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 44.36 0.36 2 16 140 119 44.93 0.07 3 16 142 121 43.98 0.18 4 16 143 122 47.95 0.40 5 16 144 123 49.16 0.02 6 16 156 135 46.16 0.48 7 16 157 136 46.41 0.57 8 16 158 137 47.01 0.88 9 16 189 170 48.57 0.07 10 16 190 171 42.45 0.83 11 16 194 175 42.57 0.88 12 17 143 121 52.97 1.56 13 17 144 122 52.97 1.56 14 17 145 123 57.38 2.48 15 17 146 124 57.38 2.48 16 17 188 167 57.40 2.48 17 17 188 168 53.06 1.52 18 17 189 169 49.09 0.05 19 17 191 171 49.31 0.01 20 17 220 195 51.58 0.41 21 17 221 196 51.61 0.40 22 18 188 166 57.42 2.47 23 18 188 167 57.37 2.49 24 19 157 133 61.25 4.41 25 19 158 134 57.36 2.49 26 20 137 112 83.34 0.46 27 20 156 131 88.80 1.49 28 20 157 132 78.79 0.46 29 20 158 133 188.58 1.13 30 20 159 134 266.11 0.36 31 21 154 128 136.81 0.02 32 21 155 129 135.79 0.35 33 21 156 130 111.28 1.74 34 22 26 4 164.42 0.32 35 22 27 5 148.51 6.63 36 22 139 112 136.69 0.08 37 22 155 128 165.63 1.12 38 22 156 129 201.21 1.42 39 23 26 3 221.03 19.45 40 24 71 44 139.74 0.31 41 25 69 41 144.68 1.81 42 25 79 51 159.57 1.33 43 25 117 89 139.71 0.28 44 27 30 3 174.93 0.18 45 27 137 105 140.26 0.01 46 27 139 107 149.80 0.62 47 27 157 125 287.16 0.23 48 28 116 85 159.52 1.31 49 28 117 86 159.39 1.28 50 28 118 87 155.56 0.77 51 28 119 88 151.52 0.30 52 29 45 14 150.88 0.62 53 29 46 15 150.12 0.90 54 29 119 87 156.59 1.78 55 29 120 88 151.56 0.28 56 29 121 89 148.44 0.06 57 29 137 103 159.53 1.29 58 29 198 166 159.38 1.29 59 29 200 168 159.19 1.40 60 30 43 11 160.77 0.76 61 30 44 12 159.59 1.33 62 30 139 104 159.59 1.32 63 30 140 105 160.33 1.02 64 30 141 106 161.58 0.77 65 30 155 120 165.73 0.81 66 30 198 165 159.43 1.30 67 31 43 10 160.84 0.73 68 31 44 11 159.62 1.33 69 31 45 12 159.61 1.32 70 31 46 13 159.62 1.33 71 31 52 19 159.62 1.32 72 31 65 32 161.64 0.81 73 31 66 33 161.53 0.83 74 31 67 34 161.38 0.82 75 31 141 105 161.66 0.76 76 32 40 6 161.82 0.75 77 32 42 8 161.63 0.76 78 32 43 9 161.33 0.74 79 32 65 31 161.69 0.79 80 32 66 32 161.69 0.79 81 32 70 35 161.68 0.79 82 32 73 38 161.80 0.76 83 32 141 104 161.66 0.76 84 33 40 5 161.88 0.74 85 33 41 6 161.83 0.76 86 33 42 7 161.66 0.77 87 33 43 8 161.65 0.77 88 33 54 19 161.62 0.75 89 33 58 23 161.72 0.79 90 33 63 28 161.79 0.77 91 33 64 29 161.76 0.76 92 33 65 30 161.71 0.78 93 33 106 70 161.67 0.78 94 34 39 3 164.31 0.47 95 34 40 4 161.88 0.74 96 34 41 5 161.88 0.74 97 34 63 27 161.81 0.77 98 34 64 28 161.78 0.76 99 34 66 30 161.78 0.75 100 37 41 4 164.61 0.57 101 37 60 23 161.91 0.75 102 37 62 25 161.90 0.76 103 45 121 75 220.72 0.35 104 46 120 73 256.78 7.90 105 46 121 74 237.22 2.60 106 47 120 72 283.91 0.87 107 47 121 73 256.86 2.80 108 47 123 75 214.46 2.17 109 47 238 186 62.90 1.42 110 48 242 189 36.14 2.08 111 51 242 186 31.14 0.41 112 51 245 189 19.53 0.45 113 71 153 80 159.93 1.31 114 71 154 81 159.56 1.34 115 71 155 82 158.97 1.60 116 72 153 79 159.91 1.32 117 72 154 80 159.81 1.28 118 73 153 78 160.96 0.80 119 74 153 77 160.97 0.80 120 87 245 154 23.73 2.54 121 89 237 144 81.48 0.67 122 89 241 148 56.23 2.71 123 89 245 152 20.41 0.01 124 91 234 139 104.83 0.42 125 91 237 142 81.41 0.62 126 92 237 141 96.73 0.49 127 98 180 80 201.04 17.93 128 99 180 79 161.02 0.55 129 100 177 75 160.15 0.33 130 100 179 77 160.31 0.27 131 100 180 78 160.88 0.55 132 101 179 76 160.25 0.28 133 101 234 129 118.72 2.40 134 102 229 123 157.75 1.54 135 103 229 122 157.74 1.54 136 103 234 127 99.45 0.86 137 103 237 130 75.25 1.43 138 103 238 131 67.84 0.34 139 105 237 128 74.28 1.92 140 105 238 129 62.78 1.35 141 105 241 132 54.62 2.54 142 105 242 133 31.12 0.40 143 107 245 134 18.11 0.27 144 122 209 83 282.80 2.73 145 123 204 81 241.44 0.48 146 123 209 82 206.08 1.51 147 123 231 104 149.52 6.40 148 123 235 108 75.30 0.42 149 123 238 111 65.25 0.25 150 123 239 112 62.84 1.45 151 124 204 80 196.65 2.71 152 124 209 81 183.64 0.49 153 124 210 82 168.58 0.12 154 124 232 104 104.56 0.21 155 124 235 107 79.53 0.70 156 127 210 80 160.12 1.03 157 128 210 79 155.54 1.20 158 129 134 4 166.61 0.22 159 129 162 32 136.17 0.15 160 129 210 78 159.72 1.08 161 130 134 3 180.75 0.35 162 130 162 31 136.88 0.01 163 132 162 30 136.84 0.03 164 132 163 31 137.04 0.07 165 132 164 32 137.08 0.07 166 133 161 28 136.97 0.04 167 133 162 29 137.05 0.07 168 134 161 27 137.05 0.07 169 134 162 28 137.09 0.08 170 135 160 25 137.06 0.07 171 135 161 26 137.08 0.08 172 136 159 23 136.94 0.03 173 136 160 24 137.02 0.05 174 136 162 26 142.10 0.90 175 137 157 20 136.75 0.06 176 137 158 21 136.89 0.06 177 137 159 22 136.95 0.03 178 138 157 19 135.09 0.40 179 138 158 20 136.71 0.09 180 138 160 22 139.38 0.38 181 138 183 45 162.12 0.61 182 138 228 88 159.56 0.96 183 139 155 16 137.23 0.06 184 139 156 17 137.05 0.09 185 139 157 18 136.67 0.09 186 140 155 15 137.23 0.07 187 140 156 16 137.05 0.09 188 141 151 10 161.13 0.77 189 141 152 11 159.59 1.32 190 141 153 12 159.49 1.31 191 141 154 13 153.81 0.40 192 141 155 14 138.78 0.68 193 142 151 9 161.18 0.76 194 142 152 10 161.13 0.77 195 142 192 52 287.16 1.31 196 142 194 54 285.85 1.80 197 143 148 5 161.77 0.76 198 143 149 6 161.44 0.76 199 143 150 7 161.35 0.79 200 143 151 8 161.24 0.79 201 143 152 9 161.25 0.79 202 143 191 50 203.97 1.19 203 143 192 51 286.95 1.22 204 144 150 6 161.49 0.78 205 144 152 8 161.36 0.76 206 144 156 12 137.25 0.14 207 145 148 3 165.84 1.03 208 145 149 4 161.66 0.81 209 145 150 5 161.53 0.79 210 146 220 71 160.94 0.67 211 146 221 72 160.85 0.72 212 146 221 73 160.85 0.72 213 151 192 43 161.20 0.76 214 151 193 44 161.21 0.77 215 152 156 4 168.97 0.85 216 158 188 32 137.13 0.11 217 158 189 33 136.91 0.14 218 159 184 26 137.43 0.14 219 160 184 24 136.99 0.10 220 160 184 25 137.33 0.18 221 161 183 22 157.44 10.11 222 161 184 23 157.48 10.08 223 161 184 24 162.46 7.58 224 162 181 19 252.78 14.54 225 162 182 20 185.48 1.44 226 162 183 21 157.53 10.14 227 162 201 41 148.72 0.32 228 163 182 19 203.39 7.52 229 163 183 20 179.62 1.46 230 163 184 21 179.34 1.31 231 163 185 23 174.25 1.79 232 163 225 60 155.03 0.98 233 167 185 19 244.25 9.75 234 171 223 50 161.08 0.74 235 171 224 51 161.08 0.74 236 171 225 52 161.08 0.74 237 172 215 41 162.66 0.44 238 172 216 42 162.58 0.41 239 172 217 43 162.54 0.40 240 172 224 50 161.09 0.74 241 172 225 51 161.09 0.74 242 172 227 53 160.84 0.67 243 175 215 38 162.68 0.43 244 176 215 37 162.67 0.43 245 176 227 49 161.03 0.72 246 178 230 50 160.16 1.02 247 178 233 53 156.97 1.81 248 179 229 48 160.16 1.06 249 179 230 49 159.62 1.28 250 179 233 52 155.32 1.30 251 179 234 53 150.81 0.78 252 180 215 33 162.57 0.41 253 180 227 45 160.97 0.79 254 180 228 46 160.55 0.87 255 180 230 48 159.62 1.28 256 181 199 20 161.65 0.71 257 181 210 27 161.32 0.70 258 181 211 28 161.32 0.70 259 181 227 44 160.64 0.86 260 181 228 45 160.15 1.06 261 181 229 46 159.91 1.15 262 181 230 47 159.58 1.29 263 182 225 41 161.00 0.73 264 182 226 42 160.87 0.75 265 182 227 43 159.76 1.22 266 182 228 44 159.75 1.21 267 183 225 40 161.06 0.75 268 183 226 41 160.84 0.78 269 183 228 43 160.10 1.03 270 184 225 39 160.95 0.81 271 184 188 5 257.73 9.44 272 185 222 34 162.09 0.58 273 185 223 35 161.69 0.77 274 185 225 37 161.06 0.77 275 186 222 33 162.09 0.58 276 187 221 30 162.25 0.62 277 187 221 31 162.22 0.60 278 187 222 32 162.17 0.62 279 188 221 29 162.52 0.68 280 188 221 28 178.06 8.43 281 189 221 27 178.06 8.43 282 189 226 33 159.42 1.24 283 190 228 34 157.96 1.56 284 199 228 25 159.87 1.15 285 209 231 22 122.35 1.53 286 210 230 20 157.30 1.32 287 210 231 21 122.36 1.53 288 210 232 22 105.05 0.39 289 211 228 17 159.89 1.14 290 211 229 18 157.80 1.52 291 211 231 20 114.13 1.01 292 212 228 16 159.13 1.07 293 212 229 17 157.68 1.53 294 212 231 19 114.43 2.31 295 213 228 15 157.80 1.51 296 214 227 13 159.90 1.13 297 214 228 14 157.97 1.59 298 214 229 15 157.75 1.50 299 215 226 11 160.62 0.90 300 215 227 12 159.89 1.16 301 216 227 11 159.59 1.28 302 217 224 7 178.83 8.08 303 221 224 3 284.52 0.29 304 231 235 4 287.16 0.04 305 231 238 7 66.81 0.07 306 232 235 3 87.67 2.23 307 234 237 3 71.34 0.94 308 234 238 4 67.70 0.12 309 235 238 3 68.75 0.16 310 235 239 4 67.09 0.66 311 236 239 3 68.75 0.16 312 236 240 4 66.22 0.23 313 237 240 3 67.19 0.35 314 237 241 4 62.70 1.38 315 238 241 3 64.89 2.24 316 238 242 4 50.09 0.27 317 239 242 3 59.46 4.95 318 239 243 4 40.77 4.39 319 240 243 3 59.46 4.95 320 240 244 4 41.42 4.07 321 241 244 3 39.52 3.42 322 241 245 4 30.16 0.12 323 242 245 3 27.45 1.53