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 2 16 14 12.98 0.90 2 3 14 11 102.89 38.40 3 4 11 7 204.29 0.96 4 4 12 8 203.37 1.43 5 4 13 9 105.45 37.28 6 5 10 5 316.59 7.53 7 5 11 6 245.57 2.98 8 5 12 7 203.37 1.44 9 5 14 9 193.10 6.48 10 5 30 25 46.62 0.22 11 5 34 29 47.09 1.00 12 6 9 3 373.43 3.07 13 6 10 4 318.78 6.44 14 6 33 27 48.92 0.25 15 7 10 3 367.42 6.08 16 7 12 5 296.14 7.91 17 7 27 20 49.62 0.21 18 7 29 22 49.24 0.39 19 7 30 23 48.85 0.21 20 7 33 26 48.97 0.27 21 12 20 8 199.80 0.09 22 12 25 13 122.08 27.32 23 12 27 15 65.17 1.13 24 12 30 18 64.48 1.47 25 13 20 7 199.81 0.09 26 13 21 8 199.78 0.10 27 13 22 9 195.40 1.98 28 14 19 5 208.78 2.16 29 14 20 6 199.81 0.09 30 14 21 7 199.78 0.09 31 15 18 3 369.07 2.73 32 15 19 4 237.31 1.07 33 15 21 6 201.69 0.85 34 17 101 84 78.03 4.55 35 17 107 90 65.32 1.02 36 18 101 83 78.03 4.56 37 19 97 78 78.28 4.68 38 19 100 81 78.07 4.58 39 19 101 82 78.05 4.57 40 19 105 86 70.31 0.69 41 19 106 87 67.84 0.51 42 19 107 88 67.80 0.53 43 20 23 3 393.62 0.81 44 20 26 6 218.72 5.49 45 20 30 10 86.94 0.11 46 20 104 84 77.97 4.53 47 23 57 34 101.69 5.24 48 23 104 81 79.70 3.96 49 23 105 82 79.70 3.95 50 23 106 83 79.66 3.94 51 25 54 29 108.63 1.92 52 26 30 4 361.04 1.28 53 26 31 5 361.04 1.28 54 26 47 21 110.81 0.82 55 26 50 24 110.77 0.90 56 26 54 28 108.64 1.92 57 26 102 76 110.76 0.91 58 26 103 77 108.58 1.91 59 26 104 78 105.69 1.40 60 27 30 3 369.82 3.09 61 27 31 4 362.58 0.54 62 28 31 3 378.13 0.57 63 28 32 4 362.56 0.54 64 28 47 19 110.66 0.86 65 29 32 3 363.17 0.24 66 29 33 4 362.50 0.53 67 30 33 3 368.38 1.91 68 30 34 4 360.55 1.07 69 31 34 3 365.18 0.76 70 31 35 4 359.80 0.82 71 31 42 11 188.69 3.79 72 31 47 16 118.07 0.04 73 31 50 19 110.88 0.86 74 31 102 71 110.78 0.91 75 32 35 3 365.07 0.81 76 32 36 4 362.51 2.18 77 32 42 10 193.72 1.28 78 33 36 3 367.44 2.00 79 33 37 4 365.18 0.87 80 34 37 3 373.14 1.54 81 34 38 4 367.25 0.17 82 34 101 67 111.14 1.01 83 34 102 68 111.14 1.00 84 35 38 3 367.26 0.17 85 35 39 4 362.12 2.39 86 35 40 5 303.42 8.14 87 35 42 7 229.53 2.24 88 35 102 67 111.21 0.97 89 36 39 3 351.63 2.79 90 38 98 60 140.30 1.61 91 38 102 64 133.34 0.41 92 40 46 6 353.42 0.43 93 40 90 50 159.59 2.04 94 40 91 51 159.16 1.90 95 40 92 52 159.19 1.90 96 40 98 58 157.58 1.15 97 40 102 62 154.14 2.27 98 41 46 5 357.39 0.10 99 42 46 4 353.43 0.43 100 42 47 5 354.42 0.93 101 42 50 8 347.94 1.49 102 42 102 60 159.37 1.79 103 43 46 3 370.08 2.36 104 43 47 4 357.41 0.09 105 44 47 3 371.16 1.82 106 44 48 4 363.87 1.14 107 45 48 3 370.35 2.23 108 45 49 4 363.88 1.14 109 45 86 41 164.02 1.64 110 45 90 45 163.34 1.60 111 46 49 3 368.73 3.04 112 46 50 4 363.89 1.13 113 46 90 44 162.28 2.10 114 46 91 45 162.27 2.11 115 47 50 3 363.88 1.12 116 47 51 4 363.89 1.12 117 48 51 3 365.04 0.55 118 48 52 4 359.39 1.14 119 48 77 29 165.84 2.04 120 49 52 3 360.28 1.83 121 49 53 4 366.03 2.18 122 49 69 20 167.44 2.08 123 49 73 24 166.80 2.06 124 49 87 38 164.00 1.58 125 49 90 41 163.98 1.61 126 49 91 42 163.94 1.60 127 49 99 50 161.18 1.65 128 50 53 3 370.50 0.04 129 50 54 4 366.02 2.19 130 50 102 52 161.19 1.65 131 50 103 53 160.72 1.74 132 51 54 3 367.88 1.26 133 51 55 4 363.81 3.29 134 52 55 3 377.40 1.36 135 52 56 4 363.57 3.40 136 52 69 17 185.35 4.58 137 52 72 20 167.56 2.16 138 52 73 21 167.27 2.10 139 52 76 24 166.96 2.13 140 53 56 3 370.46 0.04 141 53 57 4 358.18 0.70 142 53 64 11 218.50 3.92 143 53 69 16 185.13 4.70 144 53 99 46 161.88 1.92 145 53 100 47 161.30 1.63 146 53 103 50 161.19 1.65 147 53 105 52 161.03 1.58 148 54 57 3 380.16 0.01 149 54 58 4 358.23 0.72 150 54 103 49 161.19 1.65 151 55 58 3 364.36 2.33 152 55 59 4 358.22 0.72 153 56 59 3 368.01 0.51 154 56 60 4 348.02 1.61 155 56 61 5 339.50 1.72 156 56 62 6 338.35 2.27 157 56 64 8 264.47 4.21 158 57 61 4 338.36 2.28 159 57 62 5 304.49 1.03 160 57 63 6 272.41 0.24 161 57 105 48 161.22 1.65 162 58 61 3 369.24 2.76 163 63 108 45 154.46 0.39 164 64 68 4 351.37 5.05 165 64 69 5 343.42 9.03 166 65 68 3 359.96 2.01 167 65 69 4 362.56 0.52 168 65 96 31 164.41 1.69 169 66 69 3 365.48 0.94 170 66 70 4 362.62 0.54 171 66 95 29 164.48 1.70 172 66 96 30 164.41 1.69 173 67 71 4 363.51 0.98 174 68 71 3 370.23 1.43 175 68 72 4 362.61 0.55 176 69 72 3 366.44 0.48 177 69 73 4 362.57 0.57 178 69 87 18 166.55 2.16 179 69 96 27 164.19 1.61 180 69 99 30 164.16 1.60 181 70 74 4 362.89 0.41 182 70 82 12 166.74 2.10 183 70 83 13 166.74 2.10 184 71 74 3 370.62 4.26 185 71 75 4 365.34 1.63 186 72 75 3 374.44 2.35 187 72 76 4 357.12 3.21 188 73 76 3 359.64 4.48 189 73 77 4 354.87 2.10 190 74 78 4 341.58 1.26 191 74 79 5 319.42 3.45 192 74 81 7 223.66 2.93 193 74 82 8 179.50 1.94 194 75 78 3 373.66 3.99 195 77 81 4 355.62 5.79 196 77 86 9 306.20 2.98 197 78 81 3 379.07 0.41 198 80 83 3 408.66 0.41 199 81 86 5 354.98 0.03 200 82 87 5 355.79 0.41 201 83 86 3 356.04 0.28 202 83 87 4 357.80 1.16 203 84 87 3 368.56 0.27 204 84 88 4 357.79 1.16 205 85 88 3 370.42 1.20 206 85 89 4 357.58 1.26 207 86 89 3 358.23 1.23 208 86 90 4 357.81 1.43 209 87 90 3 358.19 1.02 210 87 91 4 354.99 0.17 211 87 95 8 233.19 1.14 212 88 91 3 355.55 0.23 213 88 92 4 341.47 0.65 214 88 95 7 236.56 0.32 215 91 94 3 371.22 0.33 216 91 95 4 290.76 11.03 217 91 98 7 250.05 1.59 218 91 99 8 246.19 0.32 219 91 102 11 249.62 2.71 220 93 98 5 333.79 4.21 221 94 97 3 365.19 1.74 222 94 98 4 349.25 3.06 223 95 98 3 366.06 1.64 224 95 99 4 356.73 0.47 225 96 99 3 366.06 1.64 226 96 100 4 362.56 3.39 227 97 100 3 366.14 1.59 228 97 101 4 356.62 0.54 229 98 101 3 364.93 2.19 230 98 102 4 364.01 2.46 231 99 102 3 366.00 1.52 232 99 103 4 356.78 0.46 233 100 103 3 360.35 2.29 234 100 104 4 349.75 2.89 235 100 105 5 276.62 2.81 236 100 108 8 217.28 3.29 237 101 104 3 367.92 2.29 238 109 112 3 429.04 0.06