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 52.11 2.49 2 16 140 119 52.10 2.49 3 16 142 121 60.76 1.83 4 16 143 122 65.08 0.04 5 16 144 123 65.17 0.06 6 16 156 135 64.39 0.02 7 16 157 136 62.16 1.14 8 16 158 137 59.80 0.05 9 16 189 170 63.21 0.32 10 16 190 171 51.29 2.62 11 16 194 175 45.78 0.13 12 17 143 121 65.25 0.09 13 17 144 122 65.25 0.09 14 17 145 123 65.28 0.09 15 17 146 124 65.31 0.07 16 17 188 167 65.27 0.09 17 17 188 168 65.24 0.08 18 17 189 169 65.11 0.01 19 17 191 171 65.12 0.03 20 17 220 195 65.17 0.04 21 17 221 196 65.17 0.04 22 18 158 135 65.50 0.02 23 18 188 166 65.27 0.09 24 18 188 167 65.25 0.09 25 19 157 133 65.56 0.01 26 19 158 134 65.48 0.03 27 20 137 112 80.70 0.20 28 20 156 131 123.60 17.37 29 20 157 132 117.45 20.45 30 20 158 133 183.85 0.83 31 20 159 134 277.29 1.33 32 21 154 128 148.02 5.17 33 21 155 129 159.02 0.34 34 21 156 130 135.37 11.49 35 22 26 4 172.69 1.27 36 22 27 5 163.26 0.46 37 22 139 112 135.56 1.01 38 22 155 128 159.62 0.07 39 22 156 129 196.90 2.46 40 23 26 3 176.47 0.97 41 24 71 44 142.66 1.29 42 25 28 3 174.62 1.90 43 25 69 41 144.13 2.04 44 25 79 51 156.88 0.29 45 25 117 89 140.16 0.04 46 27 30 3 181.42 1.04 47 27 137 105 140.83 0.95 48 27 139 107 152.56 1.72 49 28 116 85 156.24 0.64 50 28 117 86 156.24 0.64 51 28 118 87 155.52 0.77 52 28 119 88 153.64 0.94 53 29 45 14 150.72 1.47 54 29 46 15 150.72 1.47 55 29 119 87 155.53 0.77 56 29 120 88 152.71 0.48 57 29 121 89 147.99 0.10 58 29 137 103 156.83 0.60 59 29 198 166 156.17 0.45 60 29 200 168 156.38 0.43 61 30 43 11 157.62 0.36 62 30 44 12 156.81 0.60 63 30 139 104 157.02 0.67 64 30 140 105 157.64 0.38 65 30 141 106 158.96 0.39 66 30 155 120 198.23 11.50 67 30 198 165 156.31 0.48 68 31 43 10 157.65 0.38 69 31 44 11 156.94 0.63 70 31 45 12 156.83 0.60 71 31 46 13 156.97 0.68 72 31 52 19 156.88 0.60 73 31 65 32 159.07 0.35 74 31 65 33 159.06 0.36 75 31 66 34 158.80 0.47 76 31 141 105 159.03 0.38 77 32 40 6 159.46 0.24 78 32 42 8 159.10 0.35 79 32 65 31 159.10 0.36 80 32 65 32 159.08 0.37 81 32 73 38 159.48 0.21 82 32 141 104 159.02 0.38 83 33 40 5 159.63 0.19 84 33 41 6 159.44 0.26 85 33 42 7 159.16 0.33 86 33 43 8 159.13 0.34 87 33 52 17 159.10 0.35 88 33 54 19 159.13 0.34 89 33 58 23 159.50 0.22 90 33 63 28 159.50 0.23 91 33 64 29 159.50 0.24 92 33 65 30 159.13 0.35 93 33 104 68 159.41 0.20 94 33 106 70 159.12 0.35 95 34 39 3 172.46 0.21 96 34 40 4 159.63 0.18 97 34 41 5 159.65 0.18 98 34 63 27 159.55 0.24 99 34 64 28 159.53 0.24 100 34 65 30 159.53 0.24 101 37 41 4 183.19 7.50 102 37 60 23 172.06 0.11 103 37 62 25 165.68 1.58 104 45 121 75 221.75 4.92 105 46 120 73 255.02 1.70 106 46 121 74 236.96 2.69 107 47 121 73 256.27 1.07 108 47 123 75 203.54 1.30 109 47 238 186 52.72 0.12 110 47 242 190 31.39 0.51 111 48 242 189 31.41 0.50 112 51 242 186 31.39 0.51 113 51 245 189 21.62 0.36 114 71 153 80 157.94 0.24 115 71 154 81 156.88 0.09 116 71 155 82 155.15 0.44 117 72 153 79 157.91 0.23 118 72 154 80 157.86 0.24 119 73 153 78 157.99 0.28 120 74 153 77 158.03 0.30 121 87 245 154 21.83 0.47 122 89 237 144 76.16 2.35 123 89 241 148 33.29 0.53 124 89 245 152 21.38 0.20 125 91 234 139 104.92 0.64 126 91 237 142 82.42 0.87 127 92 237 141 100.06 0.42 128 98 180 80 277.72 4.29 129 99 180 79 220.51 24.30 130 100 177 75 220.21 24.30 131 100 179 77 220.40 24.32 132 100 180 78 220.26 24.28 133 101 179 76 220.22 24.29 134 101 234 129 120.96 3.14 135 102 229 123 156.35 0.75 136 103 229 122 156.31 0.73 137 103 234 127 100.48 0.55 138 103 237 130 72.96 0.11 139 103 238 131 69.20 0.04 140 105 237 128 71.49 0.42 141 105 238 129 60.15 3.84 142 105 241 132 32.75 0.15 143 105 242 133 31.39 0.51 144 107 245 134 16.88 0.62 145 121 209 84 286.60 0.28 146 122 204 82 284.91 0.78 147 122 209 83 263.14 4.74 148 123 204 81 233.77 0.15 149 123 209 82 199.77 0.49 150 123 231 104 252.07 8.90 151 123 235 108 71.37 0.47 152 123 238 111 61.08 3.12 153 124 204 80 188.46 1.02 154 124 209 81 171.46 0.57 155 124 210 82 167.08 1.50 156 124 232 104 189.44 40.22 157 124 235 107 80.90 0.05 158 127 210 80 158.44 0.73 159 128 210 79 156.51 1.18 160 129 134 4 172.94 1.44 161 129 162 32 136.13 0.46 162 129 210 78 157.58 1.07 163 130 134 3 179.93 0.52 164 130 162 31 136.84 0.64 165 132 162 30 136.95 0.58 166 132 163 31 136.99 0.58 167 132 164 32 137.03 0.59 168 133 161 28 136.97 0.59 169 133 162 29 137.01 0.59 170 134 161 27 137.03 0.60 171 134 162 28 137.05 0.60 172 135 160 25 137.03 0.60 173 135 161 26 137.03 0.60 174 136 159 23 136.97 0.58 175 136 160 24 137.03 0.60 176 136 162 26 142.95 0.59 177 137 157 20 136.53 0.59 178 137 158 21 136.84 0.51 179 137 159 22 137.03 0.59 180 138 157 19 135.56 1.01 181 138 158 20 136.43 0.63 182 138 160 22 137.22 0.53 183 138 228 88 157.98 0.97 184 139 155 16 137.07 0.58 185 139 156 17 136.85 0.52 186 139 157 18 135.56 1.01 187 140 155 15 137.03 0.58 188 140 156 16 136.97 0.57 189 141 151 10 157.72 0.42 190 141 152 11 157.59 0.40 191 141 153 12 157.02 0.66 192 141 154 13 152.72 1.46 193 141 155 14 137.03 0.58 194 142 151 9 157.76 0.43 195 142 152 10 157.72 0.42 196 143 148 5 159.62 0.18 197 143 149 6 158.72 0.42 198 143 150 7 158.71 0.42 199 143 151 8 157.83 0.47 200 143 191 50 205.17 3.18 201 144 150 6 158.84 0.48 202 144 152 8 158.19 0.57 203 144 156 12 137.02 0.57 204 145 148 3 165.43 0.74 205 145 149 4 159.31 0.32 206 145 150 5 158.91 0.48 207 146 220 71 157.97 0.55 208 146 221 72 158.19 0.65 209 146 221 73 158.19 0.65 210 152 156 4 166.95 1.86 211 158 184 27 137.15 0.56 212 158 188 32 136.96 0.55 213 158 189 33 136.72 0.48 214 159 184 26 137.47 0.41 215 160 184 24 136.99 0.59 216 160 184 25 137.16 0.56 217 161 183 22 180.41 1.08 218 161 184 23 154.34 9.22 219 161 184 24 157.18 7.81 220 162 181 19 238.68 3.62 221 162 182 20 196.97 7.31 222 162 183 21 180.42 1.08 223 162 201 41 149.55 2.02 224 163 182 19 218.25 6.59 225 163 183 20 182.60 0.12 226 163 184 21 182.59 0.12 227 163 185 23 180.53 1.14 228 163 225 60 153.56 0.90 229 167 185 19 269.41 1.43 230 171 223 50 158.31 0.60 231 171 224 51 158.26 0.61 232 171 225 52 158.24 0.60 233 172 215 41 167.50 1.59 234 172 216 42 165.04 0.85 235 172 217 43 165.02 0.84 236 172 224 50 158.41 0.65 237 172 225 51 158.41 0.65 238 172 227 53 157.84 0.66 239 175 215 38 167.67 1.64 240 176 215 37 167.75 1.63 241 176 227 49 158.12 0.69 242 178 230 50 157.78 0.69 243 178 233 53 156.06 0.82 244 179 229 48 157.83 0.67 245 179 230 49 157.27 0.70 246 179 233 52 152.90 0.53 247 179 234 53 150.91 1.40 248 180 215 33 168.07 1.78 249 180 227 45 158.06 0.66 250 180 228 46 157.94 0.60 251 180 230 48 157.04 0.77 252 181 199 20 158.60 0.47 253 181 210 27 158.22 0.54 254 181 211 28 158.21 0.54 255 181 227 44 158.02 0.57 256 181 228 45 157.60 0.56 257 181 229 46 157.24 0.67 258 181 230 47 156.94 0.70 259 182 225 41 158.24 0.57 260 182 226 42 158.11 0.59 261 182 227 43 157.23 0.68 262 183 225 40 158.24 0.57 263 183 226 41 158.18 0.55 264 183 228 43 157.24 0.67 265 184 188 5 282.70 0.66 266 185 222 34 159.33 0.29 267 185 223 35 158.34 0.32 268 185 225 37 158.03 0.46 269 186 222 33 159.50 0.21 270 187 221 30 165.80 1.47 271 187 221 31 165.71 1.42 272 187 222 32 159.72 0.10 273 188 221 29 166.25 1.29 274 188 221 28 167.10 1.73 275 189 221 27 176.47 6.44 276 189 226 33 157.20 0.92 277 190 228 34 157.19 0.92 278 199 228 25 157.72 1.09 279 209 231 22 120.94 0.23 280 210 230 20 156.87 1.33 281 210 231 21 123.06 0.04 282 210 232 22 112.56 0.81 283 211 228 17 157.72 1.09 284 211 229 18 157.53 1.05 285 211 231 20 117.96 1.35 286 212 228 16 157.56 1.06 287 212 229 17 156.56 1.15 288 212 231 19 117.95 1.36 289 213 228 15 157.12 0.88 290 214 227 13 157.95 0.96 291 214 228 14 157.47 0.97 292 214 229 15 156.85 1.20 293 215 226 11 158.52 0.68 294 215 227 12 158.43 0.72 295 216 226 10 158.52 0.68 296 216 227 11 158.51 0.68 297 217 224 7 178.53 2.83 298 221 224 3 286.18 0.09 299 231 235 4 273.95 6.01 300 231 238 7 69.20 0.04 301 232 235 3 87.66 0.92 302 234 237 3 72.17 0.07 303 234 238 4 69.56 0.20 304 235 238 3 69.91 0.38 305 235 239 4 68.25 0.46 306 236 239 3 71.22 0.47 307 236 240 4 68.15 0.48 308 237 240 3 69.45 0.42 309 237 241 4 51.73 0.26 310 238 241 3 51.05 8.69 311 238 242 4 31.43 0.51 312 239 242 3 36.05 1.19 313 239 243 4 31.40 0.50 314 240 243 3 31.42 0.51 315 240 244 4 31.39 0.50 316 241 244 3 73.59 0.53 317 241 245 4 29.93 0.41 318 242 245 3 33.15 0.67