TABLE 3.

Energetic and Entropic Contributions to Basin Stability

						barrierd
pfoldf basin	weight (%)	〈E〉a (kcal/mol)	〈ΔE〉b (kcal/mol)	ΔFc (kcal/mol)	−TΔS = ΔF - 〈ΔE〉 (kcal/mol)	secondary str (kcal/mol)	rmsd (kcal/mol)
native	35.0	−7.2	0	0	0	1.9	2.5
Ns-or	6.2	−6.4	0.8	1.1	0.3	1.2	1.7
Cs-or	2.6	−3.3	3.9	1.7	−2.2	0.8	1.6
Ch-curl1	2.8	−10.1	−2.9	1.7	4.6	1.0	3.2
Ch-curl2	2.1	−10.1	−2.9	1.9	4.8	1.2	2.6
helicale	11.2	2.2	9.4	0.8	−8.6	1.4	1.3
entropice	32.7	2.9	10.1	0.0	−10.1

^aAverage effective energy, that is, the sum of CHARMM param19 force field³⁸ and the SAS solvation model³⁹ contributions. The average was calculated over all snapshots in the clusters (i.e., secondary structure strings) belonging to the basin determined by the pfoldf procedure. The error of the average effective energy is less than 0.5 kcal/mol as estimated by the difference of the mean values calculated on one-half of the sample, i.e., two segments of 10 µs each.

^bAverage effective energy relative to the folded state. Note that, in any force field, the absolute value of the effective energy E is arbitrary, and only ΔE values relative to a reference state are meaningful.

^cFree energy relative to the folded state calculated as ΔF = −kT ln(weight/5.0), where 35% is the weight of the native basin as isolated by pfoldf.

^dBarrier to exit individual pfoldf basin, calculated for the secondary structure and 2.5-Å rmsd coarse-graining.

^eThese basins are stabilized mainly by entropy, as indicated in the table.