fold along well‐defined sequential pathways, whereas the “new view” sees protein folding as a highly parallel stochastic process on funnel‐shaped energy landscapes. We have analyzed parallel and sequential processes on a large number of molecular dynamics unfolding trajectories of the protein CI2 at high temperatures. Using rigorous statistical measures, we quantify the degree of sequentiality on two structural levels. The unfolding process is highly parallel on the microstructural level of individual contacts. On a coarser, macrostructural level of contact clusters, characteristic parallel and sequential events emerge. These characteristic events can be understood from loop‐closure dependencies between the contact clusters. A correlation analysis of the unfolding times of the contacts reveals a high degree of substructural cooperativity within the contact clusters. Proteins 2006. © 2006 Wiley‐Liss, Inc.