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 8 34 26 165.40 2.60 2 8 35 27 165.53 2.68 3 9 12 3 331.72 1.03 4 9 13 4 312.86 5.30 5 9 35 26 165.99 2.54 6 10 13 3 330.94 0.65 7 10 14 4 330.64 0.58 8 11 14 3 339.94 5.15 9 11 15 4 330.64 0.58 10 11 67 56 165.39 2.58 11 11 70 59 162.35 1.10 12 11 76 65 92.81 0.26 13 12 15 3 330.65 0.58 14 12 16 4 330.64 0.58 15 12 35 23 166.65 2.45 16 12 63 51 165.43 2.57 17 12 66 54 165.39 2.58 18 12 67 55 165.39 2.58 19 13 16 3 330.76 0.52 20 13 17 4 330.78 0.51 21 13 35 22 166.50 2.48 22 14 17 3 330.77 0.51 23 14 18 4 330.77 0.51 24 14 76 62 96.98 2.33 25 15 18 3 337.07 1.32 26 15 19 4 330.76 0.50 27 15 66 51 165.41 2.56 28 15 67 52 165.43 2.56 29 15 70 55 162.42 1.06 30 15 76 61 97.06 2.38 31 16 19 3 343.72 1.04 32 16 20 4 303.00 10.32 33 16 28 12 167.81 2.77 34 16 31 15 166.72 2.44 35 16 32 16 166.84 2.50 36 16 35 19 166.67 2.44 37 16 66 50 165.49 2.60 38 18 75 57 117.34 6.84 39 18 76 58 116.06 7.07 40 18 79 61 115.94 7.12 41 19 22 3 333.93 1.34 42 19 23 4 328.74 0.16 43 19 66 47 165.55 2.60 44 19 69 50 165.44 2.56 45 19 70 51 165.40 2.55 46 19 73 54 164.47 2.19 47 19 74 55 161.52 0.78 48 19 75 56 142.13 0.19 49 20 23 3 332.85 2.23 50 20 28 8 172.76 5.22 51 22 69 47 166.10 2.65 52 22 73 51 165.00 2.33 53 23 27 4 299.62 9.20 54 23 28 5 263.95 8.25 55 23 31 8 261.99 7.28 56 23 62 39 167.01 2.41 57 23 65 42 166.88 2.46 58 23 66 43 166.88 2.46 59 23 69 46 166.88 2.46 60 24 27 3 325.30 1.22 61 24 28 4 321.31 0.77 62 25 28 3 331.94 0.22 63 25 29 4 318.89 0.44 64 26 58 32 168.13 2.48 65 27 31 4 338.69 0.95 66 27 62 35 167.06 2.43 67 27 65 38 167.06 2.43 68 28 31 3 344.31 1.63 69 28 32 4 329.36 1.05 70 29 32 3 342.44 0.70 71 29 33 4 334.12 1.32 72 29 48 19 172.02 1.95 73 30 33 3 335.80 0.49 74 30 34 4 463.26 0.27 75 30 44 14 189.41 0.20 76 30 48 18 180.91 2.82 77 30 50 20 171.94 1.95 78 30 55 25 168.57 2.33 79 30 58 28 168.57 2.33 80 30 59 29 168.45 2.33 81 31 59 28 168.45 2.33 82 31 62 31 168.39 2.35 83 31 63 32 168.39 2.35 84 31 66 35 168.30 2.35 85 33 44 11 309.23 0.12 86 33 47 14 275.69 5.71 87 33 48 15 266.38 10.37 88 34 41 7 389.32 0.95 89 34 44 10 310.89 0.65 90 34 59 25 168.60 2.32 91 39 43 4 321.88 0.67 92 39 44 5 310.92 0.67 93 40 43 3 326.94 1.85 94 40 44 4 326.38 1.56 95 41 44 3 329.36 1.12 96 41 45 4 326.38 1.56 97 41 52 11 177.74 1.35 98 41 55 14 170.84 1.97 99 41 56 15 170.49 1.79 100 41 59 18 170.45 1.79 101 42 45 3 332.19 0.62 102 42 46 4 326.37 1.55 103 42 52 10 177.83 1.35 104 43 46 3 331.48 0.98 105 43 47 4 329.10 2.17 106 44 47 3 332.53 0.03 107 44 48 4 322.25 1.26 108 44 55 11 170.47 1.78 109 44 59 15 169.68 1.96 110 45 48 3 333.06 3.23 111 45 49 4 320.41 2.18 112 45 50 5 278.26 4.41 113 45 51 6 212.06 6.07 114 45 52 7 188.44 3.73 115 45 55 10 174.86 0.05 116 46 49 3 327.92 0.48 117 50 54 4 317.93 0.32 118 50 55 5 317.91 0.32 119 51 54 3 322.86 2.15 120 51 55 4 323.55 2.50 121 52 55 3 328.11 1.42 122 52 56 4 323.55 2.50 123 53 56 3 325.86 2.31 124 53 57 4 324.56 2.96 125 54 57 3 331.63 0.57 126 54 58 4 328.37 1.06 127 55 58 3 334.56 3.65 128 55 59 4 326.11 0.56 129 56 59 3 332.94 2.21 130 56 60 4 328.44 0.61 131 57 60 3 332.25 0.14 132 57 61 4 327.93 0.89 133 58 61 3 335.29 1.94 134 58 62 4 335.14 1.94 135 59 62 3 335.14 1.93 136 59 63 4 327.96 0.85 137 60 63 3 333.05 0.82 138 60 64 4 327.80 0.23 139 61 64 3 333.37 0.67 140 61 65 4 330.46 1.55 141 62 65 3 331.86 0.86 142 62 66 4 327.79 0.22 143 63 66 3 330.45 1.56 144 63 67 4 328.76 2.92 145 64 67 3 333.49 0.56 146 64 68 4 330.22 2.20 147 65 68 3 334.73 0.06 148 65 69 4 334.73 0.05 149 66 69 3 334.74 0.05 150 66 70 4 334.74 0.04 151 67 70 3 334.74 0.04 152 67 71 4 334.74 0.04 153 68 71 3 338.75 1.97 154 68 72 4 332.47 1.08 155 69 72 3 336.49 3.10 156 69 73 4 327.39 1.44 157 70 73 3 339.34 2.29 158 70 74 4 312.69 2.73 159 70 75 5 307.18 5.48 160 70 76 6 301.91 3.00 161 70 77 7 287.03 4.43 162 71 74 3 347.87 1.22 163 74 77 3 334.60 1.68 164 74 78 4 319.19 1.30 165 75 78 3 337.08 3.58 166 75 79 4 322.87 0.51 167 76 79 3 332.85 1.27 168 76 80 4 322.87 0.51 169 77 80 3 340.23 2.02 170 77 81 4 323.27 0.70 171 78 81 3 333.44 2.91 172 78 82 4 326.16 0.74 173 79 82 3 337.73 0.77 174 79 83 4 326.77 1.01 175 79 110 31 22.84 0.40 176 79 111 32 23.80 0.87 177 80 83 3 330.70 2.97 178 80 84 4 326.78 1.00 179 81 84 3 339.26 1.30 180 81 85 4 320.36 2.22 181 82 85 3 333.72 4.46 182 82 86 4 319.22 2.79 183 82 110 28 28.17 0.51 184 83 86 3 322.47 1.17 185 83 87 4 322.47 1.17 186 84 87 3 334.03 2.27 187 84 88 4 322.45 1.17 188 85 88 3 327.00 1.25 189 85 89 4 322.30 1.09 190 86 89 3 328.52 0.97 191 86 90 4 318.86 3.07 192 86 103 17 36.12 0.66 193 86 106 20 36.18 0.63 194 86 107 21 34.70 0.65 195 87 90 3 329.27 3.66 196 87 91 4 327.73 1.36 197 88 91 3 333.54 1.53 198 88 92 4 327.73 1.37 199 89 92 3 327.73 1.36 200 89 93 4 322.04 4.21 201 89 99 10 59.68 2.28 202 89 103 14 43.23 0.12 203 90 93 3 330.75 0.23 204 90 94 4 305.50 1.93 205 90 103 13 43.28 0.09 206 91 94 3 336.43 1.08 207 93 96 3 339.72 0.56 208 93 99 6 298.35 1.44 209 94 100 6 308.73 2.85 210 95 100 5 319.12 2.31 211 96 99 3 329.67 2.75 212 96 100 4 325.19 0.73 213 97 100 3 329.45 2.86 214 97 101 4 325.41 0.62 215 98 101 3 331.41 3.62 216 98 102 4 325.39 0.62 217 99 102 3 330.85 1.02 218 99 103 4 325.31 0.58 219 100 103 3 337.96 1.13 220 100 104 4 325.30 0.59 221 101 104 3 327.72 0.61 222 101 105 4 324.38 1.05 223 102 105 3 333.76 0.96 224 102 106 4 324.51 0.98 225 103 106 3 331.98 0.59 226 103 107 4 323.42 0.44 227 104 107 3 339.55 3.19 228 104 108 4 323.43 0.45 229 105 108 3 340.68 2.63 230 105 109 4 326.45 2.08 231 106 109 3 327.89 1.36 232 106 110 4 320.39 1.90 233 107 110 3 334.71 2.04 234 107 111 4 325.93 0.88 235 108 111 3 333.39 2.85 236 108 112 4 325.94 0.88 237 109 112 3 331.60 0.53