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 44.06 0.49 2 16 140 119 43.82 0.61 3 16 142 121 44.62 0.21 4 16 143 122 62.30 3.59 5 16 144 123 62.66 3.67 6 16 156 135 58.07 5.32 7 16 157 136 56.51 6.10 8 16 158 137 51.71 3.75 9 16 189 170 55.00 2.52 10 16 190 171 43.73 0.58 11 16 194 175 43.73 0.58 12 17 143 121 62.81 3.65 13 17 144 122 62.81 3.65 14 17 145 123 62.93 3.70 15 17 146 124 63.08 3.77 16 17 188 167 62.97 3.70 17 17 188 168 62.83 3.66 18 17 189 169 62.38 3.64 19 17 191 171 62.73 3.61 20 17 220 195 62.84 3.65 21 17 221 196 62.85 3.65 22 18 158 135 63.45 3.45 23 18 188 166 62.98 3.70 24 18 188 167 62.91 3.69 25 19 157 133 64.50 2.93 26 19 158 134 62.95 3.70 27 20 137 112 85.58 0.49 28 20 156 131 123.23 19.74 29 20 157 132 75.04 0.49 30 20 158 133 190.45 0.70 31 20 159 134 286.61 1.43 32 21 154 128 148.18 6.09 33 21 155 129 161.54 0.59 34 21 156 130 138.21 12.26 35 22 26 4 166.83 0.43 36 22 27 5 150.17 8.76 37 22 139 112 135.32 0.29 38 22 155 128 164.46 0.85 39 22 156 129 195.67 2.10 40 23 26 3 177.30 0.14 41 24 71 44 140.18 0.67 42 25 69 41 143.90 0.42 43 25 79 51 160.10 0.73 44 25 117 89 140.19 0.64 45 27 30 3 233.52 13.06 46 27 137 105 140.96 0.30 47 27 139 107 144.71 1.22 48 27 157 125 285.10 0.24 49 28 116 85 159.03 0.28 50 28 117 86 158.85 0.26 51 28 118 87 158.46 0.38 52 28 119 88 154.47 0.64 53 29 45 14 150.03 0.14 54 29 46 15 146.63 0.49 55 29 119 87 158.46 0.38 56 29 120 88 154.45 0.64 57 29 121 89 145.43 0.90 58 29 137 103 160.00 0.65 59 29 198 166 159.83 0.74 60 29 200 168 159.61 0.73 61 30 43 11 160.21 0.68 62 30 44 12 160.12 0.72 63 30 139 104 160.19 0.69 64 30 140 105 160.31 0.64 65 30 141 106 161.42 0.65 66 30 155 120 172.06 2.18 67 30 198 165 159.84 0.74 68 31 43 10 160.70 0.80 69 31 44 11 160.16 0.70 70 31 45 12 160.21 0.68 71 31 46 13 160.13 0.72 72 31 52 19 160.16 0.71 73 31 65 32 161.38 0.62 74 31 66 33 161.37 0.62 75 31 67 34 160.88 0.72 76 31 141 105 161.47 0.64 77 32 40 6 161.71 0.60 78 32 42 8 161.46 0.64 79 32 43 9 161.18 0.59 80 32 65 31 161.46 0.63 81 32 66 32 161.44 0.63 82 32 73 38 161.64 0.55 83 32 141 104 161.47 0.64 84 33 40 5 161.77 0.58 85 33 41 6 161.71 0.58 86 33 42 7 161.48 0.64 87 33 43 8 161.47 0.64 88 33 52 17 161.47 0.64 89 33 54 19 161.47 0.64 90 33 58 23 161.64 0.58 91 33 63 28 161.73 0.57 92 33 64 29 161.70 0.56 93 33 65 30 161.48 0.63 94 33 104 68 161.50 0.65 95 33 106 70 161.47 0.63 96 34 39 3 165.40 0.57 97 34 40 4 161.79 0.59 98 34 41 5 161.78 0.59 99 34 63 27 161.74 0.57 100 34 64 28 161.72 0.57 101 34 66 30 161.65 0.55 102 37 41 4 166.79 0.12 103 37 60 23 165.24 1.10 104 37 62 25 161.89 0.54 105 45 121 75 226.64 3.14 106 46 120 73 251.33 3.41 107 46 121 74 242.35 0.48 108 47 120 72 286.88 0.95 109 47 121 73 261.02 6.73 110 47 123 75 209.53 2.12 111 47 238 186 59.84 1.74 112 47 242 190 30.45 0.36 113 51 242 186 30.45 0.36 114 51 245 189 23.02 0.06 115 53 238 180 59.72 1.74 116 71 153 80 160.53 0.72 117 71 154 81 159.55 0.49 118 71 155 82 158.49 0.38 119 72 153 79 160.52 0.72 120 72 154 80 160.25 0.82 121 73 153 78 160.53 0.72 122 74 153 77 160.53 0.71 123 87 245 154 22.91 0.00 124 89 237 144 78.39 0.18 125 89 241 148 56.15 1.77 126 89 245 152 21.54 0.04 127 91 234 139 106.27 0.14 128 91 237 142 78.86 0.08 129 92 237 141 92.00 0.34 130 98 180 80 228.67 28.34 131 99 180 79 208.38 18.21 132 100 177 75 160.62 0.80 133 100 179 77 160.66 0.82 134 100 180 78 160.77 0.78 135 101 179 76 160.65 0.82 136 101 234 129 110.52 0.21 137 102 229 123 159.07 0.18 138 103 229 122 159.08 0.18 139 103 234 127 102.67 1.80 140 103 237 130 76.03 1.33 141 103 238 131 62.13 2.71 142 105 237 128 75.27 1.13 143 105 238 129 59.71 1.74 144 105 241 132 31.62 0.70 145 105 242 133 30.45 0.36 146 107 245 134 22.18 0.36 147 122 209 83 275.85 1.50 148 123 204 81 256.41 5.64 149 123 209 82 211.90 1.50 150 123 231 104 192.56 28.32 151 123 235 108 72.21 0.65 152 123 238 111 61.62 2.63 153 124 204 80 191.96 0.72 154 124 209 81 177.15 2.00 155 124 210 82 167.09 1.51 156 124 231 103 286.80 1.42 157 124 232 104 109.19 0.73 158 124 235 107 79.12 0.62 159 127 210 80 159.69 0.03 160 128 210 79 155.58 0.16 161 129 134 4 162.08 1.32 162 129 162 32 136.59 0.33 163 129 210 78 159.29 0.06 164 130 134 3 182.18 1.40 165 130 162 31 136.76 0.32 166 132 162 30 136.69 0.35 167 132 163 31 136.81 0.32 168 132 164 32 136.81 0.32 169 133 161 28 136.75 0.32 170 133 162 29 136.81 0.32 171 134 161 27 136.83 0.32 172 134 162 28 136.86 0.32 173 135 160 25 136.83 0.32 174 135 161 26 136.85 0.32 175 136 159 23 136.80 0.32 176 136 160 24 136.83 0.32 177 136 162 26 143.89 0.37 178 137 157 20 135.42 0.26 179 137 158 21 136.72 0.29 180 137 159 22 136.82 0.33 181 138 157 19 135.20 0.35 182 138 158 20 135.66 0.16 183 138 160 22 137.17 0.25 184 138 228 88 159.44 0.02 185 139 155 16 136.96 0.32 186 139 156 17 136.72 0.29 187 139 157 18 135.31 0.30 188 140 155 15 136.97 0.32 189 140 156 16 136.79 0.33 190 141 151 10 160.66 0.81 191 141 152 11 160.16 0.59 192 141 153 12 160.03 0.65 193 141 154 13 152.46 2.63 194 141 155 14 136.98 0.32 195 142 151 9 161.04 0.62 196 142 152 10 160.67 0.81 197 142 194 54 286.62 0.33 198 143 148 5 161.66 0.58 199 143 149 6 161.32 0.61 200 143 150 7 161.22 0.57 201 143 151 8 161.09 0.60 202 143 191 50 198.35 0.33 203 144 150 6 161.24 0.58 204 144 152 8 161.18 0.60 205 144 156 12 136.93 0.39 206 145 148 3 173.08 1.38 207 145 149 4 161.55 0.54 208 145 150 5 161.40 0.61 209 145 191 48 167.71 0.01 210 146 220 71 160.72 0.70 211 146 221 72 160.30 0.50 212 151 192 43 161.18 0.60 213 152 156 4 164.47 0.87 214 158 184 27 136.89 0.32 215 158 188 32 136.84 0.35 216 158 189 33 136.73 0.29 217 159 184 26 166.43 0.06 218 160 183 23 166.59 0.04 219 160 184 24 136.70 0.30 220 160 184 25 151.33 7.50 221 161 183 22 168.11 0.03 222 161 184 23 166.50 0.03 223 161 184 24 167.19 0.31 224 162 181 19 201.94 2.04 225 162 182 20 179.59 2.42 226 162 183 21 168.12 0.04 227 162 201 41 157.19 0.77 228 163 182 19 201.94 2.04 229 163 183 20 179.51 2.39 230 163 184 21 176.21 4.03 231 163 185 23 168.13 0.03 232 163 225 60 154.28 0.70 233 171 223 50 160.97 0.57 234 171 224 51 160.84 0.51 235 171 225 52 160.82 0.52 236 172 215 41 161.34 0.38 237 172 216 42 161.34 0.38 238 172 217 43 161.27 0.39 239 172 224 50 160.97 0.57 240 172 225 51 160.97 0.57 241 172 227 53 160.56 0.69 242 175 215 38 161.30 0.41 243 176 215 37 161.41 0.41 244 176 227 49 160.86 0.57 245 178 230 50 159.98 0.40 246 178 233 53 158.43 0.13 247 179 229 48 160.16 0.30 248 179 230 49 159.41 0.12 249 179 233 52 152.84 0.78 250 179 234 53 148.05 0.70 251 180 215 33 161.47 0.42 252 180 227 45 160.68 0.45 253 180 228 46 160.28 0.48 254 180 230 48 159.40 0.11 255 181 199 20 161.44 0.59 256 181 210 27 161.12 0.61 257 181 211 28 161.12 0.62 258 181 227 44 160.47 0.38 259 181 228 45 159.74 0.27 260 181 229 46 159.73 0.27 261 181 230 47 159.21 0.17 262 182 225 41 160.69 0.46 263 182 226 42 160.47 0.38 264 182 227 43 159.58 0.21 265 183 225 40 160.90 0.53 266 183 226 41 160.59 0.40 267 183 228 43 159.78 0.29 268 184 188 5 260.69 0.39 269 185 222 34 161.39 0.61 270 185 223 35 161.35 0.61 271 185 225 37 161.03 0.58 272 186 222 33 161.41 0.61 273 187 221 30 161.75 0.47 274 187 221 31 161.75 0.47 275 187 222 32 161.40 0.61 276 188 221 29 161.89 0.53 277 188 221 28 171.04 4.03 278 189 221 27 229.21 11.27 279 189 226 33 159.34 0.09 280 190 228 34 159.31 0.07 281 199 228 25 159.46 0.06 282 209 231 22 115.58 0.26 283 210 229 19 159.69 0.04 284 210 230 20 158.66 0.38 285 210 231 21 117.89 1.24 286 210 232 22 108.19 0.57 287 211 228 17 159.52 0.04 288 211 229 18 158.93 0.26 289 211 231 20 113.00 1.54 290 212 228 16 159.28 0.10 291 212 229 17 158.55 0.39 292 212 231 19 113.37 1.36 293 213 228 15 159.29 0.07 294 214 227 13 159.44 0.10 295 214 228 14 159.30 0.06 296 214 229 15 159.30 0.07 297 215 226 11 160.10 0.12 298 215 227 12 159.44 0.12 299 216 227 11 159.37 0.10 300 217 224 7 193.21 0.42 301 231 235 4 282.48 0.49 302 231 238 7 61.95 2.79 303 232 235 3 82.27 0.14 304 234 237 3 70.98 0.33 305 234 238 4 69.60 0.99 306 235 238 3 63.85 3.52 307 235 239 4 61.88 2.77 308 236 239 3 61.93 2.75 309 236 240 4 61.62 2.64 310 237 240 3 59.32 2.00 311 237 241 4 58.80 2.12 312 238 241 3 43.77 6.44 313 238 242 4 35.61 2.71 314 239 242 3 36.67 3.07 315 239 243 4 31.62 0.70 316 240 243 3 31.97 0.54 317 240 244 4 30.71 0.26 318 241 244 3 31.97 0.54 319 241 245 4 29.87 0.51 320 242 245 3 30.54 0.27