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 14 19 5 64.88 0.91 2 15 143 123 65.17 0.84 3 15 144 124 65.21 0.84 4 15 145 125 65.42 0.94 5 16 19 3 67.20 0.15 6 16 20 4 65.53 0.92 7 16 21 5 65.53 0.92 8 16 143 122 65.40 0.94 9 16 154 133 65.53 0.92 10 16 156 135 65.48 0.90 11 17 142 120 65.52 0.91 12 17 143 121 65.53 0.90 13 17 144 122 65.64 0.84 14 17 156 134 66.53 0.42 15 17 188 167 65.45 0.93 16 17 188 168 65.44 0.94 17 17 189 169 65.38 0.92 18 17 191 171 65.43 0.94 19 17 220 195 65.42 0.94 20 17 221 196 65.41 0.93 21 18 158 135 66.39 0.49 22 18 188 166 66.28 0.52 23 18 188 167 65.44 0.94 24 19 157 133 110.84 22.00 25 19 158 134 65.54 0.92 26 20 137 112 77.33 0.65 27 20 156 131 118.23 18.34 28 20 157 132 115.36 19.78 29 20 158 133 122.44 26.23 30 20 159 134 248.50 1.96 31 21 154 128 154.67 0.11 32 21 155 129 154.69 0.12 33 21 156 130 132.72 11.10 34 22 26 4 165.98 2.11 35 22 27 5 161.16 0.95 36 22 155 128 162.21 2.10 37 22 156 129 185.31 0.75 38 23 26 3 167.72 1.24 39 23 27 4 166.16 2.02 40 23 71 45 147.31 0.94 41 23 155 127 221.30 2.17 42 24 27 3 168.68 0.77 43 24 28 4 160.03 1.40 44 24 69 42 146.94 1.10 45 24 70 43 147.33 0.94 46 24 71 44 147.37 0.92 47 24 117 90 146.91 1.10 48 25 28 3 171.85 0.84 49 25 116 88 146.98 1.10 50 25 117 89 146.98 1.10 51 27 30 3 196.43 6.63 52 27 137 105 147.31 0.94 53 27 139 107 147.37 0.92 54 27 157 125 239.43 10.45 55 28 116 85 151.35 0.42 56 28 117 86 151.35 0.42 57 28 118 87 150.63 0.55 58 28 119 88 148.02 0.68 59 29 45 14 147.53 0.91 60 29 46 15 147.41 0.93 61 29 119 87 151.04 0.35 62 29 120 88 148.00 0.69 63 29 121 89 147.46 0.95 64 29 137 103 151.54 0.40 65 29 198 166 151.35 0.39 66 29 200 168 151.38 0.38 67 30 43 11 152.66 0.15 68 30 44 12 151.46 0.36 69 30 139 104 151.56 0.40 70 30 140 105 152.11 0.64 71 30 141 106 153.99 0.06 72 30 155 120 279.11 2.62 73 30 198 165 151.37 0.38 74 31 43 10 153.41 0.01 75 31 44 11 151.59 0.38 76 31 45 12 151.54 0.40 77 31 46 13 151.53 0.39 78 31 52 19 151.54 0.40 79 31 65 32 153.97 0.24 80 31 66 33 153.92 0.21 81 31 67 34 153.43 0.06 82 31 141 105 154.21 0.07 83 32 40 6 154.49 0.10 84 32 42 8 154.10 0.12 85 32 43 9 153.86 0.18 86 32 65 31 154.25 0.14 87 32 66 32 154.10 0.18 88 32 73 38 154.50 0.11 89 32 141 104 154.21 0.07 90 33 40 5 154.55 0.10 91 33 41 6 154.49 0.10 92 33 42 7 154.12 0.12 93 33 43 8 154.11 0.12 94 33 54 19 154.09 0.12 95 33 58 23 154.35 0.01 96 33 63 28 154.57 0.07 97 33 64 29 154.53 0.09 98 33 65 30 154.35 0.09 99 33 106 70 154.18 0.17 100 34 39 3 169.77 4.67 101 34 40 4 154.56 0.10 102 34 41 5 154.72 0.01 103 34 63 27 154.59 0.08 104 34 64 28 154.54 0.09 105 34 66 30 154.54 0.09 106 37 41 4 167.88 1.48 107 37 60 23 162.37 3.81 108 40 73 32 285.04 0.10 109 40 152 109 152.59 0.43 110 45 121 75 212.74 0.73 111 46 120 73 252.66 0.17 112 46 121 74 232.28 1.04 113 47 121 73 271.25 0.89 114 47 123 75 196.20 1.45 115 47 238 186 48.41 0.23 116 47 242 190 30.36 0.62 117 48 242 189 30.39 0.61 118 51 242 186 30.29 0.59 119 51 245 189 21.73 0.81 120 70 155 83 151.25 0.45 121 71 155 82 151.14 0.52 122 72 153 79 152.74 0.21 123 73 152 77 153.51 0.03 124 73 153 78 153.12 0.12 125 74 153 77 153.30 0.06 126 87 245 154 21.68 0.64 127 89 237 144 74.80 0.40 128 89 241 148 34.65 0.72 129 89 245 152 23.05 0.06 130 91 234 139 101.52 0.32 131 91 237 142 77.78 0.39 132 92 237 141 99.23 0.81 133 98 180 80 189.72 9.76 134 99 180 79 162.05 4.08 135 100 177 75 161.66 4.22 136 100 179 77 162.01 4.08 137 100 180 78 161.94 4.04 138 101 179 76 161.91 4.04 139 101 234 129 127.36 3.38 140 102 229 123 151.87 0.60 141 103 229 122 152.08 0.72 142 103 234 127 98.78 1.03 143 103 237 130 73.88 0.06 144 103 238 131 58.14 5.12 145 105 237 128 60.81 6.13 146 105 238 129 46.81 0.41 147 105 241 132 30.47 0.58 148 105 242 133 30.35 0.62 149 107 245 134 19.62 0.03 150 122 209 83 279.10 1.60 151 123 204 81 259.92 3.85 152 123 209 82 200.18 0.69 153 123 231 104 213.06 38.13 154 123 235 108 65.85 3.62 155 123 238 111 51.41 1.70 156 123 239 112 48.41 0.23 157 124 204 80 197.52 2.42 158 124 209 81 182.36 1.96 159 124 210 82 160.35 2.14 160 124 232 104 109.46 0.65 161 124 235 107 74.91 0.27 162 127 210 80 155.82 0.44 163 128 210 79 152.31 1.17 164 129 134 4 166.40 0.88 165 129 162 32 144.50 1.54 166 129 210 78 152.99 0.86 167 130 134 3 182.05 1.47 168 130 162 31 146.81 1.08 169 132 162 30 146.81 1.08 170 132 163 31 146.85 1.08 171 132 164 32 146.94 1.10 172 133 161 28 146.83 1.09 173 133 162 29 146.93 1.10 174 134 161 27 146.94 1.10 175 134 162 28 146.96 1.10 176 135 159 24 146.93 1.10 177 135 160 25 146.94 1.10 178 135 161 26 146.94 1.10 179 135 184 50 154.12 0.02 180 136 159 23 146.94 1.10 181 136 160 24 146.94 1.10 182 136 162 26 147.38 0.92 183 137 157 20 146.63 0.99 184 137 158 21 146.87 1.08 185 137 159 22 146.93 1.10 186 138 157 19 145.27 1.09 187 138 158 20 146.46 1.03 188 138 160 22 147.30 0.95 189 138 228 88 153.44 0.73 190 139 156 17 146.90 1.10 191 139 157 18 145.88 0.74 192 140 155 15 147.00 1.07 193 140 156 16 146.92 1.10 194 141 152 11 151.20 0.27 195 141 153 12 150.48 0.07 196 141 154 13 147.44 0.89 197 141 155 14 146.99 1.07 198 142 152 10 151.27 0.24 199 142 156 14 146.97 1.06 200 143 150 7 153.88 0.07 201 143 151 8 153.75 0.07 202 143 153 10 152.38 0.50 203 143 154 11 150.84 0.06 204 144 148 4 154.44 0.12 205 144 149 5 154.25 0.04 206 144 150 6 153.94 0.04 207 144 191 49 194.38 7.16 208 145 148 3 168.50 0.52 209 145 149 4 154.25 0.04 210 145 151 6 154.24 0.04 211 150 191 43 152.91 0.24 212 150 192 44 153.28 0.10 213 156 194 40 146.91 1.09 214 158 188 32 146.85 1.08 215 158 189 33 146.46 1.03 216 159 184 26 147.02 1.08 217 160 183 23 151.41 3.53 218 160 184 24 146.84 1.12 219 160 184 25 147.00 1.09 220 161 183 22 165.50 3.48 221 161 184 23 147.00 1.08 222 161 184 24 147.37 0.93 223 162 181 19 260.20 4.88 224 162 182 20 195.86 9.12 225 162 183 21 165.50 3.48 226 162 201 41 147.38 0.92 227 163 182 19 219.88 2.86 228 163 183 20 195.86 9.12 229 163 184 21 195.83 9.11 230 163 185 23 165.75 3.35 231 163 225 60 148.27 0.65 232 171 223 50 153.73 0.33 233 171 224 51 153.69 0.30 234 171 225 52 153.81 0.36 235 172 215 41 161.24 3.70 236 172 216 42 160.95 3.83 237 172 217 43 160.90 3.81 238 172 224 50 153.94 0.30 239 172 225 51 153.94 0.30 240 172 227 53 153.47 0.26 241 175 215 38 162.06 4.08 242 176 215 37 162.09 4.05 243 176 227 49 153.94 0.31 244 178 230 50 153.37 0.36 245 178 233 53 150.97 0.67 246 179 229 48 153.52 0.35 247 179 230 49 152.74 0.66 248 179 233 52 149.08 0.14 249 179 234 53 146.50 0.04 250 180 215 33 162.12 4.03 251 180 227 45 153.94 0.32 252 180 228 46 153.52 0.35 253 180 229 47 152.82 0.70 254 180 230 48 152.68 0.68 255 181 199 20 154.39 0.10 256 181 210 27 154.08 0.07 257 181 211 28 154.24 0.12 258 181 227 44 153.88 0.34 259 181 228 45 153.46 0.38 260 181 229 46 152.74 0.66 261 181 230 47 152.53 0.68 262 182 225 41 153.94 0.31 263 182 226 42 153.90 0.32 264 182 227 43 152.71 0.66 265 183 225 40 153.94 0.30 266 183 226 41 153.88 0.33 267 183 228 43 153.52 0.29 268 184 188 5 278.34 2.49 269 185 222 34 157.19 1.51 270 185 223 35 154.38 0.14 271 185 225 37 154.28 0.13 272 186 222 33 157.19 1.51 273 187 221 30 160.31 3.02 274 187 221 31 160.24 2.98 275 187 222 32 157.21 1.53 276 188 221 29 160.46 3.06 277 188 221 28 161.08 3.31 278 189 221 27 193.61 10.67 279 189 226 33 153.24 0.81 280 190 228 34 152.99 0.85 281 199 228 25 153.28 0.83 282 209 231 22 113.45 0.55 283 210 230 20 152.72 1.07 284 210 231 21 134.91 9.44 285 210 232 22 106.08 1.03 286 211 228 17 153.09 0.90 287 211 229 18 153.03 0.88 288 211 231 20 113.77 1.30 289 212 228 16 153.03 0.88 290 212 229 17 152.31 1.16 291 212 231 19 114.03 1.17 292 213 228 15 152.67 1.00 293 214 227 13 153.07 0.85 294 214 228 14 152.91 0.88 295 214 229 15 152.31 1.16 296 215 226 11 153.71 0.55 297 215 227 12 153.03 0.83 298 217 224 7 191.64 2.94 299 221 224 3 270.79 5.19 300 231 235 4 263.01 4.67 301 231 238 7 48.46 0.22 302 232 235 3 81.36 0.21 303 234 237 3 62.63 5.23 304 234 238 4 60.55 6.26 305 235 238 3 59.52 5.66 306 235 239 4 59.43 5.71 307 236 239 3 70.20 0.97 308 236 240 4 48.42 0.24 309 237 240 3 58.58 4.84 310 237 241 4 46.34 0.56 311 238 241 3 50.91 10.23 312 238 242 4 31.20 0.37 313 239 242 3 62.85 4.26 314 239 243 4 31.70 0.01 315 240 243 3 33.24 0.77 316 240 244 4 31.70 0.01 317 241 244 3 50.11 9.20 318 241 245 4 30.75 0.14 319 242 245 3 59.68 4.41