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 79 76 209.15 0.60 2 4 41 37 212.53 2.29 3 4 78 74 209.22 0.60 4 4 79 75 209.21 0.61 5 4 80 76 209.19 0.61 6 4 81 77 209.18 0.61 7 5 40 35 213.63 2.84 8 5 41 36 213.56 2.81 9 5 81 76 209.16 0.61 10 6 37 31 214.66 3.32 11 6 38 32 214.59 3.29 12 6 39 33 213.72 2.85 13 6 40 34 213.69 2.86 14 6 41 35 213.66 2.83 15 6 81 75 209.21 0.60 16 6 82 76 209.18 0.61 17 6 83 77 209.18 0.61 18 7 37 30 214.67 3.32 19 7 40 33 214.38 3.19 20 7 50 43 209.19 0.62 21 7 83 76 209.17 0.62 22 7 85 78 209.16 0.62 23 8 35 27 232.31 3.76 24 8 36 28 216.34 4.13 25 8 37 29 214.68 3.31 26 8 82 74 209.24 0.60 27 8 83 75 209.21 0.61 28 8 84 76 209.18 0.61 29 8 85 77 209.16 0.62 30 9 36 27 232.61 3.99 31 9 64 55 209.09 0.65 32 9 85 76 209.16 0.62 33 9 87 78 209.01 0.61 34 10 18 8 295.64 1.35 35 10 20 10 261.29 15.79 36 10 35 25 235.03 4.34 37 10 85 75 209.22 0.60 38 10 87 77 209.09 0.64 39 10 107 97 84.92 3.27 40 10 126 116 24.87 0.05 41 11 18 7 295.64 1.35 42 11 19 8 295.62 1.35 43 11 36 25 235.69 4.00 44 11 58 47 209.33 0.65 45 11 87 76 209.12 0.64 46 11 90 79 189.65 0.15 47 11 94 83 117.50 0.08 48 12 16 4 385.48 6.08 49 12 17 5 335.35 0.07 50 12 18 6 295.73 1.33 51 12 87 75 209.18 0.61 52 12 88 76 209.11 0.63 53 12 89 77 209.00 0.59 54 12 90 78 208.94 0.57 55 13 17 4 345.72 5.11 56 13 18 5 325.11 5.20 57 13 90 77 208.99 0.58 58 13 104 91 114.66 0.54 59 16 108 92 113.79 0.64 60 17 90 73 209.19 0.61 61 17 104 87 114.63 0.56 62 17 105 88 114.37 0.66 63 17 106 89 113.76 0.62 64 17 107 90 111.98 0.24 65 18 90 72 209.07 0.62 66 18 105 87 114.20 0.73 67 18 106 88 111.98 0.24 68 18 107 89 108.39 1.30 69 19 36 17 270.40 11.25 70 19 90 71 208.75 0.46 71 19 94 75 132.96 2.56 72 19 98 79 117.11 0.10 73 19 102 83 114.75 0.56 74 19 103 84 114.67 0.55 75 19 104 85 114.61 0.55 76 19 105 86 114.13 0.49 77 20 33 13 274.50 9.38 78 20 34 14 274.25 9.38 79 20 35 15 270.39 11.24 80 20 102 82 114.70 0.55 81 20 103 83 114.67 0.55 82 20 105 85 113.92 0.59 83 20 107 87 108.13 1.65 84 21 33 12 274.44 9.35 85 21 34 13 274.32 9.35 86 21 35 14 270.43 11.24 87 21 36 15 270.43 11.25 88 21 98 77 116.68 0.19 89 21 100 79 114.95 0.54 90 21 102 81 114.68 0.55 91 22 33 11 274.44 9.35 92 22 103 81 114.80 0.51 93 23 26 3 427.80 5.56 94 23 28 5 389.14 1.80 95 23 29 6 320.31 5.65 96 23 30 7 274.80 9.26 97 23 32 9 274.59 9.35 98 23 33 10 274.58 9.35 99 23 34 11 274.58 9.35 100 23 100 77 115.06 0.49 101 24 99 75 116.59 0.20 102 24 100 76 114.97 0.54 103 24 101 77 114.95 0.53 104 29 32 3 444.84 3.04 105 30 114 84 50.48 0.96 106 31 113 82 50.47 0.92 107 31 114 83 50.32 0.91 108 31 115 84 50.30 0.91 109 31 116 85 50.16 0.97 110 31 117 86 50.29 0.92 111 32 114 82 50.32 0.91 112 32 115 83 49.93 0.99 113 32 116 84 46.30 0.01 114 33 105 72 114.39 0.54 115 33 114 81 50.01 1.05 116 33 115 82 46.27 0.01 117 33 116 83 46.30 0.01 118 34 116 82 46.26 0.01 119 35 84 49 209.23 0.60 120 35 110 75 52.22 0.10 121 36 57 21 209.23 0.60 122 36 98 62 114.89 0.53 123 37 57 20 209.22 0.61 124 38 57 19 209.26 0.59 125 39 42 3 438.74 1.08 126 39 53 14 209.45 0.52 127 40 44 4 412.09 1.78 128 40 49 9 289.31 14.92 129 40 50 10 289.32 14.92 130 40 53 13 209.44 0.51 131 41 44 3 438.61 0.64 132 44 48 4 417.00 0.29 133 44 49 5 390.94 2.04 134 44 52 8 376.57 1.18 135 45 48 3 420.43 1.60 136 45 49 4 396.28 1.41 137 46 49 3 418.99 0.88 138 46 50 4 417.05 0.28 139 46 83 37 209.49 0.47 140 46 85 39 209.48 0.47 141 47 50 3 438.57 0.61 142 47 51 4 412.64 2.47 143 48 51 3 412.64 2.47 144 48 52 4 402.26 0.51 145 49 53 4 409.64 2.20 146 50 53 3 415.99 3.01 147 50 54 4 409.62 2.77 148 50 85 35 209.53 0.44 149 51 54 3 419.97 1.02 150 51 65 14 209.46 0.47 151 52 55 3 439.61 0.71 152 52 56 4 422.86 0.42 153 53 56 3 422.14 0.78 154 53 57 4 413.46 2.30 155 54 57 3 422.14 0.78 156 54 58 4 412.10 2.98 157 54 59 5 411.70 3.17 158 54 64 10 294.24 0.46 159 55 58 3 418.35 0.14 160 55 59 4 410.86 3.58 161 55 96 41 116.64 0.15 162 56 96 40 116.62 0.15 163 56 97 41 116.59 0.14 164 57 96 39 116.63 0.15 165 57 97 40 116.55 0.18 166 58 62 4 427.25 1.62 167 58 64 6 382.45 1.59 168 58 94 36 117.00 0.13 169 58 95 37 116.94 0.12 170 58 96 38 116.62 0.15 171 59 95 36 117.00 0.12 172 59 96 37 116.84 0.12 173 60 90 30 202.59 2.18 174 60 91 31 182.24 2.29 175 60 93 33 149.36 0.23 176 60 94 34 133.41 1.80 177 60 95 35 123.64 3.07 178 61 91 30 193.22 1.64 179 62 89 27 209.52 0.40 180 62 90 28 204.52 1.22 181 62 91 29 204.52 1.21 182 63 87 24 209.95 0.29 183 63 88 25 209.89 0.28 184 63 89 26 209.52 0.39 185 64 85 21 214.17 1.66 186 64 86 22 210.15 0.20 187 64 87 23 209.93 0.29 188 64 88 24 209.93 0.29 189 65 86 21 213.88 1.54 190 65 87 22 209.96 0.29 191 66 85 19 214.19 1.66 192 66 86 20 214.12 1.65 193 67 70 3 483.76 2.49 194 67 84 17 214.33 1.60 195 67 85 18 214.19 1.66 196 67 86 19 214.18 1.66 197 68 84 16 214.70 1.68 198 68 85 17 214.22 1.65 199 68 86 18 214.19 1.66 200 68 122 54 24.88 0.06 201 68 126 58 24.12 0.36 202 69 83 14 214.84 1.64 203 69 84 15 214.78 1.65 204 69 125 56 24.10 0.35 205 70 82 12 215.06 1.68 206 70 83 13 214.84 1.64 207 70 84 14 214.84 1.64 208 71 82 11 215.06 1.68 209 71 83 12 215.05 1.68 210 71 84 13 215.04 1.68 211 71 119 48 24.79 0.05 212 71 122 51 23.16 0.14 213 72 79 7 317.00 3.31 214 72 81 9 263.78 9.86 215 73 80 7 306.76 1.80 216 74 78 4 355.81 0.96 217 74 79 5 316.94 3.29 218 74 80 6 316.95 3.28 219 75 78 3 381.66 1.96 220 75 80 5 340.98 4.40 221 82 119 37 24.78 0.05 222 84 119 35 33.14 0.21 223 84 122 38 24.82 0.04 224 84 123 39 24.80 0.05 225 90 93 3 464.24 1.83 226 90 94 4 415.25 3.43 227 90 104 14 114.73 0.57 228 95 98 3 455.72 0.60 229 106 109 3 421.09 0.99 230 107 110 3 405.83 0.58 231 107 126 19 35.79 1.19 232 108 129 21 24.89 0.00 233 110 123 13 46.34 0.54 234 111 114 3 426.39 2.79 235 111 115 4 415.53 6.63 236 112 115 3 424.80 1.99 237 112 120 8 261.87 9.08 238 112 123 11 136.41 46.20 239 112 127 15 38.51 1.07 240 115 119 4 424.35 0.84 241 115 120 5 422.38 0.37 242 115 123 8 363.49 0.80 243 116 119 3 428.99 0.06 244 117 120 3 424.35 0.84 245 119 122 3 433.16 0.65 246 119 123 4 416.85 1.74 247 120 123 3 417.00 1.66 248 120 124 4 410.33 0.29 249 121 124 3 417.89 1.21 250 122 125 3 433.25 0.10 251 122 126 4 415.00 0.46 252 123 126 3 424.88 0.47 253 123 127 4 408.49 1.05 254 124 127 3 419.09 2.50 255 124 128 4 414.99 0.46 256 125 128 3 428.15 0.18 257 126 129 3 413.05 1.24