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 44.81 0.12 2 16 140 119 44.81 0.12 3 16 142 121 44.84 0.12 4 16 143 122 52.06 0.34 5 16 144 123 53.54 0.80 6 16 156 135 48.03 1.02 7 16 157 136 46.08 0.24 8 16 158 137 45.58 0.49 9 16 189 170 51.62 0.58 10 16 190 171 44.69 0.06 11 16 194 175 44.79 0.11 12 17 144 122 53.58 0.82 13 17 145 123 58.55 1.51 14 17 146 124 58.67 1.56 15 17 188 167 55.88 0.16 16 17 188 168 55.64 0.06 17 17 189 169 53.30 0.68 18 17 191 171 53.57 0.81 19 17 220 195 55.66 0.07 20 17 221 196 55.66 0.07 21 18 158 135 56.30 0.15 22 18 188 166 56.83 0.31 23 18 188 167 55.85 0.16 24 19 157 133 64.19 2.25 25 19 158 134 56.25 0.18 26 20 137 112 85.17 0.89 27 20 156 131 160.97 0.04 28 20 157 132 162.53 0.73 29 20 158 133 192.16 0.96 30 20 159 134 286.90 1.57 31 21 154 128 161.04 0.07 32 21 155 129 161.19 0.10 33 21 156 130 161.13 0.12 34 22 26 4 167.46 0.10 35 22 27 5 153.56 6.05 36 22 139 112 140.09 0.82 37 22 155 128 166.81 2.18 38 22 156 129 200.69 4.61 39 23 26 3 188.59 5.76 40 24 71 44 142.34 0.42 41 25 28 3 169.74 1.24 42 25 69 41 143.68 0.53 43 25 79 51 159.52 0.04 44 25 117 89 140.55 0.93 45 27 30 3 273.29 6.82 46 27 137 105 142.38 0.41 47 27 139 107 150.19 3.29 48 28 116 85 157.40 0.80 49 28 117 86 157.16 0.87 50 28 118 87 155.70 1.27 51 28 119 88 149.12 0.64 52 29 45 14 145.88 0.99 53 29 46 15 144.69 0.53 54 29 119 87 155.84 1.20 55 29 120 88 153.81 2.21 56 29 121 89 144.68 0.54 57 29 137 103 158.96 0.27 58 29 198 166 158.62 0.22 59 29 200 168 158.24 0.04 60 30 43 11 159.27 0.17 61 30 44 12 159.22 0.17 62 30 139 104 159.21 0.18 63 30 140 105 159.28 0.17 64 30 141 106 160.61 0.24 65 30 155 120 198.89 16.18 66 30 198 165 158.83 0.12 67 31 43 10 159.62 0.24 68 31 44 11 159.27 0.17 69 31 45 12 159.28 0.18 70 31 46 13 159.67 0.37 71 31 52 19 159.27 0.17 72 31 65 32 161.84 0.54 73 31 66 33 161.85 0.53 74 31 67 34 161.84 0.53 75 31 141 105 161.69 0.43 76 32 40 6 162.16 0.41 77 32 42 8 161.77 0.44 78 32 65 31 162.09 0.51 79 32 66 32 161.98 0.48 80 32 70 35 162.00 0.44 81 32 73 38 161.92 0.32 82 32 141 104 161.72 0.45 83 33 40 5 162.31 0.45 84 33 41 6 162.12 0.43 85 33 42 7 161.81 0.46 86 33 43 8 161.78 0.45 87 33 52 17 161.80 0.63 88 33 54 19 161.60 0.54 89 33 58 23 162.05 0.46 90 33 63 28 162.32 0.45 91 33 64 29 162.28 0.44 92 33 65 30 162.12 0.49 93 33 104 68 161.99 0.55 94 33 106 70 162.06 0.51 95 34 39 3 168.12 2.08 96 34 40 4 162.40 0.41 97 34 41 5 162.34 0.44 98 34 63 27 162.32 0.45 99 34 64 28 162.30 0.43 100 34 66 30 162.29 0.44 101 37 41 4 169.70 1.38 102 37 60 23 168.94 2.82 103 37 62 25 162.56 0.37 104 45 121 75 220.69 0.15 105 46 120 73 246.08 0.78 106 46 121 74 238.71 2.90 107 47 120 72 284.56 1.90 108 47 121 73 254.44 3.40 109 47 123 75 205.38 3.77 110 47 238 186 65.09 0.87 111 47 242 190 29.93 0.10 112 51 242 186 29.92 0.10 113 51 245 189 23.02 0.06 114 53 238 180 65.02 0.90 115 71 153 80 159.97 0.23 116 71 154 81 159.13 0.21 117 71 155 82 158.58 0.32 118 72 153 79 159.96 0.23 119 72 154 80 159.62 0.28 120 73 153 78 159.97 0.23 121 74 153 77 159.99 0.23 122 87 245 154 22.14 0.38 123 89 237 144 76.26 0.89 124 89 241 148 56.79 0.04 125 89 245 152 21.61 0.08 126 91 234 139 106.58 0.03 127 91 237 142 80.84 0.88 128 92 237 141 92.00 0.34 129 98 180 80 202.49 20.91 130 99 180 79 160.02 0.33 131 100 177 75 159.70 0.24 132 100 179 77 159.98 0.34 133 100 180 78 160.00 0.34 134 101 179 76 159.97 0.34 135 101 234 129 121.12 6.90 136 102 229 123 156.09 1.30 137 103 229 122 156.09 1.30 138 103 234 127 94.83 0.94 139 103 237 130 76.22 1.24 140 103 238 131 69.55 1.01 141 105 237 128 75.64 0.95 142 105 238 129 65.53 0.64 143 105 241 132 31.38 0.82 144 105 242 133 30.23 0.26 145 107 245 134 22.12 0.39 146 121 209 84 286.81 0.48 147 122 204 82 282.27 2.74 148 122 209 83 258.54 4.60 149 123 204 81 241.18 3.23 150 123 209 82 197.09 1.03 151 123 231 104 286.36 1.85 152 123 235 108 73.61 1.35 153 123 238 111 67.97 1.80 154 124 204 80 200.19 3.25 155 124 209 81 181.27 0.66 156 124 210 82 164.73 2.62 157 124 232 104 169.84 31.51 158 124 235 107 78.45 0.96 159 127 210 80 161.25 0.96 160 128 210 79 155.07 0.94 161 129 134 4 157.92 0.44 162 129 162 32 140.08 0.83 163 129 210 78 156.50 1.14 164 130 134 3 178.12 0.64 165 130 162 31 140.22 0.85 166 132 162 30 140.28 0.88 167 132 163 31 140.56 0.95 168 132 164 32 140.57 0.94 169 133 161 28 140.29 0.89 170 133 162 29 140.60 0.96 171 134 161 27 140.60 0.95 172 134 162 28 140.62 0.96 173 135 159 24 140.55 0.93 174 135 160 25 140.60 0.95 175 135 161 26 140.60 0.95 176 135 184 50 161.44 0.15 177 136 159 23 140.56 0.93 178 136 160 24 140.60 0.95 179 136 162 26 142.78 0.20 180 137 157 20 140.10 0.81 181 137 158 21 140.46 0.97 182 137 159 22 140.56 0.93 183 138 157 19 139.93 0.71 184 138 158 20 140.12 0.81 185 138 160 22 140.67 0.94 186 138 183 45 161.40 0.17 187 138 228 88 156.58 1.20 188 139 155 16 140.62 0.96 189 139 156 17 140.53 0.93 190 139 157 18 140.09 0.82 191 140 155 15 140.60 0.96 192 140 156 16 140.56 0.94 193 141 151 10 159.31 0.15 194 141 152 11 159.12 0.21 195 141 153 12 158.88 0.29 196 141 154 13 151.84 2.80 197 141 155 14 140.60 0.95 198 142 151 9 159.53 0.27 199 142 152 10 159.31 0.16 200 143 148 5 161.91 0.36 201 143 149 6 160.06 0.36 202 143 150 7 159.72 0.30 203 143 151 8 159.56 0.26 204 143 191 50 194.65 4.95 205 144 150 6 160.17 0.34 206 144 152 8 159.83 0.39 207 144 156 12 140.60 0.98 208 145 148 3 171.03 2.40 209 145 149 4 161.90 0.35 210 145 150 5 161.43 0.46 211 146 220 71 159.10 0.17 212 146 221 72 159.11 0.18 213 151 192 43 159.41 0.18 214 152 156 4 161.93 0.46 215 158 188 32 140.55 0.97 216 158 189 33 140.53 0.96 217 159 184 26 152.90 5.18 218 160 184 24 140.53 0.97 219 160 184 25 140.62 0.96 220 161 183 22 153.02 5.26 221 161 184 23 152.92 5.20 222 161 184 24 152.98 5.18 223 162 181 19 231.40 18.22 224 162 182 20 182.25 1.08 225 162 183 21 153.24 5.36 226 163 182 19 214.36 9.71 227 163 183 20 182.15 1.03 228 163 184 21 172.03 4.01 229 163 185 23 158.76 2.61 230 163 225 60 151.46 0.58 231 171 223 50 159.39 0.15 232 171 224 51 159.35 0.16 233 171 225 52 159.35 0.16 234 172 215 41 159.71 0.29 235 172 216 42 159.49 0.21 236 172 217 43 159.50 0.18 237 172 224 50 159.40 0.15 238 172 225 51 159.40 0.15 239 172 227 53 159.27 0.10 240 175 215 38 159.80 0.35 241 176 215 37 159.99 0.31 242 176 227 49 159.43 0.17 243 178 230 50 159.10 0.18 244 178 233 53 155.85 1.37 245 179 229 48 159.10 0.18 246 179 230 49 158.97 0.18 247 179 233 52 152.70 0.73 248 179 234 53 144.62 0.01 249 180 215 33 160.05 0.33 250 180 227 45 159.22 0.18 251 180 228 46 159.09 0.18 252 180 230 48 158.08 0.50 253 181 199 20 161.38 0.17 254 181 210 27 160.10 0.35 255 181 211 28 160.10 0.35 256 181 227 44 159.10 0.18 257 181 228 45 159.08 0.18 258 181 229 46 159.00 0.16 259 181 230 47 157.97 0.54 260 182 225 41 159.21 0.17 261 182 226 42 159.09 0.18 262 182 227 43 158.19 0.45 263 182 228 44 158.30 0.51 264 183 225 40 159.37 0.17 265 183 226 41 159.16 0.18 266 183 228 43 159.02 0.15 267 184 188 5 273.06 1.31 268 185 222 34 161.37 0.16 269 185 223 35 160.98 0.17 270 185 225 37 159.71 0.17 271 186 222 33 161.40 0.17 272 187 221 30 161.69 0.25 273 187 221 31 161.66 0.25 274 187 222 32 161.58 0.25 275 188 221 29 162.99 0.86 276 188 221 28 178.74 0.17 277 189 221 27 208.50 7.63 278 189 226 33 158.12 0.45 279 190 228 34 156.17 1.43 280 199 228 25 157.72 0.68 281 209 231 22 114.89 1.00 282 210 230 20 155.96 1.38 283 210 231 21 123.36 1.50 284 210 232 22 110.23 0.17 285 211 229 18 156.20 1.39 286 211 231 20 115.31 0.39 287 212 228 16 156.29 1.39 288 212 229 17 155.83 1.30 289 212 231 19 113.38 1.35 290 213 228 15 155.95 1.26 291 214 227 13 157.85 0.61 292 214 228 14 156.44 1.12 293 214 229 15 155.93 1.30 294 215 226 11 159.09 0.18 295 215 227 12 158.22 0.45 296 216 227 11 158.25 0.43 297 217 224 7 192.64 3.83 298 231 235 4 285.25 0.86 299 231 238 7 69.58 1.02 300 232 235 3 129.56 20.55 301 234 237 3 73.42 1.35 302 234 238 4 69.83 1.03 303 235 238 3 69.80 1.19 304 235 239 4 69.42 1.19 305 236 239 3 69.61 1.09 306 236 240 4 69.32 1.14 307 237 240 3 65.07 0.87 308 237 241 4 64.69 1.02 309 238 241 3 31.42 0.80 310 238 242 4 30.24 0.25 311 239 242 3 31.41 0.80 312 239 243 4 30.24 0.26 313 240 243 3 31.80 0.61 314 240 244 4 30.28 0.24 315 241 244 3 48.33 9.21 316 241 245 4 29.65 0.40 317 242 245 3 30.12 0.15