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 31.76 0.48 2 16 140 119 31.75 0.48 3 16 142 121 31.75 0.48 4 16 143 122 50.99 6.37 5 16 144 123 53.23 5.57 6 16 156 135 31.89 0.49 7 16 157 136 32.12 0.41 8 16 158 137 39.24 2.74 9 16 189 170 52.25 5.55 10 16 190 171 31.73 0.48 11 16 193 174 31.64 0.47 12 17 143 121 53.29 5.56 13 17 144 122 53.26 5.56 14 17 145 123 62.60 1.76 15 17 146 124 65.81 3.36 16 17 188 167 53.76 5.34 17 17 188 168 53.75 5.33 18 17 189 169 53.19 5.55 19 17 220 195 53.36 5.53 20 17 221 196 53.41 5.50 21 18 158 135 58.23 3.11 22 18 188 166 53.77 5.33 23 18 188 167 53.76 5.34 24 19 157 133 70.47 0.01 25 19 158 134 54.16 5.15 26 20 137 112 86.77 1.24 27 20 156 131 154.43 1.85 28 20 157 132 78.73 0.20 29 20 158 133 208.65 1.99 30 20 159 134 286.10 1.61 31 21 154 128 156.23 0.96 32 21 155 129 156.44 0.88 33 21 156 130 156.74 1.19 34 22 26 4 167.95 1.48 35 22 27 5 148.48 6.00 36 22 139 112 138.05 0.79 37 22 155 128 167.29 0.72 38 22 156 129 192.24 0.64 39 23 26 3 175.05 0.17 40 24 71 44 142.20 0.90 41 25 69 41 140.73 0.17 42 25 79 51 149.89 0.24 43 25 117 89 139.33 0.57 44 27 30 3 174.22 0.22 45 27 137 105 139.34 0.48 46 27 139 107 144.84 1.17 47 28 116 85 149.99 0.20 48 28 117 86 149.91 0.24 49 28 118 87 149.50 0.05 50 28 119 88 147.12 0.48 51 29 45 14 144.22 0.26 52 29 46 15 141.09 0.09 53 29 119 87 149.49 0.12 54 29 120 88 148.98 0.21 55 29 121 89 141.11 0.07 56 29 137 103 149.93 0.20 57 29 198 166 149.81 0.26 58 29 200 168 149.57 0.09 59 30 44 12 149.97 0.21 60 30 139 104 149.97 0.21 61 30 141 106 156.34 0.93 62 30 155 120 172.69 0.18 63 30 198 165 149.92 0.21 64 31 43 10 155.72 0.90 65 31 44 11 149.97 0.21 66 31 45 12 149.97 0.21 67 31 46 13 149.97 0.21 68 31 52 19 149.98 0.21 69 31 65 32 156.25 0.91 70 31 66 33 156.31 0.83 71 31 67 34 155.31 0.59 72 31 141 105 156.44 0.93 73 32 40 6 156.93 0.73 74 32 42 8 156.39 0.95 75 32 65 31 156.41 0.88 76 32 66 32 156.36 0.84 77 32 70 35 156.75 0.65 78 32 73 38 156.94 0.71 79 32 141 104 156.48 0.91 80 33 40 5 157.05 0.77 81 33 41 6 156.92 0.73 82 33 42 7 156.47 0.91 83 33 43 8 156.40 0.94 84 33 52 17 156.37 0.85 85 33 54 19 156.34 0.93 86 33 58 23 156.49 0.92 87 33 63 28 156.91 0.70 88 33 64 29 156.88 0.70 89 33 65 30 156.72 0.77 90 33 106 70 156.46 0.90 91 34 39 3 169.48 2.42 92 34 40 4 157.05 0.77 93 34 41 5 157.09 0.79 94 34 63 27 156.96 0.72 95 34 64 28 156.89 0.70 96 34 66 30 156.88 0.69 97 37 41 4 163.09 0.28 98 37 60 23 159.91 1.02 99 45 121 75 212.19 0.71 100 46 120 73 250.06 2.15 101 46 121 74 228.40 1.80 102 47 121 73 267.55 2.54 103 47 123 75 201.36 4.49 104 47 238 186 62.50 1.26 105 47 242 190 46.99 2.20 106 48 242 189 46.99 2.19 107 51 242 186 46.94 2.19 108 51 245 189 42.99 1.78 109 71 153 80 150.32 0.23 110 71 154 81 149.81 0.20 111 71 155 82 149.25 0.22 112 72 153 79 150.31 0.23 113 72 154 80 150.22 0.21 114 73 153 78 150.32 0.23 115 74 153 77 151.16 0.01 116 87 245 154 43.19 1.75 117 89 237 144 81.59 0.53 118 89 241 148 55.59 3.03 119 89 245 152 44.56 2.44 120 91 234 139 109.78 2.06 121 91 237 142 79.43 0.65 122 92 237 141 96.01 0.13 123 98 180 80 255.30 9.19 124 99 180 79 157.84 1.48 125 100 177 75 154.30 2.36 126 100 179 77 156.69 1.18 127 100 180 78 156.80 1.12 128 101 179 76 154.27 1.93 129 101 234 129 120.61 2.21 130 102 229 123 154.59 0.03 131 103 229 122 154.62 0.04 132 103 234 127 97.78 0.61 133 103 237 130 74.89 0.57 134 103 238 131 66.11 0.20 135 105 237 128 73.85 0.75 136 105 238 129 63.43 0.79 137 105 241 132 50.76 0.61 138 105 242 133 47.01 2.22 139 107 245 134 43.03 1.79 140 122 204 82 279.86 0.47 141 122 209 83 244.05 1.63 142 123 204 81 230.18 1.95 143 123 209 82 195.41 2.15 144 123 235 108 73.11 1.33 145 123 238 111 62.98 1.46 146 123 239 112 62.48 1.26 147 124 204 80 185.99 0.48 148 124 209 81 177.02 0.15 149 124 210 82 167.83 0.26 150 124 231 103 285.87 1.27 151 124 232 104 106.44 2.18 152 124 235 107 78.55 1.21 153 127 210 80 157.10 0.20 154 128 210 79 155.62 0.15 155 129 134 4 166.60 0.38 156 129 162 32 137.85 0.70 157 129 201 73 156.13 0.33 158 129 210 78 155.85 0.11 159 130 134 3 177.53 0.79 160 130 162 31 138.40 0.62 161 132 162 30 138.42 0.63 162 132 163 31 138.62 0.71 163 132 164 32 138.64 0.70 164 133 161 28 138.41 0.62 165 133 162 29 138.68 0.69 166 134 161 27 138.68 0.70 167 134 162 28 138.70 0.69 168 135 160 25 138.68 0.70 169 135 161 26 138.69 0.69 170 136 159 23 138.57 0.70 171 136 160 24 138.68 0.70 172 136 162 26 139.38 0.48 173 137 157 20 137.97 0.67 174 137 158 21 138.43 0.64 175 137 159 22 138.63 0.68 176 138 157 19 137.74 0.94 177 138 158 20 138.38 0.62 178 138 160 22 138.91 0.69 179 138 183 45 156.65 0.91 180 138 228 88 156.12 0.21 181 139 155 16 138.81 0.68 182 139 156 17 138.44 0.64 183 139 157 18 138.05 0.79 184 140 155 15 138.78 0.70 185 140 156 16 138.44 0.64 186 141 152 11 150.10 0.26 187 141 153 12 149.53 0.10 188 141 154 13 139.72 0.38 189 141 155 14 138.81 0.68 190 141 156 15 138.56 0.62 191 142 151 9 152.31 0.36 192 142 152 10 152.06 0.48 193 143 148 5 157.58 1.10 194 143 149 6 156.10 0.86 195 143 150 7 155.63 0.89 196 143 151 8 154.52 0.74 197 143 152 9 152.55 0.48 198 144 150 6 155.65 0.87 199 144 152 8 155.02 0.76 200 144 156 12 138.62 0.72 201 145 148 3 176.97 1.24 202 145 150 5 156.19 0.88 203 146 220 71 153.09 0.71 204 146 221 72 152.47 0.42 205 151 192 43 154.78 0.65 206 152 156 4 170.09 1.19 207 158 188 32 138.63 0.70 208 158 189 33 138.39 0.62 209 159 184 26 169.72 1.91 210 160 183 23 177.84 2.12 211 160 184 24 152.70 6.54 212 161 183 22 179.35 1.38 213 161 184 23 175.59 1.03 214 161 184 24 175.67 1.00 215 162 181 19 261.16 1.51 216 162 182 20 213.75 2.96 217 162 183 21 179.46 1.43 218 162 201 41 144.30 1.88 219 163 182 19 244.93 9.62 220 163 183 20 183.94 3.61 221 163 184 21 183.94 3.62 222 163 185 23 179.50 1.48 223 163 225 60 147.12 0.47 224 167 185 19 285.75 0.07 225 171 223 50 155.96 0.67 226 171 224 51 155.96 0.67 227 171 225 52 156.03 0.63 228 172 215 41 156.88 1.05 229 172 216 42 156.67 0.98 230 172 217 43 156.61 0.97 231 172 224 50 156.22 0.72 232 172 225 51 156.24 0.71 233 172 227 53 155.85 0.58 234 175 215 38 156.89 1.06 235 176 215 37 156.89 1.07 236 176 227 49 156.12 0.71 237 178 230 50 155.63 0.70 238 178 233 53 151.81 0.34 239 179 229 48 155.36 0.47 240 179 230 49 154.53 0.14 241 179 233 52 149.31 0.04 242 179 234 53 146.97 0.24 243 180 215 33 157.20 1.15 244 180 227 45 156.10 0.72 245 180 228 46 155.03 0.30 246 180 230 48 154.07 0.06 247 181 199 20 156.60 0.86 248 181 210 27 156.38 0.91 249 181 211 28 156.41 0.90 250 181 227 44 155.74 0.54 251 181 228 45 155.00 0.31 252 181 229 46 154.56 0.17 253 181 230 47 153.84 0.10 254 182 225 41 156.08 0.71 255 182 226 42 155.90 0.63 256 182 227 43 154.93 0.34 257 182 228 44 154.62 0.13 258 183 225 40 156.23 0.70 259 183 226 41 156.12 0.71 260 183 228 43 155.14 0.24 261 184 188 5 282.58 0.43 262 185 222 34 157.07 0.69 263 185 223 35 156.81 0.79 264 186 222 33 157.08 0.69 265 187 221 30 157.50 0.49 266 187 221 31 157.47 0.51 267 187 222 32 157.10 0.69 268 188 221 29 157.54 0.52 269 188 221 28 174.48 8.73 270 189 221 27 237.88 21.89 271 189 224 31 157.37 0.51 272 189 225 32 156.22 0.07 273 189 226 33 154.70 0.01 274 190 228 34 154.99 0.07 275 199 228 25 156.41 0.06 276 209 231 22 153.68 0.10 277 210 230 20 155.69 0.18 278 210 231 21 153.68 0.10 279 210 232 22 105.05 0.39 280 211 228 17 156.09 0.21 281 211 229 18 155.84 0.10 282 211 231 20 110.05 1.34 283 212 228 16 155.69 0.18 284 212 229 17 154.72 0.04 285 212 231 19 116.56 2.56 286 213 228 15 155.00 0.15 287 214 227 13 156.22 0.04 288 214 228 14 155.28 0.18 289 214 229 15 155.28 0.18 290 215 226 11 156.28 0.01 291 215 227 12 155.66 0.23 292 216 227 11 155.65 0.22 293 217 224 7 186.74 0.33 294 221 224 3 285.56 1.22 295 229 234 5 285.32 0.84 296 230 234 4 286.00 0.52 297 231 234 3 286.00 0.52 298 231 235 4 281.14 0.68 299 231 238 7 65.97 0.03 300 232 235 3 81.93 0.46 301 234 237 3 74.03 0.99 302 234 238 4 66.88 0.18 303 235 238 3 66.66 0.21 304 235 239 4 66.08 0.08 305 236 239 3 69.69 1.76 306 236 240 4 66.06 0.09 307 237 240 3 65.85 0.07 308 237 241 4 62.06 1.02 309 238 241 3 56.80 1.13 310 238 242 4 47.29 2.35 311 239 242 3 50.88 0.56 312 239 243 4 47.29 2.35 313 240 243 3 59.45 4.95 314 240 244 4 47.28 2.35 315 241 244 3 46.94 2.23 316 241 245 4 46.60 2.35 317 242 245 3 43.19 1.75