Hidden intermediates and levinthal paradox in the folding of small proteins.

Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model.

BACKGROUND The role of intermediates in protein folding has been a matter of great controversy. Although it was widely believed that intermediates play a key role in minimizing the search problem associated with the Levinthal paradox, experimental evidence has been accumulating that small proteins fold fast without any detectable intermediates. RESULTS We study the thermodynamics and kinetics...

A Criterion That Determines Fast Folding of Proteins: A Model Study

We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular (Tθ) and the folding (Tf ) transition temperatures. For our model, the typical time scale for reaching the unique native conformation is shown to scale as τf ∼ F (M) exp(σ/σ0), where σ = 1 − Tf/Tθ, M is the number of residues, and F (M...

Theoretical studies of protein-folding thermodynamics and kinetics.

Recently, protein-folding models have advanced to the point where folding simulations of protein-like chains of reasonable length (up to 125 amino acids) are feasible, and the major physical features of folding proteins, such as cooperativity in thermodynamics and nucleation mechanisms in kinetics, can be reproduced. This has allowed deep insight into the physical mechanism of folding, includin...

Structural Characteristics of Stable Folding Intermediates of Yeast Iso-1-Cytochrome-c

Cytochrome-c (cyt-c) is an electron transport protein, and it is present throughout the evolution. More than 280 sequences have been reported in the protein sequence database (www.uniprot.org). Though sequentially diverse, cyt-c has essentially retained its tertiary structure or fold. Thus a vast data set of varied sequences with retention of similar structure and fun...

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