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 53.98 4.86 2 16 140 119 54.05 4.79 3 16 142 121 54.09 4.82 4 16 143 122 58.66 3.02 5 16 144 123 59.52 2.63 6 16 156 135 54.37 4.79 7 16 157 136 54.49 4.65 8 16 158 137 54.26 4.74 9 16 189 170 58.04 2.87 10 16 190 171 53.44 4.67 11 16 194 175 53.45 4.67 12 17 143 121 59.53 2.63 13 17 144 122 59.53 2.63 14 17 145 123 59.75 2.72 15 17 146 124 59.77 2.73 16 17 188 167 59.57 2.61 17 17 188 168 59.54 2.62 18 17 189 169 59.48 2.62 19 17 191 171 59.49 2.62 20 17 220 195 59.51 2.62 21 17 221 196 59.54 2.62 22 18 158 135 59.68 2.56 23 18 188 166 59.57 2.60 24 18 188 167 59.56 2.61 25 19 157 133 59.72 2.58 26 19 158 134 59.55 2.62 27 20 137 112 82.69 0.79 28 20 156 131 93.40 1.28 29 20 157 132 74.08 0.92 30 20 158 133 133.38 28.73 31 21 154 128 135.38 0.77 32 21 155 129 135.37 0.77 33 21 156 130 123.15 1.31 34 22 26 4 168.96 0.97 35 22 27 5 162.39 1.33 36 22 139 112 135.27 0.82 37 22 155 128 163.65 0.92 38 22 156 129 201.60 0.79 39 23 26 3 176.72 1.09 40 24 71 44 140.31 0.33 41 25 28 3 173.85 0.74 42 25 69 41 140.01 0.18 43 25 79 51 153.75 1.22 44 25 117 89 139.20 0.51 45 27 30 3 212.52 22.54 46 27 137 105 138.50 0.04 47 27 139 107 146.81 0.41 48 28 117 86 153.56 1.24 49 28 118 87 149.59 2.21 50 28 119 88 143.25 0.32 51 29 45 14 143.80 0.04 52 29 46 15 140.98 0.04 53 29 119 87 150.90 0.59 54 29 120 88 147.24 2.31 55 29 121 89 141.93 0.35 56 29 137 103 154.12 1.22 57 29 198 166 154.03 1.24 58 29 200 168 154.03 1.24 59 30 43 11 154.43 1.33 60 30 44 12 154.17 1.27 61 30 139 104 154.30 1.30 62 30 140 105 154.76 1.44 63 30 141 106 156.81 0.57 64 30 155 120 172.33 0.72 65 30 198 165 154.03 1.24 66 31 43 10 155.99 0.55 67 31 44 11 154.22 1.25 68 31 45 12 154.22 1.25 69 31 46 13 154.22 1.25 70 31 52 19 154.31 1.29 71 31 65 32 156.69 0.55 72 31 66 33 156.66 0.54 73 31 67 34 156.06 0.62 74 31 141 105 156.85 0.56 75 32 40 6 157.03 0.59 76 32 42 8 156.88 0.56 77 32 65 31 156.83 0.56 78 32 66 32 156.76 0.56 79 32 73 38 156.94 0.55 80 32 141 104 156.81 0.56 81 33 40 5 157.09 0.61 82 33 41 6 156.97 0.57 83 33 42 7 156.90 0.56 84 33 43 8 156.81 0.56 85 33 54 19 156.81 0.56 86 33 58 23 156.95 0.57 87 33 63 28 156.94 0.56 88 33 64 29 156.93 0.55 89 33 65 30 156.86 0.55 90 33 104 68 156.89 0.56 91 33 106 70 156.84 0.55 92 34 39 3 162.34 1.72 93 34 40 4 157.09 0.61 94 34 41 5 157.60 0.85 95 34 63 27 156.97 0.57 96 34 64 28 156.94 0.55 97 34 66 30 156.93 0.55 98 37 41 4 164.44 0.67 99 37 60 23 163.84 0.70 100 45 121 75 219.03 0.36 101 46 120 73 248.12 1.17 102 46 121 74 239.75 3.00 103 47 120 72 284.32 0.63 104 47 121 73 255.72 3.37 105 47 123 75 202.77 3.73 106 47 238 186 61.10 2.42 107 48 242 189 36.12 2.08 108 51 242 186 31.09 0.41 109 51 245 189 21.53 1.43 110 53 238 180 61.08 2.42 111 71 153 80 154.38 1.34 112 71 154 81 154.11 1.27 113 71 155 82 152.97 1.38 114 72 153 79 154.34 1.36 115 72 154 80 154.18 1.28 116 73 153 78 154.37 1.33 117 74 153 77 154.37 1.32 118 87 245 154 24.54 2.15 119 89 237 144 79.03 0.45 120 89 241 148 55.30 2.88 121 89 245 152 24.42 2.02 122 91 234 139 109.78 2.06 123 91 237 142 81.40 0.62 124 92 237 141 95.20 0.28 125 98 180 80 171.94 4.33 126 99 180 79 165.16 0.95 127 100 177 75 164.77 1.11 128 100 179 77 164.84 1.08 129 100 180 78 164.85 1.07 130 101 179 76 164.71 1.09 131 101 234 129 120.66 3.38 132 102 229 123 154.91 0.11 133 103 229 122 154.89 0.10 134 103 234 127 100.01 1.11 135 103 237 130 76.13 0.99 136 103 238 131 61.87 2.81 137 105 237 128 74.08 0.84 138 105 238 129 61.87 2.80 139 105 241 132 45.16 7.27 140 105 242 133 31.25 0.34 141 107 245 134 19.54 0.44 142 122 209 83 281.32 2.00 143 123 204 81 251.84 4.17 144 123 209 82 202.61 1.45 145 123 231 104 192.96 27.93 146 123 235 108 74.38 0.88 147 123 238 111 61.87 2.81 148 123 239 112 61.11 2.43 149 124 204 80 188.74 0.12 150 124 209 81 176.69 0.42 151 124 210 82 168.58 0.12 152 124 232 104 104.98 0.35 153 124 235 107 78.52 1.19 154 127 210 80 161.95 2.42 155 128 210 79 153.91 0.48 156 129 134 4 167.91 0.87 157 129 162 32 135.28 0.80 158 129 210 78 156.08 0.46 159 130 134 3 192.00 1.59 160 130 162 31 135.38 0.77 161 132 162 30 135.38 0.77 162 132 163 31 135.41 0.78 163 132 164 32 135.55 0.82 164 133 161 28 135.43 0.79 165 133 162 29 135.53 0.82 166 134 161 27 135.55 0.82 167 134 162 28 135.59 0.83 168 135 159 24 135.46 0.78 169 135 160 25 135.53 0.81 170 135 161 26 135.58 0.83 171 136 159 23 135.46 0.78 172 136 160 24 135.46 0.78 173 136 162 26 139.17 0.38 174 137 157 20 135.38 0.81 175 137 158 21 135.46 0.78 176 137 159 22 135.47 0.78 177 138 157 19 135.05 0.92 178 138 158 20 135.28 0.81 179 138 160 22 136.65 0.40 180 138 228 88 156.19 0.45 181 139 155 16 135.71 0.86 182 139 156 17 135.46 0.78 183 139 157 18 135.06 0.92 184 140 155 15 135.72 0.86 185 140 156 16 135.47 0.78 186 141 152 11 154.22 1.25 187 141 153 12 154.08 1.22 188 141 154 13 148.83 2.10 189 141 155 14 135.72 0.86 190 142 151 9 156.53 0.59 191 142 152 10 155.94 0.49 192 143 148 5 161.13 0.03 193 143 149 6 156.85 0.52 194 143 150 7 156.78 0.56 195 143 151 8 156.64 0.55 196 143 191 50 208.69 3.83 197 143 192 51 279.81 4.74 198 144 150 6 156.86 0.52 199 144 152 8 156.71 0.58 200 144 156 12 135.72 0.87 201 145 148 3 163.31 1.04 202 145 149 4 158.90 0.42 203 145 150 5 156.94 0.55 204 146 220 71 156.44 0.54 205 146 221 72 156.43 0.53 206 146 221 73 156.42 0.53 207 151 192 43 156.65 0.57 208 152 156 4 167.05 2.70 209 158 188 32 135.57 0.89 210 158 189 33 135.50 0.93 211 159 184 26 136.72 0.45 212 160 184 24 135.55 0.82 213 160 184 25 135.81 0.90 214 161 183 22 174.09 1.70 215 161 184 23 135.62 0.85 216 161 184 24 139.23 0.30 217 162 181 19 213.50 3.04 218 162 182 20 184.05 3.02 219 162 183 21 174.16 1.74 220 162 201 41 142.22 0.83 221 163 182 19 203.63 1.72 222 163 183 20 183.69 2.85 223 163 184 21 183.67 2.87 224 163 185 23 174.12 1.71 225 163 225 60 143.81 1.19 226 171 223 50 156.50 0.57 227 171 224 51 156.38 0.58 228 171 225 52 156.38 0.58 229 172 215 41 163.83 1.25 230 172 217 43 162.00 0.42 231 173 217 42 162.09 0.46 232 173 224 49 156.56 0.58 233 174 215 39 164.34 1.06 234 174 217 41 163.65 0.99 235 176 215 37 164.69 1.11 236 176 227 49 156.24 0.55 237 178 230 50 156.14 0.58 238 178 233 53 153.66 0.10 239 179 229 48 156.15 0.53 240 179 230 49 156.00 0.55 241 179 233 52 150.77 0.53 242 179 234 53 145.40 0.39 243 180 215 33 164.72 1.12 244 180 227 45 156.28 0.53 245 180 228 46 156.15 0.53 246 180 230 48 155.98 0.55 247 181 199 20 156.84 0.58 248 181 210 27 156.49 0.68 249 181 211 28 156.55 0.68 250 181 227 44 156.19 0.53 251 181 228 45 156.02 0.55 252 181 229 46 156.00 0.55 253 181 230 47 155.88 0.50 254 182 225 41 156.44 0.58 255 182 226 42 156.20 0.53 256 182 227 43 155.98 0.55 257 183 225 40 156.45 0.58 258 183 226 41 156.37 0.58 259 183 228 43 156.03 0.53 260 184 188 5 269.48 3.57 261 185 222 34 157.19 0.49 262 185 223 35 156.85 0.60 263 185 225 37 156.74 0.58 264 186 222 33 157.20 0.50 265 187 221 30 159.59 1.59 266 187 221 31 157.33 0.48 267 187 222 32 157.21 0.50 268 188 221 29 162.04 0.39 269 188 221 28 163.80 1.25 270 189 221 27 180.62 7.13 271 189 226 33 155.99 0.54 272 190 228 34 155.91 0.52 273 199 228 25 156.25 0.47 274 209 231 22 132.36 10.46 275 210 230 20 155.94 0.52 276 210 231 21 145.21 4.05 277 210 232 22 108.37 0.63 278 211 228 17 156.19 0.45 279 211 229 18 155.93 0.51 280 211 231 20 113.80 1.18 281 212 228 16 155.94 0.53 282 212 229 17 154.45 0.17 283 212 231 19 115.24 1.90 284 213 228 15 155.86 0.48 285 214 227 13 156.19 0.45 286 214 228 14 155.87 0.49 287 214 229 15 154.47 0.18 288 215 227 12 156.03 0.53 289 217 224 7 189.56 4.33 290 231 235 4 285.61 0.74 291 231 238 7 61.88 2.81 292 232 235 3 81.88 0.48 293 234 237 3 74.47 0.78 294 234 238 4 61.88 2.81 295 235 238 3 72.79 0.21 296 235 239 4 61.88 2.81 297 236 239 3 75.72 1.25 298 236 240 4 66.77 0.35 299 237 240 3 67.19 0.35 300 237 241 4 60.87 2.48 301 238 241 3 57.69 4.19 302 238 242 4 37.93 2.98 303 239 242 3 71.34 0.71 304 239 243 4 31.29 0.34 305 240 243 3 45.94 5.20 306 240 244 4 31.27 0.35 307 241 244 3 36.15 2.08 308 241 245 4 29.61 0.60 309 242 245 3 30.67 0.08