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 13 3 305.79 1.80 2 10 14 4 296.31 0.85 3 11 14 3 305.79 1.80 4 11 15 4 296.31 0.85 5 12 15 3 302.72 0.42 6 12 16 4 296.24 0.89 7 13 16 3 298.47 0.23 8 13 17 4 296.33 0.83 9 14 17 3 296.08 0.81 10 14 18 4 295.63 0.67 11 15 18 3 296.00 0.85 12 15 19 4 295.82 0.76 13 16 19 3 301.42 2.04 14 16 20 4 295.94 0.70 15 17 20 3 304.76 0.37 16 17 21 4 298.44 0.02 17 18 21 3 306.63 1.30 18 18 22 4 299.16 0.34 19 18 66 48 56.43 0.42 20 19 22 3 304.24 1.19 21 19 23 4 299.53 0.15 22 19 66 47 56.41 0.41 23 19 68 49 56.28 0.46 24 19 90 71 40.74 1.41 25 20 23 3 299.53 0.14 26 20 24 4 298.81 0.21 27 20 90 70 41.75 0.92 28 21 24 3 299.84 0.30 29 22 28 6 227.99 0.92 30 22 63 41 56.84 0.40 31 22 66 44 56.84 0.41 32 22 68 46 56.84 0.41 33 23 29 6 210.23 9.79 34 23 32 9 191.26 5.70 35 23 63 40 57.03 0.48 36 23 68 45 56.87 0.40 37 23 90 67 45.43 0.91 38 25 28 3 304.02 0.96 39 25 29 4 298.45 1.81 40 26 29 3 302.09 0.03 41 26 30 4 298.45 1.81 42 27 30 3 298.48 1.83 43 27 31 4 294.84 0.90 44 27 51 24 148.88 0.82 45 28 31 3 300.18 0.96 46 28 32 4 294.84 0.90 47 28 59 31 146.25 2.10 48 28 62 34 146.24 2.10 49 28 63 35 143.94 3.24 50 29 32 3 295.94 0.35 51 29 33 4 295.98 0.33 52 29 91 62 48.09 0.53 53 30 33 3 303.88 0.40 54 30 34 4 296.05 0.35 55 30 49 19 150.43 0.43 56 30 51 21 150.43 0.43 57 31 34 3 305.67 1.56 58 31 35 4 302.72 0.09 59 31 45 14 150.38 0.42 60 31 49 18 150.44 0.42 61 31 51 20 150.44 0.42 62 31 56 25 149.40 0.66 63 31 59 28 149.37 0.65 64 31 60 29 149.33 0.65 65 31 63 32 149.30 0.64 66 32 35 3 303.43 0.44 67 32 36 4 299.66 1.45 68 32 63 31 149.29 0.64 69 32 68 36 148.94 0.79 70 32 69 37 148.89 0.77 71 32 82 50 148.05 0.38 72 32 87 55 86.48 0.22 73 32 91 59 50.04 0.42 74 33 36 3 300.72 1.98 75 33 37 4 299.66 1.45 76 33 91 58 50.88 0.10 77 34 37 3 300.10 1.67 78 34 38 4 299.65 1.44 79 34 45 11 150.88 0.64 80 34 48 14 150.94 0.65 81 34 49 15 150.91 0.64 82 35 38 3 297.13 2.69 83 35 40 5 272.55 1.86 84 35 45 10 154.21 1.01 85 35 60 25 149.75 0.53 86 35 69 34 148.96 0.79 87 35 80 45 148.81 0.36 88 35 81 46 148.09 0.36 89 35 82 47 148.06 0.37 90 36 82 46 148.06 0.38 91 36 91 55 61.19 1.40 92 36 92 56 56.86 0.58 93 39 79 40 149.49 0.27 94 39 80 41 149.37 0.29 95 39 81 42 148.90 0.32 96 40 44 4 289.89 0.35 97 40 45 5 289.89 0.35 98 40 79 39 149.44 0.25 99 40 80 40 149.36 0.28 100 41 44 3 303.06 0.44 101 41 45 4 289.98 0.39 102 41 78 37 149.64 0.27 103 41 79 38 149.47 0.22 104 42 45 3 297.88 2.81 105 42 46 4 296.81 3.02 106 42 53 11 169.10 1.60 107 42 56 14 156.52 0.15 108 42 57 15 156.53 0.15 109 42 60 18 154.91 0.88 110 42 80 38 149.47 0.21 111 43 46 3 303.44 0.30 112 43 47 4 296.86 2.99 113 43 53 10 170.36 2.19 114 44 47 3 303.78 0.47 115 44 48 4 296.82 3.00 116 45 48 3 313.44 0.74 117 45 49 4 296.99 2.90 118 45 56 11 156.71 0.16 119 45 60 15 156.60 0.20 120 45 80 35 149.44 0.21 121 46 49 3 313.63 0.84 122 46 50 4 287.67 1.26 123 46 51 5 242.30 4.89 124 46 52 6 206.66 7.88 125 46 53 7 198.44 11.98 126 46 56 10 166.19 0.16 127 47 50 3 301.75 0.52 128 51 55 4 291.35 0.21 129 51 56 5 280.89 1.31 130 52 55 3 295.95 1.40 131 52 56 4 291.48 0.26 132 53 56 3 298.05 3.02 133 53 57 4 290.55 1.35 134 54 57 3 303.41 0.34 135 54 58 4 296.77 1.32 136 55 58 3 302.10 1.64 137 55 59 4 299.30 0.42 138 56 59 3 299.68 0.41 139 56 60 4 299.30 0.42 140 57 60 3 299.50 0.33 141 57 61 4 295.99 2.08 142 58 61 3 304.50 0.09 143 58 62 4 295.99 2.08 144 59 62 3 304.41 0.94 145 59 63 4 292.95 0.57 146 60 63 3 305.31 1.89 147 60 64 4 290.82 1.61 148 60 69 9 185.56 1.05 149 60 80 20 149.44 0.06 150 61 64 3 306.23 2.16 151 61 65 4 306.23 2.16 152 62 65 3 307.99 1.28 153 62 66 4 306.50 2.02 154 63 66 3 312.11 0.78 155 63 67 4 303.16 3.69 156 63 68 5 229.67 0.58 157 63 69 6 185.58 1.04 158 64 67 3 298.56 2.37 159 64 69 5 185.60 1.04 160 64 70 6 185.58 1.05 161 64 71 7 185.58 1.04 162 67 83 16 149.10 0.14 163 68 82 14 149.12 0.14 164 68 83 15 149.09 0.14 165 68 87 19 107.28 6.02 166 68 90 22 95.64 0.20 167 69 80 11 149.81 0.07 168 69 81 12 149.49 0.00 169 69 82 13 149.09 0.13 170 69 83 14 149.08 0.12 171 70 80 10 149.81 0.07 172 70 81 11 149.75 0.10 173 70 82 12 149.53 0.02 174 70 83 13 149.05 0.11 175 71 78 7 157.44 3.58 176 71 79 8 150.00 0.09 177 71 80 9 149.81 0.07 178 72 78 6 157.45 3.58 179 72 79 7 150.01 0.09 180 73 77 4 261.36 4.38 181 73 78 5 161.78 1.43 182 74 77 3 305.83 2.06 183 74 79 5 168.53 2.69 184 82 87 5 272.12 1.04 185 82 88 6 240.59 4.49 186 83 87 4 304.38 4.42 187 84 87 3 307.48 2.87 188 84 88 4 290.19 2.68 189 85 88 3 292.05 1.75 190 85 89 4 290.05 2.75 191 86 89 3 303.08 0.64 192 86 90 4 295.28 3.26 193 87 90 3 298.84 1.49 194 87 91 4 295.55 3.12 195 88 91 3 310.86 0.42 196 88 92 4 298.16 1.75 197 89 92 3 306.74 2.48 198 89 93 4 295.47 3.08 199 90 93 3 311.60 0.80 200 90 94 4 295.45 3.08 201 91 94 3 305.58 1.99 202 91 95 4 295.24 3.18 203 92 95 3 301.38 0.10 204 92 96 4 295.25 3.17 205 93 96 3 298.38 1.60 206 93 97 4 295.25 3.17 207 94 97 3 303.41 0.92 208 94 98 4 295.34 3.21 209 95 98 3 303.51 0.88 210 95 99 4 295.12 3.33 211 96 99 3 307.82 1.28 212 96 100 4 292.81 2.18 213 97 100 3 304.53 2.94