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 54.16 4.23 2 16 140 119 53.73 4.04 3 16 142 121 54.80 4.55 4 16 143 122 60.42 3.90 5 16 144 123 61.07 3.71 6 16 156 135 55.88 4.29 7 16 157 136 54.82 4.55 8 16 158 137 54.80 4.55 9 16 189 170 59.92 3.51 10 16 190 171 53.72 4.04 11 16 194 175 53.72 4.04 12 17 143 121 61.15 3.69 13 17 144 122 61.14 3.69 14 17 145 123 62.28 3.33 15 17 146 124 62.37 3.37 16 17 188 167 62.30 3.33 17 17 188 168 62.08 3.22 18 17 189 169 60.55 3.80 19 17 191 171 61.02 3.69 20 17 220 195 62.20 3.31 21 17 221 196 62.23 3.30 22 18 158 135 67.16 1.67 23 18 188 166 62.30 3.33 24 18 188 167 62.09 3.23 25 19 157 133 67.50 1.49 26 19 158 134 67.16 1.67 27 20 137 112 85.50 0.82 28 20 156 131 86.73 2.81 29 20 157 132 78.29 0.21 30 20 158 133 184.72 2.85 31 20 159 134 269.04 3.45 32 21 154 128 139.25 0.92 33 21 155 129 138.89 0.88 34 21 156 130 156.53 0.99 35 22 26 4 161.97 0.68 36 22 27 5 149.13 4.75 37 22 139 112 138.91 0.88 38 22 155 128 161.79 1.21 39 22 156 129 204.12 0.86 40 23 26 3 232.75 27.46 41 24 71 44 139.88 0.59 42 25 28 3 174.15 4.00 43 25 69 41 139.69 0.69 44 25 117 89 139.98 0.55 45 27 30 3 177.32 2.35 46 27 137 105 140.40 0.62 47 27 139 107 147.38 0.09 48 27 157 125 285.73 1.12 49 28 116 85 154.36 0.97 50 28 117 86 153.81 0.77 51 28 118 87 151.11 0.36 52 28 119 88 146.22 0.06 53 29 45 14 143.94 1.08 54 29 46 15 140.60 0.67 55 29 119 87 151.53 0.43 56 29 120 88 143.42 0.52 57 29 121 89 140.81 0.57 58 29 137 103 154.51 0.98 59 29 198 166 153.72 1.31 60 29 200 168 153.50 1.42 61 30 43 11 154.56 0.98 62 30 44 12 154.52 0.99 63 30 139 104 154.56 0.98 64 30 140 105 154.62 0.95 65 30 141 106 155.66 0.97 66 30 155 120 171.72 0.45 67 30 198 165 154.31 1.02 68 31 43 10 154.60 0.97 69 31 44 11 154.56 0.98 70 31 45 12 154.56 0.98 71 31 46 13 154.53 0.97 72 31 52 19 154.56 0.98 73 31 65 32 155.59 0.98 74 31 66 33 155.47 0.96 75 31 67 34 154.62 0.95 76 31 141 105 155.69 0.98 77 32 40 6 156.22 0.96 78 32 42 8 155.64 0.96 79 32 65 31 156.03 0.86 80 32 66 32 155.65 0.97 81 32 73 38 156.27 0.89 82 32 141 104 155.69 0.99 83 33 40 5 156.36 0.92 84 33 41 6 156.16 0.97 85 33 42 7 155.68 0.97 86 33 43 8 155.66 0.96 87 33 52 17 155.69 0.95 88 33 54 19 155.65 0.96 89 33 58 23 155.84 1.02 90 33 63 28 156.34 0.91 91 33 64 29 156.32 0.90 92 33 65 30 156.14 0.92 93 33 106 70 155.85 1.01 94 34 39 3 168.01 2.45 95 34 40 4 156.36 0.92 96 34 41 5 156.88 1.19 97 34 63 27 156.34 0.91 98 34 64 28 156.33 0.90 99 34 66 30 156.29 0.88 100 37 41 4 162.02 0.20 101 37 60 23 171.06 1.05 102 37 62 25 163.99 1.16 103 45 121 75 221.62 1.25 104 46 120 73 252.30 2.15 105 46 121 74 246.74 0.64 106 47 120 72 283.27 1.02 107 47 121 73 257.86 3.40 108 47 123 75 205.62 3.37 109 47 238 186 59.35 1.55 110 47 242 190 35.21 1.92 111 48 120 71 286.73 0.41 112 48 242 189 35.80 2.22 113 51 242 186 35.20 1.93 114 51 245 189 19.16 0.27 115 53 238 180 59.31 1.56 116 67 118 50 287.72 0.93 117 71 153 80 154.55 0.93 118 71 154 81 154.04 1.02 119 71 155 82 144.55 0.24 120 72 153 79 154.54 0.93 121 72 154 80 154.38 0.92 122 73 153 78 154.58 0.93 123 74 153 77 154.66 0.91 124 81 118 37 287.97 0.96 125 87 245 154 20.27 2.12 126 89 237 144 76.51 0.81 127 89 241 148 50.80 0.64 128 89 245 152 20.79 1.86 129 91 234 139 102.98 0.47 130 91 237 142 77.25 0.46 131 92 237 141 92.54 1.04 132 98 180 80 219.77 24.18 133 99 180 79 162.65 4.36 134 100 177 75 155.52 0.82 135 100 179 77 155.56 0.85 136 100 180 78 155.61 0.86 137 101 179 76 155.12 1.01 138 101 234 129 110.03 0.16 139 102 229 123 154.16 0.04 140 103 229 122 154.00 0.04 141 103 234 127 93.95 0.67 142 103 237 130 75.53 0.32 143 103 238 131 63.65 3.70 144 105 237 128 73.36 1.00 145 105 238 129 59.29 1.57 146 105 241 132 36.30 2.46 147 107 245 134 16.74 0.89 148 121 209 84 285.46 1.50 149 122 204 82 279.57 1.45 150 122 209 83 259.79 5.49 151 123 204 81 253.56 8.60 152 123 209 82 207.73 4.09 153 123 231 104 159.41 2.71 154 123 235 108 75.53 0.32 155 123 238 111 62.84 3.29 156 123 239 112 59.36 1.55 157 124 204 80 189.87 1.49 158 124 209 81 178.42 0.32 159 124 210 82 170.65 0.92 160 124 232 104 105.42 0.67 161 124 235 107 76.85 0.27 162 127 210 80 164.69 0.40 163 128 210 79 154.05 0.08 164 129 134 4 167.62 0.41 165 129 162 32 139.09 0.80 166 129 210 78 156.94 0.34 167 130 134 3 178.77 0.14 168 130 162 31 139.31 0.89 169 132 162 30 139.31 0.90 170 132 163 31 139.44 0.83 171 132 164 32 139.52 0.81 172 133 161 28 139.31 0.89 173 133 162 29 139.56 0.79 174 134 161 27 139.59 0.77 175 134 162 28 139.63 0.75 176 135 160 25 139.60 0.77 177 135 161 26 139.62 0.76 178 136 159 23 139.33 0.89 179 136 160 24 139.59 0.77 180 136 162 26 140.75 0.53 181 137 157 20 138.81 0.83 182 137 158 21 139.30 0.90 183 137 159 22 139.35 0.89 184 138 157 19 138.81 0.93 185 138 158 20 138.91 0.88 186 138 160 22 139.72 0.72 187 138 183 45 156.40 1.11 188 138 228 88 156.35 0.73 189 139 155 16 139.72 0.72 190 139 156 17 139.31 0.90 191 139 157 18 138.91 0.88 192 140 155 15 139.69 0.71 193 140 156 16 139.50 0.80 194 141 152 11 154.56 0.96 195 141 153 12 154.51 0.98 196 141 154 13 148.94 0.67 197 141 155 14 139.71 0.70 198 142 151 9 155.06 0.83 199 142 152 10 154.69 1.01 200 143 148 5 158.13 1.88 201 143 149 6 155.73 0.94 202 143 150 7 155.65 0.94 203 143 151 8 154.88 0.94 204 143 191 50 217.46 3.31 205 143 192 51 283.18 3.30 206 144 150 6 155.73 0.94 207 144 152 8 155.10 0.81 208 144 156 12 139.71 0.73 209 145 148 3 173.84 3.12 210 145 149 4 155.94 0.89 211 145 150 5 155.87 0.92 212 146 220 71 155.79 0.91 213 146 221 72 155.81 0.90 214 146 221 73 155.86 0.87 215 152 156 4 159.91 1.59 216 158 184 27 139.62 0.74 217 158 188 32 139.40 0.85 218 158 189 33 139.22 0.78 219 159 184 26 148.74 5.25 220 160 184 24 148.41 5.17 221 160 184 25 148.53 5.19 222 161 183 22 176.81 4.67 223 161 184 23 165.91 0.64 224 161 184 24 165.09 1.00 225 162 181 19 259.66 13.71 226 162 182 20 214.09 13.88 227 162 183 21 176.88 4.70 228 162 201 41 146.40 0.16 229 163 182 19 249.75 8.76 230 163 183 20 214.06 13.89 231 163 184 21 214.08 13.88 232 163 185 23 179.79 3.23 233 163 225 60 147.18 0.23 234 171 223 50 155.95 0.88 235 171 225 52 155.89 0.90 236 172 215 41 157.01 1.38 237 172 216 42 156.85 1.29 238 172 217 43 156.85 1.29 239 172 224 50 155.99 0.89 240 172 225 51 155.99 0.89 241 172 227 53 155.25 0.77 242 175 215 38 157.11 1.42 243 176 215 37 157.11 1.42 244 176 227 49 155.93 0.89 245 178 230 50 155.56 0.85 246 178 233 53 153.06 0.39 247 179 229 48 155.59 0.84 248 179 230 49 154.63 0.88 249 179 233 52 151.49 0.57 250 179 234 53 149.31 0.95 251 180 215 33 157.00 1.37 252 180 227 45 155.90 0.91 253 180 228 46 155.68 0.91 254 180 230 48 153.96 0.56 255 181 199 20 156.00 0.92 256 181 210 27 155.72 0.94 257 181 211 28 155.74 0.93 258 181 227 44 155.80 0.92 259 181 228 45 155.48 0.82 260 181 229 46 155.03 0.69 261 181 230 47 153.28 0.39 262 182 225 41 155.91 0.90 263 182 226 42 155.83 0.90 264 182 227 43 155.07 0.68 265 183 225 40 155.91 0.91 266 183 226 41 155.86 0.91 267 183 228 43 155.41 0.85 268 184 188 5 264.62 5.83 269 185 222 34 156.90 1.06 270 185 223 35 156.15 0.94 271 185 225 37 156.05 0.89 272 186 222 33 156.90 1.06 273 187 221 30 157.09 1.04 274 187 221 31 156.97 1.07 275 187 222 32 156.94 1.05 276 188 221 29 160.58 2.77 277 188 221 28 170.22 2.05 278 189 221 27 186.23 5.05 279 189 226 33 154.12 0.09 280 190 228 34 154.10 0.09 281 199 228 25 156.35 0.76 282 209 231 22 116.88 1.11 283 210 229 19 156.38 0.76 284 210 230 20 155.86 0.70 285 210 231 21 134.66 9.77 286 210 232 22 105.47 0.65 287 211 228 17 156.34 0.75 288 211 229 18 156.21 0.71 289 211 231 20 112.31 0.21 290 212 228 16 156.03 0.80 291 212 229 17 154.00 0.10 292 212 231 19 112.30 0.21 293 213 228 15 154.09 0.07 294 214 227 13 156.32 0.76 295 214 228 14 154.35 0.05 296 214 229 15 154.24 0.01 297 215 226 11 157.67 0.09 298 215 227 12 156.15 0.66 299 216 227 11 154.56 0.14 300 217 224 7 176.86 2.55 301 221 224 3 285.53 1.02 302 231 235 4 286.35 0.74 303 231 238 7 62.84 3.29 304 232 235 3 120.00 18.05 305 234 237 3 75.53 0.32 306 234 238 4 63.66 3.69 307 235 238 3 62.97 3.35 308 235 239 4 62.88 3.31 309 236 239 3 62.98 3.35 310 236 240 4 62.85 3.33 311 237 240 3 59.29 1.58 312 237 241 4 59.01 1.72 313 238 241 3 49.15 3.47 314 238 242 4 35.39 2.01 315 239 242 3 56.97 8.45 316 239 243 4 35.38 2.00 317 240 243 3 36.12 2.38 318 240 244 4 35.38 2.00 319 241 244 3 35.66 2.15 320 241 245 4 32.37 1.66 321 242 245 3 56.71 8.38