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 7 3 421.29 2.27 2 4 8 4 401.97 1.24 3 5 8 3 400.51 0.53 4 5 9 4 397.00 1.49 5 5 10 5 336.12 10.77 6 5 14 9 234.19 5.24 7 6 9 3 396.52 1.25 8 8 14 6 269.62 12.38 9 8 55 47 19.09 0.65 10 10 13 3 409.95 1.88 11 10 14 4 395.27 1.21 12 11 14 3 395.27 1.22 13 11 15 4 398.90 0.60 14 12 15 3 417.31 0.35 15 12 16 4 388.15 1.80 16 13 16 3 393.81 3.15 17 13 17 4 392.38 3.87 18 13 98 85 74.64 1.81 19 14 17 3 399.63 0.41 20 14 18 4 392.55 3.95 21 15 18 3 397.62 1.42 22 15 19 4 392.55 3.95 23 16 19 3 397.62 1.42 24 16 20 4 396.44 2.00 25 16 98 82 86.03 0.34 26 17 20 3 398.04 1.21 27 17 21 4 392.91 0.24 28 17 51 34 82.42 0.89 29 17 94 77 84.19 0.60 30 17 98 81 86.05 0.34 31 18 21 3 395.29 1.39 32 18 22 4 393.57 2.23 33 19 22 3 400.69 4.06 34 19 23 4 395.80 1.69 35 20 23 3 399.91 0.36 36 20 24 4 399.91 0.36 37 20 94 74 87.53 0.99 38 20 97 77 87.57 1.00 39 21 24 3 399.93 0.36 40 21 25 4 399.92 0.36 41 21 47 26 87.52 0.99 42 21 50 29 87.50 0.98 43 21 87 66 87.58 1.02 44 21 90 69 87.59 1.02 45 21 91 70 87.55 1.00 46 22 25 3 400.65 0.01 47 22 26 4 399.95 0.35 48 22 40 18 87.91 0.98 49 22 43 21 87.68 1.05 50 22 47 25 87.50 0.98 51 23 26 3 399.97 0.35 52 23 27 4 394.29 2.48 53 24 27 3 394.22 2.52 54 24 28 4 394.11 2.58 55 24 90 66 87.64 1.02 56 24 93 69 87.67 1.03 57 24 94 70 87.66 1.03 58 25 28 3 396.81 1.23 59 25 31 6 275.12 7.04 60 25 35 10 205.92 0.57 61 25 47 22 87.66 1.05 62 26 32 6 243.11 3.48 63 26 35 9 206.13 0.67 64 28 31 3 405.87 1.32 65 28 32 4 374.98 0.74 66 28 86 58 87.95 1.00 67 29 32 3 385.25 3.95 68 30 33 3 437.65 1.01 69 31 34 3 401.95 1.88 70 31 35 4 401.11 1.78 71 31 83 52 88.05 0.96 72 31 87 56 87.98 0.99 73 32 35 3 400.36 2.16 74 32 36 4 379.24 3.75 75 33 36 3 387.00 3.42 76 34 38 4 398.47 1.23 77 34 77 43 88.89 0.61 78 34 79 45 88.97 0.57 79 35 38 3 398.72 1.08 80 35 43 8 239.30 12.17 81 38 43 5 390.84 0.99 82 39 42 3 407.30 1.35 83 39 43 4 394.50 0.77 84 40 43 3 394.50 0.77 85 40 44 4 394.86 0.96 86 41 44 3 400.92 0.78 87 41 45 4 399.62 1.43 88 42 45 3 400.94 0.79 89 42 46 4 394.85 0.96 90 43 46 3 394.85 0.96 91 43 47 4 394.83 0.96 92 44 48 4 386.40 0.81 93 45 48 3 400.13 0.14 94 45 49 4 392.60 3.91 95 46 49 3 398.53 0.94 96 46 50 4 392.60 3.91 97 47 50 3 395.38 2.52 98 47 51 4 392.59 3.92 99 48 51 3 396.59 1.92 100 48 52 4 392.07 4.17 101 49 52 3 391.19 3.73 102 49 53 4 382.78 0.46 103 50 53 3 397.45 0.60 104 50 54 4 384.47 0.07 105 50 84 34 150.73 12.31 106 50 87 37 150.95 12.38 107 50 88 38 151.01 12.36 108 50 91 41 152.91 13.23 109 51 54 3 395.55 0.70 110 51 55 4 390.12 2.02 111 51 91 40 151.06 12.34 112 52 55 3 393.47 0.35 113 52 56 4 390.12 2.02 114 53 56 3 399.16 0.44 115 53 57 4 341.44 5.85 116 53 58 5 372.12 4.88 117 53 111 58 156.22 14.86 118 53 112 59 156.16 14.86 119 53 117 64 155.83 14.73 120 54 91 37 156.15 14.75 121 54 108 54 156.37 14.86 122 54 111 57 156.19 14.85 123 54 112 58 155.98 14.81 124 55 95 40 156.68 14.82 125 55 108 53 156.38 14.86 126 55 111 56 156.37 14.86 127 56 111 55 156.38 14.86 128 57 111 54 156.38 14.86 129 57 117 60 156.30 14.82 130 58 117 59 156.31 14.82 131 59 116 57 156.31 14.82 132 59 117 58 156.31 14.82 133 61 66 5 394.41 0.96 134 63 66 3 403.48 0.75 135 63 67 4 396.69 1.05 136 64 67 3 396.69 1.05 137 64 68 4 385.82 3.33 138 65 68 3 394.39 0.95 139 65 69 4 393.04 0.34 140 66 69 3 401.96 1.53 141 66 70 4 393.05 0.34 142 67 70 3 396.53 1.40 143 67 71 4 378.31 0.24 144 67 119 52 157.05 14.72 145 67 120 53 157.00 14.74 146 67 123 56 156.74 14.71 147 68 71 3 397.32 0.96 148 68 72 4 393.72 2.75 149 69 72 3 397.75 1.59 150 69 73 4 396.90 1.17 151 70 73 3 398.62 1.16 152 70 74 4 395.29 1.97 153 70 121 51 157.04 14.74 154 70 123 53 157.01 14.73 155 71 74 3 394.27 1.46 156 71 75 4 394.27 1.46 157 71 123 52 157.00 14.73 158 72 75 3 405.23 0.21 159 72 76 4 382.78 2.69 160 73 76 3 384.80 3.09 161 73 77 4 359.41 9.12 162 73 78 5 359.40 9.12 163 73 79 6 246.64 0.48 164 74 78 4 274.12 13.25 165 74 79 5 212.72 0.78 166 74 122 48 157.19 14.69 167 78 83 5 392.65 2.42 168 79 83 4 389.54 0.86 169 80 83 3 400.96 2.83 170 80 84 4 389.55 0.86 171 80 122 42 157.60 14.62 172 81 84 3 392.18 2.18 173 81 85 4 389.54 0.86 174 81 122 41 157.63 14.63 175 82 85 3 393.44 1.09 176 82 86 4 390.87 2.37 177 83 86 3 393.80 1.32 178 83 87 4 390.88 2.38 179 84 87 3 397.82 1.92 180 84 88 4 390.38 2.62 181 84 118 34 157.97 14.49 182 84 122 38 157.66 14.64 183 85 88 3 391.14 2.25 184 85 89 4 385.89 4.80 185 85 118 33 158.08 14.48 186 86 89 3 394.94 2.95 187 86 90 4 391.38 2.04 188 87 90 3 405.69 2.42 189 87 91 4 403.04 3.77 190 88 91 3 405.72 2.44 191 88 92 4 403.03 3.77 192 89 92 3 405.67 2.46 193 89 93 4 403.04 3.79 194 90 93 3 405.70 2.46 195 90 94 4 404.26 3.17 196 91 94 3 409.54 0.53 197 91 95 4 400.47 1.27 198 92 95 3 405.25 1.11 199 92 96 4 393.47 2.23 200 92 105 13 177.36 5.60 201 92 109 17 162.96 12.31 202 93 96 3 400.99 3.25 203 93 97 4 399.21 4.13 204 94 97 3 407.43 0.03 205 94 98 4 395.66 0.15 206 95 98 3 397.05 0.43 207 95 99 4 391.57 1.00 208 95 100 5 347.79 5.78 209 95 105 10 190.01 0.28 210 95 108 13 196.63 3.59 211 96 99 3 389.73 1.92 212 96 105 9 200.68 1.61 213 100 104 4 396.42 0.74 214 100 105 5 388.53 1.05 215 101 104 3 406.99 1.37 216 101 105 4 394.13 2.04 217 102 105 3 396.57 0.82 218 102 106 4 394.12 2.04 219 103 106 3 401.19 3.12 220 103 107 4 390.35 0.14 221 104 107 3 396.81 3.37 222 104 108 4 388.54 0.97 223 105 108 3 402.20 0.57 224 105 109 4 392.69 1.10 225 106 109 3 405.44 1.04 226 106 110 4 392.97 1.23 227 107 110 3 392.72 1.09 228 107 111 4 392.70 1.10 229 108 111 3 399.54 0.92 230 109 112 3 402.43 0.38 231 109 113 4 382.73 1.89 232 110 113 3 390.28 5.66 233 110 114 4 382.61 1.82 234 111 114 3 412.91 1.84 235 111 117 6 364.29 9.20 236 112 117 5 361.50 10.59 237 113 118 5 388.51 0.93 238 114 117 3 404.09 2.79 239 114 118 4 393.44 0.69 240 115 118 3 393.44 0.69 241 115 119 4 392.61 1.10 242 116 119 3 407.81 0.05 243 116 120 4 401.62 3.15 244 117 120 3 407.85 2.34 245 117 121 4 398.82 2.00 246 118 121 3 401.97 3.32 247 118 122 4 386.56 1.85 248 119 122 3 396.75 3.02 249 119 123 4 375.28 3.52 250 120 123 3 390.69 6.34