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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
2
|
| pubmed:dateCreated |
1996-12-23
|
| pubmed:abstractText |
A simple continuum model of a de novo designed model of a four-helix bundle is presented. The thermodynamics and kinetics of the model are studied using Langevin simulations. We use a three-letter minimal off-lattice representation of a de novo designed four-helix bundle protein. The native state of the model, which can be thought of as an alpha-carbon representation of the peptide chain, is a caricature of the sequence designed by Ho and Degrado and shows several characteristics found in the naturally occurring four-helix bundles. These include the structural aspects and the relative stability of the native conformation. The model four-helix bundle shows two characteristic temperatures T theta and Tf. The former is the temperature above which the structure resembles that of the random coil. Below the first-order folding transition temperature Tf the chain adopts the native conformation corresponding to the four-helix bundle. It is shown that in order to obtain a unique native structure a proper free energy balance between secondary and tertiary interactions is needed. The thermal denaturation starting from the unique native conformation indicates that at least a three-state analysis is required. The intermediates in the equilibrium thermal denaturation are all found to be native-like. The kinetics of refolding starting from an ensemble of denatured states shows that the acquisition of the native conformation takes place via a kinetic partitioning mechanism. A fraction of molecules, phi, reaches the native state by a topology inducing nucleation collapse mechanism, while the remainder (1-phi) follows a complex three-stage multipathway process. We suggest, in accord with our earlier studies, that phi is essentially determined by the intrinsic temperature scales T theta and Tf. Our studies indicate that better design of proteins can be achieved by making T theta as close to Tf as possible. Experimental implications for de novo design of proteins are briefly discussed.
|
| pubmed:language |
eng
|
| pubmed:journal | |
| pubmed:citationSubset |
IM
|
| pubmed:status |
MEDLINE
|
| pubmed:month |
Oct
|
| pubmed:issn |
0022-2836
|
| pubmed:author | |
| pubmed:issnType |
Print
|
| pubmed:day |
25
|
| pubmed:volume |
263
|
| pubmed:owner |
NLM
|
| pubmed:authorsComplete |
Y
|
| pubmed:pagination |
323-43
|
| pubmed:dateRevised |
2006-11-15
|
| pubmed:meshHeading | |
| pubmed:year |
1996
|
| pubmed:articleTitle |
Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein.
|
| pubmed:affiliation |
Chemical Physics Program, Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA.
|
| pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, Non-P.H.S.
|