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 5 3 343.08 0.38 2 2 6 4 336.46 2.93 3 3 6 3 338.95 1.69 4 3 7 4 343.00 0.34 5 3 94 91 18.36 0.56 6 4 7 3 343.08 0.30 7 4 8 4 340.91 1.39 8 4 94 90 21.16 0.57 9 5 8 3 336.55 2.96 10 5 9 4 328.36 1.14 11 6 9 3 345.26 1.40 12 6 10 4 334.60 1.99 13 7 10 3 346.05 1.01 14 7 87 80 28.22 0.02 15 7 90 83 27.75 0.17 16 7 91 84 27.38 0.07 17 7 94 87 25.11 1.21 18 10 14 4 238.63 5.74 19 10 87 77 38.50 0.69 20 11 15 4 290.63 9.44 21 11 18 7 265.88 11.47 22 12 15 3 350.12 5.01 23 12 18 6 264.76 13.27 24 12 53 41 88.52 2.08 25 12 54 42 88.50 2.08 26 12 57 45 88.42 2.10 27 12 59 47 88.45 2.09 28 13 19 6 263.50 12.64 29 13 22 9 236.97 0.62 30 13 59 46 88.50 2.10 31 13 83 70 70.22 1.24 32 13 84 71 69.03 1.83 33 13 87 74 68.78 1.94 34 14 87 73 68.91 1.88 35 15 18 3 337.92 1.09 36 15 19 4 327.98 0.65 37 15 50 35 159.58 0.57 38 16 19 3 334.33 0.38 39 16 20 4 325.62 1.84 40 17 20 3 337.60 1.25 41 17 21 4 332.34 0.27 42 17 42 25 170.02 0.35 43 17 50 33 159.69 0.54 44 18 21 3 334.33 0.39 45 18 22 4 332.35 0.27 46 18 50 32 162.21 1.79 47 18 53 35 159.71 0.54 48 18 54 36 159.67 0.55 49 19 22 3 337.15 2.14 50 19 23 4 328.85 2.01 51 19 87 68 69.05 1.83 52 19 88 69 69.02 1.84 53 19 91 72 68.94 1.87 54 20 23 3 331.82 0.52 55 20 24 4 330.01 0.40 56 21 24 3 335.82 2.48 57 21 25 4 335.85 2.46 58 21 40 19 171.75 0.68 59 21 42 21 171.71 0.66 60 21 47 26 171.16 0.84 61 21 50 29 171.11 0.84 62 21 51 30 170.99 0.83 63 21 54 33 170.98 0.83 64 22 25 3 341.00 2.47 65 22 26 4 336.19 2.29 66 22 54 32 171.00 0.83 67 22 59 37 170.87 0.82 68 22 60 38 170.84 0.82 69 22 76 54 169.18 0.00 70 22 80 58 141.34 1.02 71 22 84 62 89.72 1.01 72 23 26 3 341.00 2.47 73 23 27 4 344.09 0.93 74 23 88 65 70.33 1.20 75 24 27 3 368.33 0.34 76 24 28 4 332.12 0.64 77 24 31 7 291.31 11.78 78 24 36 12 172.13 0.70 79 24 39 15 172.18 0.71 80 24 40 16 172.16 0.71 81 25 28 3 346.77 2.68 82 25 29 4 317.83 1.47 83 25 30 5 317.82 1.47 84 25 31 6 259.87 3.95 85 25 36 11 189.57 9.40 86 25 60 35 171.23 0.88 87 25 74 49 171.79 0.66 88 25 76 51 170.41 0.61 89 26 76 50 171.10 0.95 90 26 81 55 136.06 0.86 91 26 84 58 121.66 0.83 92 26 85 59 121.64 0.84 93 26 88 62 100.27 3.46 94 29 75 46 171.50 0.82 95 29 76 47 171.29 0.91 96 29 77 48 171.30 0.92 97 29 78 49 171.23 0.93 98 29 81 52 143.84 0.76 99 30 63 33 172.22 0.68 100 30 73 43 172.18 0.68 101 30 74 44 171.97 0.74 102 30 75 45 171.71 0.71 103 31 36 5 321.51 2.92 104 31 73 42 172.22 0.69 105 31 74 43 172.09 0.71 106 32 35 3 335.15 1.74 107 32 36 4 333.20 1.68 108 32 72 40 172.29 0.66 109 32 73 41 172.22 0.69 110 33 36 3 334.48 2.07 111 33 37 4 327.23 0.07 112 33 44 11 188.08 7.01 113 33 47 14 172.55 0.64 114 33 48 15 172.46 0.68 115 33 51 18 172.35 0.66 116 33 72 39 172.30 0.67 117 33 74 41 172.26 0.67 118 34 37 3 339.78 1.61 119 34 38 4 327.23 0.07 120 35 38 3 335.74 1.72 121 35 39 4 326.92 0.23 122 36 39 3 337.88 0.65 123 36 40 4 320.00 1.99 124 36 47 11 203.40 1.76 125 36 74 38 172.25 0.67 126 37 41 4 319.88 2.02 127 37 42 5 226.69 0.43 128 37 43 6 225.44 1.05 129 37 44 7 208.94 1.00 130 37 47 10 186.97 6.45 131 38 41 3 330.79 0.48 132 42 47 5 321.11 2.27 133 43 46 3 345.24 4.67 134 43 47 4 331.41 0.35 135 44 47 3 339.03 0.09 136 44 48 4 326.95 0.48 137 45 48 3 339.51 0.15 138 45 49 4 334.69 1.99 139 46 49 3 339.89 0.04 140 46 50 4 338.20 0.23 141 47 50 3 338.78 0.52 142 47 51 4 330.28 0.24 143 48 51 3 336.13 1.95 144 48 52 4 330.27 0.24 145 49 52 3 332.50 0.12 146 49 53 4 331.75 0.50 147 50 53 3 334.45 0.52 148 50 54 4 331.49 0.65 149 51 54 3 336.51 1.85 150 51 55 4 334.07 0.64 151 51 60 9 208.62 0.88 152 51 62 11 201.24 1.65 153 51 74 23 195.25 0.69 154 52 55 3 335.88 1.44 155 52 56 4 335.77 1.49 156 53 56 3 338.88 1.24 157 53 57 4 334.08 0.64 158 54 57 3 338.76 2.69 159 54 58 4 334.04 0.66 160 54 59 5 241.45 3.32 161 54 60 6 221.14 5.36 162 55 58 3 335.62 1.56 163 55 60 5 227.29 2.28 164 55 61 6 208.66 0.88 165 55 62 7 208.62 0.88 166 57 79 22 195.06 0.70 167 58 77 19 195.25 0.65 168 58 79 21 195.06 0.70 169 59 76 17 195.31 0.68 170 59 77 18 195.25 0.65 171 59 79 20 195.06 0.69 172 59 80 21 194.91 0.69 173 59 83 24 194.91 0.69 174 60 74 14 195.40 0.68 175 60 75 15 195.35 0.69 176 60 76 16 195.25 0.65 177 60 77 17 195.25 0.65 178 61 74 13 195.63 0.80 179 61 75 14 195.38 0.68 180 61 77 16 195.28 0.67 181 62 72 10 195.93 0.78 182 62 73 11 195.85 0.80 183 62 74 12 195.64 0.80 184 63 72 9 195.95 0.77 185 63 73 10 195.90 0.79 186 63 75 12 195.90 0.79 187 64 71 7 196.20 0.73 188 64 72 8 195.99 0.79 189 65 69 4 318.87 2.06 190 65 70 5 210.09 6.20 191 65 71 6 196.37 0.65 192 65 73 8 196.16 0.74 193 76 80 4 319.33 0.87 194 76 81 5 319.76 0.67 195 77 80 3 330.14 2.05 196 77 81 4 330.14 2.04 197 78 81 3 339.39 0.01 198 78 82 4 340.29 2.92 199 79 82 3 342.80 1.67 200 79 83 4 340.29 2.92 201 80 83 3 343.57 1.28 202 80 84 4 335.90 5.12 203 81 84 3 343.57 1.28 204 81 85 4 342.80 1.67 205 82 85 3 337.19 1.50 206 82 86 4 334.95 2.25 207 83 86 3 340.75 0.19 208 83 87 4 335.41 2.48 209 84 87 3 346.43 2.98 210 84 88 4 332.42 0.99 211 85 88 3 336.19 0.89 212 85 89 4 332.42 0.99 213 86 89 3 332.72 2.63 214 86 90 4 326.69 0.58 215 87 90 3 332.56 3.50 216 87 91 4 332.55 3.50 217 88 91 3 330.62 2.54 218 88 92 4 325.47 0.04 219 89 92 3 331.84 1.78 220 89 93 4 325.47 0.04 221 90 93 3 334.33 0.53 222 90 94 4 329.60 2.10 223 91 94 3 333.89 0.01 224 91 95 4 329.60 2.10 225 92 95 3 337.66 1.46 226 92 96 4 337.28 1.63 227 93 96 3 344.48 1.96 228 93 97 4 337.30 1.64 229 94 97 3 342.06 1.28 230 94 98 4 340.02 0.28 231 95 98 3 342.05 1.28 232 95 99 4 342.05 1.28 233 95 100 5 327.81 1.79 234 96 99 3 349.94 2.66