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Pathways to folding, nucleation events, and native geometry
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Image of FIG. 1.
FIG. 1.

Three dimensional representations of geometry 1 (top, left) and geometry 2 (bottom, left), and their respective contact maps (right). In the contact maps each circle represents a native contact. Nonlocal LR contacts are shown in white.

Image of FIG. 2.
FIG. 2.

Probability distribution for the fraction of native contacts, , for geometry 1 (left) and geometry 2 (right) as a function of . A conformation is considered unfolded when .

Image of FIG. 3.
FIG. 3.

(Color online) Time to fold as a function of the reaction coordinate . Long lived trapped states are observed in geometry 1 (left) at very high , but are absent in geometry 2 (right). To measure of each conformation we considered only folding events in which the protein folded before unfolding. is the mean time-to-fold averaged over these folding events. The horizontal black lines indicate the cutoff times below which a conformation is committed to fold. For geometries 1 and 2 there are, respectively, 4724 and 4162 conformers with .

Image of FIG. 4.
FIG. 4.

Density plots of the probability (left column) and fraction of conformations (right column), where contact is present and is not for geometry 1 (top) and geometry 2 (bottom). Native contacts are ordered according to their relative values of (the order is the same for the and plots). The groups of contacts forming sections A, B, and C are identified. Contacts that were not assigned to any section (“free” contacts) are identified by the letter F. The range of lies between 0 (black) and 1 (white), while varies between 0 (black) and 0.54 (white) in geometry 1 and between 0 (black) and 0.64 (white) in geometry 2.

Image of FIG. 5.
FIG. 5.

(Color) Protein sections identified for geometry 1 (top row) and geometry 2 (bottom row). Native contacts forming sections A, B, and C are, respectively, colored red, blue, and green, in the three dimensional representations (left) and contact maps (right). Note that the protein sections identified as groups of correlated native bonds are grouped together in the protein’s three dimensional native structure.

Image of FIG. 6.
FIG. 6.

(Color) Density plots of the probability for having a certain as a function of for the sections A, B, and C in geometry 1 (top) and geometry 2 (bottom).

Image of FIG. 7.
FIG. 7.

(Color online) Average fraction of native bonds in each protein section, , as a function of in geometry 1 (a) and geometry 2 (b). Also shown is the dependence of the protein’s average fraction of native bonds on the reaction coordinate, , for both geometries. Note that when folding is near completion at high , there is a sharp increase in the fraction of native contacts for geometry 1.


Generic image for table
Table I.

Absolute contact order (ACO), fraction of long-range (LR) contacts, optimal folding temperature , and folding time for geometries 1 and 2.

Generic image for table
Table II.

Number of native bonds forming each protein section, absolute contact order (ACO), and fraction of long-range (LR) contacts of each protein section.

Generic image for table
Table III.

Folding pathways at the macrostructural level of section formation (showing the first, second, and third sections to fold) and their relative probabilities of occurrence. The probabilities do not add to one, since there are some events in which two sections fold simultaneously. The average time elapsing between the formation of the first section and the formation of the last section in each pathway is given in units of .


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Pathways to folding, nucleation events, and native geometry