16405339

Source:http://linkedlifedata.com/resource/pubmed/id/16405339

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0162847, umls-concept:C0456389, umls-concept:C1280500, umls-concept:C1521828
pubmed:issue	2
pubmed:dateCreated	2006-1-12
pubmed:abstractText	We analyze the dependence of cooperativity of the thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N, using lattice models with side chains, off-lattice Go models, and the available experimental data. A dimensionless measure of cooperativity, Omega(c) (0 < Omega(c) < infinity), scales as Omega(c) approximately N(zeta). The results of simulations and the analysis of experimental data further confirm the earlier prediction that zeta is universal with zeta = 1 + gamma, where exponent gamma characterizes the susceptibility of a self-avoiding walk. This finding suggests that the structural characteristics in the denaturated state are manifested in the folding cooperativity at the transition temperature. The folding rates k(F) for the Go models and a dataset of 69 proteins can be fit using k(F) = k(F)0 exp(-cN(beta)). Both beta = 1/2 and 2/3 provide a good fit of the data. We find that k(F) = k(F)0 exp(-cN(1/2)), with the average (over the dataset of proteins) k(F)0 approximately (0.2 micros)(-1) and c approximately 1.1, can be used to estimate folding rates to within an order of magnitude in most cases. The minimal models give identical N dependence with c approximately 1. The prefactor for off-lattice Go models is nearly 4 orders of magnitude larger than the experimental value.
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/9890903
pubmed:citationSubset	IM
pubmed:status	MEDLINE
pubmed:month	Jan
pubmed:issn	1089-5639
pubmed:author	pubmed-author:HuChin-KunCK, pubmed-author:KouzaMaksimM, pubmed-author:LiMai SuanMS, pubmed-author:O'brienEdward PEPJr, pubmed-author:ThirumalaiDD
pubmed:issnType	Print
pubmed:day	19
pubmed:volume	110
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	671-6
pubmed:dateRevised	2008-11-21
pubmed:meshHeading	pubmed-meshheading:16405339-Hot Temperature, pubmed-meshheading:16405339-Kinetics, pubmed-meshheading:16405339-Models, Theoretical, pubmed-meshheading:16405339-Protein Denaturation, pubmed-meshheading:16405339-Protein Folding
pubmed:year	2006
pubmed:articleTitle	Effect of finite size on cooperativity and rates of protein folding.
pubmed:affiliation	Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
pubmed:publicationType	Journal Article, Research Support, U.S. Gov't, Non-P.H.S., Research Support, Non-U.S. Gov't