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 3 7 4 146.36 1.72 2 4 7 3 157.06 1.43 3 4 8 4 154.94 0.38 4 5 8 3 154.96 0.38 5 5 9 4 154.95 0.37 6 5 108 103 38.30 0.48 7 5 113 108 31.04 1.25 8 6 9 3 154.96 0.37 9 6 10 4 154.96 0.37 10 6 50 44 42.14 0.73 11 6 54 48 40.42 0.14 12 6 111 105 39.44 0.10 13 6 112 106 39.18 0.04 14 6 113 107 35.74 1.09 15 7 10 3 158.71 2.25 16 7 11 4 154.94 0.37 17 8 11 3 158.02 1.18 18 8 12 4 150.90 1.54 19 9 12 3 155.03 0.51 20 9 13 4 148.88 0.56 21 9 53 44 46.17 1.55 22 9 112 103 42.27 0.83 23 9 113 104 40.83 0.14 24 9 114 105 40.77 0.12 25 9 115 106 40.77 0.12 26 10 13 3 155.63 1.43 27 10 14 4 144.16 1.40 28 10 50 40 47.71 1.98 29 11 33 22 44.75 0.76 30 12 40 28 44.74 0.77 31 12 43 31 44.74 0.76 32 12 45 33 44.80 0.75 33 13 44 31 44.74 0.77 34 13 45 32 44.74 0.77 35 13 46 33 45.09 0.91 36 13 115 102 44.76 0.76 37 14 33 19 115.39 4.74 38 14 46 32 45.72 1.20 39 14 48 34 49.59 2.06 40 14 50 36 49.52 2.08 41 14 53 39 49.49 2.08 42 15 18 3 166.28 3.69 43 15 25 10 130.46 2.75 44 15 29 14 123.34 0.77 45 15 33 18 122.92 0.97 46 15 45 30 49.53 2.06 47 15 46 31 49.53 2.06 48 15 47 32 49.55 2.06 49 16 47 31 49.59 2.06 50 16 48 32 49.60 2.06 51 18 21 3 170.15 1.57 52 18 25 7 131.16 2.70 53 18 47 29 103.59 1.69 54 20 25 5 131.34 2.78 55 21 25 4 144.47 0.48 56 21 47 26 131.15 2.69 57 21 77 56 131.15 2.69 58 21 78 57 131.16 2.70 59 21 79 58 131.16 2.70 60 21 96 75 139.66 0.39 61 21 98 77 131.13 2.69 62 21 99 78 131.16 2.69 63 22 25 3 152.60 0.58 64 22 26 4 152.91 0.25 65 22 96 74 144.53 2.04 66 23 26 3 157.65 1.34 67 23 27 4 252.52 0.46 68 23 94 71 167.17 3.92 69 23 95 72 155.59 1.57 70 23 96 73 151.17 0.20 71 24 27 3 348.30 0.80 72 24 28 4 260.50 2.31 73 25 28 3 337.40 4.66 74 25 29 4 267.50 1.20 75 25 45 20 219.08 1.77 76 25 47 22 166.85 0.18 77 25 79 54 245.17 4.82 78 26 29 3 348.30 0.80 79 26 30 4 258.77 1.54 80 26 94 68 226.55 0.45 81 26 96 70 208.03 2.30 82 27 30 3 343.99 1.36 83 27 31 4 298.58 0.12 84 27 94 67 226.52 0.43 85 28 31 3 349.00 0.00 86 28 32 4 309.56 6.92 87 29 32 3 348.75 1.12 88 29 33 4 282.72 1.58 89 29 45 16 227.23 0.54 90 30 34 4 309.94 6.73 91 30 35 5 228.43 0.09 92 30 36 6 227.70 0.46 93 30 40 10 227.65 0.47 94 30 43 13 227.50 0.45 95 30 45 15 227.28 0.55 96 30 94 64 227.01 0.55 97 31 34 3 343.33 0.66 98 31 36 5 227.71 0.45 99 33 45 12 227.49 0.47 100 35 39 4 231.94 2.59 101 35 40 5 227.72 0.48 102 35 43 8 227.65 0.47 103 36 39 3 231.93 2.60 104 36 92 56 260.75 4.23 105 39 83 44 227.65 0.48 106 39 88 49 246.72 2.19 107 40 83 43 227.65 0.47 108 41 82 41 227.62 0.47 109 41 83 42 227.63 0.47 110 41 121 80 79.14 0.29 111 42 80 38 227.58 0.46 112 42 81 39 227.50 0.47 113 42 82 40 227.50 0.47 114 42 117 75 79.42 0.23 115 42 120 78 79.30 0.23 116 42 121 79 79.06 0.26 117 43 80 37 227.47 0.46 118 43 81 38 227.44 0.46 119 43 117 74 79.39 0.24 120 44 78 34 227.57 0.46 121 44 79 35 227.47 0.46 122 44 80 36 227.25 0.55 123 44 115 71 79.47 0.23 124 44 117 73 79.38 0.25 125 44 120 76 79.04 0.26 126 45 78 33 227.50 0.47 127 45 79 34 227.46 0.47 128 45 81 36 227.41 0.47 129 46 53 7 242.18 5.26 130 46 76 30 227.56 0.46 131 46 77 31 227.50 0.47 132 46 78 32 227.42 0.47 133 46 103 57 184.24 4.41 134 46 115 69 79.49 0.22 135 47 77 30 227.43 0.46 136 47 78 31 227.31 0.52 137 47 79 32 227.30 0.52 138 52 76 24 227.05 0.53 139 53 76 23 226.71 0.42 140 53 112 59 84.45 0.18 141 54 111 57 84.45 0.17 142 54 112 58 84.45 0.18 143 55 61 6 272.13 0.17 144 55 62 7 260.09 0.08 145 56 61 5 237.33 0.80 146 56 62 6 227.02 0.57 147 56 70 14 227.04 0.57 148 56 72 16 226.64 0.40 149 56 76 20 217.17 1.06 150 57 70 13 227.03 0.56 151 57 110 53 91.33 2.42 152 57 111 54 91.31 2.42 153 57 112 55 85.02 0.40 154 58 61 3 256.52 1.04 155 58 62 4 227.56 0.38 156 58 70 12 227.22 0.51 157 59 62 3 242.50 2.02 158 59 70 11 227.40 0.47 159 59 73 14 226.80 0.40 160 60 73 13 226.88 0.43 161 61 72 11 227.03 0.51 162 61 73 12 226.80 0.40 163 61 74 13 226.76 0.42 164 61 76 15 226.76 0.42 165 62 70 8 227.46 0.45 166 62 71 9 227.25 0.52 167 62 72 10 227.10 0.48 168 62 73 11 227.00 0.49 169 63 70 7 227.50 0.47 170 63 71 8 227.37 0.46 171 63 73 10 227.24 0.52 172 64 69 5 227.62 0.46 173 64 70 6 227.59 0.46 174 65 69 4 227.62 0.46 175 65 70 5 227.62 0.46 176 65 71 6 227.61 0.46 177 65 104 39 227.25 0.53 178 66 69 3 239.94 0.80 179 66 118 52 82.13 0.24 180 69 104 35 227.23 0.51 181 69 105 36 227.16 0.52 182 69 106 37 227.02 0.56 183 70 104 34 227.15 0.51 184 70 105 35 227.13 0.51 185 70 107 37 226.95 0.54 186 71 102 31 227.23 0.51 187 71 103 32 227.15 0.51 188 71 104 33 226.98 0.54 189 72 76 4 244.82 1.33 190 72 102 30 227.13 0.51 191 72 103 31 227.13 0.51 192 73 102 29 227.13 0.51 193 74 102 28 226.97 0.54 194 75 100 25 227.13 0.51 195 75 101 26 226.66 0.39 196 75 102 27 222.98 1.22 197 76 100 24 226.70 0.41 198 76 101 25 226.50 0.42 199 76 103 27 211.50 0.56 200 77 99 22 226.97 0.54 201 77 100 23 225.14 0.39 202 78 98 20 226.93 0.52 203 78 99 21 225.79 0.07 204 78 101 23 212.81 0.08 205 78 103 25 177.00 1.35 206 78 120 42 78.81 0.18 207 79 96 17 227.11 0.53 208 79 97 18 226.68 0.42 209 79 98 19 217.77 0.98 210 80 96 16 226.68 0.42 211 80 97 17 225.78 0.07 212 80 120 40 75.15 1.35 213 81 94 13 227.03 0.55 214 81 95 14 226.66 0.42 215 82 94 12 227.11 0.52 216 82 95 13 227.06 0.51 217 83 88 5 227.65 0.46 218 83 92 9 227.46 0.46 219 83 93 10 227.38 0.42 220 83 94 11 227.13 0.52 221 84 93 9 227.46 0.46 222 84 94 10 227.44 0.46 223 84 95 11 227.23 0.51 224 97 122 25 68.45 1.49 225 101 119 18 79.36 0.25 226 101 120 19 79.31 0.24 227 101 122 21 79.24 0.23 228 102 119 17 79.36 0.25 229 103 115 12 81.11 0.70 230 103 120 17 79.39 0.24 231 104 115 11 81.23 0.68 232 104 116 12 79.98 0.14 233 104 119 15 79.47 0.21 234 105 112 7 84.47 0.17 235 105 114 9 82.34 0.23 236 105 115 10 81.28 0.70 237 106 112 6 84.50 0.15 238 106 113 7 84.39 0.12 239 106 114 8 83.56 0.20 240 107 111 4 92.87 1.64 241 107 112 5 84.72 0.26 242 108 111 3 152.62 7.59 243 108 113 5 91.20 2.46 244 116 119 3 249.92 0.22 245 117 120 3 161.00 0.03 246 117 121 4 158.10 0.93 247 118 121 3 161.00 0.03 248 119 122 3 169.68 2.08