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 46.83 0.55 2 16 140 119 47.40 0.26 3 16 142 121 47.41 0.26 4 16 143 122 52.00 0.09 5 16 144 123 54.06 0.95 6 16 156 135 50.59 0.27 7 16 157 136 49.73 0.70 8 16 158 137 50.59 0.27 9 16 189 170 51.06 0.07 10 16 190 171 46.61 0.66 11 16 194 175 46.63 0.64 12 17 143 121 54.72 1.22 13 17 144 122 54.18 0.95 14 17 145 123 55.23 1.17 15 17 146 124 65.11 1.71 16 17 188 167 54.95 1.28 17 17 188 168 54.81 1.22 18 17 189 169 53.87 1.05 19 17 191 171 54.10 0.96 20 17 220 195 54.83 1.23 21 17 221 196 54.95 1.28 22 18 188 166 56.04 1.06 23 18 188 167 54.95 1.28 24 19 157 133 63.69 2.60 25 19 158 134 55.02 1.24 26 20 137 112 82.56 0.33 27 20 156 131 87.36 0.40 28 20 157 132 72.17 0.86 29 20 158 133 120.66 23.38 30 20 159 134 238.28 2.54 31 21 71 47 139.68 1.06 32 21 154 128 145.99 2.11 33 21 155 129 151.94 0.79 34 21 156 130 137.34 6.44 35 22 26 4 167.09 0.28 36 22 27 5 158.15 0.32 37 22 71 46 139.96 0.93 38 22 155 128 167.66 0.72 39 22 156 129 205.58 2.75 40 23 26 3 172.53 2.43 41 24 71 44 144.31 0.37 42 25 28 3 178.63 1.07 43 25 69 41 144.17 0.30 44 25 79 51 149.90 1.15 45 25 117 89 141.26 0.28 46 27 30 3 178.12 0.97 47 27 137 105 142.56 0.03 48 27 139 107 143.00 0.16 49 27 157 125 278.13 3.24 50 28 116 85 149.88 1.12 51 28 117 86 149.84 1.13 52 28 118 87 149.24 0.99 53 28 119 88 145.75 0.00 54 29 44 13 149.54 0.98 55 29 45 14 145.18 0.28 56 29 46 15 144.62 0.57 57 29 119 87 149.24 0.99 58 29 120 88 145.75 0.00 59 29 121 89 144.21 0.36 60 29 137 103 149.88 1.15 61 29 198 166 148.66 0.57 62 29 200 168 149.09 1.17 63 30 43 11 149.91 1.14 64 30 44 12 149.88 1.14 65 30 139 104 149.91 1.15 66 30 140 105 150.01 1.17 67 30 141 106 152.09 0.73 68 30 155 120 173.72 2.87 69 30 198 165 149.85 1.14 70 31 43 10 149.99 1.15 71 31 44 11 149.90 1.14 72 31 45 12 149.91 1.14 73 31 46 13 149.91 1.14 74 31 52 19 149.91 1.14 75 31 65 32 152.24 0.78 76 31 65 33 152.21 0.78 77 31 66 34 151.79 0.70 78 31 141 105 152.22 0.80 79 32 40 6 153.12 1.05 80 32 42 8 152.25 0.82 81 32 43 9 151.99 0.72 82 32 64 30 152.74 0.95 83 32 65 31 152.34 0.83 84 32 65 32 152.24 0.79 85 32 73 38 152.57 0.79 86 32 141 104 152.21 0.78 87 33 40 5 153.18 1.08 88 33 41 6 153.09 1.09 89 33 42 7 152.28 0.83 90 33 43 8 152.28 0.83 91 33 52 17 152.34 0.83 92 33 54 19 152.30 0.83 93 33 58 23 152.71 1.02 94 33 63 28 152.75 0.99 95 33 64 29 152.74 0.95 96 33 65 30 152.44 0.88 97 33 104 68 152.70 1.01 98 33 106 70 152.65 0.98 99 34 39 3 171.05 0.83 100 34 40 4 153.85 1.42 101 34 41 5 153.19 1.08 102 34 63 27 152.81 0.96 103 34 64 28 152.75 0.95 104 34 65 30 152.81 0.91 105 37 41 4 163.82 0.07 106 37 60 23 161.97 0.27 107 40 73 32 285.81 0.56 108 45 121 75 221.77 1.17 109 46 120 73 284.19 0.57 110 46 121 74 252.03 1.54 111 47 121 73 274.94 3.04 112 47 123 75 200.33 2.12 113 47 238 186 65.11 0.27 114 47 242 190 32.24 1.02 115 48 242 189 32.24 1.02 116 51 242 186 30.70 0.25 117 51 245 189 22.07 0.42 118 71 153 80 150.24 1.18 119 71 154 81 150.00 1.19 120 71 155 82 148.46 1.34 121 72 153 79 150.12 1.19 122 72 154 80 150.02 1.19 123 73 153 78 150.13 1.18 124 74 153 77 150.15 1.18 125 89 237 144 78.93 0.10 126 89 241 148 44.74 7.21 127 89 245 152 23.73 0.39 128 90 237 143 80.38 0.82 129 91 234 139 105.90 0.19 130 91 237 142 80.38 0.82 131 92 237 141 95.54 2.16 132 98 180 80 151.56 0.84 133 99 180 79 151.53 0.83 134 100 177 75 149.56 1.11 135 100 179 77 149.83 1.14 136 100 180 78 150.40 1.40 137 101 179 76 149.60 1.14 138 101 234 129 108.10 0.51 139 102 229 123 150.32 1.36 140 103 229 122 150.81 1.03 141 103 234 127 103.40 1.44 142 103 237 130 77.42 0.76 143 103 238 131 69.84 1.15 144 105 237 128 75.84 1.05 145 105 238 129 65.12 0.29 146 105 241 132 42.98 6.38 147 105 242 133 30.73 0.27 148 107 245 134 22.03 0.45 149 122 209 83 285.33 0.73 150 123 209 82 190.88 1.41 151 123 231 104 135.10 1.26 152 123 235 108 76.77 0.32 153 123 238 111 66.86 0.16 154 123 239 112 65.10 0.27 155 124 204 80 178.18 1.82 156 124 209 81 175.35 3.23 157 124 210 82 164.20 0.50 158 124 231 103 172.59 0.24 159 124 232 104 105.16 0.83 160 124 235 107 78.23 0.41 161 125 204 79 181.11 3.45 162 127 210 80 158.68 2.20 163 128 210 79 151.46 0.90 164 129 134 4 164.20 0.51 165 129 162 32 139.61 1.07 166 129 210 78 152.04 0.82 167 130 134 3 179.85 0.98 168 130 162 31 139.67 1.05 169 132 162 30 139.66 1.04 170 132 163 31 139.73 1.06 171 132 164 32 139.91 0.97 172 133 162 29 139.75 1.04 173 134 161 27 139.73 1.05 174 134 162 28 139.75 1.05 175 135 159 24 139.66 1.06 176 135 160 25 139.73 1.05 177 135 161 26 139.74 1.05 178 136 158 22 139.65 1.07 179 136 159 23 139.65 1.07 180 136 160 24 139.71 1.04 181 136 162 26 142.93 0.14 182 137 157 20 139.59 1.07 183 137 158 21 139.65 1.07 184 138 157 19 139.58 1.08 185 138 158 20 139.60 1.07 186 138 160 22 142.48 0.01 187 138 183 45 152.15 0.71 188 138 228 88 152.33 0.93 189 139 155 16 142.37 0.05 190 139 156 17 139.65 1.07 191 139 157 18 139.52 1.05 192 140 155 15 142.03 0.07 193 140 156 16 139.72 1.07 194 141 151 10 149.91 1.17 195 141 152 11 149.81 1.18 196 141 153 12 149.56 1.16 197 141 154 13 145.75 0.70 198 141 155 14 141.74 0.10 199 142 152 10 149.88 1.15 200 142 194 54 281.24 1.40 201 143 148 5 157.47 0.18 202 143 149 6 151.79 0.59 203 143 150 7 151.43 0.69 204 143 191 50 196.85 5.83 205 143 192 51 283.56 0.21 206 144 150 6 151.74 0.61 207 144 152 8 150.42 1.25 208 144 156 12 140.03 0.94 209 145 148 3 183.60 1.64 210 145 149 4 156.34 0.81 211 145 150 5 152.01 0.70 212 146 220 71 151.38 0.73 213 146 221 72 151.38 0.74 214 152 156 4 165.43 0.03 215 158 188 32 140.00 0.95 216 158 189 33 139.71 1.08 217 158 190 34 139.71 1.08 218 159 184 26 164.74 0.12 219 160 183 23 166.21 0.12 220 160 184 24 164.66 0.09 221 160 184 25 164.66 0.10 222 161 183 22 169.06 1.30 223 161 184 23 165.09 0.29 224 161 184 24 164.96 0.23 225 162 181 19 275.90 2.23 226 162 182 20 208.50 2.37 227 162 183 21 180.66 1.77 228 162 201 41 142.93 0.15 229 163 182 19 267.81 1.22 230 163 183 20 195.38 0.20 231 163 184 21 191.89 1.91 232 163 185 23 184.27 0.03 233 163 225 60 145.06 1.10 234 167 185 19 283.65 1.67 235 171 223 50 151.87 0.74 236 171 225 52 151.75 0.77 237 172 216 42 151.73 0.59 238 172 217 43 151.78 0.62 239 172 224 50 151.84 0.76 240 172 225 51 151.81 0.75 241 172 227 53 151.33 0.82 242 176 227 49 151.66 0.78 243 178 230 50 151.55 0.81 244 178 233 53 149.84 1.13 245 179 229 48 151.58 0.82 246 179 230 49 151.34 0.82 247 179 233 52 147.44 1.93 248 179 234 53 148.51 1.40 249 180 227 45 151.70 0.80 250 180 228 46 151.63 0.79 251 180 230 48 150.93 0.94 252 181 227 44 151.69 0.80 253 181 228 45 151.59 0.77 254 181 230 47 150.04 1.14 255 182 225 41 151.77 0.79 256 182 226 42 151.69 0.80 257 182 227 43 151.41 0.82 258 183 199 18 151.97 0.65 259 183 226 41 151.69 0.80 260 183 228 43 151.63 0.80 261 184 188 5 268.88 6.90 262 185 222 34 152.24 0.77 263 185 223 35 152.14 0.74 264 185 225 37 151.91 0.69 265 186 222 33 152.24 0.76 266 187 221 30 152.59 0.83 267 187 221 31 152.39 0.76 268 187 222 32 152.28 0.74 269 188 221 29 152.62 0.83 270 188 221 28 152.65 0.83 271 189 221 27 152.65 0.85 272 189 226 33 152.10 0.80 273 190 228 34 152.08 0.81 274 199 228 25 152.10 0.81 275 209 231 22 115.98 0.46 276 210 230 20 151.89 0.90 277 210 231 21 117.19 0.01 278 210 232 22 109.01 0.83 279 211 228 17 152.06 0.82 280 211 229 18 151.91 0.89 281 211 231 20 110.85 0.04 282 212 228 16 151.81 0.85 283 212 229 17 151.44 0.91 284 212 231 19 112.23 0.64 285 213 228 15 151.77 0.83 286 214 227 13 152.07 0.82 287 214 228 14 151.83 0.80 288 214 229 15 151.77 0.83 289 215 226 11 152.12 0.80 290 215 227 12 152.09 0.81 291 216 226 10 152.11 0.81 292 216 227 11 152.10 0.80 293 217 224 7 171.84 6.39 294 221 224 3 276.69 0.06 295 231 235 4 284.43 0.55 296 231 238 7 69.60 0.99 297 232 235 3 83.36 0.65 298 234 237 3 71.34 0.46 299 234 238 4 69.89 1.14 300 235 238 3 74.36 0.81 301 235 239 4 71.23 0.18 302 236 239 3 71.53 0.33 303 236 240 4 66.92 0.13 304 237 240 3 65.12 0.29 305 237 241 4 64.12 0.38 306 238 241 3 61.61 0.77 307 238 242 4 32.26 1.02 308 239 242 3 36.52 3.15 309 239 243 4 32.25 1.02 310 240 243 3 36.70 3.06 311 240 244 4 30.76 0.28 312 241 244 3 30.69 0.25 313 241 245 4 30.22 0.25 314 242 245 3 26.12 2.44