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 18 16 141.56 0.34 2 2 19 17 141.33 0.27 3 2 64 62 141.62 0.31 4 2 68 66 141.74 0.29 5 3 17 14 141.75 0.29 6 3 18 15 141.66 0.29 7 3 20 17 141.53 0.33 8 3 57 54 141.49 0.33 9 3 62 59 141.57 0.33 10 3 63 60 141.62 0.31 11 3 64 61 141.64 0.32 12 3 67 64 141.66 0.29 13 4 16 12 141.80 0.29 14 4 17 13 141.75 0.29 15 4 67 63 141.69 0.29 16 4 68 64 141.75 0.29 17 4 69 65 141.77 0.29 18 4 72 68 141.69 0.29 19 4 73 69 141.68 0.29 20 5 15 10 141.81 0.29 21 5 16 11 141.80 0.29 22 5 18 13 141.79 0.29 23 5 27 22 141.66 0.29 24 5 57 52 141.75 0.28 25 5 62 57 141.77 0.29 26 5 67 62 141.78 0.30 27 5 72 67 141.71 0.29 28 5 73 68 141.68 0.29 29 5 75 70 141.65 0.28 30 6 14 8 175.45 16.50 31 6 15 9 141.81 0.29 32 6 72 66 141.76 0.29 33 6 73 67 141.74 0.29 34 6 74 68 141.69 0.29 35 6 75 69 141.67 0.29 36 7 13 6 176.09 16.76 37 7 14 7 175.47 16.50 38 7 16 9 175.45 16.52 39 7 27 20 141.73 0.28 40 7 31 24 141.66 0.29 41 7 44 37 141.66 0.29 42 7 75 68 141.68 0.29 43 7 77 70 141.62 0.28 44 8 12 4 282.56 3.77 45 8 13 5 225.28 1.54 46 8 74 66 141.77 0.29 47 8 75 67 141.72 0.29 48 8 76 68 141.68 0.29 49 8 77 69 141.66 0.29 50 8 90 82 57.86 1.18 51 8 91 83 55.70 0.10 52 8 93 85 55.50 0.11 53 9 12 3 330.87 1.94 54 9 77 68 141.69 0.29 55 9 78 69 141.68 0.29 56 9 79 70 141.68 0.29 57 9 86 77 59.21 1.10 58 9 89 80 58.49 1.32 59 10 89 79 58.49 1.32 60 10 90 80 58.09 1.28 61 10 91 81 57.87 1.18 62 11 91 80 57.68 1.09 63 13 93 80 52.98 0.42 64 14 34 20 190.48 0.74 65 14 35 21 190.48 0.74 66 15 72 57 141.77 0.29 67 16 27 11 191.03 0.84 68 18 22 4 306.06 1.89 69 18 57 39 195.30 0.15 70 19 22 3 327.09 0.18 71 19 57 38 198.50 1.45 72 20 56 36 205.44 3.25 73 20 57 37 198.39 1.40 74 20 58 38 195.30 0.15 75 20 63 43 172.37 0.04 76 20 64 44 175.14 0.24 77 21 56 35 205.47 3.23 78 22 26 4 328.23 1.44 79 22 56 34 206.35 3.50 80 22 57 35 206.33 3.50 81 23 26 3 329.14 1.83 82 23 27 4 330.53 0.66 83 23 53 30 208.24 2.86 84 23 54 31 208.14 2.82 85 23 55 32 207.87 2.78 86 23 56 33 207.73 2.82 87 23 57 34 207.73 2.82 88 24 27 3 332.33 0.23 89 24 28 4 330.63 0.64 90 24 44 20 212.13 0.92 91 24 51 27 208.26 2.85 92 24 52 28 208.26 2.87 93 24 53 29 208.24 2.86 94 24 55 31 208.13 2.83 95 24 57 33 207.77 2.81 96 24 60 36 207.96 2.75 97 25 28 3 332.28 0.25 98 25 29 4 330.64 0.64 99 25 39 14 248.52 2.81 100 25 53 28 208.22 2.87 101 26 29 3 330.63 0.63 102 26 30 4 330.63 0.63 103 27 30 3 333.78 0.95 104 27 31 4 330.63 0.63 105 27 44 17 213.48 0.25 106 27 57 30 208.11 2.79 107 27 75 48 182.25 1.76 108 28 31 3 329.25 0.04 109 28 32 4 328.32 0.50 110 28 39 11 253.56 0.34 111 28 42 14 237.84 0.41 112 28 44 16 213.51 0.27 113 28 53 25 208.44 2.89 114 29 32 3 335.81 2.77 115 29 33 4 329.25 0.04 116 29 39 10 254.07 0.24 117 30 33 3 340.51 0.41 118 30 34 4 329.25 0.04 119 31 34 3 336.44 1.62 120 31 35 4 327.27 0.07 121 31 42 11 250.97 1.73 122 31 77 46 182.18 1.76 123 32 36 4 306.85 0.41 124 32 37 5 286.92 0.01 125 32 38 6 258.42 2.41 126 32 39 7 263.91 0.34 127 32 42 10 258.08 2.54 128 33 36 3 338.12 1.93 129 35 77 42 182.34 1.75 130 35 79 44 182.13 1.78 131 37 41 4 320.18 3.50 132 37 42 5 313.93 2.22 133 37 79 42 182.09 1.80 134 37 80 43 182.07 1.81 135 38 41 3 334.17 0.52 136 38 42 4 328.71 0.77 137 39 42 3 332.29 1.02 138 40 80 40 181.82 1.95 139 41 79 38 181.81 1.94 140 41 80 39 181.72 1.90 141 42 77 35 182.21 1.77 142 42 78 36 182.12 1.78 143 42 79 37 181.81 1.84 144 42 80 38 181.69 1.89 145 43 50 7 254.45 1.04 146 43 77 34 182.18 1.75 147 43 78 35 182.09 1.76 148 43 80 37 181.79 1.83 149 43 85 42 60.23 0.63 150 43 87 44 58.73 1.35 151 43 88 45 58.68 1.36 152 44 50 6 254.54 0.99 153 44 51 7 254.44 1.03 154 44 75 31 182.28 1.73 155 44 76 32 182.18 1.75 156 44 77 33 182.11 1.77 157 45 48 3 345.81 3.91 158 45 49 4 298.95 5.49 159 45 50 5 255.72 0.41 160 45 51 6 255.72 0.41 161 45 75 30 182.27 1.73 162 45 76 31 182.18 1.74 163 45 78 33 182.16 1.75 164 45 88 43 58.58 1.31 165 46 49 3 336.21 0.10 166 46 51 5 287.56 0.96 167 46 60 14 209.28 2.60 168 46 61 15 209.27 2.60 169 46 62 16 209.25 2.61 170 47 88 41 58.62 1.30 171 51 60 9 216.02 5.59 172 51 62 11 216.02 5.59 173 51 75 24 182.28 1.74 174 52 55 3 337.56 0.06 175 55 59 4 315.11 2.41 176 55 60 5 305.30 2.45 177 56 59 3 328.43 0.66 178 56 60 4 324.83 2.46 179 57 60 3 332.80 1.52 180 57 61 4 329.94 0.10 181 57 62 5 305.22 2.43 182 58 61 3 328.24 0.75 183 58 62 4 305.28 2.44 184 62 73 11 182.36 1.74 185 62 75 13 182.28 1.74 186 63 66 3 338.40 0.05 187 63 67 4 303.06 7.21 188 64 68 4 303.06 7.21 189 66 71 5 298.16 4.10 190 67 72 5 252.19 10.73 191 67 73 6 234.90 2.47 192 68 71 3 326.58 3.55 193 68 72 4 267.17 3.25 194 69 72 3 343.43 1.78 195 74 90 16 57.86 1.19 196 76 88 12 58.55 1.32 197 76 90 14 57.89 1.20 198 77 88 11 58.58 1.31 199 78 86 8 58.77 1.32 200 78 88 10 58.58 1.31 201 79 86 7 59.10 1.20 202 81 84 3 324.28 0.65 203 98 104 6 315.71 0.10 204 99 103 4 320.54 1.80 205 99 104 5 307.30 1.41 206 100 103 3 333.49 1.25 207 100 104 4 320.56 1.79 208 101 104 3 327.04 1.45