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 1 37 36 94.28 1.03 2 3 10 7 233.91 9.04 3 3 18 15 94.47 1.06 4 3 37 34 94.48 1.07 5 3 40 37 94.42 1.08 6 4 9 5 265.30 6.64 7 4 10 6 233.92 9.05 8 4 14 10 216.69 3.75 9 4 40 36 94.67 1.15 10 4 44 40 94.65 1.16 11 5 9 4 315.87 2.94 12 5 44 39 94.66 1.16 13 6 9 3 319.03 1.36 14 6 10 4 315.88 2.94 15 6 44 38 94.67 1.15 16 7 10 3 310.26 1.53 17 7 15 8 276.62 0.98 18 7 44 37 94.68 1.15 19 7 45 38 94.67 1.15 20 7 72 65 94.67 1.15 21 7 76 69 92.03 0.12 22 7 83 76 52.06 0.42 23 7 84 77 51.75 0.35 24 8 82 74 52.15 0.48 25 8 83 75 52.05 0.42 26 8 84 76 51.80 0.37 27 8 85 77 51.73 0.35 28 9 14 5 305.85 1.22 29 9 85 76 51.74 0.35 30 10 14 4 302.53 0.41 31 10 15 5 302.12 0.60 32 10 18 8 288.50 2.23 33 10 40 30 110.94 1.28 34 10 44 34 100.59 1.41 35 10 84 74 51.81 0.39 36 10 85 75 51.65 0.32 37 11 14 3 307.46 0.77 38 11 15 4 305.85 1.22 39 11 84 73 51.85 0.41 40 11 85 74 51.63 0.35 41 12 15 3 308.50 0.70 42 12 16 4 307.69 0.30 43 12 69 57 106.58 1.59 44 12 73 61 106.67 1.54 45 12 84 72 51.86 0.41 46 13 16 3 311.99 1.03 47 13 17 4 311.19 0.65 48 14 17 3 311.19 0.65 49 14 18 4 311.19 0.65 50 14 85 71 51.84 0.42 51 15 18 3 309.00 1.75 52 15 19 4 305.81 0.18 53 15 41 26 111.93 1.62 54 15 44 29 111.87 1.67 55 15 45 30 111.80 1.65 56 15 69 54 111.77 1.64 57 15 72 57 111.73 1.66 58 15 84 69 51.85 0.41 59 16 19 3 311.80 2.10 60 16 20 4 304.32 0.56 61 16 65 49 112.18 1.48 62 16 69 53 111.81 1.66 63 17 20 3 310.33 1.37 64 17 21 4 309.63 1.72 65 18 21 3 311.21 0.93 66 18 22 4 309.58 1.75 67 18 44 26 112.98 1.57 68 19 22 3 309.58 1.74 69 19 23 4 304.13 0.98 70 19 41 22 113.03 1.55 71 19 54 35 113.01 1.57 72 19 65 46 112.97 1.60 73 19 68 49 112.98 1.58 74 19 69 50 112.98 1.58 75 20 23 3 311.78 0.68 76 20 24 4 309.62 1.76 77 20 65 45 113.16 1.56 78 21 24 3 309.98 1.94 79 21 25 4 309.64 1.77 80 21 37 16 114.07 1.94 81 22 25 3 315.47 0.20 82 22 26 4 314.12 0.48 83 22 34 12 114.16 1.97 84 22 37 15 114.08 1.94 85 22 38 16 114.07 1.94 86 22 41 19 113.80 1.80 87 22 54 32 113.73 1.81 88 23 26 3 314.12 0.48 89 23 27 4 314.12 0.48 90 23 65 42 113.30 1.59 91 24 27 3 314.12 0.48 92 24 28 4 314.11 0.48 93 25 28 3 305.52 3.81 94 25 33 8 114.47 1.99 95 25 34 9 114.38 1.97 96 25 37 12 114.38 1.96 97 26 34 8 114.42 1.99 98 26 55 29 114.32 1.99 99 31 34 3 296.18 0.20 100 31 35 4 291.29 0.81 101 32 36 4 301.06 0.79 102 33 36 3 312.18 1.92 103 33 37 4 307.75 4.13 104 34 37 3 311.11 2.46 105 34 38 4 307.75 4.13 106 34 55 21 196.47 2.06 107 35 38 3 310.05 2.98 108 35 39 4 297.25 0.26 109 36 39 3 317.32 0.65 110 36 40 4 308.75 3.35 111 37 40 3 309.05 3.50 112 37 41 4 308.87 0.90 113 38 41 3 308.88 0.90 114 38 42 4 306.30 2.19 115 38 51 13 197.13 2.39 116 38 54 16 197.13 2.38 117 38 55 17 197.14 2.39 118 39 42 3 311.55 2.25 119 39 43 4 308.99 3.54 120 40 43 3 311.72 2.17 121 40 44 4 311.56 2.25 122 41 44 3 322.33 3.14 123 41 45 4 306.55 4.75 124 41 50 9 197.34 2.44 125 41 51 10 197.33 2.44 126 41 53 12 197.34 2.44 127 41 54 13 197.31 2.43 128 41 68 27 195.68 2.20 129 41 72 31 195.53 2.21 130 42 45 3 313.33 1.36 131 42 46 4 299.17 5.73 132 42 50 8 197.33 2.44 133 42 51 9 197.33 2.44 134 43 46 3 315.88 3.27 135 44 76 32 195.51 2.21 136 45 72 27 195.54 2.21 137 45 75 30 195.53 2.21 138 45 76 31 195.51 2.20 139 46 75 29 195.54 2.21 140 46 76 30 195.52 2.21 141 46 81 35 137.19 1.54 142 47 50 3 302.62 1.94 143 47 53 6 227.96 6.94 144 47 75 28 195.54 2.21 145 48 75 27 195.61 2.21 146 49 52 3 314.92 0.98 147 50 53 3 323.75 0.73 148 51 54 3 317.07 0.09 149 51 55 4 298.23 0.01 150 52 55 3 308.44 1.06 151 52 56 4 270.16 1.99 152 52 57 5 270.16 1.99 153 53 61 8 204.56 0.33 154 53 68 15 195.81 2.25 155 53 71 18 195.78 2.25 156 53 72 19 195.77 2.25 157 54 57 3 323.47 0.05 158 54 68 14 195.81 2.25 159 57 61 4 307.38 2.33 160 57 63 6 195.90 2.24 161 58 61 3 319.68 1.97 162 61 67 6 199.74 0.35 163 61 68 7 203.96 2.46 164 61 71 10 195.95 2.24 165 62 67 5 208.86 4.90 166 64 67 3 307.32 5.58 167 64 68 4 297.41 0.62 168 65 68 3 307.60 5.45 169 65 69 4 297.56 0.58 170 66 69 3 304.36 3.52 171 66 70 4 297.58 0.57 172 67 70 3 309.49 2.54 173 67 71 4 299.48 1.52 174 68 71 3 316.50 0.97 175 68 72 4 297.59 0.57 176 69 72 3 301.11 1.82 177 69 73 4 302.57 0.89 178 69 84 15 88.38 18.60 179 70 73 3 304.12 1.67 180 70 74 4 304.13 1.67 181 71 74 3 312.29 1.46 182 71 75 4 304.12 1.67 183 72 75 3 313.32 0.95 184 72 76 4 305.99 2.73 185 72 84 12 86.21 17.50 186 73 76 3 306.28 2.58 187 73 77 4 301.10 1.07 188 73 84 11 86.21 17.50 189 74 77 3 307.34 2.05 190 74 78 4 307.33 2.05 191 75 78 3 317.56 0.19 192 75 79 4 308.00 1.72 193 75 81 6 299.10 0.60 194 76 79 3 310.87 3.15 195 76 80 4 300.81 1.22 196 76 81 5 269.97 1.64 197 76 82 6 269.63 1.80 198 77 80 3 301.69 0.56