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 58.93 1.35 2 16 140 119 58.83 1.30 3 16 142 121 59.25 1.36 4 16 143 122 62.91 2.04 5 16 144 123 63.56 2.07 6 16 156 135 60.31 1.90 7 16 157 136 59.36 1.43 8 16 158 137 59.34 1.43 9 16 189 170 60.44 0.98 10 16 190 171 58.75 1.33 11 16 194 175 58.79 1.31 12 17 143 121 63.88 1.96 13 17 144 122 63.79 2.00 14 17 145 123 65.25 1.45 15 17 146 124 65.27 1.45 16 17 188 167 65.36 1.40 17 17 188 168 65.17 1.41 18 17 189 169 63.10 2.21 19 17 191 171 63.58 2.01 20 17 220 195 65.12 1.50 21 17 221 196 65.20 1.46 22 18 158 135 65.43 1.30 23 18 188 166 68.55 0.18 24 18 188 167 65.34 1.39 25 19 157 133 65.92 1.55 26 19 158 134 65.41 1.29 27 20 137 112 83.48 0.05 28 20 156 131 129.99 13.72 29 20 157 132 74.70 0.70 30 20 158 133 137.66 30.62 31 20 159 134 277.77 0.77 32 21 154 128 147.31 5.05 33 21 155 129 147.04 5.21 34 21 156 130 138.75 9.34 35 22 26 4 165.80 0.79 36 22 27 5 162.78 0.27 37 22 139 112 137.51 0.21 38 22 155 128 163.68 0.14 39 22 156 129 196.30 1.12 40 23 26 3 174.03 1.03 41 24 71 44 139.87 0.74 42 25 28 3 172.22 1.59 43 25 69 41 141.85 0.28 44 25 79 51 156.48 1.06 45 25 117 89 141.73 0.84 46 27 30 3 175.97 0.10 47 27 137 105 140.64 0.30 48 27 139 107 145.19 0.06 49 28 116 85 155.70 0.50 50 28 117 86 155.43 0.43 51 28 118 87 153.46 0.46 52 28 119 88 151.53 0.20 53 29 45 14 149.55 0.44 54 29 46 15 147.12 0.77 55 29 119 87 153.50 0.45 56 29 120 88 150.31 0.80 57 29 121 89 147.15 0.74 58 29 137 103 155.87 0.56 59 29 198 166 155.50 0.46 60 29 200 168 155.75 0.54 61 30 43 11 156.67 0.95 62 30 44 12 156.65 0.95 63 30 139 104 156.31 0.76 64 30 140 105 156.94 0.76 65 30 141 106 157.84 0.47 66 30 155 120 207.39 17.30 67 30 198 165 155.70 0.51 68 31 43 10 157.13 0.77 69 31 44 11 156.66 0.95 70 31 45 12 156.72 0.97 71 31 46 13 156.72 0.98 72 31 52 19 156.71 0.96 73 31 65 32 159.50 0.76 74 31 66 33 159.49 0.76 75 31 67 34 158.25 1.14 76 31 141 105 158.27 0.29 77 32 40 6 159.75 0.77 78 32 42 8 158.72 0.34 79 32 65 31 159.73 0.82 80 32 66 32 159.62 0.82 81 32 70 35 159.88 0.95 82 32 73 38 160.06 0.93 83 32 141 104 158.25 0.38 84 33 40 5 159.78 0.77 85 33 41 6 159.60 0.70 86 33 42 7 158.72 0.33 87 33 43 8 158.69 0.33 88 33 52 17 159.22 0.59 89 33 54 19 158.70 0.33 90 33 58 23 159.60 0.70 91 33 63 28 160.05 0.93 92 33 64 29 159.98 0.90 93 33 65 30 159.73 0.82 94 33 104 68 159.38 0.59 95 33 106 70 159.67 0.79 96 34 39 3 172.71 0.52 97 34 40 4 160.09 0.91 98 34 41 5 159.84 0.78 99 34 63 27 160.06 0.93 100 34 64 28 160.00 0.91 101 34 66 30 159.99 0.91 102 37 41 4 172.81 0.47 103 37 60 23 173.78 0.98 104 37 62 25 164.47 1.21 105 45 121 75 214.67 0.06 106 46 120 73 246.23 0.69 107 46 121 74 236.26 0.80 108 47 121 73 250.84 2.77 109 47 123 75 204.82 1.73 110 47 238 186 56.88 4.85 111 47 242 190 30.29 0.48 112 48 242 189 30.49 0.39 113 51 242 186 30.29 0.48 114 51 245 189 22.71 0.45 115 71 153 80 157.50 1.28 116 71 154 81 156.81 1.28 117 71 155 82 156.48 1.44 118 72 153 79 157.47 1.27 119 72 154 80 157.16 1.21 120 73 153 78 157.51 1.28 121 74 153 77 157.57 1.25 122 87 245 154 24.82 0.54 123 89 237 144 74.58 0.04 124 89 241 148 31.57 0.45 125 89 245 152 23.80 0.02 126 91 234 139 106.44 0.39 127 91 237 142 81.98 2.99 128 92 237 141 103.09 1.62 129 98 180 80 251.22 2.06 130 99 180 79 201.55 21.50 131 100 177 75 166.77 4.57 132 100 179 77 167.26 4.40 133 100 180 78 167.26 4.38 134 101 179 76 167.25 4.39 135 101 234 129 111.55 2.12 136 102 229 123 154.68 0.01 137 103 229 122 154.65 0.01 138 103 234 127 103.48 1.40 139 103 237 130 73.53 0.57 140 103 238 131 57.32 4.86 141 105 237 128 71.14 0.24 142 105 238 129 56.69 4.99 143 105 241 132 32.47 0.90 144 105 242 133 30.27 0.48 145 107 245 134 21.93 0.96 146 122 204 82 279.96 0.73 147 122 209 83 267.73 5.38 148 123 204 81 239.07 1.02 149 123 209 82 201.34 0.07 150 123 231 104 183.41 14.05 151 123 235 108 73.64 0.69 152 123 238 111 57.55 4.87 153 123 239 112 56.89 4.87 154 124 204 80 190.31 2.60 155 124 209 81 183.53 3.33 156 124 210 82 162.56 1.72 157 124 232 104 138.22 10.53 158 124 235 107 81.59 0.52 159 127 210 80 156.02 0.34 160 128 210 79 153.13 0.02 161 129 134 4 163.83 0.48 162 129 162 32 137.06 0.20 163 129 210 78 154.99 0.04 164 130 134 3 180.83 1.64 165 130 162 31 137.91 0.18 166 132 162 30 137.93 0.18 167 132 163 31 137.95 0.18 168 132 164 32 137.98 0.18 169 133 161 28 137.91 0.18 170 133 162 29 138.00 0.15 171 134 161 27 137.97 0.18 172 134 162 28 138.06 0.17 173 135 160 25 137.97 0.18 174 135 161 26 138.03 0.16 175 136 159 23 137.93 0.18 176 136 160 24 137.98 0.18 177 136 162 26 142.37 0.54 178 137 157 20 137.46 0.00 179 137 158 21 137.88 0.19 180 137 159 22 137.93 0.18 181 138 157 19 137.50 0.22 182 138 158 20 137.62 0.17 183 138 160 22 138.16 0.12 184 138 228 88 155.02 0.14 185 139 155 16 138.05 0.17 186 139 156 17 137.84 0.16 187 139 157 18 137.51 0.21 188 140 155 15 138.06 0.16 189 140 156 16 137.82 0.18 190 141 151 10 157.03 0.68 191 141 152 11 156.09 0.65 192 141 153 12 156.03 0.67 193 141 154 13 154.43 0.93 194 141 155 14 138.06 0.16 195 142 151 9 157.25 0.59 196 142 152 10 156.99 0.69 197 143 148 5 158.68 0.29 198 143 149 6 157.88 0.59 199 143 150 7 157.65 0.48 200 143 151 8 157.38 0.53 201 143 191 50 194.21 3.04 202 143 192 51 283.04 2.69 203 144 150 6 157.96 0.44 204 144 152 8 157.41 0.54 205 144 156 12 138.10 0.12 206 145 148 3 167.53 1.67 207 145 149 4 158.63 0.29 208 145 150 5 158.44 0.32 209 146 220 71 156.72 0.34 210 146 221 72 156.69 0.35 211 146 221 73 156.68 0.35 212 151 192 43 157.34 0.51 213 152 156 4 164.70 0.39 214 158 184 27 150.41 6.01 215 158 188 32 137.84 0.22 216 158 189 33 137.68 0.18 217 158 190 34 137.66 0.18 218 159 184 26 150.46 6.03 219 160 184 24 150.34 6.05 220 160 184 25 150.43 6.01 221 161 183 22 151.09 6.41 222 161 184 23 150.83 6.23 223 161 184 24 151.40 5.71 224 162 181 19 226.56 2.88 225 162 182 20 168.33 15.01 226 162 183 21 151.10 6.40 227 162 201 41 148.71 0.87 228 163 182 19 218.38 1.21 229 163 183 20 159.60 10.60 230 163 184 21 162.93 7.13 231 163 185 23 159.40 2.29 232 163 225 60 150.40 0.89 233 171 223 50 156.80 0.42 234 171 224 51 156.74 0.40 235 171 225 52 156.69 0.39 236 172 215 41 167.12 4.24 237 172 216 42 158.85 0.57 238 172 217 43 157.91 0.07 239 172 224 50 156.81 0.42 240 172 225 51 156.81 0.42 241 172 227 53 156.30 0.53 242 175 215 38 167.16 4.22 243 176 215 37 167.17 4.22 244 176 227 49 156.74 0.41 245 178 230 50 155.97 0.36 246 178 233 53 154.53 0.06 247 179 229 48 156.01 0.35 248 179 230 49 155.81 0.38 249 179 233 52 152.27 0.40 250 179 234 53 146.83 1.43 251 180 215 33 167.20 4.24 252 180 227 45 156.59 0.34 253 180 228 46 156.01 0.35 254 180 230 48 155.48 0.21 255 181 199 20 158.25 0.51 256 181 210 27 157.25 0.73 257 181 211 28 157.25 0.73 258 181 227 44 156.56 0.33 259 181 228 45 156.00 0.35 260 181 229 46 155.96 0.36 261 181 230 47 155.17 0.10 262 182 225 41 156.69 0.38 263 182 226 42 156.56 0.33 264 182 227 43 155.95 0.36 265 183 225 40 156.84 0.44 266 183 226 41 156.61 0.35 267 183 228 43 156.37 0.26 268 184 188 5 258.94 6.73 269 185 222 34 157.50 0.59 270 185 223 35 157.38 0.59 271 185 225 37 157.30 0.59 272 186 222 33 157.80 0.49 273 187 221 30 167.02 4.07 274 187 221 31 160.97 1.06 275 187 222 32 157.79 0.49 276 188 221 29 172.43 1.36 277 188 221 28 177.35 0.98 278 189 221 27 202.95 12.24 279 189 226 33 154.72 0.01 280 190 228 34 154.90 0.07 281 199 228 25 155.05 0.14 282 209 231 22 118.24 1.39 283 210 230 20 154.03 0.30 284 210 231 21 122.97 1.54 285 210 232 22 109.14 0.89 286 211 228 17 154.94 0.06 287 211 229 18 154.90 0.07 288 211 231 20 118.98 0.78 289 212 228 16 154.90 0.08 290 212 229 17 154.05 0.29 291 212 231 19 116.03 0.12 292 213 228 15 154.68 0.01 293 214 227 13 155.83 0.28 294 214 228 14 154.71 0.03 295 214 229 15 154.69 0.03 296 215 226 11 156.10 0.29 297 215 227 12 155.81 0.27 298 217 224 7 229.78 15.92 299 231 235 4 286.12 2.93 300 231 238 7 57.61 4.89 301 232 235 3 81.61 0.51 302 234 237 3 71.37 0.39 303 234 238 4 69.48 0.99 304 235 238 3 69.42 1.02 305 235 239 4 69.25 1.10 306 236 239 3 71.92 0.23 307 236 240 4 69.25 1.10 308 237 240 3 56.87 5.07 309 237 241 4 56.17 5.16 310 238 241 3 34.16 0.06 311 238 242 4 30.62 0.45 312 239 242 3 49.10 9.36 313 239 243 4 30.62 0.46 314 240 243 3 30.88 0.58 315 240 244 4 30.62 0.46 316 241 244 3 50.50 10.22 317 241 245 4 29.64 0.04 318 242 245 3 23.75 1.27