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 44.42 0.86 2 16 140 119 44.36 0.83 3 16 142 121 44.40 0.94 4 16 143 122 56.30 3.71 5 16 144 123 58.91 2.58 6 16 156 135 55.41 3.73 7 16 157 136 55.33 3.77 8 16 158 137 52.73 2.41 9 16 189 170 57.44 2.61 10 16 190 171 44.11 0.93 11 16 194 175 44.13 0.94 12 17 143 121 58.95 2.60 13 17 144 122 58.92 2.58 14 17 145 123 59.91 2.15 15 17 146 124 59.91 2.15 16 17 188 167 59.91 2.04 17 17 188 168 59.70 2.14 18 17 189 169 58.75 2.51 19 17 191 171 58.76 2.51 20 17 220 195 59.84 2.12 21 17 221 196 59.79 2.10 22 18 158 135 63.95 0.07 23 18 188 166 59.91 2.04 24 18 188 167 59.80 2.10 25 19 157 133 63.95 0.07 26 19 158 134 62.08 1.01 27 20 137 112 85.00 1.07 28 20 156 131 87.42 0.15 29 20 157 132 78.09 0.30 30 20 158 133 197.62 4.11 31 20 159 134 274.05 0.96 32 21 154 128 136.91 0.58 33 21 155 129 148.69 7.07 34 21 156 130 138.08 10.85 35 22 26 4 166.19 0.28 36 22 27 5 148.02 7.51 37 22 139 112 135.82 0.66 38 22 155 128 163.52 0.34 39 22 156 129 201.88 1.98 40 23 26 3 274.56 6.07 41 24 71 44 137.80 0.24 42 25 69 41 140.60 0.07 43 25 79 51 157.44 0.06 44 25 117 89 138.87 0.49 45 27 30 3 259.73 8.21 46 27 137 105 138.62 0.12 47 27 139 107 148.08 0.36 48 28 116 85 155.97 0.62 49 28 117 86 155.88 0.59 50 28 118 87 150.71 1.46 51 28 119 88 148.17 0.64 52 29 45 14 146.16 0.02 53 29 46 15 145.31 0.45 54 29 119 87 151.43 1.10 55 29 120 88 148.16 0.63 56 29 121 89 145.31 0.45 57 29 137 103 156.78 0.24 58 29 198 166 156.21 0.51 59 29 200 168 156.12 0.49 60 30 43 11 157.58 0.03 61 30 44 12 157.44 0.06 62 30 139 104 157.44 0.02 63 30 140 105 157.85 0.12 64 30 141 106 159.19 0.28 65 30 155 120 238.24 2.54 66 30 198 165 156.78 0.24 67 31 43 10 158.41 0.18 68 31 44 11 157.56 0.04 69 31 45 12 157.58 0.04 70 31 46 13 157.56 0.04 71 31 52 19 157.58 0.03 72 31 65 32 161.52 0.35 73 31 65 33 161.57 0.35 74 31 66 34 161.54 0.34 75 31 141 105 159.21 0.28 76 32 40 6 161.41 0.73 77 32 42 8 159.29 0.24 78 32 65 31 161.62 0.35 79 32 65 32 161.60 0.35 80 32 73 38 161.98 0.40 81 32 141 104 159.33 0.22 82 33 40 5 162.06 0.43 83 33 41 6 161.41 0.70 84 33 42 7 160.19 0.21 85 33 43 8 159.38 0.20 86 33 52 17 160.27 0.24 87 33 54 19 160.11 0.17 88 33 58 23 161.85 0.48 89 33 63 28 162.06 0.43 90 33 64 29 162.05 0.42 91 33 65 30 161.65 0.37 92 33 106 70 160.63 0.42 93 34 39 3 162.81 0.17 94 34 40 4 162.06 0.43 95 34 41 5 162.06 0.43 96 34 63 27 162.09 0.43 97 34 64 28 162.06 0.42 98 34 65 30 162.05 0.42 99 37 41 4 164.97 0.07 100 37 60 23 165.27 0.56 101 37 62 25 162.22 0.45 102 45 121 75 217.05 1.94 103 46 120 73 263.31 1.53 104 46 121 74 234.88 3.69 105 47 120 72 280.88 2.12 106 47 121 73 259.08 6.00 107 47 123 75 196.83 0.57 108 47 238 186 57.79 1.32 109 47 242 190 31.98 0.31 110 48 242 189 31.98 0.31 111 51 242 186 31.98 0.31 112 51 245 189 19.34 0.54 113 66 118 50 286.80 0.95 114 71 153 80 159.47 0.08 115 71 154 81 157.58 0.25 116 71 155 82 157.31 0.12 117 72 153 79 159.44 0.07 118 72 154 80 158.47 0.20 119 73 153 78 159.49 0.09 120 74 153 77 159.47 0.09 121 87 245 154 23.26 0.24 122 89 237 144 76.80 1.28 123 89 241 148 50.44 0.83 124 89 245 152 25.32 1.00 125 91 234 139 104.85 0.39 126 91 237 142 83.10 0.17 127 92 237 141 93.09 0.77 128 98 180 80 162.43 2.13 129 99 180 79 162.38 2.13 130 100 177 75 161.98 2.31 131 100 179 77 162.31 2.14 132 100 180 78 162.32 2.14 133 101 179 76 162.22 2.10 134 101 234 129 112.00 0.53 135 102 229 123 150.74 1.67 136 103 229 122 150.74 1.67 137 103 234 127 95.62 0.52 138 103 237 130 75.71 0.73 139 103 238 131 72.31 0.46 140 104 237 129 76.72 1.24 141 105 237 128 74.75 0.45 142 105 238 129 61.75 3.35 143 105 241 132 40.93 3.82 144 107 245 134 18.25 0.01 145 122 204 82 286.24 2.27 146 122 209 83 270.61 4.20 147 123 204 81 239.24 1.51 148 123 209 82 198.77 3.38 149 123 231 104 211.19 37.36 150 123 235 108 74.36 0.49 151 123 238 111 68.58 0.00 152 123 239 112 57.77 1.31 153 124 204 80 191.36 2.04 154 124 209 81 174.74 2.18 155 124 210 82 166.66 1.07 156 124 232 104 110.94 0.35 157 124 235 107 77.97 0.69 158 127 210 80 161.06 1.71 159 128 210 79 149.69 1.74 160 129 134 4 166.15 0.64 161 129 162 32 136.72 0.44 162 129 210 78 151.04 1.46 163 130 134 3 181.95 0.78 164 130 162 31 136.99 0.57 165 132 162 30 136.97 0.56 166 132 163 31 137.04 0.59 167 132 164 32 137.10 0.58 168 133 162 29 137.08 0.58 169 134 161 27 137.08 0.58 170 134 162 28 137.11 0.59 171 135 159 24 137.06 0.58 172 135 160 25 137.08 0.58 173 135 161 26 137.10 0.59 174 135 184 50 159.19 0.24 175 136 159 23 137.06 0.58 176 136 160 24 137.08 0.58 177 136 162 26 139.38 0.26 178 137 157 20 136.64 0.47 179 137 158 21 136.97 0.57 180 137 159 22 137.06 0.58 181 138 157 19 135.15 0.97 182 138 158 20 136.67 0.45 183 138 160 22 138.56 0.14 184 138 228 88 150.88 1.56 185 139 155 16 137.12 0.57 186 139 156 17 137.03 0.57 187 139 157 18 135.82 0.66 188 140 155 15 137.12 0.57 189 140 156 16 137.03 0.59 190 141 151 10 158.66 0.30 191 141 152 11 157.50 0.03 192 141 153 12 157.38 0.03 193 141 154 13 147.99 0.57 194 141 155 14 137.12 0.57 195 142 151 9 158.67 0.30 196 142 152 10 158.47 0.26 197 143 148 5 161.93 0.49 198 143 149 6 159.11 0.29 199 143 150 7 158.84 0.34 200 143 151 8 158.68 0.30 201 143 191 50 199.80 0.48 202 144 150 6 159.12 0.29 203 144 152 8 158.75 0.34 204 144 156 12 137.09 0.56 205 145 148 3 176.22 0.70 206 145 149 4 161.24 0.57 207 145 150 5 159.31 0.29 208 146 220 71 158.27 0.36 209 146 221 72 158.24 0.36 210 146 221 73 158.24 0.36 211 151 192 43 158.75 0.35 212 152 156 4 165.10 1.01 213 158 188 32 137.05 0.57 214 158 189 33 136.78 0.50 215 159 184 26 151.12 6.44 216 160 184 24 151.05 6.47 217 160 184 25 151.10 6.43 218 161 183 22 161.78 11.78 219 161 184 23 155.49 8.62 220 161 184 24 155.50 8.61 221 162 181 19 238.31 8.03 222 162 182 20 180.62 2.62 223 162 183 21 161.78 11.78 224 162 201 41 146.27 0.10 225 163 182 19 220.14 17.13 226 163 183 20 179.86 2.77 227 163 184 21 179.83 2.76 228 163 185 23 179.41 2.91 229 163 225 60 149.52 1.25 230 167 185 19 235.15 6.37 231 171 223 50 158.19 0.39 232 171 224 51 158.13 0.36 233 171 225 52 158.13 0.36 234 172 215 41 162.00 2.10 235 172 216 42 161.95 2.12 236 172 217 43 161.83 2.18 237 172 224 50 158.21 0.39 238 172 225 51 158.22 0.39 239 172 227 53 157.93 0.28 240 175 215 38 162.18 2.04 241 176 215 37 162.31 2.05 242 176 227 49 158.19 0.39 243 178 230 50 156.56 0.56 244 178 233 53 150.12 1.41 245 179 229 48 156.56 0.56 246 179 230 49 156.40 0.58 247 179 233 52 149.47 1.27 248 179 234 53 149.01 1.04 249 180 215 33 162.41 2.08 250 180 227 45 157.59 0.10 251 180 228 46 157.12 0.27 252 180 230 48 155.90 0.66 253 181 199 20 159.25 0.21 254 181 210 27 158.89 0.32 255 181 211 28 158.86 0.34 256 181 227 44 157.50 0.09 257 181 228 45 156.90 0.38 258 181 229 46 156.44 0.60 259 181 230 47 155.65 0.77 260 182 225 41 157.62 0.09 261 182 226 42 157.49 0.09 262 182 227 43 156.41 0.61 263 183 225 40 158.22 0.39 264 183 226 41 157.59 0.10 265 183 228 43 157.12 0.27 266 184 225 39 158.22 0.39 267 184 188 5 272.17 4.36 268 185 222 34 159.09 0.26 269 185 223 35 158.90 0.31 270 185 225 37 158.87 0.32 271 186 222 33 159.19 0.27 272 187 221 30 162.10 1.66 273 187 221 31 162.05 1.64 274 187 222 32 159.10 0.26 275 188 221 29 162.41 1.79 276 188 221 28 162.45 1.79 277 189 220 26 286.93 0.92 278 189 221 27 178.54 9.86 279 189 226 33 153.95 0.05 280 190 228 34 150.87 1.50 281 199 228 25 150.89 1.57 282 209 231 22 117.52 1.93 283 210 230 20 149.97 1.50 284 210 231 21 121.16 0.27 285 210 232 22 110.45 0.24 286 211 228 17 150.98 1.54 287 211 229 18 150.59 1.64 288 211 231 20 110.98 0.51 289 212 228 16 150.87 1.59 290 212 229 17 150.33 1.57 291 212 231 19 115.54 0.96 292 213 228 15 150.63 1.62 293 214 227 13 155.78 0.84 294 214 228 14 150.87 1.59 295 214 229 15 150.58 1.45 296 215 226 11 156.90 0.38 297 215 227 12 155.78 0.72 298 217 224 7 178.68 10.22 299 231 235 4 282.65 0.56 300 231 238 7 71.00 0.67 301 232 235 3 83.61 0.05 302 234 237 3 74.55 0.39 303 234 238 4 72.80 1.25 304 235 238 3 71.83 0.77 305 235 239 4 67.37 0.61 306 236 239 3 71.67 0.33 307 236 240 4 67.93 0.33 308 237 240 3 65.45 1.57 309 237 241 4 55.86 2.27 310 238 241 3 52.77 2.10 311 238 242 4 32.95 0.17 312 239 242 3 50.76 7.30 313 239 243 4 33.83 0.27 314 240 243 3 53.13 9.92 315 240 244 4 33.82 0.27 316 241 244 3 32.86 0.75 317 241 245 4 32.59 0.88 318 242 245 3 30.29 2.04