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 59.48 1.25 2 16 140 119 59.53 1.27 3 16 142 121 59.56 1.26 4 16 143 122 63.14 2.15 5 16 144 123 63.80 2.06 6 16 156 135 60.88 1.20 7 16 157 136 60.34 0.93 8 16 158 137 60.34 0.93 9 16 189 170 60.49 0.85 10 16 190 171 58.89 0.95 11 16 194 175 58.90 0.96 12 17 143 121 64.67 1.64 13 17 144 122 64.75 1.59 14 17 145 123 65.31 1.33 15 17 146 124 65.42 1.31 16 17 188 167 68.46 0.22 17 17 188 168 65.29 1.32 18 17 189 169 63.73 2.01 19 17 191 171 63.68 1.96 20 17 220 195 65.31 1.34 21 17 221 196 65.31 1.34 22 18 158 135 68.44 0.23 23 18 188 166 68.53 0.18 24 18 188 167 65.31 1.32 25 19 157 133 65.59 1.38 26 19 158 134 65.41 1.29 27 20 137 112 85.34 1.57 28 20 156 131 86.81 0.14 29 20 157 132 73.16 1.51 30 20 158 133 185.66 1.21 31 20 159 134 277.77 0.77 32 21 154 128 137.77 0.12 33 21 155 129 137.25 0.12 34 21 156 130 112.72 1.34 35 22 26 4 165.02 1.06 36 22 27 5 150.22 6.36 37 22 139 112 137.44 0.02 38 22 155 128 165.38 0.01 39 22 156 129 201.39 3.01 40 23 26 3 176.43 1.35 41 24 71 44 140.25 1.01 42 25 28 3 170.15 1.88 43 25 69 41 142.73 0.16 44 25 117 89 139.64 0.80 45 27 30 3 196.22 12.31 46 27 137 105 139.69 0.77 47 27 139 107 148.62 1.77 48 28 116 85 160.03 0.22 49 28 117 86 159.91 0.28 50 28 118 87 156.64 0.46 51 28 119 88 150.39 0.57 52 29 45 14 148.29 1.61 53 29 46 15 145.21 0.29 54 29 119 87 157.66 0.40 55 29 120 88 150.34 0.55 56 29 121 89 147.18 0.71 57 29 137 103 160.15 0.24 58 29 198 166 159.83 0.11 59 29 200 168 160.06 0.23 60 30 43 11 160.22 0.24 61 30 44 12 160.09 0.23 62 30 139 104 160.18 0.23 63 30 140 105 160.28 0.24 64 30 141 106 161.08 0.18 65 30 155 120 171.76 2.21 66 30 198 165 160.05 0.21 67 31 43 10 160.78 0.23 68 31 44 11 160.14 0.20 69 31 45 12 160.16 0.23 70 31 46 13 160.13 0.24 71 31 52 19 160.10 0.21 72 31 65 32 161.05 0.15 73 31 66 33 161.03 0.14 74 31 67 34 160.51 0.17 75 31 141 105 161.10 0.19 76 32 40 6 161.43 0.20 77 32 42 8 161.13 0.20 78 32 43 9 160.93 0.19 79 32 65 31 161.10 0.17 80 32 66 32 161.08 0.17 81 32 73 38 161.27 0.14 82 32 141 104 161.10 0.20 83 33 40 5 161.47 0.21 84 33 41 6 161.46 0.22 85 33 42 7 161.15 0.20 86 33 43 8 161.12 0.18 87 33 54 19 161.14 0.20 88 33 58 23 161.43 0.20 89 33 63 28 161.56 0.12 90 33 64 29 161.50 0.12 91 33 65 30 161.22 0.21 92 33 104 68 161.31 0.17 93 33 106 70 161.18 0.20 94 34 39 3 169.78 3.88 95 34 40 4 161.47 0.21 96 34 41 5 161.48 0.21 97 34 63 27 161.56 0.12 98 34 64 28 161.53 0.12 99 34 66 30 161.43 0.14 100 37 41 4 167.63 0.36 101 37 60 23 178.54 3.36 102 37 62 25 164.25 1.32 103 40 73 32 286.32 0.29 104 45 121 75 215.21 1.14 105 46 120 73 247.47 4.80 106 46 121 74 236.17 0.76 107 47 121 73 259.95 0.89 108 47 123 75 200.87 3.73 109 47 238 186 55.65 5.11 110 47 242 190 30.29 0.48 111 48 242 189 30.37 0.45 112 51 242 186 30.29 0.48 113 51 245 189 22.82 0.51 114 71 153 80 160.24 0.27 115 71 154 81 159.88 0.27 116 71 155 82 157.27 0.14 117 72 153 79 160.16 0.24 118 72 154 80 160.13 0.24 119 73 153 78 160.19 0.26 120 74 153 77 160.24 0.24 121 87 245 154 23.91 0.03 122 89 237 144 78.55 2.02 123 89 241 148 31.57 0.45 124 89 245 152 23.80 0.02 125 91 234 139 118.35 6.34 126 91 237 142 79.37 1.69 127 92 237 141 102.23 0.79 128 98 180 80 190.60 9.23 129 99 180 79 183.30 11.41 130 100 177 75 163.59 1.77 131 100 179 77 163.83 1.68 132 100 180 78 163.81 1.67 133 101 179 76 163.69 1.61 134 101 234 129 122.66 0.25 135 102 229 123 158.59 0.95 136 103 229 122 158.12 0.71 137 103 234 127 104.06 1.58 138 103 237 130 73.53 0.57 139 103 238 131 56.41 5.44 140 105 237 128 69.79 0.91 141 105 238 129 55.70 5.08 142 105 241 132 31.96 1.15 143 105 242 133 30.28 0.48 144 107 245 134 22.30 0.78 145 122 209 83 267.82 4.30 146 123 204 81 250.69 4.79 147 123 209 82 198.49 1.48 148 123 231 104 133.69 0.62 149 123 235 108 71.48 0.39 150 123 238 111 56.27 5.37 151 124 204 80 190.31 2.60 152 124 209 81 183.21 6.15 153 124 210 82 167.68 0.03 154 124 232 104 111.05 2.50 155 124 235 107 74.36 0.36 156 127 210 80 161.26 0.17 157 128 210 79 156.07 1.34 158 129 134 4 166.37 1.08 159 129 162 32 137.76 0.14 160 129 201 73 154.08 1.34 161 129 210 78 158.71 0.83 162 130 134 3 182.81 1.02 163 130 162 31 138.03 0.18 164 132 162 30 138.06 0.18 165 132 163 31 138.24 0.10 166 132 164 32 138.26 0.11 167 133 161 28 138.19 0.12 168 133 162 29 138.25 0.12 169 134 161 27 138.27 0.12 170 134 162 28 138.31 0.13 171 135 159 24 138.22 0.11 172 135 160 25 138.25 0.12 173 135 161 26 138.28 0.12 174 136 159 23 138.10 0.17 175 136 160 24 138.22 0.14 176 136 162 26 140.87 1.29 177 137 157 20 137.96 0.14 178 137 158 21 138.10 0.16 179 137 159 22 138.21 0.14 180 138 157 19 135.74 0.89 181 138 158 20 137.73 0.13 182 138 160 22 138.37 0.14 183 138 228 88 158.94 0.95 184 139 155 16 138.32 0.12 185 139 156 17 138.17 0.12 186 139 157 18 137.43 0.01 187 140 155 15 138.31 0.12 188 140 156 16 138.21 0.10 189 141 151 10 160.69 0.13 190 141 152 11 160.18 0.22 191 141 153 12 160.12 0.21 192 141 154 13 150.80 0.80 193 141 155 14 138.31 0.12 194 142 151 9 160.92 0.23 195 142 152 10 160.56 0.12 196 143 148 5 161.42 0.26 197 143 149 6 161.10 0.21 198 143 150 7 160.99 0.21 199 143 151 8 160.88 0.20 200 143 191 50 203.12 2.87 201 144 150 6 161.07 0.19 202 144 152 8 160.89 0.21 203 144 156 12 138.31 0.13 204 145 148 3 163.51 1.30 205 145 150 5 161.13 0.21 206 146 220 71 160.73 0.21 207 146 221 72 160.72 0.22 208 146 221 73 160.69 0.22 209 151 192 43 160.94 0.23 210 152 156 4 164.72 0.39 211 158 184 27 138.31 0.14 212 158 188 32 138.31 0.14 213 158 189 33 138.13 0.10 214 158 190 34 137.94 0.00 215 159 184 26 138.43 0.14 216 160 184 24 138.28 0.13 217 160 184 25 138.33 0.14 218 161 183 22 138.30 0.14 219 161 184 23 138.33 0.14 220 161 184 24 139.71 0.76 221 162 181 19 243.72 12.40 222 162 182 20 179.56 20.75 223 162 183 21 138.31 0.13 224 162 201 41 145.36 0.93 225 163 182 19 217.08 2.00 226 163 183 20 173.12 1.51 227 163 184 21 164.18 5.99 228 163 185 23 159.22 0.66 229 163 225 60 149.25 0.31 230 171 223 50 160.70 0.24 231 171 224 51 160.69 0.24 232 171 225 52 160.67 0.25 233 172 215 41 163.23 1.39 234 172 216 42 162.99 1.34 235 172 217 43 162.53 1.24 236 172 224 50 160.72 0.24 237 172 225 51 160.72 0.23 238 172 227 53 160.50 0.16 239 175 215 38 163.50 1.40 240 176 215 37 163.62 1.47 241 176 227 49 160.62 0.18 242 178 230 50 160.31 0.26 243 178 233 53 158.12 0.74 244 179 229 48 160.34 0.26 245 179 230 49 160.20 0.32 246 179 233 52 152.89 0.70 247 179 234 53 151.99 1.16 248 180 215 33 163.75 1.54 249 180 227 45 160.59 0.24 250 180 228 46 160.26 0.33 251 180 230 48 159.72 0.55 252 181 199 20 160.99 0.21 253 181 210 27 160.87 0.20 254 181 211 28 160.88 0.20 255 181 227 44 160.35 0.26 256 181 228 45 160.22 0.32 257 181 229 46 160.21 0.32 258 181 230 47 158.77 0.86 259 182 225 41 160.60 0.27 260 182 226 42 160.37 0.25 261 182 227 43 160.21 0.32 262 183 225 40 160.71 0.24 263 183 226 41 160.58 0.26 264 183 228 43 160.22 0.32 265 184 225 39 160.74 0.24 266 184 188 5 286.39 0.44 267 185 222 34 161.23 0.35 268 185 223 35 161.00 0.24 269 185 225 37 160.88 0.23 270 186 222 33 161.25 0.35 271 187 221 30 163.02 1.03 272 187 221 31 162.94 1.02 273 187 222 32 162.10 0.78 274 188 221 29 163.05 1.03 275 188 221 28 167.72 0.14 276 189 221 27 235.41 1.47 277 189 226 33 158.90 0.92 278 189 228 35 158.95 0.95 279 190 228 34 158.31 0.80 280 199 228 25 158.97 0.94 281 209 231 22 116.77 0.65 282 210 231 21 122.80 1.94 283 210 232 22 109.79 0.35 284 211 228 17 158.97 0.94 285 211 229 18 158.16 0.73 286 211 231 20 112.66 1.80 287 212 228 16 158.69 0.91 288 212 229 17 158.00 0.69 289 212 231 19 113.61 1.33 290 213 228 15 158.31 0.80 291 214 227 13 159.75 0.55 292 214 228 14 158.59 0.95 293 214 229 15 158.27 0.82 294 215 226 11 160.39 0.41 295 215 227 12 160.19 0.44 296 217 224 7 189.62 2.50 297 221 224 3 282.45 4.05 298 231 238 7 69.23 1.09 299 232 235 3 81.57 0.51 300 234 237 3 71.32 0.39 301 234 238 4 69.42 1.02 302 235 238 3 69.75 1.18 303 235 239 4 69.25 1.10 304 236 239 3 71.92 0.24 305 236 240 4 69.17 1.15 306 237 240 3 55.43 5.70 307 237 241 4 53.86 5.90 308 238 241 3 37.98 1.75 309 238 242 4 30.50 0.39 310 239 242 3 53.02 7.39 311 239 243 4 30.50 0.39 312 240 243 3 30.50 0.39 313 240 244 4 30.50 0.39 314 241 244 3 30.46 0.36 315 241 245 4 30.39 0.34 316 242 245 3 50.34 10.30