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 4 10 6 331.56 0.01 2 4 13 9 301.69 2.21 3 4 21 17 96.65 0.03 4 5 10 5 350.21 4.01 5 5 24 19 96.73 0.01 6 5 77 72 96.64 0.04 7 5 78 73 96.78 0.00 8 6 9 3 362.08 1.92 9 6 10 4 350.61 3.82 10 6 76 70 96.69 0.01 11 6 77 71 96.74 0.01 12 7 10 3 362.16 1.88 13 7 11 4 355.16 1.55 14 7 76 69 96.75 0.01 15 7 86 79 96.78 0.00 16 7 87 80 96.74 0.01 17 7 88 81 96.44 0.01 18 7 98 91 58.04 0.48 19 7 99 92 58.05 0.48 20 7 100 93 57.76 0.57 21 7 109 102 24.48 0.91 22 8 11 3 362.08 1.91 23 8 12 4 355.14 1.98 24 8 109 101 26.21 0.06 25 8 110 102 23.45 0.39 26 9 12 3 362.76 1.43 27 9 13 4 362.47 1.69 28 10 13 3 362.49 1.68 29 10 14 4 362.38 1.64 30 10 20 10 305.07 4.44 31 10 24 14 183.22 42.27 32 10 74 64 97.28 0.06 33 10 76 66 98.38 0.33 34 10 88 78 96.84 0.07 35 11 14 3 362.94 1.44 36 11 15 4 362.38 1.63 37 11 88 77 97.19 0.10 38 11 96 85 66.89 0.32 39 11 109 98 25.89 0.11 40 11 110 99 21.02 0.49 41 12 15 3 365.25 0.29 42 12 16 4 356.67 4.48 43 12 110 98 22.34 0.16 44 13 16 3 360.94 2.37 45 13 17 4 356.65 4.49 46 13 18 5 355.58 3.96 47 13 19 6 344.04 0.77 48 13 20 7 333.22 0.64 49 13 21 8 310.13 1.90 50 14 18 4 345.06 1.28 51 14 19 5 338.64 3.33 52 14 20 6 338.61 3.33 53 14 88 74 98.73 0.16 54 14 90 76 95.55 0.81 55 14 94 80 72.36 0.03 56 14 96 82 70.72 0.47 57 15 18 3 351.39 4.29 58 15 94 79 72.36 0.03 59 15 96 81 72.24 0.02 60 15 110 95 22.33 0.16 61 18 94 76 73.38 0.03 62 20 24 4 334.39 5.17 63 20 52 32 100.56 0.81 64 20 53 33 98.98 0.15 65 20 74 54 98.98 0.15 66 20 90 70 98.45 0.04 67 21 24 3 364.27 0.46 68 23 49 26 158.81 0.71 69 23 50 27 158.81 0.71 70 24 50 26 158.81 0.71 71 24 52 28 158.46 0.64 72 24 74 50 158.48 0.64 73 24 75 51 158.71 0.72 74 25 29 4 354.21 2.50 75 25 30 5 354.51 2.35 76 25 33 8 344.99 1.37 77 25 49 24 159.02 0.75 78 25 50 25 158.94 0.76 79 25 51 26 158.90 0.74 80 25 52 27 158.88 0.74 81 26 29 3 366.76 0.60 82 26 30 4 358.44 1.95 83 26 51 25 158.96 0.76 84 26 52 26 158.93 0.76 85 26 53 27 158.95 0.74 86 26 54 28 158.80 0.70 87 27 30 3 376.89 0.55 88 27 31 4 358.43 1.96 89 27 35 8 339.17 0.05 90 27 51 24 159.03 0.74 91 27 54 27 158.99 0.74 92 28 31 3 359.45 1.45 93 28 32 4 357.04 1.27 94 28 35 7 343.62 2.27 95 29 32 3 367.56 1.95 96 29 33 4 360.12 1.11 97 30 33 3 361.69 0.98 98 30 34 4 358.53 0.32 99 30 35 5 343.70 2.33 100 30 42 12 159.28 0.76 101 30 51 21 159.09 0.72 102 31 34 3 357.49 0.21 103 31 35 4 344.44 1.95 104 33 46 13 159.64 0.80 105 33 49 16 159.63 0.80 106 34 45 11 159.75 0.81 107 35 42 7 159.49 0.68 108 35 45 10 159.75 0.81 109 36 39 3 394.69 2.25 110 36 41 5 280.94 6.59 111 38 82 44 160.18 0.83 112 39 82 43 160.16 0.83 113 39 83 44 160.06 0.84 114 40 82 42 160.18 0.83 115 41 44 3 352.79 0.30 116 41 45 4 359.63 0.30 117 42 45 3 369.55 1.94 118 42 46 4 350.75 4.75 119 42 51 9 217.62 27.41 120 42 78 36 172.22 4.45 121 42 83 41 170.43 4.03 122 43 46 3 361.97 0.96 123 43 47 4 318.90 3.00 124 43 79 36 178.95 7.81 125 44 47 3 372.35 2.32 126 46 49 3 380.22 0.47 127 50 75 25 252.69 1.04 128 50 78 28 252.99 1.00 129 51 54 3 468.85 0.27 130 51 74 23 252.84 0.97 131 51 75 24 252.75 1.02 132 51 83 32 253.16 1.11 133 52 73 21 253.40 1.04 134 52 74 22 252.74 1.03 135 52 75 23 253.12 0.95 136 53 73 20 253.49 1.07 137 53 74 21 253.41 1.03 138 53 90 37 253.14 0.90 139 54 72 18 253.69 1.09 140 54 73 19 253.51 1.07 141 55 70 15 254.03 1.14 142 55 71 16 254.01 1.13 143 55 72 17 253.75 1.07 144 56 63 7 278.49 1.79 145 56 71 15 254.00 1.12 146 56 72 16 254.00 1.12 147 56 73 17 253.99 1.12 148 56 89 33 253.64 0.95 149 56 103 47 55.25 0.43 150 56 106 50 52.28 0.03 151 58 61 3 346.22 0.86 152 58 62 4 348.58 0.32 153 58 63 5 325.53 0.21 154 60 104 44 62.22 0.12 155 62 106 44 51.96 0.18 156 63 71 8 257.63 2.83 157 63 89 26 253.74 0.93 158 63 97 34 229.97 2.48 159 63 106 43 51.91 0.21 160 64 69 5 366.19 2.02 161 64 71 7 284.57 1.56 162 64 95 31 253.09 0.92 163 64 97 33 252.06 1.00 164 65 69 4 358.04 2.05 165 65 71 6 292.56 1.57 166 66 69 3 371.49 0.62 167 69 91 22 254.56 0.48 168 69 93 24 253.48 0.96 169 69 95 26 253.14 1.03 170 71 89 18 256.60 0.76 171 71 90 19 256.36 0.82 172 71 91 20 254.31 0.35 173 71 95 24 235.68 3.32 174 71 97 26 211.31 6.78 175 72 89 17 256.61 0.76 176 72 90 18 256.53 0.73 177 72 91 19 255.82 0.87 178 73 87 14 256.85 0.78 179 73 88 15 256.75 0.79 180 73 89 16 256.62 0.76 181 73 90 17 256.62 0.76 182 73 103 30 52.29 0.03 183 74 87 13 256.86 0.78 184 74 88 14 256.79 0.79 185 74 90 16 256.74 0.78 186 75 78 3 411.29 0.86 187 75 87 12 256.89 0.77 188 76 84 8 257.06 0.80 189 76 86 10 256.98 0.77 190 76 87 11 256.93 0.78 191 76 88 12 256.93 0.78 192 77 84 7 257.10 0.79 193 77 86 9 257.04 0.79 194 78 83 5 263.10 3.77 195 78 84 6 263.08 3.77 196 83 87 4 443.86 0.14 197 84 87 3 503.30 2.58 198 85 101 16 54.09 0.41 199 85 102 17 52.06 0.10 200 86 99 13 109.89 25.72 201 86 100 14 54.97 0.72 202 87 98 11 257.49 0.83 203 87 99 12 208.55 23.58 204 87 102 15 52.27 0.04 205 87 103 16 52.10 0.12 206 88 96 8 260.26 1.01 207 88 97 9 258.52 0.53 208 88 98 10 257.49 0.83 209 88 109 21 30.05 0.14 210 89 95 6 276.63 9.13 211 89 96 7 260.61 1.19 212 89 97 8 258.58 0.55 213 89 99 10 258.46 0.53 214 89 103 14 154.10 50.86 215 89 106 17 43.36 0.74 216 90 94 4 307.69 3.38 217 90 95 5 268.91 5.26 218 90 96 6 260.32 1.33 219 91 94 3 358.12 2.34 220 91 95 4 275.98 1.74 221 94 110 16 27.14 0.29 222 95 108 13 34.66 0.12 223 96 107 11 35.37 0.40 224 96 108 12 33.89 0.17 225 96 109 13 29.16 0.27 226 96 110 14 26.19 0.46 227 97 106 9 146.59 55.97 228 97 107 10 35.31 0.42 229 97 108 11 33.89 0.17 230 97 109 12 31.21 1.12 231 98 105 7 276.44 3.26 232 98 106 8 146.59 55.97 233 98 107 9 34.98 0.24 234 98 109 11 29.65 0.35 235 99 102 3 377.62 0.45 236 99 103 4 315.78 6.46 237 99 104 5 315.76 6.48 238 99 105 6 265.12 2.39 239 99 106 7 260.56 0.46 240 101 104 3 362.65 3.12 241 101 105 4 348.83 0.36 242 103 106 3 389.00 0.71