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 52.77 3.29 2 16 140 119 52.72 3.32 3 16 142 121 54.51 4.21 4 16 143 122 58.33 2.71 5 16 144 123 58.97 2.66 6 16 156 135 54.73 4.20 7 16 157 136 55.34 3.79 8 16 158 137 54.56 4.17 9 16 189 170 58.26 2.61 10 16 190 171 52.64 3.30 11 16 194 175 52.64 3.30 12 17 143 121 59.02 2.65 13 17 144 122 58.99 2.66 14 17 145 123 60.36 2.47 15 17 146 124 61.95 1.68 16 17 188 167 59.94 2.21 17 17 188 168 59.89 2.22 18 17 189 169 58.55 2.75 19 17 191 171 58.72 2.78 20 17 220 195 59.71 2.25 21 17 221 196 59.84 2.21 22 18 158 135 64.08 0.14 23 18 188 166 59.94 2.21 24 18 188 167 59.90 2.22 25 19 157 133 66.56 0.13 26 19 158 134 63.93 0.21 27 20 137 112 88.53 0.70 28 20 156 131 124.81 17.05 29 20 157 132 78.09 0.31 30 20 158 133 187.09 1.16 31 20 159 134 255.37 8.62 32 21 154 128 148.51 5.20 33 21 155 129 157.75 0.60 34 21 156 130 137.66 10.64 35 22 26 4 164.34 0.65 36 22 27 5 158.96 0.89 37 22 139 112 136.78 0.41 38 22 155 128 161.28 0.35 39 22 156 129 199.30 0.39 40 23 26 3 177.88 0.14 41 24 71 44 139.17 0.64 42 25 28 3 165.95 0.92 43 25 69 41 139.68 0.40 44 25 79 51 154.19 1.07 45 25 117 89 139.19 0.65 46 27 30 3 209.84 16.74 47 27 137 105 138.62 0.12 48 27 139 107 150.90 2.12 49 27 157 125 284.78 0.96 50 28 116 85 153.81 1.28 51 28 117 86 153.80 1.28 52 28 118 87 150.52 0.34 53 28 119 88 148.62 0.41 54 29 45 14 148.42 0.33 55 29 46 15 148.41 0.34 56 29 119 87 150.84 0.18 57 29 120 88 149.22 0.10 58 29 121 89 147.24 0.27 59 29 137 103 154.26 1.05 60 29 198 166 153.76 1.28 61 29 200 168 153.76 1.28 62 30 43 11 154.87 1.02 63 30 44 12 154.34 1.09 64 30 139 104 154.38 1.11 65 30 141 106 157.52 0.70 66 30 155 120 197.99 14.08 67 30 198 165 153.83 1.29 68 31 43 10 156.34 0.94 69 31 44 11 154.37 1.10 70 31 45 12 154.36 1.10 71 31 46 13 154.37 1.09 72 31 52 19 154.37 1.09 73 31 65 32 157.63 0.70 74 31 66 33 157.56 0.72 75 31 67 34 157.22 0.74 76 31 141 105 157.61 0.70 77 32 40 6 158.00 0.69 78 32 42 8 157.61 0.70 79 32 43 9 157.22 0.59 80 32 65 31 157.65 0.70 81 32 66 32 157.62 0.70 82 32 70 35 157.58 0.71 83 32 73 38 157.66 0.76 84 32 141 104 157.61 0.70 85 33 40 5 158.03 0.69 86 33 41 6 157.88 0.62 87 33 42 7 157.65 0.70 88 33 43 8 157.64 0.70 89 33 52 17 157.65 0.70 90 33 54 19 157.64 0.70 91 33 58 23 157.82 0.61 92 33 63 28 157.98 0.70 93 33 64 29 157.94 0.70 94 33 65 30 157.77 0.67 95 33 106 70 157.75 0.66 96 34 39 3 165.72 3.18 97 34 40 4 158.05 0.68 98 34 41 5 158.05 0.68 99 34 63 27 157.98 0.71 100 34 64 28 157.97 0.71 101 34 66 30 157.93 0.69 102 37 41 4 161.21 0.84 103 37 60 23 161.02 0.76 104 40 73 32 286.00 0.04 105 45 121 75 214.16 0.72 106 46 120 73 250.14 8.11 107 46 121 74 237.17 4.92 108 47 120 72 287.27 0.82 109 47 121 73 266.19 9.55 110 47 123 75 196.82 0.57 111 47 238 186 57.80 1.32 112 47 242 190 36.91 2.77 113 48 242 189 36.91 2.77 114 51 242 186 36.80 2.73 115 51 245 189 20.66 1.12 116 53 238 180 57.76 1.33 117 71 153 80 155.34 0.80 118 71 154 81 154.17 1.03 119 71 155 82 154.12 1.05 120 72 153 79 155.32 0.79 121 72 154 80 155.19 0.82 122 73 153 78 155.69 0.68 123 74 153 77 155.81 0.66 124 87 245 154 28.78 2.98 125 89 237 144 81.09 0.94 126 89 241 148 51.25 1.34 127 89 245 152 29.03 2.86 128 91 234 139 105.85 0.12 129 91 237 142 81.33 1.05 130 92 237 141 93.02 0.83 131 98 180 80 160.89 1.16 132 99 180 79 160.74 1.08 133 100 177 75 159.78 1.49 134 100 179 77 160.66 1.06 135 100 180 78 160.67 1.04 136 101 179 76 160.62 1.07 137 101 234 129 119.95 3.17 138 102 229 123 152.52 0.85 139 103 229 122 152.52 0.85 140 103 234 127 97.45 2.18 141 103 237 130 74.66 0.25 142 103 238 131 69.88 0.66 143 105 237 128 73.31 0.92 144 105 238 129 58.09 1.50 145 105 241 132 39.98 4.29 146 107 245 134 19.86 0.75 147 122 204 82 279.41 4.47 148 122 209 83 258.66 5.90 149 123 204 81 239.33 2.69 150 123 209 82 194.91 2.23 151 123 231 104 192.12 29.70 152 123 235 108 73.20 0.96 153 123 238 111 57.84 1.29 154 124 204 80 189.44 0.59 155 124 209 81 176.90 3.25 156 124 210 82 167.16 0.08 157 124 232 104 111.54 1.60 158 124 235 107 80.64 2.02 159 127 210 80 156.97 0.10 160 128 210 79 151.75 1.22 161 129 134 4 167.32 1.52 162 129 162 32 136.25 0.20 163 129 210 78 153.85 0.34 164 130 134 3 187.10 4.17 165 130 162 31 136.99 0.51 166 132 162 30 137.05 0.54 167 132 163 31 137.19 0.49 168 132 164 32 137.34 0.44 169 133 162 29 137.24 0.49 170 134 161 27 137.25 0.48 171 134 162 28 137.30 0.47 172 135 159 24 137.20 0.48 173 135 160 25 137.25 0.48 174 135 161 26 137.25 0.48 175 136 159 23 137.21 0.48 176 136 160 24 137.25 0.49 177 136 162 26 143.34 1.57 178 137 157 20 136.77 0.41 179 137 158 21 137.19 0.47 180 137 159 22 137.21 0.48 181 138 157 19 136.70 0.44 182 138 158 20 136.78 0.41 183 138 160 22 138.61 0.11 184 138 228 88 152.77 0.96 185 139 155 16 137.34 0.44 186 139 156 17 137.20 0.48 187 139 157 18 136.77 0.41 188 140 155 15 137.37 0.42 189 140 156 16 137.20 0.48 190 141 151 10 156.56 0.73 191 141 152 11 155.02 0.76 192 141 153 12 154.33 1.08 193 141 154 13 151.51 1.76 194 141 155 14 137.37 0.43 195 142 151 9 157.04 0.52 196 142 152 10 156.55 0.77 197 143 148 5 159.02 0.11 198 143 149 6 157.46 0.65 199 143 150 7 157.42 0.67 200 143 151 8 157.08 0.54 201 143 191 50 198.35 1.21 202 144 150 6 157.47 0.67 203 144 152 8 157.29 0.60 204 144 156 12 137.13 0.52 205 145 148 3 169.44 1.09 206 145 149 4 157.81 0.70 207 145 150 5 157.56 0.64 208 146 220 71 156.21 0.66 209 146 221 72 156.19 0.66 210 146 221 73 156.15 0.63 211 151 192 43 157.06 0.53 212 151 193 44 157.09 0.53 213 152 156 4 167.05 2.17 214 158 188 32 137.16 0.52 215 158 189 33 136.94 0.42 216 159 184 26 138.54 0.15 217 160 184 24 137.22 0.46 218 160 184 25 138.53 0.15 219 161 183 22 171.93 2.86 220 161 184 23 137.37 0.44 221 161 184 24 138.58 0.15 222 162 181 19 243.08 8.48 223 162 182 20 179.27 1.94 224 162 183 21 172.47 2.83 225 162 201 41 147.37 0.32 226 163 182 19 228.25 13.08 227 163 183 20 189.25 3.04 228 163 184 21 186.78 4.28 229 163 185 23 172.09 2.93 230 163 225 60 148.56 0.41 231 167 185 19 286.22 0.32 232 171 223 50 156.15 0.61 233 171 224 51 156.15 0.61 234 171 225 52 156.13 0.60 235 172 215 41 160.44 1.02 236 172 216 42 159.97 0.85 237 172 217 43 159.85 0.80 238 172 224 50 156.17 0.62 239 172 225 51 156.18 0.62 240 172 227 53 155.87 0.70 241 175 215 38 160.60 1.06 242 176 215 37 160.75 0.99 243 176 227 49 156.14 0.61 244 178 230 50 155.56 0.50 245 178 233 53 150.58 0.32 246 179 229 48 155.61 0.48 247 179 230 49 155.43 0.46 248 179 233 52 149.68 0.10 249 179 234 53 146.87 0.03 250 180 215 33 160.72 0.94 251 180 227 45 156.16 0.60 252 180 228 46 155.71 0.53 253 180 230 48 155.38 0.48 254 181 199 20 157.47 0.64 255 181 210 27 156.84 0.87 256 181 211 28 156.84 0.88 257 181 227 44 156.05 0.59 258 181 228 45 155.58 0.51 259 181 229 46 155.56 0.51 260 181 230 47 155.16 0.49 261 182 225 41 156.16 0.61 262 182 226 42 156.04 0.63 263 182 227 43 155.58 0.49 264 183 225 40 156.19 0.60 265 183 226 41 156.16 0.60 266 183 228 43 155.60 0.53 267 184 188 5 281.12 0.11 268 185 222 34 157.48 0.60 269 185 223 35 157.33 0.63 270 185 225 37 156.78 0.77 271 186 222 33 157.49 0.60 272 187 221 30 160.01 0.64 273 187 221 31 159.89 0.58 274 187 222 32 157.59 0.56 275 188 221 29 160.10 0.60 276 188 221 28 160.22 0.64 277 189 221 27 187.37 0.84 278 189 226 33 152.11 1.18 279 190 228 34 152.65 0.92 280 199 228 25 152.78 0.96 281 209 231 22 116.69 2.34 282 210 229 19 155.24 0.25 283 210 230 20 152.06 1.06 284 210 231 21 120.27 0.56 285 210 232 22 108.05 0.96 286 211 228 17 152.85 0.92 287 211 229 18 152.52 0.85 288 211 231 20 114.56 2.29 289 212 228 16 152.68 0.93 290 212 229 17 152.09 1.05 291 212 231 19 114.17 0.28 292 213 228 15 152.16 1.03 293 214 227 13 155.07 0.17 294 214 228 14 152.63 0.80 295 214 229 15 152.06 1.01 296 215 226 11 155.74 0.42 297 215 227 12 155.37 0.48 298 217 224 7 169.66 6.13 299 221 224 3 286.42 0.09 300 231 235 4 285.41 0.48 301 231 238 7 69.05 0.24 302 232 235 3 85.65 1.07 303 234 237 3 71.96 1.32 304 234 238 4 69.81 0.61 305 235 238 3 69.18 0.12 306 235 239 4 58.76 1.79 307 236 239 3 69.14 0.28 308 236 240 4 58.70 1.80 309 237 240 3 61.11 3.08 310 237 241 4 57.11 1.60 311 238 241 3 59.80 3.74 312 238 242 4 39.97 4.29 313 239 242 3 57.93 4.68 314 239 243 4 39.96 4.29 315 240 243 3 40.08 4.25 316 240 244 4 39.96 4.30 317 241 244 3 43.95 0.42 318 241 245 4 36.49 2.83 319 242 245 3 34.56 4.23