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 11 14 3 316.11 3.39 2 11 15 4 293.99 4.63 3 12 15 3 316.10 3.39 4 12 16 4 289.06 2.17 5 12 66 54 48.83 2.25 6 12 69 57 49.55 2.10 7 12 70 58 49.37 2.18 8 12 73 61 50.81 2.19 9 12 84 72 51.00 2.12 10 13 16 3 299.45 1.90 11 13 17 4 297.72 2.17 12 13 87 74 50.38 1.81 13 14 17 3 297.72 2.16 14 14 18 4 297.72 2.16 15 15 18 3 302.18 0.07 16 15 19 4 294.39 0.51 17 16 19 3 296.98 0.04 18 16 20 4 296.18 0.38 19 16 66 50 57.10 1.20 20 16 87 71 61.16 1.30 21 16 88 72 61.13 1.31 22 16 91 75 53.78 0.91 23 17 20 3 297.00 0.02 24 17 21 4 296.19 0.38 25 17 87 70 62.81 1.41 26 18 21 3 296.19 0.39 27 18 22 4 296.19 0.39 28 19 22 3 296.18 0.39 29 19 23 4 296.18 0.39 30 19 62 43 64.22 1.70 31 19 63 44 64.04 1.61 32 19 66 47 63.76 1.47 33 19 91 72 63.14 1.25 34 20 23 3 301.54 2.29 35 20 24 4 296.07 0.45 36 20 87 67 63.68 1.41 37 20 90 70 63.61 1.40 38 20 91 71 62.91 1.36 39 20 94 74 62.91 1.35 40 21 24 3 308.60 1.24 41 21 25 4 296.55 0.13 42 22 25 3 296.54 0.12 43 22 26 4 296.32 0.01 44 22 59 37 65.70 2.30 45 22 63 41 64.95 1.95 46 23 26 3 301.27 2.38 47 23 27 4 296.50 0.07 48 23 91 68 63.62 1.39 49 23 94 71 62.91 1.35 50 23 95 72 62.90 1.35 51 23 98 75 49.66 4.34 52 24 27 3 312.58 2.27 53 24 28 4 296.61 0.04 54 24 90 66 63.71 1.42 55 24 94 70 63.17 1.23 56 25 28 3 301.53 2.42 57 25 29 4 301.48 2.39 58 26 29 3 311.42 2.56 59 26 30 4 312.43 2.06 60 26 52 26 87.63 1.17 61 26 55 29 80.09 2.10 62 26 59 33 70.20 0.21 63 27 30 3 312.43 2.06 64 27 31 4 302.56 2.88 65 27 98 71 56.77 0.77 66 28 31 3 301.16 2.18 67 28 32 4 296.64 0.07 68 29 32 3 306.23 4.71 69 29 33 4 296.11 0.34 70 29 51 22 95.77 1.82 71 30 33 3 316.51 0.43 72 30 48 18 95.68 1.75 73 30 52 22 95.07 2.02 74 31 34 3 317.70 0.16 75 32 35 3 330.38 0.09 76 33 44 11 100.84 1.74 77 33 47 14 100.80 1.73 78 33 48 15 98.03 2.10 79 33 51 18 99.79 1.45 80 34 44 10 100.84 1.74 81 36 40 4 291.81 1.73 82 37 40 3 308.17 1.11 83 37 41 4 291.50 1.57 84 38 41 3 294.34 0.47 85 38 42 4 294.74 0.36 86 39 42 3 334.98 1.46 87 40 43 3 311.50 2.69 88 40 44 4 292.94 0.64 89 41 44 3 297.23 1.51 90 41 45 4 297.32 1.44 91 42 45 3 307.12 0.60 92 42 46 4 303.08 1.44 93 43 46 3 303.37 1.58 94 43 47 4 303.08 1.45 95 44 47 3 305.06 2.17 96 44 48 4 304.80 2.31 97 45 48 3 309.68 0.12 98 45 49 4 304.80 2.31 99 45 105 60 48.27 4.65 100 46 49 3 311.98 0.17 101 46 50 4 305.89 2.88 102 47 50 3 310.79 0.43 103 47 51 4 305.86 2.90 104 48 51 3 305.88 1.77 105 48 52 4 298.79 0.61 106 48 55 7 289.87 0.98 107 49 52 3 309.06 0.18 108 49 53 4 303.12 2.79 109 49 102 53 49.13 4.53 110 49 105 56 43.87 2.46 111 49 106 57 28.18 0.94 112 50 53 3 307.38 1.55 113 50 54 4 306.53 1.08 114 51 54 3 305.53 0.92 115 51 55 4 303.24 0.57 116 52 55 3 308.68 0.66 117 52 56 4 303.76 0.32 118 52 102 50 48.98 4.58 119 53 56 3 311.56 0.79 120 53 57 4 308.85 2.13 121 54 57 3 312.77 0.70 122 54 58 4 310.76 1.17 123 55 58 3 312.36 0.37 124 55 59 4 307.16 2.15 125 56 59 3 311.53 0.04 126 56 60 4 307.16 2.14 127 56 95 39 63.80 1.45 128 56 99 43 60.38 0.96 129 57 60 3 316.14 0.70 130 57 61 4 310.22 0.61 131 58 61 3 315.73 1.98 132 58 62 4 308.03 1.71 133 59 62 3 308.73 1.53 134 59 63 4 307.19 2.07 135 59 95 36 63.79 1.45 136 60 63 3 309.60 0.87 137 60 64 4 303.74 0.36 138 60 95 35 63.80 1.44 139 60 99 39 61.96 0.57 140 61 64 3 305.23 0.23 141 61 65 4 302.51 1.03 142 62 65 3 306.50 0.38 143 62 66 4 308.50 1.39 144 63 66 3 314.81 0.03 145 63 67 4 305.12 0.27 146 63 91 28 63.83 1.44 147 63 95 32 63.73 1.46 148 64 67 3 306.50 0.39 149 64 68 4 302.56 1.01 150 65 68 3 311.41 2.37 151 65 69 4 303.95 1.67 152 66 69 3 303.95 1.67 153 66 70 4 303.95 1.67 154 66 88 22 64.12 1.36 155 67 70 3 308.38 2.33 156 67 71 4 305.50 0.90 157 67 88 21 64.12 1.35 158 67 92 25 64.07 1.34 159 68 71 3 305.50 0.89 160 68 72 4 305.48 0.90 161 69 72 3 308.99 2.13 162 69 73 4 305.47 0.90 163 70 73 3 305.48 0.90 164 70 74 4 305.44 0.89 165 70 81 11 124.39 0.76 166 71 74 3 305.69 1.00 167 71 75 4 305.44 0.88 168 72 75 3 306.08 1.20 169 72 76 4 305.44 0.88 170 73 76 3 304.36 1.42 171 73 77 4 300.17 3.50 172 73 78 5 277.71 1.54 173 73 81 8 132.18 0.57 174 73 84 11 129.53 0.24 175 74 77 3 300.07 3.56 176 74 78 4 245.53 7.43 177 74 81 7 136.50 1.05 178 77 80 3 344.79 0.92 179 77 81 4 299.57 1.54 180 78 81 3 308.86 0.39 181 78 82 4 285.33 4.77 182 80 83 3 316.41 1.46 183 81 84 3 308.02 0.24 184 81 85 4 308.02 0.24 185 82 85 3 305.77 0.88 186 82 86 4 305.64 0.94 187 83 86 3 305.76 0.88 188 83 87 4 305.64 0.94 189 84 87 3 305.75 0.88 190 84 88 4 301.16 1.29 191 85 88 3 307.50 2.18 192 85 89 4 303.96 0.93 193 86 89 3 310.03 0.92 194 86 90 4 310.03 0.92 195 87 90 3 310.02 0.92 196 87 91 4 310.02 0.92 197 88 91 3 311.60 0.12 198 88 92 4 306.98 2.43 199 89 92 3 309.69 1.07 200 89 93 4 303.95 0.97 201 90 93 3 307.79 2.01 202 90 94 4 303.44 2.06 203 91 94 3 306.78 0.39 204 91 95 4 303.42 2.07 205 92 95 3 309.72 1.86 206 92 96 4 299.14 0.02 207 93 96 3 302.56 1.72 208 93 97 4 299.14 0.01 209 94 97 3 310.19 1.90 210 94 98 4 302.76 1.82 211 95 98 3 302.12 1.50 212 95 99 4 301.20 1.03 213 96 99 3 307.10 2.97 214 96 100 4 300.63 1.32 215 97 100 3 300.63 1.32 216 97 101 4 300.62 1.31 217 98 101 3 303.90 0.32 218 98 102 4 303.83 0.30 219 99 102 3 308.83 1.65 220 99 103 4 296.56 3.93 221 100 103 3 308.38 1.87 222 100 104 4 295.75 3.52 223 101 104 3 308.55 1.78 224 101 105 4 301.87 0.46 225 102 105 3 308.43 2.48 226 102 106 4 301.80 0.49 227 103 106 3 311.73 5.46 228 103 107 4 302.89 1.04 229 104 107 3 315.87 3.40