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 38.31 2.90 2 16 140 119 38.19 2.84 3 16 142 121 38.80 3.23 4 16 143 122 44.41 3.08 5 16 144 123 46.56 3.04 6 16 156 135 40.66 3.38 7 16 157 136 40.79 3.33 8 16 158 137 42.84 3.85 9 16 189 170 45.09 2.73 10 16 190 171 37.91 2.79 11 16 194 175 38.05 2.85 12 17 143 121 51.62 5.33 13 17 144 122 51.38 5.45 14 17 145 123 53.29 4.53 15 17 146 124 59.18 1.58 16 17 188 167 52.21 5.05 17 17 188 168 51.66 5.30 18 17 189 169 45.93 2.73 19 17 191 171 46.52 2.79 20 17 220 195 47.31 3.06 21 17 221 196 47.17 3.00 22 18 188 166 52.68 5.28 23 18 188 167 51.75 5.28 24 19 157 133 57.72 2.76 25 19 158 134 51.88 5.35 26 20 137 112 82.69 0.78 27 20 156 131 93.86 1.05 28 20 157 132 77.25 0.29 29 20 158 133 189.12 5.36 30 20 159 134 266.17 0.33 31 21 154 128 147.39 3.87 32 21 155 129 147.05 4.05 33 21 156 130 135.97 9.58 34 22 26 4 165.10 0.03 35 22 27 5 150.53 5.78 36 22 139 112 137.58 0.70 37 22 155 128 162.62 0.39 38 22 156 129 196.20 1.91 39 23 26 3 186.51 3.81 40 24 71 44 147.62 1.95 41 25 69 41 146.17 1.07 42 25 70 42 154.81 0.39 43 25 79 51 158.39 1.80 44 25 117 89 141.81 0.38 45 27 30 3 176.98 2.48 46 27 137 105 140.61 0.18 47 27 139 107 148.71 0.08 48 27 157 125 287.25 0.18 49 28 116 85 158.41 1.88 50 28 117 86 158.18 1.90 51 28 118 87 157.14 1.55 52 28 119 88 151.67 0.38 53 29 45 14 150.81 0.78 54 29 46 15 150.11 0.89 55 29 119 87 157.15 1.56 56 29 120 88 153.12 0.18 57 29 121 89 148.02 0.14 58 29 137 103 158.30 1.96 59 29 198 166 157.99 1.98 60 29 200 168 157.88 2.04 61 30 43 11 158.56 1.85 62 30 44 12 158.32 1.95 63 30 139 104 158.40 1.93 64 30 140 105 158.52 1.88 65 30 141 106 160.08 1.46 66 30 155 120 172.59 0.13 67 30 198 165 158.17 1.89 68 31 43 10 159.27 1.52 69 31 44 11 158.36 1.95 70 31 45 12 158.36 1.96 71 31 46 13 158.46 1.91 72 31 52 19 158.36 1.95 73 31 65 32 160.06 1.45 74 31 66 33 160.05 1.45 75 31 67 34 159.58 1.59 76 31 141 105 160.09 1.46 77 32 40 6 160.62 1.27 78 32 42 8 160.08 1.47 79 32 43 9 159.50 1.46 80 32 65 31 160.13 1.44 81 32 66 32 160.13 1.44 82 32 73 38 160.55 1.31 83 32 141 104 160.09 1.46 84 33 40 5 160.66 1.27 85 33 41 6 160.59 1.25 86 33 42 7 160.10 1.47 87 33 43 8 160.09 1.46 88 33 52 17 160.09 1.45 89 33 54 19 160.08 1.45 90 33 58 23 160.55 1.25 91 33 63 28 160.55 1.25 92 33 64 29 160.53 1.26 93 33 65 30 160.16 1.44 94 33 106 70 160.15 1.44 95 34 39 3 164.99 0.90 96 34 40 4 160.66 1.27 97 34 41 5 161.25 0.96 98 34 63 27 160.63 1.24 99 34 64 28 160.55 1.25 100 34 66 30 160.53 1.26 101 37 41 4 170.22 3.38 102 37 60 23 164.71 0.77 103 37 62 25 161.26 0.96 104 45 121 75 223.62 2.42 105 46 120 73 259.18 6.70 106 46 121 74 244.69 2.12 107 47 121 73 259.16 2.40 108 47 123 75 214.56 2.12 109 47 238 186 65.75 0.01 110 47 242 190 41.44 4.88 111 48 242 189 45.74 2.73 112 51 242 186 41.12 5.04 113 51 245 189 32.59 6.98 114 71 153 80 158.71 1.88 115 71 154 81 158.07 1.95 116 71 155 82 157.12 1.54 117 72 153 79 158.69 1.89 118 72 154 80 158.51 1.86 119 73 153 78 159.12 1.68 120 74 153 77 159.13 1.68 121 87 245 154 33.49 6.63 122 89 237 144 79.16 0.50 123 89 241 148 58.04 1.80 124 89 245 152 35.57 7.59 125 91 234 139 109.78 2.06 126 91 237 142 81.40 0.62 127 92 237 141 96.73 0.49 128 98 180 80 203.58 19.46 129 99 180 79 165.85 0.62 130 100 177 75 165.74 0.66 131 100 179 77 165.80 0.64 132 100 180 78 165.77 0.65 133 101 179 76 165.71 0.63 134 101 234 129 114.33 2.35 135 102 229 123 157.98 1.42 136 103 229 122 157.99 1.42 137 103 234 127 99.45 0.86 138 103 237 130 74.21 0.91 139 103 238 131 67.82 0.30 140 105 237 128 74.06 0.85 141 105 238 129 63.66 0.91 142 105 241 132 54.62 2.54 143 105 242 133 41.26 5.12 144 107 245 134 32.59 6.98 145 122 209 83 280.67 2.71 146 123 204 81 240.74 5.99 147 123 209 82 203.59 3.56 148 123 231 104 220.70 28.89 149 123 235 108 74.37 0.88 150 123 238 111 66.03 0.08 151 123 239 112 62.84 1.45 152 124 204 80 190.32 0.89 153 124 209 81 178.15 0.33 154 124 210 82 170.81 1.24 155 124 232 104 111.79 3.75 156 124 235 107 79.52 0.70 157 127 210 80 159.87 1.14 158 128 210 79 156.27 0.83 159 129 134 4 166.62 0.22 160 129 162 32 138.01 0.61 161 129 210 78 159.44 1.23 162 130 134 3 180.70 0.33 163 130 162 31 138.25 0.70 164 132 162 30 138.22 0.71 165 132 163 31 138.74 0.80 166 132 164 32 138.85 0.82 167 133 161 28 138.64 0.77 168 133 162 29 138.72 0.80 169 134 161 27 138.88 0.83 170 134 162 28 138.90 0.83 171 135 160 25 138.88 0.83 172 135 161 26 138.88 0.83 173 136 159 23 138.80 0.84 174 136 160 24 138.90 0.83 175 136 162 26 144.30 1.62 176 137 157 20 138.18 0.73 177 137 158 21 138.71 0.80 178 137 159 22 138.74 0.81 179 138 157 19 137.03 0.96 180 138 158 20 138.19 0.72 181 138 160 22 140.37 0.27 182 138 183 45 160.16 1.36 183 138 228 88 159.58 1.26 184 139 155 16 138.92 0.83 185 139 156 17 138.68 0.90 186 139 157 18 137.09 0.95 187 140 155 15 139.05 0.91 188 140 156 16 138.64 0.88 189 141 151 10 159.38 1.50 190 141 152 11 158.34 1.94 191 141 153 12 158.25 1.93 192 141 154 13 153.81 0.39 193 141 155 14 139.91 0.47 194 142 151 9 159.40 1.50 195 142 152 10 159.38 1.50 196 143 148 5 160.53 1.29 197 143 149 6 160.09 1.46 198 143 150 7 159.52 1.49 199 143 151 8 159.40 1.50 200 143 191 50 206.06 4.49 201 144 150 6 160.08 1.46 202 144 152 8 159.46 1.49 203 144 156 12 139.81 0.41 204 145 148 3 165.12 0.23 205 145 149 4 160.48 1.29 206 145 150 5 160.34 1.36 207 146 220 71 158.95 1.46 208 146 221 72 159.03 1.50 209 152 156 4 163.74 1.04 210 158 188 32 138.69 0.79 211 158 189 33 138.21 0.71 212 159 184 26 139.08 0.90 213 160 184 24 138.56 0.87 214 160 184 25 139.08 0.90 215 161 183 22 173.81 0.32 216 161 184 23 138.87 0.83 217 161 184 24 140.36 0.27 218 162 181 19 234.62 1.74 219 162 182 20 196.50 11.57 220 162 183 21 177.62 2.21 221 162 201 41 147.99 0.21 222 163 182 19 217.13 1.27 223 163 183 20 177.84 2.24 224 163 184 21 177.83 2.23 225 163 185 23 177.61 2.21 226 163 225 60 152.58 0.08 227 167 185 19 245.23 6.79 228 171 223 50 159.68 1.31 229 171 224 51 159.68 1.31 230 171 225 52 159.66 1.31 231 172 215 41 164.49 0.30 232 172 216 42 163.99 0.07 233 172 217 43 163.53 0.14 234 172 224 50 159.69 1.31 235 172 225 51 159.69 1.30 236 172 227 53 159.50 1.37 237 175 215 38 165.55 0.72 238 176 215 37 165.55 0.71 239 176 227 49 159.69 1.30 240 178 230 50 159.31 1.43 241 178 233 53 157.27 1.67 242 179 229 48 159.34 1.44 243 179 230 49 159.31 1.43 244 179 233 52 155.15 1.39 245 179 234 53 150.75 0.18 246 180 215 33 165.62 0.68 247 180 227 45 159.67 1.31 248 180 228 46 159.53 1.33 249 180 230 48 159.27 1.42 250 181 199 20 159.93 1.29 251 181 210 27 159.62 1.38 252 181 211 28 159.68 1.35 253 181 227 44 159.58 1.32 254 181 228 45 159.34 1.42 255 181 229 46 159.33 1.43 256 181 230 47 159.13 1.48 257 182 225 41 159.66 1.31 258 182 226 42 159.59 1.32 259 182 227 43 159.29 1.43 260 182 228 44 159.31 1.42 261 183 225 40 159.66 1.29 262 183 226 41 159.62 1.30 263 183 228 43 159.47 1.34 264 184 188 5 257.73 9.45 265 185 222 34 160.31 1.28 266 185 223 35 159.79 1.19 267 185 225 37 159.65 1.25 268 186 222 33 162.83 0.03 269 187 221 30 163.65 0.14 270 187 221 31 163.41 0.26 271 187 222 32 160.31 1.28 272 188 221 29 163.70 0.14 273 188 221 28 164.60 0.30 274 189 221 27 183.59 9.17 275 189 226 33 159.53 1.28 276 190 228 34 158.90 0.98 277 199 228 25 159.60 1.27 278 209 231 22 122.42 1.50 279 210 229 19 159.62 1.27 280 210 230 20 156.95 0.89 281 210 231 21 120.67 0.62 282 210 232 22 111.68 1.02 283 211 228 17 159.59 1.27 284 211 229 18 158.82 1.01 285 211 231 20 113.09 0.49 286 212 228 16 159.43 1.30 287 212 229 17 157.71 1.28 288 212 231 19 116.89 2.40 289 213 228 15 158.19 1.32 290 214 227 13 159.62 1.27 291 214 228 14 159.47 1.29 292 214 229 15 158.77 0.97 293 215 226 11 159.71 1.30 294 215 227 12 159.62 1.28 295 216 226 10 159.66 1.29 296 216 227 11 159.62 1.28 297 217 224 7 179.00 0.44 298 221 224 3 286.07 0.43 299 231 235 4 286.63 0.68 300 231 238 7 67.47 0.48 301 232 235 3 81.97 0.43 302 234 237 3 74.03 0.99 303 234 238 4 71.30 0.96 304 235 238 3 69.08 0.15 305 235 239 4 67.48 0.64 306 236 239 3 71.31 0.95 307 236 240 4 66.27 0.04 308 237 240 3 66.88 0.50 309 237 241 4 62.58 1.31 310 238 241 3 59.38 0.16 311 238 242 4 42.69 5.51 312 239 242 3 55.03 0.65 313 239 243 4 50.68 0.57 314 240 243 3 64.59 0.71 315 240 244 4 41.45 5.18 316 241 244 3 53.78 1.28 317 241 245 4 40.90 5.14 318 242 245 3 33.80 6.37