The importance of explicit chain representation in protein folding models: an examination of Ising-like models.
A class of models that represents a protein chain as a sequence of "folded" and "unfolded" residues has recently been used to correlate rates and mechanisms of protein folding with the protein native structure. In order to better understand the conditions under which these "Ising-like" models apply, we compare results from this model to those obtained from an off-lattice model which uses the same potential function. We find that Ising-like models by construction impose folding via a highly sequential nucleation-condensation mechanism, which in turn leads to more rugged energy landscapes, fewer "pathways" to the native state, and in the specific case examined here, the cold shock protein A from Escherichia coli, a qualitative difference in the most likely order of events in folding.
Karanicolas
John
J
Department of Molecular Biology (TPC6), Center for Theoretical Biological Physics, The Scripps Research Institute, La Jolla, California 92037, USA.
Brooks
Charles L
CL
D000596:Amino Acids / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry
D000596:Amino Acids; D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D011506:Proteins; C062260:cold shock protein CS7.4, Bacteria