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 2 117 115 25.41 1.12 2 2 143 141 25.45 1.14 3 2 144 142 25.41 1.12 4 3 93 90 25.43 1.12 5 3 95 92 28.09 0.13 6 3 106 103 25.42 1.12 7 3 108 105 25.43 1.12 8 3 117 114 25.42 1.12 9 3 143 140 25.45 1.14 10 5 95 90 31.77 0.11 11 5 139 134 31.64 0.17 12 6 80 74 32.09 0.12 13 6 81 75 32.06 0.12 14 6 93 87 32.01 0.13 15 6 94 88 32.02 0.15 16 6 95 89 31.85 0.07 17 7 10 3 143.97 19.90 18 7 80 73 33.09 0.14 19 7 94 87 32.05 0.14 20 7 95 88 32.05 0.14 21 7 96 89 32.05 0.14 22 7 97 90 32.05 0.14 23 10 15 5 102.31 0.54 24 10 79 69 71.19 0.55 25 10 80 70 70.44 0.23 26 10 82 72 73.86 0.73 27 10 94 84 70.28 0.14 28 10 97 87 70.25 0.14 29 10 99 89 70.31 0.12 30 11 14 3 142.88 20.34 31 11 15 4 102.62 0.40 32 11 99 88 80.10 0.70 33 12 15 3 144.50 19.52 34 12 48 36 71.62 0.38 35 12 52 40 76.95 0.80 36 12 54 42 71.14 0.51 37 12 82 70 74.81 0.51 38 13 16 3 152.31 15.87 39 13 48 35 81.62 2.26 40 13 49 36 86.78 0.03 41 13 50 37 86.86 0.01 42 14 99 85 91.89 1.54 43 14 124 110 165.69 2.44 44 15 19 4 206.24 0.03 45 15 46 31 87.01 0.08 46 15 54 39 87.06 0.08 47 15 99 84 92.22 1.70 48 15 103 88 88.77 0.73 49 15 124 109 168.91 0.83 50 16 46 30 87.02 0.09 51 16 48 32 87.03 0.06 52 16 124 108 179.62 1.32 53 17 45 28 87.20 0.15 54 17 46 29 87.20 0.15 55 17 124 107 179.63 1.33 56 18 44 26 87.21 0.15 57 18 45 27 87.20 0.15 58 18 124 106 179.72 1.31 59 19 43 24 87.32 0.21 60 19 44 25 87.34 0.18 61 19 45 26 87.61 0.21 62 19 46 27 89.24 0.85 63 19 99 80 179.78 1.32 64 19 102 83 179.77 1.33 65 19 103 84 179.69 1.36 66 19 122 103 179.68 1.36 67 19 123 104 179.75 1.32 68 19 124 105 179.74 1.30 69 20 121 101 179.84 1.35 70 20 122 102 179.80 1.34 71 20 123 103 179.78 1.31 72 20 124 104 180.19 1.10 73 20 125 105 180.20 1.09 74 20 126 106 180.19 1.08 75 20 156 136 86.98 0.14 76 20 157 137 86.36 0.33 77 21 24 3 230.29 3.83 78 21 42 21 87.76 0.14 79 21 43 22 89.20 0.86 80 21 120 99 179.75 1.37 81 21 121 100 179.86 1.34 82 21 122 101 180.24 1.15 83 21 151 130 89.59 0.68 84 21 156 135 87.00 0.14 85 21 161 140 52.33 1.05 86 22 121 99 180.32 1.16 87 22 123 101 180.30 1.12 88 22 128 106 180.19 1.07 89 22 129 107 180.19 1.07 90 22 133 111 179.83 0.97 91 22 150 128 92.06 1.25 92 22 151 129 89.30 0.82 93 22 156 134 87.02 0.15 94 23 120 97 180.34 1.15 95 23 121 98 180.34 1.15 96 23 133 110 179.88 0.97 97 23 136 113 178.75 0.68 98 23 149 126 93.92 1.85 99 23 150 127 92.17 1.25 100 24 32 8 172.15 2.03 101 24 40 16 162.78 0.35 102 24 41 17 126.59 18.25 103 24 42 18 93.02 1.56 104 24 119 95 180.41 1.18 105 24 120 96 180.35 1.16 106 24 136 112 179.86 0.93 107 24 148 124 94.14 1.85 108 24 149 125 94.02 1.85 109 24 151 127 93.93 1.85 110 25 32 7 177.00 0.39 111 25 118 93 180.43 1.18 112 25 119 94 180.43 1.19 113 25 136 111 179.87 0.93 114 25 140 115 160.55 0.89 115 25 145 120 149.45 0.01 116 25 147 122 102.86 2.36 117 25 148 123 94.14 1.85 118 26 31 5 180.13 1.18 119 26 32 6 177.01 0.38 120 26 117 91 180.52 1.20 121 26 118 92 180.49 1.21 122 26 145 119 149.72 0.01 123 26 146 120 149.48 0.04 124 26 147 121 116.16 0.79 125 27 114 87 180.57 1.28 126 27 117 90 180.59 1.21 127 27 144 117 153.38 0.99 128 27 145 118 151.51 0.88 129 27 146 119 149.66 0.02 130 28 31 3 180.50 1.13 131 28 114 86 180.74 1.23 132 28 115 87 180.74 1.24 133 28 146 118 152.82 0.83 134 28 147 119 151.55 0.86 135 29 32 3 212.30 1.52 136 29 33 4 202.62 0.49 137 29 146 117 153.34 0.98 138 29 147 118 150.72 0.45 139 30 33 3 210.49 0.71 140 30 37 7 196.21 0.06 141 30 38 8 195.95 0.07 142 31 37 6 196.25 0.07 143 31 38 7 195.95 0.07 144 31 39 8 195.86 0.10 145 31 40 9 194.76 0.45 146 32 37 5 198.34 0.06 147 32 39 7 197.15 0.67 148 32 40 8 191.27 1.25 149 32 147 115 153.94 1.28 150 32 149 117 152.79 0.84 151 33 37 4 207.96 0.60 152 33 40 7 198.58 0.01 153 33 147 114 154.25 1.28 154 34 37 3 208.81 1.05 155 34 40 6 200.99 0.57 156 35 40 5 205.87 1.62 157 35 61 26 126.89 1.10 158 36 61 25 126.89 1.10 159 37 40 3 213.82 2.27 160 37 60 23 126.98 1.11 161 38 60 22 127.02 1.13 162 39 107 68 242.20 13.03 163 39 118 79 207.96 0.61 164 40 60 20 128.90 2.08 165 40 149 109 154.34 1.49 166 41 58 17 137.62 2.18 167 41 59 18 131.82 0.64 168 41 60 19 128.90 2.08 169 41 107 66 215.33 1.56 170 41 120 79 221.98 0.06 171 42 58 16 138.15 1.93 172 42 59 17 131.88 0.64 173 42 151 109 154.41 1.35 174 42 160 118 104.28 3.86 175 42 161 119 101.65 2.55 176 43 46 3 309.51 1.45 177 43 56 13 149.21 0.22 178 43 57 14 142.79 1.49 179 43 58 15 138.36 1.95 180 43 120 77 207.16 0.97 181 43 122 79 210.83 0.10 182 44 57 13 145.81 0.23 183 44 58 14 140.69 0.80 184 44 59 15 140.82 0.85 185 45 57 12 149.22 0.22 186 46 54 8 154.85 1.22 187 46 55 9 154.09 1.52 188 46 56 10 153.28 1.24 189 46 103 57 201.06 1.26 190 46 122 76 200.98 1.27 191 47 54 7 154.86 1.22 192 47 55 8 154.12 1.50 193 47 57 10 154.05 1.50 194 48 53 5 161.75 0.42 195 48 54 6 154.52 1.40 196 49 52 3 197.97 2.29 197 49 53 4 169.69 0.46 198 51 75 24 272.82 0.34 199 52 75 23 272.82 0.34 200 53 73 20 272.81 0.35 201 53 74 21 272.81 0.34 202 53 75 22 272.83 0.34 203 54 72 18 272.81 0.35 204 54 73 19 272.82 0.34 205 55 70 15 272.73 0.32 206 55 71 16 272.81 0.34 207 55 72 17 272.81 0.34 208 56 69 13 272.81 0.34 209 56 70 14 272.81 0.34 210 56 71 15 272.81 0.34 211 56 73 17 272.85 0.34 212 57 69 12 272.81 0.34 213 57 70 13 272.81 0.34 214 58 68 10 272.80 0.34 215 58 69 11 272.81 0.34 216 58 71 13 272.86 0.34 217 59 66 7 271.20 0.64 218 59 67 8 272.80 0.34 219 59 68 9 272.80 0.34 220 59 159 100 237.56 2.58 221 59 160 101 176.08 2.05 222 60 67 7 272.80 0.34 223 60 69 9 272.85 0.34 224 61 64 3 272.86 0.34 225 61 65 4 272.82 0.34 226 61 66 5 272.79 0.34 227 61 160 99 272.74 0.36 228 62 65 3 272.83 0.34 229 62 67 5 272.83 0.34 230 71 84 13 230.81 20.59 231 72 84 12 230.90 20.55 232 72 85 13 230.81 20.59 233 73 82 9 234.25 18.95 234 73 83 10 234.16 19.00 235 73 84 11 231.86 20.12 236 74 82 8 234.40 18.88 237 74 83 9 234.28 18.95 238 75 82 7 234.43 18.87 239 76 81 5 347.17 2.00 240 76 82 6 289.19 2.20 241 76 83 7 262.17 5.02 242 80 93 13 189.77 32.48 243 80 94 14 189.05 32.70 244 81 91 10 190.06 32.55 245 81 92 11 189.99 32.55 246 81 93 12 189.21 32.77 247 82 91 9 190.12 32.63 248 82 92 10 189.45 32.83 249 83 89 6 265.77 4.15 250 83 90 7 204.25 25.58 251 83 91 8 204.00 25.70 252 84 90 6 265.78 4.15 253 84 92 8 204.80 25.98 254 88 110 22 201.80 1.71 255 89 110 21 201.85 1.71 256 90 108 18 208.28 4.91 257 90 109 19 208.28 4.92 258 91 107 16 217.92 5.92 259 91 108 17 211.16 3.57 260 92 105 13 256.89 8.30 261 92 106 14 255.03 8.73 262 92 107 15 221.52 4.13 263 93 105 12 256.90 8.30 264 93 106 13 255.69 8.42 265 93 108 15 255.52 8.50 266 94 103 9 257.10 8.25 267 94 104 10 257.01 8.27 268 94 105 11 256.90 8.30 269 95 104 9 257.02 8.28 270 95 105 10 256.98 8.28 271 95 106 11 256.98 8.28 272 95 139 44 222.19 25.03 273 96 102 6 354.87 2.98 274 96 103 7 265.64 3.98 275 96 104 8 257.08 8.25 276 97 102 5 348.69 4.99 277 97 103 6 274.26 8.29 278 102 132 30 194.40 1.25 279 102 135 33 194.31 1.29 280 104 135 31 187.96 3.27 281 104 136 32 187.15 3.55 282 104 139 35 177.88 8.18 283 106 143 37 166.40 6.01 284 114 144 30 156.93 0.91 285 117 143 26 158.04 0.35 286 117 144 27 155.78 0.75 287 117 145 28 153.23 0.93 288 118 145 27 152.81 0.83 289 119 136 17 187.56 2.93 290 119 140 21 170.00 4.33 291 119 143 24 154.06 1.33 292 119 145 26 149.72 0.01 293 120 136 16 187.55 3.32 294 121 132 11 188.13 3.18 295 121 133 12 187.97 3.11 296 121 136 15 184.71 4.75 297 123 127 4 357.45 0.07 298 123 129 6 207.45 1.45 299 123 132 9 194.49 1.28 300 126 153 27 86.34 0.33 301 126 156 30 86.19 0.41 302 126 157 31 85.73 0.53 303 128 153 25 87.03 0.67 304 137 148 11 144.49 23.37 305 140 143 3 356.95 1.55 306 140 145 5 311.97 7.49 307 151 155 4 354.75 1.56 308 151 156 5 354.03 1.27 309 151 161 10 200.40 1.90 310 155 161 6 215.96 0.10 311 155 162 7 215.95 0.10 312 156 161 5 237.11 1.46 313 158 162 4 312.35 20.17