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 4 374.99 1.16 2 5 69 64 75.80 6.09 3 6 9 3 396.38 2.25 4 7 10 3 387.79 0.04 5 7 11 4 383.81 1.44 6 8 11 3 383.81 1.44 7 8 12 4 383.81 1.44 8 8 62 54 99.61 0.77 9 8 65 57 99.66 0.73 10 8 66 58 99.66 0.73 11 8 69 61 100.28 0.42 12 8 71 63 100.30 0.42 13 9 12 3 391.14 1.64 14 9 13 4 383.73 1.34 15 10 13 3 392.89 1.65 16 10 14 4 383.88 1.41 17 10 52 42 102.73 0.28 18 11 14 3 394.14 3.04 19 11 15 4 383.89 1.41 20 11 46 35 102.93 0.34 21 11 47 36 102.67 0.24 22 11 52 41 102.73 0.28 23 11 62 51 102.06 0.07 24 11 66 55 101.66 0.09 25 12 15 3 390.66 4.78 26 12 16 4 381.50 0.20 27 12 66 54 101.69 0.10 28 12 71 59 101.64 0.10 29 13 16 3 386.35 0.98 30 13 17 4 381.51 0.20 31 14 17 3 401.99 1.65 32 14 21 7 244.19 1.90 33 14 46 32 103.03 0.33 34 14 52 38 102.95 0.29 35 15 21 6 244.19 1.91 36 15 22 7 244.18 1.90 37 15 43 28 102.98 0.35 38 15 46 31 103.03 0.33 39 15 66 51 102.56 0.29 40 15 72 57 102.06 0.07 41 15 102 87 85.81 0.75 42 16 106 90 78.72 1.23 43 17 21 4 267.55 5.83 44 17 22 5 267.55 5.83 45 18 22 4 322.84 8.77 46 18 23 5 259.26 2.04 47 20 46 26 113.53 2.25 48 21 46 25 113.54 2.25 49 22 38 16 113.64 2.25 50 22 43 21 113.56 2.25 51 22 46 24 113.56 2.25 52 22 102 80 113.30 2.33 53 24 36 12 113.64 2.25 54 24 37 13 113.64 2.25 55 24 38 14 113.64 2.25 56 25 37 12 113.70 2.26 57 26 33 7 120.65 0.12 58 26 34 8 118.97 0.14 59 27 39 12 121.64 0.41 60 27 99 72 122.54 0.05 61 28 31 3 393.25 1.55 62 28 32 4 366.26 2.67 63 28 33 5 257.44 5.07 64 28 34 6 257.44 5.07 65 29 77 48 124.21 0.66 66 29 97 68 125.39 1.25 67 29 99 70 124.84 0.97 68 30 77 47 130.05 1.65 69 34 37 3 412.00 4.25 70 34 75 41 170.53 1.38 71 34 77 43 177.70 0.16 72 36 101 65 173.44 0.08 73 36 102 66 169.35 0.79 74 37 75 38 180.22 1.09 75 37 99 62 184.79 0.70 76 37 100 63 180.16 1.08 77 37 101 64 174.53 0.14 78 38 42 4 373.40 0.36 79 38 43 5 371.29 1.42 80 38 72 34 184.30 0.94 81 38 99 61 190.47 0.96 82 38 100 62 181.82 0.30 83 38 101 63 180.28 1.06 84 39 42 3 381.16 0.50 85 39 43 4 380.76 4.04 86 39 95 56 202.53 0.95 87 39 96 57 202.03 0.72 88 39 98 59 193.59 0.47 89 39 99 60 191.19 0.63 90 40 43 3 387.84 0.50 91 40 44 4 380.76 4.04 92 40 92 52 201.19 0.83 93 40 95 55 202.53 0.95 94 40 98 58 196.53 0.95 95 40 99 59 193.65 0.49 96 40 100 60 191.44 0.60 97 41 44 3 385.50 1.67 98 41 45 4 372.12 0.99 99 41 94 53 202.55 0.96 100 41 95 54 202.54 0.96 101 41 96 55 202.53 0.96 102 42 45 3 391.24 3.06 103 42 46 4 376.99 3.43 104 43 46 3 384.49 0.32 105 43 47 4 371.26 0.85 106 43 63 20 266.56 1.51 107 43 66 23 266.55 1.51 108 43 72 29 252.27 0.09 109 43 92 49 203.47 1.29 110 44 47 3 384.30 0.42 111 44 48 4 382.79 0.31 112 44 56 12 272.07 0.42 113 44 59 15 266.74 1.51 114 44 60 16 266.76 1.50 115 44 92 48 203.50 1.28 116 44 94 50 203.51 1.27 117 45 48 3 382.31 0.57 118 45 49 4 380.89 1.26 119 46 49 3 384.47 0.53 120 46 50 4 380.89 1.26 121 46 52 6 374.76 4.32 122 47 50 3 388.79 2.69 123 47 51 4 380.89 1.26 124 47 52 5 353.51 0.64 125 47 53 6 346.71 4.04 126 47 59 12 271.57 0.67 127 47 62 15 267.82 1.66 128 47 63 16 267.14 1.52 129 47 66 19 267.62 1.76 130 48 51 3 380.89 1.26 131 48 53 5 311.73 0.38 132 48 55 7 294.60 0.89 133 48 56 8 290.25 3.04 134 48 59 11 277.81 2.35 135 52 62 10 278.13 2.53 136 53 58 5 293.56 3.79 137 53 59 6 287.88 1.36 138 53 62 9 281.83 4.38 139 54 58 4 361.70 0.18 140 55 58 3 386.37 5.24 141 55 59 4 376.93 0.85 142 56 59 3 378.66 1.30 143 56 60 4 377.37 0.64 144 56 94 38 222.20 1.81 145 57 60 3 377.38 0.64 146 57 61 4 377.37 0.64 147 58 61 3 384.01 2.38 148 58 62 4 377.34 0.61 149 59 62 3 377.35 0.61 150 59 63 4 379.26 1.34 151 60 63 3 383.04 0.54 152 60 64 4 379.72 1.13 153 60 92 32 228.39 3.27 154 60 94 34 226.83 3.89 155 61 64 3 379.72 1.13 156 61 65 4 379.72 1.12 157 61 90 29 228.55 3.28 158 62 65 3 386.42 2.23 159 62 66 4 386.41 2.23 160 63 66 3 392.95 1.01 161 63 67 4 389.74 0.58 162 63 72 9 292.99 5.01 163 63 92 29 228.52 3.31 164 64 67 3 395.90 0.47 165 64 68 4 389.75 0.58 166 64 88 24 230.47 3.47 167 64 89 25 230.46 3.47 168 64 90 26 230.34 3.44 169 64 91 27 229.38 3.61 170 64 92 28 228.56 3.29 171 65 68 3 392.95 1.01 172 65 69 4 389.75 0.59 173 65 88 23 230.47 3.46 174 66 69 3 385.10 2.92 175 66 70 4 385.05 2.93 176 66 71 5 315.99 1.98 177 66 72 6 296.57 3.22 178 67 70 3 383.62 3.66 179 67 72 5 292.99 5.01 180 67 73 6 292.99 5.01 181 67 74 7 292.99 5.01 182 67 91 24 230.46 3.47 183 67 92 25 230.45 3.47 184 67 100 33 226.75 3.75 185 68 85 17 230.87 3.33 186 68 86 18 230.88 3.34 187 68 87 19 230.87 3.35 188 68 88 20 230.55 3.49 189 70 103 33 224.16 2.64 190 70 105 35 223.94 2.66 191 70 106 36 212.47 2.03 192 71 102 31 225.13 3.12 193 71 103 32 224.87 3.00 194 72 101 29 225.21 3.14 195 72 102 30 225.13 3.12 196 72 103 31 224.17 2.64 197 73 100 27 226.78 3.77 198 73 101 28 226.05 3.54 199 73 102 29 225.21 3.14 200 73 103 30 225.13 3.10 201 74 79 5 316.48 7.27 202 74 80 6 287.98 0.03 203 74 83 9 234.62 1.82 204 74 99 25 227.15 3.73 205 74 100 26 227.06 3.75 206 75 79 4 376.42 0.06 207 75 80 5 323.48 10.77 208 75 99 24 227.20 3.75 209 75 100 25 227.15 3.73 210 75 101 26 227.15 3.73 211 76 80 4 365.86 5.33 212 77 80 3 418.36 1.77 213 77 97 20 229.42 3.71 214 77 99 22 228.67 3.36 215 78 93 15 230.56 3.48 216 78 97 19 229.30 3.64 217 78 98 20 228.66 3.36 218 79 93 14 230.51 3.46 219 79 98 19 228.63 3.37 220 79 100 21 228.61 3.37 221 80 83 3 395.87 0.76 222 84 91 7 230.68 3.44 223 92 100 8 238.33 0.04 224 93 98 5 269.64 15.58 225 93 100 7 244.56 1.11 226 103 106 3 418.55 2.91