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 20 46 26 131.30 51.76 2 20 122 102 110.02 1.46 3 21 122 101 111.31 1.86 4 22 121 99 111.34 1.86 5 22 122 100 111.31 1.87 6 23 48 25 177.59 31.23 7 23 49 26 177.56 31.23 8 23 51 28 175.18 30.04 9 23 121 98 111.36 1.85 10 23 122 99 111.33 1.86 11 23 123 100 111.31 1.87 12 23 125 102 111.31 1.86 13 24 46 22 179.71 32.27 14 24 47 23 179.53 32.19 15 24 48 24 177.59 31.23 16 24 49 25 177.59 31.23 17 24 122 98 111.37 1.86 18 24 123 99 111.36 1.86 19 24 124 100 111.33 1.86 20 24 125 101 111.31 1.86 21 25 46 21 180.50 32.64 22 25 47 22 179.53 32.19 23 25 49 24 177.75 31.30 24 25 55 30 174.75 29.83 25 25 60 35 170.90 27.93 26 25 63 38 109.04 0.70 27 25 87 62 111.31 1.86 28 25 125 100 111.33 1.86 29 26 44 18 182.24 33.45 30 26 45 19 181.25 32.99 31 26 46 20 180.50 32.65 32 26 125 99 111.36 1.86 33 26 126 100 111.33 1.86 34 26 127 101 111.31 1.86 35 26 128 102 111.31 1.86 36 27 43 16 182.53 33.44 37 27 44 17 182.24 33.45 38 27 45 18 181.27 32.99 39 27 47 20 181.25 32.99 40 27 63 36 111.37 1.84 41 27 64 37 111.34 1.84 42 27 67 40 111.24 1.78 43 27 127 100 111.33 1.86 44 28 42 14 255.34 0.71 45 28 43 15 182.53 33.44 46 28 44 16 182.32 33.48 47 28 127 99 111.36 1.86 48 28 128 100 111.32 1.86 49 28 129 101 111.31 1.86 50 29 42 13 255.39 0.72 51 29 43 14 255.32 0.72 52 29 68 39 112.41 1.33 53 29 129 100 111.33 1.86 54 29 131 102 111.30 1.87 55 30 38 8 311.34 0.21 56 30 40 10 299.66 2.44 57 30 42 12 265.00 1.93 58 30 129 99 111.36 1.86 59 30 130 100 111.31 1.86 60 30 131 101 111.31 1.87 61 31 38 7 317.70 3.30 62 31 39 8 310.93 0.42 63 31 40 9 300.69 2.42 64 31 131 100 111.32 1.87 65 31 133 102 111.07 1.78 66 32 36 4 331.78 3.12 67 32 37 5 318.82 2.75 68 32 38 6 317.71 3.30 69 32 39 7 311.41 0.18 70 32 130 98 111.37 1.86 71 32 131 99 111.35 1.86 72 32 132 100 111.31 1.87 73 32 133 101 111.31 1.87 74 33 36 3 397.78 2.55 75 33 37 4 339.85 0.91 76 33 39 6 318.81 2.75 77 33 132 99 111.35 1.86 78 33 133 100 111.33 1.87 79 34 132 98 111.36 1.86 80 38 41 3 431.08 0.92 81 39 73 34 178.96 0.34 82 39 133 94 111.30 1.87 83 40 43 3 451.34 2.18 84 40 68 28 203.86 12.10 85 40 71 31 180.99 1.29 86 40 73 33 179.19 0.46 87 43 67 24 182.18 0.92 88 43 70 27 182.37 0.92 89 43 71 28 182.22 0.92 90 45 67 22 182.21 0.92 91 47 63 16 182.51 1.07 92 47 66 19 182.77 1.01 93 47 67 20 182.84 1.03 94 49 55 6 329.31 5.86 95 49 113 64 180.72 1.47 96 49 125 76 114.67 3.54 97 50 53 3 407.99 2.27 98 50 113 63 181.14 1.29 99 51 113 62 180.72 1.48 100 51 114 63 180.10 1.78 101 51 115 64 173.11 0.09 102 52 112 60 181.47 1.29 103 52 113 61 181.37 1.32 104 53 59 6 390.62 1.78 105 53 112 59 182.13 1.60 106 53 113 60 181.47 1.28 107 54 59 5 393.48 0.35 108 54 109 55 186.65 2.66 109 54 110 56 184.76 1.76 110 54 111 57 183.62 1.21 111 54 112 58 182.14 1.60 112 55 59 4 390.62 1.78 113 55 60 5 390.60 1.77 114 55 63 8 384.85 1.33 115 55 110 55 185.24 1.99 116 55 111 56 184.13 1.45 117 55 113 58 182.37 1.79 118 56 59 3 393.48 0.35 119 56 60 4 393.46 0.35 120 56 107 51 186.80 2.70 121 56 108 52 186.79 2.69 122 56 109 53 186.78 2.70 123 56 110 54 186.59 2.67 124 57 60 3 397.22 1.52 125 57 61 4 393.48 0.35 126 57 106 49 186.84 2.71 127 57 107 50 186.83 2.69 128 57 108 51 186.83 2.69 129 58 61 3 402.97 1.26 130 58 62 4 390.64 1.79 131 59 62 3 397.34 1.55 132 59 63 4 397.36 1.54 133 60 63 3 397.37 1.54 134 60 64 4 397.38 1.53 135 60 81 21 188.52 2.79 136 60 87 27 186.82 2.69 137 60 106 46 186.86 2.71 138 60 127 67 111.44 1.88 139 61 64 3 392.95 0.69 140 61 65 4 390.37 1.99 141 61 78 17 188.93 2.99 142 61 81 20 188.52 2.79 143 62 65 3 393.90 2.35 144 62 66 4 391.84 1.24 145 63 66 3 391.84 1.25 146 63 67 4 391.84 1.24 147 64 67 3 389.67 0.15 148 64 68 4 389.66 0.15 149 64 78 14 189.40 2.79 150 64 81 17 188.80 2.91 151 64 127 63 111.58 1.95 152 64 131 67 109.78 2.67 153 65 68 3 393.81 0.55 154 65 69 4 389.60 0.12 155 65 78 13 189.44 2.77 156 66 69 3 400.12 2.54 157 67 70 3 409.14 0.91 158 67 71 4 399.36 1.55 159 68 71 3 396.58 2.33 160 68 73 5 349.28 4.48 161 68 74 6 314.68 4.62 162 68 78 10 266.44 2.41 163 68 133 65 108.58 3.25 164 69 74 5 322.53 0.71 165 71 74 3 402.15 3.93 166 73 76 3 387.32 0.44 167 73 133 60 109.10 3.02 168 75 136 61 108.25 3.09 169 76 133 57 109.65 2.75 170 76 134 58 109.08 3.01 171 76 135 59 108.83 3.10 172 76 136 60 108.69 3.13 173 77 133 56 109.20 2.97 174 77 134 57 109.11 3.01 175 77 135 58 109.09 3.02 176 77 136 59 108.28 3.05 177 78 81 3 479.01 1.82 178 78 132 54 110.41 2.38 179 78 133 55 109.23 2.95 180 79 132 53 110.94 2.12 181 79 133 54 109.76 2.69 182 79 134 55 109.27 2.93 183 80 131 51 111.30 1.95 184 80 132 52 111.26 1.94 185 81 130 49 111.42 1.89 186 81 131 50 111.25 1.94 187 82 85 3 391.70 0.18 188 82 129 47 111.46 1.90 189 82 130 48 111.42 1.89 190 85 106 21 216.16 12.96 191 85 127 42 121.48 6.89 192 85 129 44 120.42 6.39 193 86 103 17 220.03 11.53 194 86 104 18 219.55 11.43 195 86 105 19 219.23 11.43 196 86 106 20 219.22 11.43 197 86 127 41 121.48 6.90 198 87 103 16 221.27 12.15 199 87 104 17 219.69 11.36 200 87 106 19 219.39 11.35 201 87 111 24 211.40 10.70 202 87 125 38 122.11 7.18 203 87 126 39 122.05 7.17 204 87 127 40 121.53 6.93 205 88 101 13 229.59 12.98 206 88 102 14 226.97 14.21 207 88 103 15 222.03 11.77 208 88 125 37 122.19 7.21 209 88 126 38 122.03 7.17 210 89 101 12 229.59 12.98 211 89 102 13 227.19 14.17 212 89 104 15 227.05 14.22 213 89 116 27 203.28 7.37 214 89 123 34 122.73 7.42 215 89 124 35 122.41 7.32 216 89 125 36 122.17 7.24 217 90 99 9 271.90 4.17 218 90 100 10 261.14 1.08 219 90 101 11 229.58 12.98 220 91 99 8 274.85 2.69 221 91 100 9 269.17 2.81 222 91 116 25 203.44 7.47 223 91 119 28 198.44 5.23 224 91 120 29 186.12 11.36 225 92 97 5 345.61 2.18 226 92 98 6 316.35 0.47 227 92 99 7 274.85 2.69 228 93 96 3 392.70 0.51 229 93 97 4 358.31 1.53 230 93 98 5 330.67 4.36 231 93 119 26 198.33 5.28 232 94 97 3 369.61 5.04 233 96 100 4 430.24 0.46 234 104 111 7 234.44 0.94 235 104 114 10 215.95 8.23 236 104 125 21 122.19 7.21 237 105 111 6 276.69 1.09 238 106 127 21 121.48 6.90 239 107 110 3 379.40 1.75 240 113 125 12 121.62 6.99 241 114 125 11 220.58 13.10 242 115 118 3 483.29 0.85 243 116 119 3 406.61 2.56 244 116 120 4 387.32 2.92 245 116 123 7 290.08 5.14 246 116 125 9 284.98 7.69 247 117 120 3 389.87 1.99 248 117 121 4 349.00 2.65 249 120 123 3 404.51 0.30