BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 3 7 4 327.80 0.87 2 4 7 3 323.70 1.18 3 4 8 4 320.26 2.90 4 4 44 40 84.66 0.71 5 4 45 41 85.39 0.35 6 4 50 46 90.97 0.14 7 5 8 3 331.05 2.50 8 5 9 4 327.80 0.88 9 5 41 36 84.08 1.01 10 5 45 40 90.89 0.17 11 5 54 49 89.98 0.21 12 5 66 61 89.23 0.62 13 6 9 3 331.05 2.50 14 6 10 4 331.05 2.50 15 6 66 60 89.25 0.61 16 6 69 63 94.17 0.24 17 6 70 64 93.41 0.22 18 7 10 3 333.44 2.28 19 7 11 4 327.16 0.85 20 7 44 37 91.53 0.04 21 7 70 63 94.51 0.13 22 8 11 3 335.51 0.36 23 8 12 4 326.96 0.76 24 8 37 29 91.16 0.22 25 8 40 32 91.17 0.22 26 8 41 33 91.17 0.22 27 8 44 36 91.50 0.06 28 8 59 51 93.72 0.29 29 8 97 89 26.91 0.06 30 9 12 3 329.16 0.35 31 9 59 50 94.02 0.21 32 9 66 57 94.23 0.28 33 9 67 58 93.93 0.15 34 9 70 61 94.78 0.03 35 10 70 60 94.78 0.03 36 10 90 80 52.16 0.39 37 11 44 33 93.84 0.28 38 11 89 78 55.30 1.29 39 11 90 79 50.73 0.81 40 11 92 81 48.66 0.20 41 11 93 82 37.68 0.96 42 11 96 85 34.37 0.11 43 11 97 86 31.73 1.21 44 12 37 25 93.80 0.32 45 12 67 55 94.89 0.01 46 12 72 60 95.17 0.09 47 12 87 75 87.19 1.01 48 12 88 76 68.83 0.24 49 12 89 77 60.26 1.18 50 12 90 78 55.29 1.29 51 13 87 74 90.14 1.23 52 13 88 75 72.28 0.07 53 13 90 77 62.50 0.54 54 14 72 58 95.20 0.08 55 14 73 59 95.19 0.08 56 14 86 72 93.73 0.29 57 14 87 73 93.13 0.01 58 15 19 4 305.68 6.36 59 15 20 5 192.42 5.12 60 15 86 71 93.78 0.30 61 15 88 73 93.73 0.29 62 17 86 69 104.23 0.71 63 18 75 57 105.34 1.26 64 18 76 58 105.63 1.33 65 18 77 59 105.73 1.38 66 18 84 66 105.75 1.39 67 18 85 67 105.62 1.34 68 18 86 68 104.73 0.96 69 19 84 65 105.92 1.34 70 19 85 66 105.78 1.37 71 19 86 67 105.56 1.33 72 20 84 64 106.88 1.07 73 20 85 65 105.89 1.33 74 20 86 66 105.72 1.37 75 20 87 67 105.55 1.33 76 20 88 68 105.39 1.27 77 21 33 12 245.83 3.91 78 21 34 13 245.82 3.91 79 21 35 14 245.82 3.91 80 21 36 15 245.81 3.90 81 21 37 16 245.79 3.90 82 21 40 19 245.80 3.90 83 21 84 63 106.94 1.08 84 21 85 64 106.78 1.04 85 21 87 66 105.77 1.40 86 21 88 67 105.59 1.35 87 21 89 68 105.66 1.39 88 22 35 13 245.84 3.91 89 22 36 14 245.81 3.90 90 22 37 15 245.81 3.90 91 22 79 57 107.95 1.10 92 22 81 59 107.95 1.09 93 22 82 60 107.87 1.06 94 22 83 61 107.66 1.12 95 22 84 62 106.92 1.08 96 23 37 14 245.81 3.89 97 23 56 33 160.21 1.22 98 23 59 36 160.08 1.16 99 23 63 40 157.00 1.40 100 23 74 51 107.91 1.06 101 23 83 60 107.75 1.11 102 23 85 62 107.20 1.18 103 24 28 4 320.80 4.30 104 24 36 12 245.88 3.91 105 24 38 14 245.86 3.91 106 24 56 32 160.26 1.20 107 25 28 3 335.66 0.90 108 25 38 13 245.88 3.92 109 25 39 14 245.89 3.92 110 25 56 31 160.23 1.21 111 26 31 5 305.97 3.11 112 26 38 12 246.05 3.85 113 28 31 3 346.92 1.74 114 28 36 8 246.64 3.77 115 28 39 11 246.55 3.77 116 31 39 8 246.72 3.75 117 31 42 11 246.61 3.74 118 32 35 3 318.75 0.36 119 32 36 4 286.31 14.83 120 32 39 7 246.74 3.75 121 33 39 6 246.74 3.75 122 33 40 7 246.72 3.74 123 33 43 10 246.68 3.73 124 33 98 65 28.45 0.44 125 33 99 66 27.18 0.18 126 34 94 60 72.59 11.76 127 34 98 64 29.64 0.15 128 36 39 3 330.53 0.22 129 36 40 4 318.07 0.82 130 37 40 3 323.29 1.79 131 37 41 4 319.04 0.37 132 37 59 22 160.12 1.14 133 37 63 26 156.85 1.47 134 37 85 48 107.73 1.11 135 37 87 50 106.89 1.08 136 38 41 3 320.80 1.05 137 38 42 4 319.12 0.40 138 38 53 15 161.78 0.72 139 38 54 16 161.75 0.71 140 38 55 17 161.54 0.73 141 38 56 18 160.27 1.20 142 38 59 21 160.13 1.14 143 39 42 3 324.80 2.44 144 39 43 4 323.39 1.73 145 40 43 3 324.81 2.43 146 40 44 4 323.03 1.54 147 40 89 49 105.94 1.35 148 40 97 57 29.53 0.10 149 41 44 3 324.81 1.56 150 41 45 4 320.00 0.83 151 41 53 12 161.78 0.72 152 41 54 13 161.78 0.72 153 41 59 18 161.12 0.77 154 42 45 3 328.06 3.19 155 42 46 4 319.29 1.20 156 42 53 11 161.78 0.71 157 43 46 3 331.35 4.23 158 43 47 4 318.38 0.73 159 43 97 54 27.52 0.12 160 43 99 56 25.03 0.89 161 44 47 3 316.59 0.17 162 44 48 4 314.70 1.10 163 44 97 53 25.89 0.49 164 45 48 3 316.90 0.64 165 45 49 4 314.69 1.10 166 45 50 5 286.99 0.71 167 45 53 8 163.56 1.47 168 46 49 3 319.35 1.26 169 46 50 4 314.49 1.14 170 47 97 50 25.27 0.78 171 54 58 4 306.51 2.71 172 54 59 5 288.63 1.18 173 55 58 3 317.95 0.68 174 55 59 4 316.78 1.15 175 56 59 3 323.71 1.78 176 56 60 4 322.06 1.40 177 57 60 3 323.27 2.00 178 57 61 4 323.28 2.00 179 58 61 3 328.88 0.80 180 58 62 4 327.86 0.29 181 59 62 3 327.87 0.29 182 59 63 4 327.86 0.29 183 60 63 3 332.94 1.28 184 60 64 4 332.49 1.05 185 61 64 3 353.88 1.47 186 61 65 4 332.49 1.05 187 62 65 3 332.86 0.72 188 62 66 4 326.80 0.73 189 63 66 3 332.97 0.78 190 63 67 4 324.08 0.59 191 63 74 11 170.22 2.63 192 63 87 24 108.01 1.09 193 64 67 3 329.78 0.50 194 64 68 4 327.15 0.03 195 64 74 10 144.12 8.32 196 65 68 3 326.59 0.25 197 65 69 4 326.12 0.49 198 66 69 3 326.12 0.49 199 66 70 4 326.11 0.49 200 67 70 3 326.10 0.49 201 67 71 4 326.09 0.49 202 67 72 5 281.50 2.23 203 67 74 7 217.80 12.47 204 67 87 20 110.48 1.49 205 68 71 3 321.68 1.68 206 68 72 4 301.86 1.58 207 68 73 5 288.24 3.38 208 73 86 13 116.66 0.59 209 74 85 11 118.81 0.28 210 74 86 12 116.67 0.59 211 74 87 13 116.64 0.59 212 75 85 10 118.81 0.28 213 75 86 11 116.67 0.59 214 76 83 7 138.00 2.06 215 76 84 8 127.09 1.52 216 76 85 9 118.81 0.28 217 77 83 6 138.01 2.06 218 77 84 7 128.62 1.56 219 78 82 4 254.78 0.75 220 78 83 5 169.06 2.53 221 79 82 3 297.86 7.13 222 79 84 5 173.60 0.27 223 89 93 4 326.82 2.88 224 89 94 5 324.81 3.89 225 89 97 8 283.59 1.53 226 89 98 9 190.84 2.34 227 90 93 3 344.09 2.77 228 90 94 4 333.06 0.21 229 91 94 3 341.85 3.90 230 92 95 3 333.62 0.07 231 92 96 4 318.12 2.68 232 93 96 3 325.93 1.59 233 93 97 4 316.94 2.21 234 93 98 5 279.30 3.80 235 94 98 4 258.17 6.77