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 10 14 4 340.43 3.29 2 10 51 41 110.97 0.02 3 10 72 62 88.72 0.77 4 11 14 3 346.21 1.73 5 11 15 4 340.43 3.29 6 11 51 40 110.98 0.02 7 11 65 54 94.14 0.01 8 11 68 57 89.09 0.62 9 11 69 58 89.05 0.61 10 11 72 61 89.00 0.64 11 12 15 3 353.01 1.29 12 12 16 4 343.82 1.59 13 12 72 60 89.00 0.64 14 12 77 65 88.66 0.74 15 12 89 77 87.79 0.48 16 12 93 81 73.17 0.38 17 12 94 82 73.17 0.38 18 13 16 3 345.49 2.08 19 13 17 4 343.83 1.59 20 14 17 3 345.16 2.25 21 14 18 4 343.81 1.58 22 14 47 33 114.35 1.07 23 14 50 36 114.41 1.04 24 14 51 37 114.28 1.06 25 14 54 40 114.34 1.08 26 15 18 3 348.03 0.86 27 15 19 4 344.71 2.02 28 15 29 14 205.44 1.18 29 15 39 24 205.55 1.16 30 15 47 32 114.31 1.05 31 15 89 74 88.81 0.60 32 16 19 3 350.76 3.61 33 16 20 4 343.81 1.57 34 16 89 73 88.36 0.57 35 16 94 78 74.75 1.18 36 16 95 79 73.08 0.40 37 16 96 80 69.11 0.83 38 17 20 3 345.43 1.67 39 17 21 4 337.14 1.48 40 18 21 3 335.93 0.88 41 18 24 6 263.83 2.21 42 18 25 7 240.07 1.49 43 18 28 10 205.61 1.10 44 18 29 11 205.59 1.10 45 18 47 29 153.80 20.60 46 18 50 32 151.86 19.61 47 19 29 10 205.61 1.10 48 19 30 11 205.72 1.15 49 19 31 12 205.74 1.15 50 19 39 20 205.73 1.14 51 19 89 70 111.45 2.13 52 20 31 11 217.15 2.48 53 21 24 3 359.57 1.67 54 21 25 4 331.25 0.28 55 22 25 3 341.16 4.12 56 24 50 26 206.09 0.86 57 25 28 3 359.31 1.53 58 25 29 4 350.70 0.95 59 26 43 17 226.26 0.42 60 27 42 15 226.35 0.40 61 27 43 16 226.32 0.39 62 28 41 13 226.53 0.42 63 28 42 14 226.36 0.40 64 28 43 15 226.31 0.39 65 28 46 18 226.09 0.38 66 28 47 19 226.09 0.37 67 28 50 22 225.56 0.64 68 29 39 10 230.83 0.15 69 29 40 11 228.34 0.40 70 29 41 12 226.55 0.42 71 29 42 13 226.47 0.45 72 29 47 18 226.23 0.42 73 30 39 9 230.83 0.15 74 30 40 10 230.65 0.10 75 30 42 12 227.29 0.52 76 31 34 3 361.87 1.50 77 31 37 6 248.59 0.87 78 31 38 7 243.25 2.75 79 31 39 8 234.19 1.72 80 32 38 6 244.06 3.14 81 32 39 7 234.24 1.73 82 32 40 8 234.22 1.72 83 33 36 3 339.83 0.37 84 33 37 4 271.07 1.14 85 33 38 5 246.12 2.12 86 34 37 3 336.86 1.11 87 34 96 62 85.42 0.24 88 35 96 61 104.11 8.81 89 36 88 52 172.64 0.44 90 36 96 60 104.12 8.81 91 37 88 51 172.57 0.48 92 37 89 52 172.53 0.48 93 37 96 59 76.92 0.42 94 38 86 48 172.74 0.49 95 38 87 49 172.62 0.50 96 38 88 50 172.53 0.49 97 39 78 39 172.57 0.51 98 39 86 47 172.63 0.50 99 39 87 48 172.59 0.49 100 39 88 49 172.54 0.49 101 39 89 50 172.53 0.49 102 40 85 45 172.66 0.49 103 40 86 46 172.56 0.50 104 41 44 3 342.81 0.63 105 41 47 6 308.80 1.86 106 41 62 21 172.87 0.47 107 41 85 44 172.62 0.49 108 41 87 46 172.58 0.49 109 43 46 3 347.07 2.74 110 43 47 4 337.21 2.19 111 44 47 3 344.23 1.31 112 44 48 4 338.70 1.44 113 44 62 18 172.78 0.49 114 44 85 41 172.65 0.50 115 45 48 3 354.59 0.12 116 45 49 4 337.12 1.87 117 46 49 3 345.06 2.10 118 46 50 4 338.98 0.96 119 47 50 3 347.75 3.31 120 47 51 4 342.00 0.55 121 47 62 15 172.92 0.45 122 47 65 18 172.88 0.48 123 48 51 3 342.01 0.55 124 48 52 4 342.00 0.55 125 48 60 12 173.03 0.46 126 48 61 13 172.93 0.45 127 48 62 14 172.90 0.47 128 48 65 17 172.85 0.46 129 49 52 3 352.00 1.71 130 49 53 4 345.85 1.37 131 50 53 3 350.91 1.16 132 50 54 4 350.89 1.16 133 51 54 3 350.90 1.16 134 51 55 4 345.77 1.40 135 51 60 9 173.06 0.46 136 51 65 14 172.91 0.43 137 52 55 3 341.63 0.21 138 52 56 4 341.62 0.21 139 52 57 5 287.17 11.81 140 52 60 8 173.05 0.47 141 53 56 3 334.55 0.74 142 57 60 3 332.94 5.20 143 57 64 7 321.61 2.52 144 59 64 5 331.24 2.26 145 60 64 4 333.54 3.40 146 60 65 5 331.22 2.26 147 61 64 3 344.97 0.46 148 61 65 4 345.95 0.83 149 62 65 3 345.97 0.83 150 62 66 4 335.50 4.40 151 62 69 7 326.63 1.66 152 62 85 23 175.96 1.32 153 62 87 25 176.43 1.10 154 63 66 3 355.44 0.86 155 64 67 3 352.45 0.63 156 65 68 3 355.94 2.38 157 65 69 4 340.18 0.09 158 66 69 3 334.92 2.47 159 66 70 4 333.33 2.87 160 67 71 4 340.54 1.06 161 68 71 3 344.01 0.67 162 68 72 4 340.85 0.91 163 69 72 3 348.11 0.88 164 69 73 4 348.63 1.14 165 69 78 9 240.83 1.33 166 69 87 18 176.46 1.10 167 70 73 3 354.51 1.93 168 71 74 3 357.62 1.53 169 71 75 4 348.90 0.50 170 72 75 3 354.11 2.10 171 72 76 4 333.94 2.30 172 72 77 5 269.27 3.83 173 72 78 6 241.26 1.54 174 73 76 3 338.43 3.95 175 73 78 5 250.93 5.33 176 73 79 6 241.81 1.82 177 73 80 7 240.83 1.32 178 73 87 14 177.18 1.19 179 75 92 17 176.41 1.01 180 76 90 14 176.60 1.07 181 76 92 16 176.40 1.00 182 77 89 12 176.87 1.20 183 77 90 13 176.51 1.03 184 77 92 15 176.25 1.12 185 77 93 16 175.33 1.20 186 78 87 9 177.14 1.21 187 78 88 10 176.92 1.21 188 78 89 11 176.55 1.03 189 78 90 12 176.51 1.03 190 79 88 9 177.00 1.24 191 79 90 11 176.50 1.03 192 81 86 5 242.12 0.72 193 81 87 6 177.38 1.10 194 81 88 7 177.38 1.10 195 83 86 3 338.41 3.26 196 89 93 4 274.00 5.53 197 89 96 7 235.85 0.53 198 90 96 6 263.54 1.57 199 91 97 6 247.66 1.92 200 93 96 3 424.31 8.23 201 93 97 4 352.76 0.04