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Influence of the native topology on the folding barrier for small proteins
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Image of FIG. 1.
FIG. 1.

(Color online) Set of eight proteins used in the present study. The ribbon structure for each protein lays at the left side of the corresponding contact map. Every spot in the latter indicates the presence of a native contact between residues and . Dotted lines separate elements of secondary structure, according to the PDB file headers.

Image of FIG. 2.
FIG. 2.

Simulation results for the constant volume heat capacity as a function of temperature for protein 1BBL.

Image of FIG. 3.
FIG. 3.

(Color online) Free energy profiles (solid lines) and energy histograms (dotted lines) for protein 1BBL, at its folding temperature , and at temperatures below and above it.

Image of FIG. 4.
FIG. 4.

(Color online) Free energy profiles for all the proteins in Fig. 1 at their folding temperatures, obtained through WHAM analysis of the simulation results. The (numerically meaningless) scales for the free energy axes are the same in all the plots.

Image of FIG. 5.
FIG. 5.

(Color online) Free energy profile and energy histogram for protein 1VII at its folding temperature.

Image of FIG. 6.
FIG. 6.

(Color online) Free energy profiles at the folding temperature for the indicated proteins, with native and reweighted contributions of long range interactions, as indicated in every panel.

Image of FIG. 7.
FIG. 7.

(Color online) Native contact order histograms for all the proteins in Fig. 1, with and being the residue positions along the sequence which define a contact. The values of the histogram scale are divided by the total number of long range contacts for every protein.

Image of FIG. 8.
FIG. 8.

(Color online) Average contact order histograms for a large set of monomeric protein structures: (a) With up to 60 residues, and (b) with more than 60 residues.


Generic image for table
Table I.

Structural and folding transition temperature values for the proteins of the set (Fig. 1). is the number of amino acids, is the proportion of long range energy in the native state, is the number of total contacts in the native structure, and and are the number of long range contacts per residue in the native state calculated under Zuo et al. (Ref. 38) and our contact classification, respectively.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Influence of the native topology on the folding barrier for small proteins