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. 2009 Sep 16;97(6):1737–1746. doi: 10.1016/j.bpj.2009.06.047

Table 2.

Properties of the 50 most populated causally grouped mesostates sorted according to statistical weight Pi

Rank Pi [%] ΔGi [kcal/mol] ΔEi [kcal/mol] TΔSi [kcal/mol] Mi1 [ns] α-Helix [%] β-Sheet [%]
1 3.5 −1.0 −12.4 11.4 1 25 44
49 2.7 −0.9 −4.8 3.9 11 24 41
127 2.5 −0.8 −2.5 1.7 90 64 4
147 2.1 −0.7 3.0 −3.7 95 57 5
133 1.8 −0.6 3.7 −4.3 92 51 9
128 1.8 −0.6 3.9 −4.5 90 53 8
35 1.6 −0.5 −8.8 8.3 9 26 44
186 1.6 −0.5 0.9 −1.4 101 64 3
183 1.6 −0.5 2.9 −3.4 98 53 10
16 1.6 −0.5 −4.8 4.3 4 29 38
119 1.6 −0.5 −7.9 7.4 87 55 13
182 1.5 −0.5 1.6 −2.1 98 67 3
134 1.4 −0.4 4.3 −4.7 92 52 8
153 1.3 −0.4 −0.2 −0.2 96 63 4
125 1.3 −0.4 1.6 −2.0 89 53 10
164 1.2 −0.3 −6.2 5.9 96 42 29
139 1.1 −0.3 6.6 −6.9 94 38 16
123 1.1 −0.3 1.9 −2.2 89 53 10
24 1.0 −0.2 2.2 −2.4 6 35 27
179 1.0 −0.2 0.5 −0.7 97 43 21
174 1.0 −0.2 6.1 −6.3 97 40 15
171 1.0 −0.2 7.3 −7.5 96 39 19
152 1.0 −0.2 6.7 −6.9 96 43 13
138 1.0 −0.2 6.0 −6.2 94 32 24
105 1.0 −0.2 3.3 −3.5 83 47 14
48 0.9 −0.1 −5.9 5.8 11 22 44
4 0.9 −0.1 −10.4 10.3 2 25 37
200 0.9 −0.2 −1.4 1.2 314 0 74
198 0.9 −0.1 −2.7 2.6 201 2 60
172 0.9 −0.1 7.7 −7.8 97 31 22
132 0.9 −0.1 1.2 −1.3 92 31 31
129 0.9 −0.1 2.0 −2.1 90 46 15
121 0.9 −0.1 0.0 −0.1 88 32 32
116 0.9 −0.1 2.9 −3.0 87 51 9
10 0.9 −0.1 −5.9 5.8 3 28 39
91 0.8 −0.1 4.8 −4.9 73 12 45
87 0.8 −0.0 1.8 −1.8 68 31 30
75 0.8 −0.1 8.4 −8.5 38 34 20
21 0.8 −0.1 1.9 −2.0 5 28 31
184 0.8 −0.0 0.6 −0.6 99 41 23
161 0.8 −0.1 −1.0 0.9 96 27 37
76 0.7 −0.0 4.7 −4.7 43 32 21
47 0.7 0.0 −0.5 0.5 11 25 38
29 0.7 0.0 −0.6 0.6 7 32 28
162 0.7 0.1 −6.5 6.6 96 43 26
151 0.7 0.0 3.7 −3.7 96 39 20
137 0.7 0.0 0.6 −0.6 93 26 34
124 0.7 0.1 −1.6 1.7 89 59 7
118 0.7 0.1 0.4 −0.3 87 47 16
113 0.7 0.0 7.9 −7.9 87 39 13

Average effective energy (sum of force field and SAS solvation energy) relative to the whole simulation ΔEi = 〈Ei〉 – 〈E〉, where the 〈Ei〉 and 〈E〉 values are calculated over the snapshots in the causally grouped mesostate i and the whole trajectory, respectively. Note that, in any force field, the absolute value of the effective energy is arbitrary and only ΔE values relative to a reference state are meaningful. The free energy differences are calculated by the relation ΔGi=kBTjPjln(Pi/Pj). Consequently, the entropy contribution to the free energy difference, TΔSi, is calculated using the relation −TΔSi = ΔGi – ΔEi.

The rank reflects the folding time Mi1 calculated by the equilibrium evolutions of the Markov chain. Structures in mesostates with rank in boldface are shown in Figs. 3 and 4.