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 47.98 7.86 2 16 140 119 47.95 7.83 3 16 142 121 47.93 7.83 4 16 143 122 51.86 6.42 5 16 144 123 53.11 6.03 6 16 156 135 48.48 7.80 7 16 157 136 48.22 7.87 8 16 158 137 48.79 7.58 9 16 189 170 50.98 6.37 10 16 190 171 47.55 7.65 11 16 194 175 47.55 7.65 12 17 143 121 53.16 6.01 13 17 144 122 53.16 6.01 14 17 145 123 53.27 6.01 15 17 146 124 54.70 5.30 16 17 188 167 53.27 6.01 17 17 188 168 53.21 5.99 18 17 189 169 52.77 5.85 19 17 191 171 52.93 5.90 20 17 220 195 53.19 6.00 21 17 221 196 53.26 6.01 22 18 158 135 53.78 5.75 23 18 188 166 53.70 5.80 24 18 188 167 53.23 6.00 25 19 157 133 53.81 5.87 26 19 158 134 53.26 6.01 27 20 137 112 82.00 1.12 28 20 156 131 97.14 0.23 29 20 157 132 74.36 1.74 30 20 158 133 131.65 26.91 31 21 154 128 138.05 0.66 32 21 155 129 137.85 0.75 33 21 156 130 110.55 1.26 34 22 26 4 150.87 5.46 35 22 27 5 146.89 7.44 36 22 139 112 137.63 0.66 37 22 155 128 159.90 1.06 38 22 156 129 196.76 1.63 39 23 26 3 172.38 0.34 40 24 71 44 142.29 0.89 41 25 28 3 170.47 2.56 42 25 69 41 146.19 1.05 43 25 70 42 149.85 0.60 44 25 117 89 139.74 0.31 45 27 30 3 217.77 25.16 46 27 137 105 140.44 0.10 47 27 139 107 150.38 0.40 48 28 116 85 156.31 0.83 49 28 117 86 156.06 0.95 50 28 118 87 154.57 1.10 51 28 119 88 148.49 0.09 52 29 45 14 149.12 0.23 53 29 46 15 145.97 1.17 54 29 119 87 154.13 0.89 55 29 120 88 150.08 0.88 56 29 121 89 142.81 0.45 57 29 137 103 156.66 1.27 58 29 198 166 156.49 1.23 59 29 200 168 155.41 0.69 60 30 43 11 157.42 0.91 61 30 44 12 156.71 1.16 62 30 139 104 156.88 1.18 63 30 140 105 157.68 1.28 64 30 141 106 159.27 0.96 65 30 155 120 215.58 21.61 66 30 198 165 156.49 1.23 67 31 43 10 158.17 1.02 68 31 44 11 156.82 1.20 69 31 45 12 156.82 1.20 70 31 46 13 157.03 1.11 71 31 52 19 156.82 1.20 72 31 65 32 159.36 0.99 73 31 66 33 159.35 0.99 74 31 67 34 159.29 0.96 75 31 141 105 159.31 0.97 76 32 40 6 159.88 1.05 77 32 42 8 159.34 0.99 78 32 65 31 159.59 0.91 79 32 66 32 159.47 0.94 80 32 73 38 159.81 0.88 81 32 141 104 159.31 0.97 82 33 40 5 160.00 0.99 83 33 41 6 159.81 1.08 84 33 42 7 159.37 0.99 85 33 43 8 159.35 0.99 86 33 52 17 159.38 1.02 87 33 54 19 159.35 1.00 88 33 58 23 159.94 1.01 89 33 63 28 159.99 0.99 90 33 64 29 159.98 0.99 91 33 65 30 159.72 0.97 92 33 106 70 159.56 1.05 93 34 39 3 161.48 1.08 94 34 40 4 160.00 0.99 95 34 41 5 160.04 0.97 96 34 63 27 160.00 1.00 97 34 64 28 160.00 1.00 98 34 66 30 159.98 0.98 99 37 41 4 168.74 1.38 100 37 60 23 161.57 1.16 101 37 62 25 160.60 0.76 102 45 121 75 215.18 0.77 103 46 120 73 234.41 0.96 104 46 121 74 229.72 0.95 105 47 120 72 268.35 2.10 106 47 121 73 237.17 2.52 107 47 123 75 201.36 4.49 108 47 238 186 60.32 2.57 109 47 242 190 41.13 5.19 110 48 120 71 286.76 0.34 111 48 242 189 45.90 2.81 112 51 242 186 41.13 5.19 113 51 245 189 34.77 7.92 114 67 118 50 286.41 1.49 115 69 117 48 287.44 0.94 116 69 118 49 286.00 1.64 117 71 153 80 159.03 0.99 118 71 154 81 157.30 0.77 119 71 155 82 154.81 0.39 120 72 153 79 158.98 0.97 121 72 154 80 158.74 1.08 122 73 153 78 158.97 0.97 123 74 153 77 158.97 0.97 124 81 118 37 287.41 0.95 125 87 245 154 39.74 5.43 126 89 237 144 82.22 1.03 127 89 241 148 55.59 3.03 128 89 245 152 35.91 7.75 129 91 234 139 109.79 2.06 130 91 237 142 81.75 0.51 131 92 237 141 96.01 0.13 132 98 180 80 223.70 13.01 133 99 180 79 159.81 2.19 134 100 177 75 158.34 2.90 135 100 179 77 159.71 2.23 136 100 180 78 159.78 2.19 137 101 179 76 159.54 2.31 138 101 234 129 130.68 3.53 139 102 229 123 156.50 0.68 140 103 229 122 156.94 0.89 141 103 234 127 99.23 1.33 142 103 237 130 76.50 0.81 143 103 238 131 70.94 0.23 144 104 237 129 76.36 0.88 145 105 237 128 75.98 1.06 146 105 238 129 60.71 3.12 147 105 241 132 45.24 7.23 148 105 242 133 41.37 5.30 149 107 245 134 32.63 6.99 150 121 209 84 287.44 0.57 151 122 204 82 286.46 1.49 152 122 209 83 274.26 5.52 153 123 204 81 241.99 0.75 154 123 209 82 197.59 0.79 155 123 231 104 283.75 3.00 156 123 235 108 75.30 0.42 157 123 238 111 62.69 3.31 158 123 239 112 59.70 2.88 159 124 204 80 196.83 1.22 160 124 209 81 183.60 0.52 161 124 210 82 172.27 0.51 162 124 232 104 282.70 3.52 163 124 235 107 78.53 1.20 164 125 204 79 205.49 2.65 165 127 210 80 162.83 1.97 166 128 210 79 156.47 0.73 167 129 134 4 172.36 1.74 168 129 162 32 137.74 0.64 169 129 210 78 157.21 0.98 170 130 134 3 183.96 2.43 171 130 162 31 138.56 0.70 172 132 162 30 138.56 0.71 173 132 163 31 138.58 0.70 174 132 164 32 138.63 0.71 175 133 161 28 138.57 0.71 176 133 162 29 138.61 0.72 177 134 161 27 138.61 0.72 178 134 162 28 138.65 0.71 179 135 159 24 138.61 0.72 180 135 160 25 138.62 0.72 181 135 161 26 138.63 0.72 182 136 159 23 138.59 0.72 183 136 160 24 138.63 0.72 184 136 162 26 140.31 0.03 185 137 157 20 137.62 0.56 186 137 158 21 138.28 0.83 187 138 157 19 133.62 0.21 188 138 158 20 137.75 0.60 189 138 160 22 138.78 0.76 190 138 183 45 159.50 1.06 191 138 228 88 157.78 0.77 192 139 155 16 138.67 0.74 193 139 156 17 138.26 0.69 194 139 157 18 137.41 0.77 195 140 155 15 138.66 0.74 196 140 156 16 138.33 0.68 197 141 151 10 158.71 1.09 198 141 152 11 157.28 1.40 199 141 153 12 156.55 1.22 200 141 154 13 148.44 0.07 201 141 155 14 138.59 0.73 202 142 151 9 158.78 1.11 203 142 152 10 158.68 1.07 204 142 192 52 285.59 1.59 205 143 148 5 159.66 1.06 206 143 149 6 159.31 0.96 207 143 150 7 158.93 1.14 208 143 151 8 158.80 1.11 209 143 152 9 158.80 1.11 210 143 191 50 199.11 1.25 211 143 192 51 276.17 2.77 212 144 150 6 159.31 0.97 213 144 152 8 158.94 1.14 214 144 156 12 138.54 0.74 215 145 148 3 162.60 1.49 216 145 149 4 159.53 1.01 217 145 150 5 159.45 1.03 218 146 220 71 158.26 1.33 219 146 221 72 158.59 1.16 220 146 221 73 158.23 1.33 221 151 192 43 158.84 1.10 222 152 156 4 163.74 1.04 223 158 188 32 138.55 0.74 224 158 189 33 137.78 0.61 225 159 184 26 152.14 5.94 226 160 184 24 151.13 5.59 227 160 184 25 151.20 5.56 228 161 183 22 165.98 0.03 229 161 184 23 152.57 6.25 230 161 184 24 152.55 6.12 231 162 181 19 242.02 14.28 232 162 182 20 198.49 4.55 233 162 183 21 166.00 0.01 234 162 201 41 149.01 0.70 235 163 182 19 210.41 4.62 236 163 183 20 173.22 3.43 237 163 184 21 173.22 3.43 238 163 185 23 165.98 0.05 239 163 225 60 153.19 1.45 240 167 185 19 236.12 2.23 241 171 223 50 158.72 1.05 242 171 224 51 158.67 1.01 243 171 225 52 158.66 1.02 244 172 215 41 159.50 1.28 245 172 216 42 159.22 1.18 246 172 217 43 159.27 1.16 247 172 224 50 158.76 1.04 248 172 225 51 158.76 1.04 249 172 227 53 157.94 0.84 250 175 215 38 159.67 1.41 251 176 215 37 160.09 1.61 252 176 227 49 158.65 1.07 253 178 230 50 157.86 0.79 254 178 233 53 155.62 1.14 255 179 229 48 158.28 0.95 256 179 230 49 157.75 0.73 257 179 233 52 152.81 0.50 258 179 234 53 151.50 0.14 259 180 215 33 160.47 1.80 260 180 227 45 158.66 1.08 261 180 228 46 158.31 0.93 262 180 230 48 157.30 0.95 263 181 199 20 159.15 0.98 264 181 210 27 158.91 1.02 265 181 211 28 158.78 1.09 266 181 227 44 158.62 1.05 267 181 228 45 157.81 0.75 268 181 229 46 157.77 0.77 269 181 230 47 157.25 0.96 270 182 225 41 158.71 1.03 271 182 226 42 158.62 1.05 272 182 227 43 157.90 0.80 273 183 225 40 158.75 1.04 274 183 226 41 158.68 1.03 275 183 228 43 158.41 1.10 276 184 188 5 257.73 9.44 277 185 222 34 159.28 1.02 278 185 223 35 159.10 1.08 279 185 225 37 158.94 0.99 280 186 222 33 159.40 1.03 281 187 221 30 159.70 1.06 282 187 221 31 159.68 1.06 283 187 222 32 159.45 0.98 284 188 221 29 159.80 1.05 285 188 221 28 169.21 5.65 286 189 221 27 187.69 3.60 287 189 226 33 157.18 1.06 288 189 228 35 157.19 1.05 289 190 228 34 156.78 0.81 290 199 228 25 157.78 0.77 291 209 231 22 120.50 0.59 292 210 229 19 158.65 0.98 293 210 230 20 156.53 0.69 294 210 231 21 123.47 0.96 295 210 232 22 110.02 1.95 296 211 228 17 157.78 0.77 297 211 229 18 157.30 0.92 298 211 231 20 114.13 1.01 299 212 228 16 157.27 0.96 300 212 229 17 156.54 0.70 301 212 231 19 114.13 1.01 302 213 228 15 156.59 0.70 303 214 227 13 157.94 0.72 304 214 228 14 157.32 0.94 305 214 229 15 157.12 1.01 306 215 226 11 158.88 0.95 307 215 227 12 157.83 0.68 308 216 227 11 158.08 0.58 309 217 224 7 181.31 4.36 310 221 224 3 286.26 1.54 311 231 238 7 70.40 0.52 312 232 235 3 81.96 0.43 313 234 237 3 74.34 0.84 314 234 238 4 72.91 0.20 315 235 238 3 72.95 0.19 316 235 239 4 72.92 0.20 317 236 239 3 72.94 0.19 318 236 240 4 67.81 0.80 319 237 240 3 59.55 3.01 320 237 241 4 59.30 3.08 321 238 241 3 59.85 1.02 322 238 242 4 43.23 5.78 323 239 242 3 56.93 0.43 324 239 243 4 51.63 1.04 325 240 243 3 52.18 1.31 326 240 244 4 41.37 5.30 327 241 244 3 46.54 3.12 328 241 245 4 40.87 5.32 329 242 245 3 41.93 5.51