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 16 139 118 54.90 3.93 2 16 140 119 55.41 4.19 3 16 142 121 54.96 4.26 4 16 143 122 58.66 3.02 5 16 144 123 59.69 2.75 6 16 156 135 55.62 4.08 7 16 157 136 55.59 4.11 8 16 158 137 55.59 4.11 9 16 189 170 58.05 2.88 10 16 190 171 42.87 1.78 11 16 194 175 42.87 1.78 12 17 143 121 59.72 2.74 13 17 144 122 59.72 2.74 14 17 145 123 61.38 2.46 15 17 146 124 62.16 2.76 16 17 188 167 60.34 2.68 17 17 188 168 59.91 2.69 18 17 189 169 59.42 2.65 19 17 191 171 59.64 2.70 20 17 220 195 60.09 2.81 21 17 221 196 60.29 2.70 22 18 158 135 60.21 2.70 23 18 188 166 61.44 2.48 24 18 188 167 60.28 2.70 25 19 157 133 61.55 3.31 26 19 158 134 60.09 2.76 27 20 137 112 84.16 1.52 28 20 156 131 88.71 1.44 29 20 157 132 77.91 0.60 30 20 158 133 188.72 1.06 31 20 159 134 279.29 5.01 32 21 154 128 147.17 5.01 33 21 155 129 147.72 5.60 34 21 156 130 138.63 9.21 35 22 26 4 167.98 1.47 36 22 27 5 148.48 6.00 37 22 139 112 136.76 0.06 38 22 155 128 161.90 0.04 39 22 156 129 196.76 1.63 40 23 26 3 171.72 1.11 41 24 71 44 146.12 1.23 42 25 69 41 146.19 1.05 43 25 70 42 155.42 2.16 44 25 79 51 155.86 2.12 45 25 117 89 140.88 0.83 46 27 30 3 171.92 2.95 47 27 137 105 139.94 0.35 48 27 139 107 150.77 1.57 49 28 116 85 155.34 1.88 50 28 117 86 155.16 1.79 51 28 118 87 153.19 1.26 52 28 119 88 150.00 1.15 53 29 45 14 151.52 1.60 54 29 46 15 146.78 1.02 55 29 119 87 153.60 1.17 56 29 120 88 150.11 0.91 57 29 121 89 147.85 2.03 58 29 137 103 155.84 2.09 59 29 198 166 154.50 1.47 60 29 200 168 154.88 1.66 61 30 43 11 156.08 2.02 62 30 44 12 155.90 2.12 63 30 139 104 156.02 2.06 64 30 140 105 157.53 1.33 65 30 141 106 160.15 0.77 66 30 155 120 173.07 0.35 67 30 198 165 155.44 1.93 68 31 43 10 158.88 1.18 69 31 44 11 155.95 2.10 70 31 45 12 155.96 2.10 71 31 46 13 155.96 2.08 72 31 52 19 155.93 2.10 73 31 65 32 160.28 0.78 74 31 66 33 160.19 0.77 75 31 67 34 159.27 0.86 76 31 141 105 160.28 0.83 77 32 40 6 160.53 0.80 78 32 42 8 160.27 0.82 79 32 43 9 159.66 0.92 80 32 65 31 160.43 0.77 81 32 66 32 160.29 0.82 82 32 73 38 160.31 0.84 83 32 141 104 160.25 0.81 84 33 40 5 160.64 0.78 85 33 41 6 160.52 0.81 86 33 42 7 160.35 0.82 87 33 43 8 160.28 0.83 88 33 52 17 160.34 0.82 89 33 54 19 160.30 0.82 90 33 58 23 160.47 0.77 91 33 63 28 160.59 0.78 92 33 64 29 160.58 0.78 93 33 65 30 160.44 0.78 94 33 106 70 160.35 0.82 95 34 39 3 161.00 0.90 96 34 40 4 160.65 0.78 97 34 41 5 160.66 0.77 98 34 63 27 160.60 0.78 99 34 64 28 160.60 0.78 100 34 66 30 160.56 0.79 101 37 41 4 169.45 1.83 102 37 60 23 162.34 0.04 103 37 62 25 162.10 0.07 104 45 121 75 217.83 1.10 105 46 120 73 242.59 3.13 106 46 121 74 230.87 1.44 107 47 120 72 283.05 0.43 108 47 121 73 252.19 0.88 109 47 123 75 215.17 2.42 110 47 238 186 59.51 2.75 111 47 242 190 32.59 0.47 112 48 242 189 37.02 1.63 113 51 242 186 32.32 0.59 114 51 245 189 19.54 0.45 115 69 118 49 286.44 1.60 116 71 153 80 157.96 1.18 117 71 154 81 155.81 2.12 118 71 155 82 155.46 2.15 119 72 153 79 156.34 1.97 120 72 154 80 156.08 2.03 121 73 153 78 158.02 1.21 122 74 153 77 158.24 1.25 123 87 245 154 22.14 1.75 124 89 237 144 79.33 0.59 125 89 241 148 54.80 2.63 126 89 245 152 20.41 0.01 127 91 234 139 109.65 1.99 128 91 237 142 81.41 0.62 129 92 237 141 94.56 0.59 130 98 180 80 205.34 18.51 131 99 180 79 163.87 1.03 132 100 177 75 163.28 1.28 133 100 179 77 163.82 1.03 134 100 180 78 163.83 1.02 135 101 179 76 163.75 1.06 136 101 234 129 118.72 2.40 137 102 229 123 157.16 0.18 138 103 229 122 157.16 0.18 139 103 234 127 98.83 1.18 140 103 237 130 75.25 1.44 141 103 238 131 60.81 3.18 142 105 237 128 75.23 1.44 143 105 238 129 59.85 2.69 144 105 241 132 54.62 2.54 145 105 242 133 32.34 0.60 146 107 245 134 19.54 0.45 147 122 204 82 286.59 1.42 148 122 209 83 279.29 3.41 149 123 204 81 251.67 5.59 150 123 209 82 204.58 0.47 151 123 231 104 281.76 3.03 152 123 235 108 74.38 0.88 153 123 238 111 60.28 2.72 154 123 239 112 59.40 2.81 155 124 204 80 187.78 0.58 156 124 209 81 177.13 0.19 157 124 210 82 170.81 1.24 158 124 232 104 188.69 42.27 159 124 235 107 79.53 0.70 160 127 210 80 159.04 0.38 161 128 210 79 155.33 1.14 162 129 134 4 166.13 0.01 163 129 162 32 136.38 0.12 164 129 210 78 158.58 0.28 165 130 134 3 180.75 0.35 166 130 162 31 137.01 0.07 167 132 162 30 137.02 0.07 168 132 163 31 137.18 0.01 169 132 164 32 137.21 0.00 170 133 161 28 137.06 0.07 171 133 162 29 137.18 0.01 172 134 161 27 137.24 0.03 173 134 162 28 137.28 0.01 174 135 160 25 137.24 0.02 175 135 161 26 137.26 0.01 176 136 159 23 137.05 0.07 177 136 160 24 137.22 0.03 178 136 162 26 144.57 1.35 179 137 157 20 136.85 0.01 180 137 158 21 137.03 0.07 181 137 159 22 137.09 0.04 182 138 157 19 135.25 0.60 183 138 158 20 137.02 0.06 184 138 160 22 138.25 0.35 185 138 183 45 160.54 0.82 186 138 228 88 158.96 0.40 187 139 155 16 137.53 0.06 188 139 156 17 137.15 0.01 189 139 157 18 136.81 0.01 190 140 155 15 137.53 0.06 191 140 156 16 137.16 0.00 192 141 151 10 158.58 1.34 193 141 152 11 155.91 2.09 194 141 153 12 155.47 1.91 195 141 154 13 151.56 1.94 196 141 155 14 137.52 0.06 197 142 151 9 158.96 1.16 198 142 152 10 158.53 1.35 199 143 148 5 160.92 0.58 200 143 149 6 160.27 0.81 201 143 150 7 159.86 0.83 202 143 151 8 158.99 1.17 203 143 191 50 207.93 3.55 204 143 192 51 285.31 2.17 205 144 150 6 160.28 0.81 206 144 152 8 159.00 1.16 207 144 156 12 137.94 0.40 208 145 148 3 164.56 1.67 209 145 149 4 160.40 0.84 210 145 150 5 160.38 0.84 211 146 220 71 158.33 1.44 212 146 221 72 158.33 1.44 213 151 192 43 159.03 1.15 214 151 193 44 158.97 1.17 215 152 156 4 169.86 1.29 216 158 188 32 137.38 0.12 217 158 189 33 136.96 0.07 218 158 190 34 136.94 0.07 219 159 184 26 137.56 0.10 220 160 184 24 137.15 0.00 221 160 184 25 137.51 0.09 222 161 183 22 169.56 1.47 223 161 184 23 151.71 7.04 224 161 184 24 152.37 6.71 225 162 181 19 217.22 5.18 226 162 182 20 191.81 4.68 227 162 183 21 169.77 1.40 228 162 201 41 148.81 0.80 229 163 182 19 213.26 3.21 230 163 183 20 175.24 0.96 231 163 184 21 174.74 0.71 232 163 185 23 170.03 1.53 233 163 225 60 150.74 1.67 234 167 185 19 272.20 6.70 235 171 223 50 159.66 0.73 236 171 224 51 159.45 0.84 237 171 225 52 159.46 0.84 238 172 215 41 162.09 0.06 239 172 216 42 161.21 0.22 240 172 217 43 161.16 0.24 241 172 224 50 159.69 0.75 242 172 225 51 159.69 0.74 243 172 227 53 159.47 0.72 244 175 215 38 162.19 0.14 245 176 215 37 163.34 0.72 246 176 227 49 159.62 0.73 247 178 230 50 159.10 0.50 248 178 233 53 153.90 1.15 249 179 229 48 159.16 0.52 250 179 230 49 158.84 0.58 251 179 233 52 152.53 0.70 252 179 234 53 151.75 0.32 253 180 215 33 163.49 0.81 254 180 227 45 159.50 0.65 255 180 228 46 159.12 0.49 256 180 230 48 158.72 0.59 257 181 199 20 160.24 0.87 258 181 210 27 160.03 0.85 259 181 211 28 160.03 0.85 260 181 227 44 159.13 0.48 261 181 228 45 158.91 0.57 262 181 229 46 158.84 0.58 263 181 230 47 158.34 0.57 264 182 225 41 159.54 0.67 265 182 226 42 159.38 0.61 266 182 227 43 158.81 0.60 267 182 228 44 158.84 0.58 268 183 225 40 159.64 0.71 269 183 226 41 159.39 0.61 270 183 228 43 158.87 0.57 271 184 188 5 280.13 2.38 272 185 222 34 160.38 0.90 273 185 223 35 160.19 0.86 274 185 225 37 159.94 0.79 275 186 222 33 161.12 0.57 276 187 221 30 162.09 0.10 277 187 221 31 162.05 0.12 278 187 222 32 160.60 0.83 279 188 221 29 162.10 0.11 280 188 221 28 162.47 0.01 281 189 221 27 174.08 5.78 282 189 226 33 158.68 0.24 283 190 228 34 158.55 0.29 284 199 228 25 158.84 0.36 285 209 231 22 137.72 9.21 286 210 229 19 159.07 0.42 287 210 230 20 156.42 0.75 288 210 231 21 122.36 1.53 289 210 232 22 110.50 0.43 290 211 228 17 158.85 0.35 291 211 229 18 158.36 0.22 292 211 231 20 112.81 0.35 293 212 228 16 158.55 0.32 294 212 229 17 157.20 0.20 295 212 231 19 116.90 2.40 296 213 228 15 157.62 0.15 297 214 227 13 159.06 0.44 298 214 228 14 158.46 0.24 299 214 229 15 158.39 0.22 300 215 226 11 159.19 0.44 301 215 227 12 159.13 0.44 302 216 226 10 159.16 0.45 303 216 227 11 159.13 0.43 304 217 224 7 176.77 2.08 305 221 224 3 286.79 0.76 306 231 235 4 286.63 0.68 307 231 238 7 60.54 3.31 308 232 235 3 82.46 0.73 309 234 237 3 73.22 1.40 310 234 238 4 70.34 1.44 311 235 238 3 71.14 1.03 312 235 239 4 59.85 3.03 313 236 239 3 71.14 1.03 314 236 240 4 59.84 3.04 315 237 240 3 62.84 2.52 316 237 241 4 59.03 2.97 317 238 241 3 67.14 4.67 318 238 242 4 42.86 3.35 319 239 242 3 63.59 2.89 320 239 243 4 33.51 0.89 321 240 243 3 69.61 5.91 322 240 244 4 33.51 0.89 323 241 244 3 40.08 3.14 324 241 245 4 30.84 0.26 325 242 245 3 35.37 5.49