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 55.95 4.08 2 16 140 119 55.70 3.96 3 16 142 121 55.89 4.05 4 16 143 122 61.54 4.40 5 16 144 123 62.42 4.17 6 16 156 135 58.86 5.48 7 16 157 136 56.13 4.13 8 16 158 137 56.00 4.06 9 16 189 170 58.71 2.79 10 16 190 171 55.52 3.87 11 16 194 175 55.37 3.94 12 17 143 121 62.54 4.13 13 17 144 122 62.54 4.13 14 17 145 123 62.91 4.01 15 17 146 124 63.79 3.57 16 17 188 167 62.90 4.00 17 17 188 168 62.72 3.97 18 17 189 169 61.98 4.07 19 17 191 171 62.09 4.03 20 17 220 195 62.53 4.12 21 17 221 196 62.52 4.11 22 18 158 135 62.71 4.07 23 18 188 166 62.90 4.01 24 18 188 167 62.84 4.03 25 19 157 133 64.22 3.33 26 19 158 134 62.70 4.07 27 20 137 112 83.34 0.46 28 20 156 131 95.25 1.66 29 20 157 132 75.91 1.60 30 20 158 133 185.90 0.21 31 20 159 134 266.31 0.41 32 21 154 128 155.28 0.07 33 21 155 129 155.29 0.07 34 21 156 130 155.27 0.07 35 22 26 4 165.09 0.01 36 22 27 5 159.01 0.77 37 22 139 112 137.73 0.61 38 22 155 128 163.16 1.18 39 22 156 129 197.97 0.05 40 23 26 3 176.43 1.24 41 24 71 44 142.24 0.92 42 25 28 3 175.79 3.18 43 25 69 41 140.03 0.19 44 25 79 51 152.16 0.35 45 25 117 89 139.34 0.57 46 27 30 3 175.59 1.61 47 27 137 105 139.62 0.34 48 27 139 107 145.78 0.70 49 27 157 125 286.29 0.30 50 28 117 86 152.30 0.37 51 28 118 87 150.81 0.55 52 28 119 88 146.75 1.14 53 29 45 14 143.71 0.01 54 29 46 15 142.29 0.69 55 29 119 87 150.81 0.55 56 29 120 88 146.73 1.12 57 29 121 89 142.33 0.68 58 29 137 103 152.34 0.34 59 29 198 166 152.19 0.33 60 29 200 168 152.17 0.34 61 30 43 11 152.43 0.33 62 30 44 12 152.31 0.37 63 30 139 104 152.35 0.35 64 30 141 106 155.91 0.36 65 30 155 120 180.39 6.52 66 30 198 165 152.19 0.34 67 31 43 10 154.99 0.29 68 31 44 11 152.42 0.33 69 31 45 12 152.38 0.35 70 31 46 13 152.38 0.35 71 31 52 19 152.38 0.35 72 31 65 32 155.73 0.42 73 31 66 33 155.72 0.42 74 31 67 34 155.28 0.48 75 31 141 105 155.94 0.36 76 32 40 6 156.27 0.32 77 32 42 8 155.91 0.38 78 32 65 31 155.97 0.36 79 32 66 32 155.84 0.41 80 32 73 38 156.38 0.35 81 32 141 104 155.92 0.38 82 33 40 5 156.41 0.35 83 33 41 6 156.26 0.31 84 33 42 7 155.96 0.37 85 33 43 8 155.91 0.38 86 33 54 19 155.91 0.38 87 33 58 23 156.24 0.33 88 33 63 28 156.28 0.35 89 33 64 29 156.27 0.34 90 33 65 30 156.05 0.38 91 33 106 70 155.97 0.35 92 34 39 3 163.54 0.56 93 34 40 4 156.41 0.36 94 34 41 5 156.46 0.33 95 34 63 27 156.34 0.32 96 34 64 28 156.33 0.33 97 34 66 30 156.32 0.32 98 37 41 4 169.10 3.08 99 37 60 23 160.85 0.79 100 37 62 25 160.60 0.67 101 45 121 75 223.80 1.75 102 46 120 73 243.82 2.58 103 46 121 74 228.47 0.01 104 47 120 72 279.79 0.43 105 47 121 73 239.75 1.88 106 47 123 75 201.36 4.49 107 47 238 186 58.82 2.64 108 47 242 190 31.61 0.43 109 48 120 71 287.26 0.58 110 48 242 189 36.38 1.96 111 51 242 186 31.53 0.46 112 51 245 189 24.97 0.29 113 71 153 80 153.96 0.91 114 71 154 81 151.97 0.46 115 71 155 82 150.81 0.77 116 72 153 79 153.96 0.91 117 72 154 80 152.53 0.26 118 73 153 78 153.97 0.92 119 74 153 77 154.88 0.52 120 87 245 154 24.54 2.15 121 89 237 144 82.22 1.03 122 89 241 148 55.26 2.23 123 89 245 152 27.00 0.72 124 91 234 139 109.66 2.00 125 91 237 142 81.40 0.62 126 92 237 141 95.48 0.11 127 98 180 80 208.30 20.71 128 99 180 79 161.77 2.54 129 100 177 75 160.84 2.95 130 100 179 77 161.63 2.55 131 100 180 78 161.64 2.54 132 101 179 76 161.51 2.55 133 101 234 129 129.53 3.00 134 102 229 123 154.64 0.31 135 103 229 122 154.62 0.30 136 103 234 127 101.08 1.03 137 103 237 130 75.31 0.35 138 103 238 131 60.89 3.21 139 105 237 128 74.06 0.85 140 105 238 129 59.52 2.53 141 105 241 132 32.45 0.42 142 105 242 133 31.61 0.42 143 107 245 134 23.00 1.28 144 122 204 82 275.47 1.73 145 122 209 83 258.56 4.80 146 123 204 81 235.44 4.05 147 123 209 82 199.72 0.27 148 123 231 104 274.30 6.21 149 123 235 108 74.38 0.88 150 123 238 111 59.50 2.87 151 124 204 80 184.37 1.31 152 124 209 81 179.42 0.93 153 124 210 82 168.82 0.01 154 124 232 104 104.53 0.20 155 124 235 107 79.52 0.70 156 127 210 80 155.58 0.45 157 128 210 79 154.61 0.31 158 129 162 32 138.19 0.53 159 129 210 78 154.91 0.40 160 130 134 3 184.62 2.10 161 130 162 31 138.34 0.59 162 132 162 30 138.34 0.59 163 132 163 31 138.58 0.70 164 132 164 32 138.66 0.70 165 133 162 29 138.66 0.70 166 134 161 27 138.63 0.68 167 134 162 28 138.70 0.69 168 135 159 24 138.57 0.70 169 135 160 25 138.65 0.68 170 135 161 26 138.69 0.69 171 136 159 23 138.59 0.70 172 136 160 24 138.67 0.70 173 136 162 26 139.37 0.48 174 137 157 20 137.85 0.57 175 137 158 21 138.41 0.66 176 137 159 22 138.56 0.70 177 138 157 19 137.70 0.62 178 138 158 20 138.06 0.78 179 138 160 22 138.75 0.67 180 138 228 88 155.00 0.51 181 139 155 16 138.72 0.66 182 139 156 17 138.45 0.66 183 139 157 18 137.73 0.61 184 140 155 15 138.72 0.66 185 140 156 16 138.24 0.71 186 141 151 10 155.46 0.29 187 141 152 11 152.38 0.33 188 141 153 12 152.34 0.35 189 141 154 13 144.88 0.61 190 141 155 14 138.70 0.65 191 142 151 9 155.46 0.29 192 142 152 10 155.46 0.29 193 143 148 5 158.53 0.70 194 143 149 6 155.85 0.40 195 143 150 7 155.76 0.39 196 143 151 8 155.62 0.34 197 143 191 50 203.97 1.19 198 144 150 6 155.85 0.40 199 144 152 8 155.62 0.38 200 144 156 12 138.54 0.77 201 145 148 3 166.51 0.42 202 145 149 4 158.39 0.68 203 145 150 5 155.87 0.40 204 146 220 71 155.35 0.20 205 146 221 72 155.35 0.20 206 146 221 73 155.32 0.21 207 151 192 43 155.68 0.35 208 152 156 4 168.18 2.14 209 158 188 32 138.37 0.63 210 158 189 33 138.09 0.77 211 159 184 26 138.72 0.68 212 160 184 24 138.43 0.65 213 160 184 25 138.71 0.68 214 161 183 22 158.85 9.40 215 161 184 23 158.84 9.39 216 161 184 24 153.16 6.44 217 162 181 19 237.01 0.23 218 162 182 20 189.74 3.83 219 162 183 21 158.86 9.40 220 162 201 41 142.12 0.88 221 163 182 19 224.96 2.65 222 163 183 20 189.72 3.83 223 163 184 21 188.83 4.28 224 163 185 23 169.35 4.71 225 163 225 60 140.84 0.09 226 167 185 19 232.66 3.95 227 167 225 56 154.95 0.40 228 168 225 55 154.97 0.41 229 168 226 56 154.98 0.41 230 168 227 57 154.87 0.39 231 171 223 50 154.97 0.33 232 171 224 51 155.01 0.30 233 174 215 39 161.44 2.33 234 175 215 38 161.46 2.33 235 176 215 37 161.46 2.32 236 176 227 49 155.61 0.43 237 178 230 50 155.27 0.51 238 178 233 53 153.34 0.26 239 179 229 48 155.28 0.51 240 179 230 49 154.91 0.39 241 179 233 52 151.42 0.15 242 179 234 53 150.27 0.45 243 180 215 33 161.47 2.31 244 180 227 45 155.59 0.45 245 180 228 46 155.27 0.52 246 180 229 47 154.90 0.40 247 180 230 48 154.87 0.41 248 181 199 20 156.08 0.40 249 181 210 27 155.93 0.35 250 181 211 28 155.94 0.35 251 181 227 44 155.44 0.43 252 181 228 45 155.08 0.47 253 181 229 46 154.90 0.40 254 181 230 47 154.59 0.33 255 182 225 41 155.59 0.45 256 182 226 42 155.50 0.42 257 183 225 40 155.67 0.42 258 183 226 41 155.57 0.45 259 183 228 43 155.12 0.45 260 184 225 39 155.67 0.41 261 184 188 5 278.33 0.86 262 184 225 38 155.68 0.41 263 185 222 34 156.15 0.45 264 185 223 35 156.10 0.46 265 185 225 37 155.77 0.35 266 186 222 33 156.16 0.45 267 187 221 30 160.67 1.67 268 187 221 31 156.28 0.48 269 187 222 32 156.18 0.45 270 188 221 29 160.72 1.65 271 188 221 28 162.08 2.29 272 189 221 27 238.99 20.55 273 189 226 33 154.90 0.39 274 190 228 34 154.89 0.39 275 199 228 25 154.99 0.50 276 209 231 22 153.75 0.34 277 210 230 20 154.63 0.32 278 210 231 21 153.94 0.34 279 210 232 22 109.92 1.90 280 211 228 17 155.00 0.49 281 211 229 18 154.84 0.42 282 211 231 20 115.58 1.74 283 212 228 16 154.97 0.49 284 212 229 17 154.59 0.32 285 212 231 19 114.56 2.47 286 213 228 15 154.61 0.33 287 214 227 13 155.07 0.46 288 214 228 14 154.67 0.29 289 214 229 15 154.62 0.31 290 215 226 11 155.24 0.54 291 215 227 12 155.00 0.46 292 217 224 7 217.55 19.41 293 221 224 3 285.15 0.03 294 231 235 4 284.83 0.23 295 231 238 7 60.52 2.68 296 232 235 3 82.50 0.70 297 234 237 3 74.20 0.91 298 234 238 4 70.19 1.52 299 235 238 3 72.80 0.21 300 235 239 4 59.63 3.04 301 236 239 3 70.30 1.46 302 236 240 4 59.63 3.04 303 237 240 3 59.06 2.77 304 237 241 4 58.78 2.62 305 238 241 3 59.46 4.96 306 238 242 4 38.95 2.83 307 239 242 3 61.16 5.80 308 239 243 4 32.02 0.63 309 240 243 3 59.45 4.95 310 240 244 4 31.62 0.43 311 241 244 3 40.94 4.31 312 241 245 4 30.27 0.18 313 242 245 3 22.73 0.83