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 6 14 8 269.27 1.27 2 6 93 87 43.37 0.35 3 7 11 4 335.44 5.92 4 8 11 3 363.17 4.86 5 10 13 3 378.83 1.24 6 10 101 91 44.29 0.02 7 10 105 95 36.98 0.43 8 11 14 3 382.88 0.79 9 11 17 6 338.70 0.62 10 12 17 5 364.52 4.71 11 12 18 6 340.10 7.50 12 12 44 32 104.80 0.67 13 12 58 46 104.64 0.65 14 13 18 5 367.74 3.15 15 13 58 45 104.70 0.68 16 13 59 46 104.69 0.68 17 13 93 80 55.21 1.46 18 13 101 88 51.25 0.12 19 13 104 91 46.82 0.26 20 13 108 95 45.68 0.63 21 14 17 3 382.16 2.25 22 14 18 4 375.19 0.49 23 14 93 79 55.21 1.46 24 15 18 3 381.35 1.84 25 15 19 4 368.23 2.99 26 15 36 21 180.31 29.88 27 15 40 25 171.91 34.05 28 16 19 3 381.17 1.75 29 16 20 4 368.11 2.97 30 17 20 3 377.31 0.46 31 17 21 4 376.86 0.70 32 18 21 3 387.26 1.63 33 18 22 4 386.92 1.80 34 18 39 21 176.74 31.64 35 18 42 24 176.67 31.61 36 18 44 26 176.54 31.55 37 18 58 40 116.64 1.59 38 18 86 68 116.64 1.58 39 19 22 3 388.36 1.08 40 19 35 16 181.94 29.07 41 19 36 17 181.95 29.08 42 19 39 20 176.84 31.59 43 20 23 3 425.18 5.03 44 21 44 23 182.36 28.73 45 21 45 24 182.30 28.69 46 22 35 13 182.56 28.82 47 22 38 16 182.62 28.80 48 22 39 17 182.59 28.79 49 22 43 21 182.59 28.78 50 22 44 22 182.43 28.70 51 22 45 23 182.37 28.67 52 23 45 22 186.97 26.43 53 24 28 4 386.75 0.42 54 25 28 3 404.98 1.10 55 25 33 8 253.00 0.31 56 25 38 13 252.96 0.32 57 25 52 27 223.93 7.81 58 25 53 28 223.87 7.81 59 25 54 29 223.86 7.81 60 25 55 30 223.77 7.78 61 25 67 42 222.38 6.80 62 26 53 27 224.08 7.73 63 27 31 4 313.17 5.27 64 27 33 6 253.02 0.30 65 27 34 7 253.03 0.30 66 27 35 8 253.03 0.29 67 27 53 26 224.18 7.68 68 27 67 40 222.42 6.79 69 27 68 41 222.41 6.77 70 27 69 42 222.34 6.75 71 28 34 6 253.02 0.30 72 28 35 7 253.02 0.29 73 30 69 39 228.91 3.47 74 31 34 3 398.38 1.04 75 31 69 38 228.90 3.46 76 32 37 5 345.37 10.98 77 32 70 38 228.16 3.06 78 32 71 39 228.16 3.06 79 32 72 40 228.11 3.04 80 32 73 41 228.11 3.04 81 33 37 4 362.97 2.19 82 33 38 5 320.68 0.31 83 33 67 34 229.14 3.42 84 33 68 35 229.10 3.40 85 33 71 38 228.18 3.00 86 34 37 3 362.97 2.19 87 34 38 4 366.93 0.21 88 35 38 3 377.17 1.09 89 35 39 4 366.94 0.21 90 36 39 3 378.31 0.52 91 36 40 4 367.00 0.17 92 37 40 3 379.98 1.35 93 37 73 36 227.81 2.81 94 38 41 3 389.01 5.71 95 38 42 4 375.01 0.01 96 38 43 5 309.66 0.76 97 38 55 17 232.30 2.56 98 38 67 29 229.27 3.46 99 38 73 35 227.75 2.78 100 39 42 3 366.72 2.83 101 39 43 4 316.18 1.74 102 39 86 47 201.30 3.90 103 40 74 34 227.78 2.77 104 40 86 46 198.14 2.33 105 41 57 16 232.65 2.23 106 41 73 32 227.81 2.78 107 41 74 33 227.78 2.77 108 41 84 43 207.25 4.52 109 41 86 45 198.17 2.31 110 41 87 46 188.69 0.87 111 42 57 15 232.63 2.22 112 42 58 16 232.62 2.19 113 42 84 42 207.93 4.84 114 42 86 44 201.30 3.91 115 43 55 12 232.67 2.24 116 43 56 13 232.65 2.23 117 43 57 14 232.61 2.21 118 43 64 21 232.36 2.10 119 43 67 24 232.11 2.06 120 43 73 30 227.82 2.77 121 43 76 33 227.78 2.75 122 43 77 34 226.56 2.16 123 44 56 12 232.66 2.21 124 44 58 14 232.71 2.16 125 46 54 8 236.02 3.71 126 46 56 10 232.87 2.14 127 47 51 4 339.86 9.38 128 47 52 5 253.22 1.13 129 47 54 7 236.01 3.72 130 48 51 3 370.47 0.52 131 48 52 4 291.75 0.28 132 48 54 6 249.45 2.99 133 51 54 3 389.81 1.90 134 51 65 14 232.99 1.81 135 53 65 12 232.99 1.77 136 53 66 13 232.97 1.78 137 54 63 9 233.18 1.78 138 54 64 10 233.06 1.78 139 54 65 11 232.95 1.75 140 55 64 9 233.11 1.76 141 55 67 12 232.88 1.72 142 56 62 6 252.77 1.09 143 56 63 7 233.13 1.74 144 57 60 3 387.13 0.80 145 57 61 4 293.39 4.63 146 57 62 5 252.78 1.09 147 57 77 20 226.59 2.16 148 57 84 27 208.11 4.89 149 58 61 3 371.38 1.84 150 58 84 26 208.18 4.87 151 59 83 24 209.29 5.42 152 59 84 25 208.18 4.87 153 59 85 26 208.18 4.87 154 59 104 45 57.02 2.18 155 59 107 48 56.91 2.21 156 59 108 49 56.30 2.27 157 60 77 17 227.66 2.66 158 60 83 23 208.41 4.99 159 60 84 24 208.19 4.88 160 60 111 51 56.30 2.27 161 61 111 50 56.31 2.27 162 61 112 51 56.30 2.27 163 61 115 54 56.18 2.23 164 62 80 18 226.02 1.88 165 64 67 3 449.03 4.52 166 64 76 12 226.62 2.15 167 64 77 13 226.59 2.15 168 64 80 16 222.42 0.14 169 67 71 4 336.54 11.26 170 67 73 6 328.80 7.54 171 67 76 9 272.26 3.71 172 68 71 3 377.72 0.83 173 71 76 5 320.86 3.62 174 72 75 3 370.80 4.81 175 72 76 4 335.26 9.96 176 73 76 3 360.37 0.41 177 73 77 4 358.19 1.50 178 74 78 4 365.26 2.97 179 74 87 13 191.81 0.69 180 75 78 3 372.67 0.10 181 75 79 4 365.25 2.98 182 76 79 3 372.64 0.10 183 76 80 4 369.53 0.85 184 77 80 3 381.80 4.48 185 77 81 4 365.22 3.00 186 77 83 6 323.25 2.46 187 77 84 7 306.73 4.54 188 77 87 10 243.30 24.88 189 78 81 3 365.16 3.02 190 78 82 4 341.74 6.42 191 78 87 9 269.42 9.09 192 82 87 5 314.63 7.04 193 83 111 28 56.90 2.21 194 84 87 3 377.05 1.32 195 85 104 19 57.06 2.19 196 85 107 22 57.01 2.17 197 86 89 3 350.25 10.42 198 86 104 18 57.02 2.17 199 89 100 11 60.77 1.28 200 91 95 4 328.42 10.77 201 91 96 5 282.04 5.26 202 91 100 9 279.20 6.68 203 92 95 3 353.39 4.88 204 92 96 4 346.80 1.58 205 93 96 3 390.28 1.50 206 93 101 8 282.00 5.25 207 97 100 3 377.45 4.07 208 97 101 4 362.64 3.99 209 98 101 3 369.26 0.69 210 98 102 4 371.85 0.18 211 99 103 4 371.87 0.18 212 100 103 3 374.24 0.38 213 100 104 4 372.76 0.35 214 101 104 3 379.47 0.48 215 101 105 4 373.79 0.14 216 102 105 3 376.00 0.96 217 102 106 4 376.88 1.60 218 103 106 3 380.82 0.36 219 103 107 4 376.88 1.60 220 104 107 3 376.88 1.60 221 104 108 4 376.88 1.60 222 105 108 3 380.81 0.36 223 105 109 4 376.87 1.60 224 106 109 3 381.79 0.84 225 106 110 4 372.24 0.70 226 107 110 3 372.25 0.70 227 107 111 4 372.24 0.70 228 108 111 3 381.49 3.94 229 108 112 4 381.38 3.99 230 109 112 3 386.63 1.36 231 109 113 4 381.38 3.99 232 110 113 3 386.34 1.50 233 110 114 4 381.37 3.98 234 111 114 3 381.37 3.98 235 111 115 4 386.46 1.44 236 112 115 3 386.46 1.44 237 112 116 4 386.46 1.44 238 113 116 3 390.64 3.53 239 113 117 4 371.30 0.04 240 114 117 3 382.30 1.60