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 5 9 4 313.30 4.33 2 5 69 64 39.03 0.67 3 5 71 66 39.56 0.39 4 7 10 3 362.62 1.99 5 7 11 4 334.06 1.24 6 8 11 3 354.22 2.21 7 8 12 4 343.06 5.75 8 8 65 57 56.95 0.95 9 8 66 58 56.94 0.96 10 8 69 61 56.95 0.95 11 8 71 63 56.94 0.96 12 9 12 3 352.51 1.35 13 9 13 4 343.26 5.85 14 9 71 62 56.99 0.93 15 10 13 3 356.83 0.90 16 10 14 4 356.38 0.67 17 11 14 3 358.65 1.66 18 11 15 4 356.46 0.63 19 11 46 35 69.09 0.96 20 11 47 36 68.94 0.94 21 11 52 41 68.94 0.94 22 11 62 51 65.98 0.99 23 11 66 55 64.64 1.18 24 12 15 3 362.13 0.09 25 12 16 4 356.45 0.63 26 12 66 54 64.57 1.21 27 12 71 59 64.54 1.21 28 12 101 89 64.55 1.21 29 12 102 90 64.54 1.22 30 13 16 3 362.38 0.04 31 14 17 3 357.64 1.32 32 14 21 7 68.94 0.89 33 14 46 32 73.11 1.03 34 15 21 6 68.95 0.88 35 15 22 7 68.81 0.95 36 15 43 28 68.94 0.89 37 15 46 31 69.17 0.93 38 15 66 51 65.25 1.39 39 15 72 57 64.95 1.31 40 15 101 86 64.63 1.18 41 16 101 85 64.62 1.19 42 17 20 3 350.23 9.61 43 17 21 4 266.80 1.97 44 17 22 5 266.80 1.97 45 18 22 4 276.06 3.48 46 20 46 26 104.86 0.26 47 21 46 25 104.86 0.26 48 22 38 16 104.77 0.27 49 22 43 21 104.85 0.26 50 22 46 24 104.85 0.26 51 22 101 79 95.87 0.49 52 23 38 15 104.86 0.26 53 24 36 12 104.81 0.24 54 24 37 13 104.83 0.24 55 24 38 14 104.87 0.26 56 24 101 77 104.79 0.26 57 25 34 9 105.34 0.27 58 25 37 12 104.87 0.26 59 26 33 7 172.56 33.85 60 26 34 8 105.34 0.27 61 26 35 9 105.17 0.33 62 27 33 6 204.92 19.57 63 27 34 7 172.53 33.86 64 27 38 11 105.38 0.26 65 27 39 12 105.46 0.30 66 27 98 71 105.28 0.36 67 28 31 3 377.20 0.53 68 28 32 4 316.98 3.45 69 28 33 5 257.62 9.21 70 29 32 3 367.30 1.03 71 29 34 5 338.56 2.23 72 29 98 69 107.34 0.58 73 34 37 3 366.72 0.37 74 34 75 41 130.06 0.38 75 34 76 42 130.25 0.29 76 34 106 72 63.48 0.85 77 35 105 70 64.62 1.16 78 35 106 71 63.19 0.91 79 36 100 64 131.13 0.99 80 36 104 68 65.11 1.40 81 36 105 69 64.36 1.22 82 37 99 62 136.20 1.09 83 37 100 63 131.53 0.79 84 37 106 69 63.16 0.92 85 38 43 5 337.77 3.89 86 38 72 34 136.77 0.84 87 38 98 60 137.53 1.07 88 38 99 61 136.41 1.02 89 38 100 62 136.41 1.02 90 38 101 63 136.41 1.02 91 39 42 3 344.22 3.58 92 39 43 4 345.10 3.14 93 39 97 58 149.38 4.76 94 39 98 59 138.94 0.43 95 39 99 60 138.90 0.41 96 40 43 3 361.05 1.01 97 40 44 4 345.15 3.12 98 40 91 51 151.09 5.00 99 40 92 52 150.84 4.86 100 40 94 54 151.73 5.32 101 40 97 57 149.38 4.76 102 40 99 59 142.78 1.47 103 41 44 3 364.83 2.94 104 41 45 4 345.12 3.12 105 41 56 15 200.59 22.32 106 41 93 52 151.77 5.32 107 41 94 53 151.77 5.31 108 41 95 54 151.75 5.32 109 42 45 3 347.70 1.84 110 42 46 4 352.44 0.70 111 43 46 3 365.52 2.33 112 43 47 4 359.09 0.88 113 43 63 20 158.93 1.99 114 43 72 29 151.66 5.38 115 43 91 48 159.40 1.98 116 44 47 3 359.09 0.88 117 44 48 4 352.25 4.30 118 44 56 12 200.67 22.29 119 44 59 15 159.35 1.96 120 44 60 16 159.41 1.98 121 44 63 19 159.06 1.81 122 44 91 47 159.41 1.98 123 44 93 49 159.41 1.98 124 45 48 3 359.09 0.88 125 45 49 4 346.88 1.61 126 46 49 3 346.88 1.61 127 46 50 4 346.88 1.61 128 46 52 6 336.39 0.70 129 47 50 3 361.05 0.97 130 47 51 4 337.94 0.27 131 47 52 5 319.24 9.03 132 47 53 6 319.22 9.04 133 47 59 12 200.59 22.24 134 47 63 16 200.44 22.27 135 48 51 3 337.69 0.19 136 48 53 5 318.81 9.25 137 48 55 7 261.74 3.85 138 48 56 8 252.61 1.28 139 53 58 5 338.30 1.06 140 53 59 6 322.42 6.87 141 53 62 9 280.75 2.85 142 54 58 4 356.62 0.03 143 55 58 3 361.71 0.30 144 55 59 4 358.89 1.10 145 56 59 3 358.89 1.11 146 56 60 4 358.90 1.11 147 56 93 37 231.73 0.41 148 57 60 3 358.90 1.11 149 57 61 4 358.91 1.11 150 58 61 3 359.30 0.94 151 58 62 4 358.32 1.40 152 59 62 3 358.36 1.41 153 59 63 4 358.32 1.40 154 60 63 3 358.88 1.14 155 60 64 4 358.94 1.17 156 60 89 29 233.72 1.21 157 60 91 31 233.68 1.21 158 60 92 32 233.65 1.22 159 60 93 33 233.38 1.08 160 61 64 3 365.21 0.16 161 61 65 4 358.94 1.17 162 62 65 3 358.94 1.17 163 62 66 4 358.94 1.17 164 63 66 3 358.31 1.48 165 63 67 4 354.95 3.15 166 63 91 28 233.74 1.19 167 64 67 3 358.31 1.47 168 64 68 4 351.93 1.72 169 64 90 26 233.75 1.19 170 64 91 27 233.74 1.19 171 65 68 3 364.91 1.86 172 65 69 4 350.30 0.90 173 66 69 3 358.41 0.61 174 66 70 4 350.27 0.91 175 66 71 5 335.09 2.63 176 66 72 6 332.83 3.76 177 67 70 3 347.30 0.25 178 67 71 4 338.67 0.86 179 67 72 5 314.18 5.57 180 67 74 7 296.79 1.23 181 67 90 23 233.84 1.21 182 67 91 24 233.83 1.20 183 67 99 32 233.65 1.21 184 70 102 32 232.56 1.02 185 71 101 30 232.96 1.19 186 71 102 31 232.93 1.21 187 72 91 19 234.00 1.24 188 72 99 27 233.65 1.21 189 72 100 28 233.52 1.21 190 72 101 29 232.59 1.01 191 73 99 26 233.70 1.23 192 73 100 27 233.56 1.20 193 73 102 29 232.98 1.18 194 74 79 5 260.02 3.46 195 74 80 6 245.47 5.92 196 74 98 24 233.85 1.24 197 74 99 25 233.77 1.22 198 74 100 26 233.69 1.20 199 75 79 4 344.75 1.83 200 75 98 23 233.84 1.24 201 75 100 25 233.84 1.24 202 77 80 3 350.98 1.28 203 77 81 4 339.13 1.36 204 78 81 3 352.52 5.12 205 78 82 4 351.30 1.45 206 78 92 14 234.62 1.06 207 78 96 18 234.47 1.12 208 78 97 19 234.19 1.18 209 79 82 3 355.61 3.60 210 79 83 4 351.31 1.45 211 79 92 13 234.60 1.05 212 79 97 18 234.26 1.14 213 79 99 20 234.13 1.17 214 80 83 3 351.85 1.72 215 80 84 4 351.31 1.46 216 81 84 3 351.31 1.46 217 81 85 4 351.31 1.46 218 81 86 5 345.09 1.63 219 82 85 3 354.67 0.51 220 82 86 4 345.06 1.65 221 82 90 8 234.78 1.07 222 82 92 10 234.78 1.08 223 83 90 7 234.78 1.07 224 91 99 8 235.55 1.29 225 92 97 5 298.04 13.55 226 92 99 7 264.89 3.02 227 94 97 3 365.37 3.65 228 95 98 3 419.16 5.04 229 100 105 5 249.74 3.14 230 100 106 6 260.72 2.35 231 101 104 3 363.00 1.76 232 101 105 4 284.24 0.65