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 43.33 0.04 2 16 140 119 43.54 0.14 3 16 142 121 43.41 0.01 4 16 143 122 53.15 0.42 5 16 144 123 54.63 0.46 6 16 156 135 48.24 1.12 7 16 157 136 44.95 0.33 8 16 158 137 46.48 1.11 9 16 189 170 53.11 0.29 10 16 190 171 43.29 0.06 11 16 194 175 43.29 0.06 12 17 143 121 54.65 0.46 13 17 144 122 54.65 0.46 14 17 145 123 55.23 0.48 15 17 146 124 55.63 0.35 16 17 188 167 56.52 0.02 17 17 188 168 55.33 0.40 18 17 189 169 53.86 0.30 19 17 191 171 54.62 0.47 20 17 220 195 54.91 0.58 21 17 221 196 54.91 0.59 22 18 158 135 56.35 0.05 23 18 188 166 56.59 0.02 24 18 188 167 55.34 0.40 25 19 157 133 57.56 0.76 26 19 158 134 55.69 0.21 27 20 137 112 82.45 0.68 28 20 156 131 124.89 17.02 29 20 157 132 71.05 1.43 30 20 158 133 198.30 6.57 31 20 159 134 264.58 7.79 32 21 154 128 159.46 0.14 33 21 155 129 159.50 0.12 34 21 156 130 136.19 11.46 35 22 26 4 166.27 1.95 36 22 27 5 160.12 0.06 37 22 139 112 135.36 0.89 38 22 155 128 164.86 1.69 39 22 156 129 197.29 2.27 40 23 26 3 174.40 0.83 41 24 71 44 141.93 0.93 42 25 28 3 173.45 1.30 43 25 69 41 140.18 0.39 44 25 79 51 156.50 0.49 45 25 117 89 137.96 0.11 46 27 30 3 199.76 9.78 47 27 137 105 137.88 0.15 48 27 139 107 148.97 0.08 49 27 157 125 288.00 0.70 50 28 116 85 156.22 0.63 51 28 117 86 155.91 0.79 52 28 118 87 155.16 0.95 53 28 119 88 153.41 1.04 54 29 45 14 148.22 0.20 55 29 46 15 146.58 0.62 56 29 119 87 155.50 0.79 57 29 120 88 153.66 0.88 58 29 121 89 146.41 0.71 59 29 137 103 156.46 0.43 60 29 198 166 156.12 0.47 61 29 200 168 156.12 0.45 62 30 43 11 157.12 0.22 63 30 44 12 156.53 0.46 64 30 139 104 156.74 0.55 65 30 140 105 157.53 0.33 66 30 141 106 159.38 0.18 67 30 155 120 261.07 0.42 68 30 198 165 156.41 0.46 69 31 43 10 158.12 0.18 70 31 44 11 156.60 0.48 71 31 45 12 156.74 0.55 72 31 46 13 156.72 0.55 73 31 52 19 156.61 0.48 74 31 65 32 159.48 0.17 75 31 65 33 159.48 0.17 76 31 66 34 158.58 0.59 77 31 141 105 159.43 0.18 78 32 40 6 159.79 0.10 79 32 42 8 159.48 0.17 80 32 65 31 159.53 0.14 81 32 65 32 159.51 0.15 82 32 73 38 159.66 0.12 83 32 141 104 159.43 0.18 84 33 40 5 159.85 0.08 85 33 41 6 159.78 0.10 86 33 42 7 159.49 0.17 87 33 43 8 159.49 0.17 88 33 54 19 159.49 0.14 89 33 58 23 159.80 0.09 90 33 63 28 159.80 0.10 91 33 64 29 159.79 0.10 92 33 65 30 159.56 0.15 93 33 104 68 159.66 0.07 94 33 106 70 159.51 0.14 95 34 39 3 166.05 3.00 96 34 40 4 159.85 0.08 97 34 41 5 159.85 0.08 98 34 63 27 159.82 0.09 99 34 64 28 159.81 0.10 100 34 65 30 159.81 0.09 101 37 41 4 170.12 0.96 102 37 60 23 167.16 2.34 103 37 62 25 169.31 4.79 104 45 121 75 209.04 0.95 105 46 120 73 240.21 2.08 106 46 121 74 236.95 2.69 107 47 120 72 283.61 0.85 108 47 121 73 240.31 2.02 109 47 123 75 200.18 2.97 110 47 238 186 68.53 0.32 111 47 242 190 32.39 0.03 112 48 120 71 287.31 0.07 113 48 242 189 32.38 0.03 114 51 242 186 32.36 0.02 115 51 245 189 20.98 0.04 116 53 238 180 68.53 0.32 117 69 118 49 286.96 0.12 118 71 153 80 157.18 0.51 119 71 154 81 156.22 0.48 120 71 155 82 155.31 0.35 121 72 153 79 157.13 0.49 122 72 154 80 157.00 0.54 123 73 153 78 157.19 0.50 124 74 153 77 157.54 0.36 125 79 117 38 287.81 0.10 126 87 245 154 22.75 0.93 127 89 237 144 77.28 1.70 128 89 241 148 63.45 2.58 129 89 245 152 21.40 0.21 130 91 234 139 114.67 4.26 131 91 237 142 82.44 0.86 132 92 237 141 100.10 0.46 133 98 180 80 259.05 1.72 134 99 180 79 213.80 20.89 135 100 177 75 164.68 3.48 136 100 179 77 165.67 3.10 137 100 180 78 165.68 3.11 138 101 179 76 164.60 3.59 139 101 234 129 117.13 3.03 140 102 229 123 155.90 0.98 141 103 229 122 155.71 1.02 142 103 234 127 100.70 0.58 143 103 237 130 73.17 0.01 144 103 238 131 71.03 0.68 145 105 237 128 71.98 0.35 146 105 238 129 69.11 0.10 147 105 241 132 32.75 0.15 148 105 242 133 32.36 0.02 149 107 245 134 18.69 0.29 150 121 209 84 287.76 0.12 151 122 204 82 287.31 0.07 152 122 209 83 273.29 5.03 153 123 204 81 228.31 1.46 154 123 209 82 191.28 0.21 155 123 235 108 72.51 0.07 156 123 238 111 69.64 0.16 157 123 239 112 69.05 0.06 158 124 204 80 186.34 0.55 159 124 209 81 168.58 2.55 160 124 210 82 164.75 2.66 161 124 232 104 277.53 5.18 162 124 235 107 78.67 1.16 163 127 210 80 158.69 1.32 164 128 210 79 155.64 1.08 165 129 134 4 162.88 1.31 166 129 162 32 135.84 0.60 167 129 210 78 156.09 0.92 168 130 134 3 180.69 1.34 169 130 162 31 137.19 0.23 170 132 162 30 137.43 0.11 171 132 163 31 137.57 0.12 172 132 164 32 137.59 0.12 173 133 161 28 137.55 0.12 174 133 162 29 137.59 0.13 175 134 161 27 137.59 0.13 176 134 162 28 137.63 0.12 177 135 160 25 137.59 0.13 178 135 161 26 137.62 0.12 179 136 159 23 137.41 0.22 180 136 160 24 137.56 0.15 181 136 162 26 138.88 0.31 182 137 157 20 137.04 0.34 183 137 158 21 137.28 0.26 184 137 159 22 137.56 0.14 185 138 157 19 133.96 0.21 186 138 158 20 136.94 0.10 187 138 160 22 137.69 0.10 188 138 228 88 156.52 1.02 189 139 155 16 137.65 0.11 190 139 156 17 137.55 0.15 191 139 157 18 135.36 0.89 192 140 155 15 137.65 0.10 193 140 156 16 137.55 0.15 194 141 151 10 158.59 0.43 195 141 152 11 156.86 0.61 196 141 153 12 156.85 0.62 197 141 154 13 149.47 0.84 198 141 155 14 137.66 0.10 199 142 151 9 158.66 0.45 200 142 152 10 158.59 0.42 201 143 148 5 159.59 0.15 202 143 149 6 158.78 0.41 203 143 150 7 158.73 0.42 204 143 151 8 158.68 0.44 205 143 191 50 206.62 7.88 206 144 150 6 158.80 0.40 207 144 152 8 158.72 0.42 208 144 156 12 137.66 0.10 209 145 148 3 165.13 0.79 210 145 150 5 159.12 0.30 211 146 220 71 158.44 0.27 212 146 221 72 158.66 0.38 213 146 221 73 158.41 0.26 214 151 192 43 158.72 0.42 215 152 156 4 165.24 2.72 216 158 184 27 137.66 0.12 217 158 188 32 137.62 0.10 218 158 189 33 137.47 0.11 219 159 184 26 137.66 0.12 220 160 184 24 137.59 0.12 221 160 184 25 137.66 0.12 222 161 183 22 148.88 5.74 223 161 184 23 137.66 0.12 224 161 184 24 139.16 0.49 225 162 181 19 230.41 14.12 226 162 182 20 178.72 1.82 227 162 183 21 168.52 3.17 228 162 201 41 149.05 2.26 229 163 182 19 220.47 19.05 230 163 183 20 178.72 1.82 231 163 184 21 178.72 1.82 232 163 185 23 176.56 0.86 233 163 225 60 152.38 0.57 234 171 223 50 159.30 0.12 235 171 224 51 159.12 0.10 236 171 225 52 159.09 0.11 237 172 215 41 165.40 2.64 238 172 216 42 163.42 1.72 239 172 217 43 163.41 1.72 240 172 224 50 159.32 0.11 241 172 225 51 159.31 0.11 242 172 227 53 158.99 0.07 243 175 215 38 165.56 2.72 244 176 215 37 165.63 2.77 245 176 227 49 159.24 0.07 246 178 230 50 157.57 0.78 247 178 233 53 155.92 0.89 248 179 229 48 157.33 0.90 249 179 230 49 156.68 0.71 250 179 233 52 153.47 0.11 251 179 234 53 151.48 1.11 252 180 215 33 165.81 2.98 253 180 227 45 158.18 0.51 254 180 228 46 157.35 0.89 255 180 230 48 156.28 0.87 256 181 199 20 159.40 0.12 257 181 210 27 159.33 0.10 258 181 211 28 159.34 0.10 259 181 227 44 157.40 0.88 260 181 228 45 156.87 0.64 261 181 229 46 156.85 0.65 262 181 230 47 156.22 0.88 263 182 225 41 158.24 0.54 264 182 226 42 157.40 0.88 265 182 227 43 156.81 0.64 266 183 225 40 158.77 0.23 267 183 226 41 157.94 0.41 268 183 228 43 157.06 0.76 269 184 188 5 282.91 0.70 270 185 222 34 159.37 0.02 271 185 223 35 159.16 0.03 272 185 225 37 159.12 0.03 273 186 222 33 159.34 0.01 274 187 221 30 163.91 2.15 275 187 221 31 163.24 1.84 276 187 222 32 159.35 0.02 277 188 221 29 164.95 2.68 278 188 221 28 168.30 3.67 279 189 221 27 244.10 7.75 280 189 226 33 156.69 0.71 281 190 228 34 156.09 0.90 282 199 228 25 156.55 1.03 283 209 231 22 123.06 0.30 284 210 230 20 155.74 1.08 285 210 231 21 125.66 1.61 286 210 232 22 111.14 0.60 287 211 228 17 156.31 0.92 288 211 229 18 155.98 0.95 289 211 231 20 114.71 0.26 290 212 228 16 156.03 0.93 291 212 229 17 155.75 1.05 292 212 231 19 116.47 0.62 293 213 228 15 155.93 0.97 294 214 227 13 157.02 0.81 295 214 228 14 156.09 0.90 296 214 229 15 156.08 0.91 297 215 226 11 157.50 1.02 298 215 227 12 157.19 0.97 299 216 227 11 156.69 0.71 300 217 224 7 172.62 5.79 301 221 224 3 285.54 0.33 302 231 235 4 277.99 0.07 303 231 238 7 70.14 0.10 304 232 235 3 80.90 0.05 305 234 237 3 72.37 0.01 306 234 238 4 72.35 0.00 307 235 238 3 71.29 0.51 308 235 239 4 69.41 0.18 309 236 239 3 71.36 0.47 310 236 240 4 69.38 0.05 311 237 240 3 69.12 0.10 312 237 241 4 68.41 0.36 313 238 241 3 59.59 0.77 314 238 242 4 32.40 0.02 315 239 242 3 51.24 9.40 316 239 243 4 32.39 0.02 317 240 243 3 32.40 0.02 318 240 244 4 32.39 0.03 319 241 244 3 52.77 9.14 320 241 245 4 30.45 0.29 321 242 245 3 52.77 9.14