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 53 43 69.78 1.93 2 10 57 47 69.95 0.10 3 10 60 50 70.25 0.08 4 11 14 3 293.14 5.81 5 11 15 4 285.34 4.54 6 11 57 46 71.84 0.87 7 11 72 61 70.86 0.04 8 11 79 68 68.99 0.48 9 12 15 3 288.79 3.63 10 12 16 4 288.76 3.62 11 13 16 3 307.35 0.75 12 13 17 4 295.51 1.23 13 14 17 3 298.82 0.42 14 14 18 4 295.51 1.23 15 14 50 36 73.36 1.32 16 14 53 39 73.50 1.05 17 14 54 40 73.31 1.16 18 14 57 43 73.71 0.95 19 14 79 65 70.97 0.07 20 14 83 69 70.52 0.06 21 15 18 3 300.43 1.22 22 15 19 4 295.51 1.23 23 16 19 3 301.76 0.55 24 16 20 4 288.83 2.04 25 17 20 3 303.35 1.34 26 17 21 4 283.50 0.62 27 17 46 29 78.48 3.64 28 17 50 33 74.08 1.33 29 17 53 36 74.20 1.14 30 18 21 3 287.73 2.21 31 18 22 4 285.70 1.77 32 18 86 68 70.34 0.37 33 19 22 3 292.34 0.18 34 19 23 4 285.78 1.73 35 20 23 3 302.75 3.83 36 20 24 4 294.88 0.10 37 21 24 3 294.88 0.10 38 21 25 4 293.48 0.62 39 21 43 22 99.44 0.48 40 21 46 25 99.44 0.48 41 21 47 26 86.03 7.16 42 21 86 65 70.45 0.34 43 22 25 3 294.90 0.09 44 22 26 4 296.56 0.94 45 22 86 64 70.45 0.33 46 23 26 3 298.69 0.71 47 23 27 4 298.13 1.71 48 24 27 3 299.41 1.07 49 24 28 4 297.36 1.32 50 24 39 15 109.78 0.48 51 24 42 18 107.22 0.80 52 24 43 19 107.13 0.79 53 25 28 3 306.59 2.51 54 25 29 4 310.08 0.76 55 25 43 18 107.17 0.81 56 25 86 61 70.96 0.35 57 25 89 64 69.81 0.65 58 25 90 65 69.25 0.89 59 25 93 68 68.14 1.20 60 26 29 3 320.47 1.72 61 26 30 4 304.04 1.95 62 27 30 3 304.04 1.95 63 27 31 4 296.47 0.95 64 28 31 3 297.37 1.39 65 28 36 8 157.40 2.04 66 28 39 11 141.52 1.91 67 28 40 12 141.52 1.91 68 28 93 65 69.14 0.84 69 28 94 66 68.13 1.20 70 29 36 7 199.93 2.57 71 29 93 64 69.16 0.84 72 29 96 67 67.20 1.08 73 29 98 69 41.77 0.89 74 31 35 4 275.81 1.73 75 31 36 5 228.53 4.97 76 31 39 8 189.74 2.53 77 32 35 3 298.26 0.66 78 32 36 4 276.92 3.33 79 33 36 3 288.47 1.22 80 33 37 4 285.81 2.54 81 34 38 4 304.07 1.29 82 35 38 3 303.86 1.18 83 35 39 4 295.63 2.92 84 36 39 3 300.13 0.68 85 36 40 4 295.64 2.92 86 36 93 57 69.36 0.94 87 36 94 58 68.22 1.19 88 36 96 60 68.05 1.15 89 37 40 3 307.82 3.18 90 37 41 4 300.12 0.68 91 38 41 3 300.32 0.57 92 38 42 4 296.95 2.25 93 39 42 3 293.29 0.41 94 39 43 4 293.28 0.42 95 40 44 4 295.22 1.70 96 40 90 50 69.80 0.91 97 40 94 54 67.75 1.01 98 41 44 3 297.02 0.80 99 41 45 4 299.60 3.21 100 42 45 3 309.31 2.04 101 42 46 4 299.60 3.21 102 43 46 3 299.61 3.21 103 43 47 4 289.52 0.49 104 43 90 47 69.54 1.03 105 44 47 3 299.67 3.17 106 44 48 4 296.07 1.36 107 44 90 46 69.91 1.15 108 45 48 3 298.81 0.01 109 45 49 4 298.53 2.58 110 46 49 3 298.54 2.58 111 46 50 4 298.56 2.59 112 47 50 3 306.82 1.49 113 47 51 4 306.03 1.09 114 47 83 36 75.42 2.27 115 47 86 39 71.06 0.77 116 47 90 43 69.95 1.17 117 48 51 3 306.03 1.09 118 48 52 4 306.04 1.09 119 49 52 3 318.33 1.43 120 49 53 4 306.06 1.10 121 50 53 3 306.06 1.10 122 50 54 4 306.05 1.08 123 50 83 33 79.41 4.29 124 51 54 3 307.96 0.85 125 51 55 4 303.31 0.84 126 51 83 32 79.42 4.29 127 52 55 3 298.93 1.35 128 52 56 4 298.88 1.37 129 53 56 3 303.93 1.16 130 53 57 4 298.55 1.21 131 54 57 3 300.08 0.77 132 54 58 4 296.65 2.16 133 54 76 22 87.17 2.50 134 54 79 25 85.06 1.67 135 54 80 26 86.67 2.62 136 54 83 29 79.55 4.34 137 55 58 3 302.92 2.19 138 55 59 4 291.75 0.29 139 56 59 3 291.87 0.25 140 56 60 4 291.51 0.20 141 57 60 3 300.99 0.29 142 57 61 4 295.71 2.35 143 57 72 15 109.84 2.66 144 57 76 19 98.58 8.19 145 58 61 3 297.83 1.30 146 58 62 4 297.82 1.30 147 58 76 18 88.00 2.20 148 58 80 22 87.23 2.58 149 60 63 3 306.95 1.28 150 60 64 4 282.94 7.30 151 61 64 3 287.95 4.80 152 61 69 8 133.00 1.22 153 61 72 11 119.20 1.29 154 61 76 15 109.89 2.65 155 64 68 4 261.10 2.71 156 64 69 5 161.36 5.41 157 64 72 8 155.96 8.10 158 65 68 3 301.19 2.84 159 65 69 4 261.08 2.71 160 66 69 3 291.26 2.10 161 69 72 3 295.41 2.98 162 69 73 4 277.20 3.89 163 71 74 3 297.04 0.85 164 71 75 4 290.56 1.82 165 72 75 3 298.80 0.03 166 72 76 4 292.28 2.67 167 73 76 3 292.28 2.67 168 73 77 4 292.28 2.67 169 74 77 3 308.09 0.68 170 74 78 4 303.92 1.97 171 75 78 3 303.92 1.97 172 75 79 4 296.30 2.39 173 76 79 3 305.55 1.16 174 76 80 4 296.27 2.41 175 77 80 3 300.73 0.18 176 77 81 4 296.25 2.41 177 78 81 3 305.08 3.19 178 78 82 4 296.19 2.44 179 79 82 3 302.22 0.67 180 79 83 4 293.23 2.15 181 80 83 3 299.00 0.64 182 80 84 4 292.24 2.78 183 81 84 3 303.40 1.56 184 81 85 4 294.04 1.88 185 82 85 3 301.75 1.98 186 82 86 4 292.70 2.54 187 83 86 3 304.50 1.07 188 83 87 4 298.32 0.96 189 84 87 3 300.45 0.10 190 84 88 4 300.45 0.10 191 85 88 3 300.45 0.10 192 85 89 4 293.75 3.25 193 86 90 4 301.60 2.06 194 87 90 3 302.98 1.39 195 87 91 4 301.61 2.06 196 88 91 3 301.61 2.07 197 88 92 4 301.56 2.09 198 89 92 3 296.95 4.40 199 89 93 4 296.95 4.39 200 90 93 3 304.00 0.84 201 90 94 4 304.00 0.84 202 91 94 3 304.00 0.84 203 91 95 4 303.99 0.84 204 92 95 3 307.51 0.92 205 93 96 3 303.85 0.79 206 96 100 4 232.94 9.90