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 58.58 1.08 2 16 140 119 58.47 1.15 3 16 142 121 58.22 0.97 4 16 143 122 62.21 1.86 5 16 144 123 62.56 1.83 6 16 156 135 61.01 2.02 7 16 157 136 59.89 0.85 8 16 158 137 59.01 1.30 9 16 189 170 61.02 1.27 10 16 190 171 58.02 0.94 11 16 194 175 58.02 0.94 12 17 143 121 62.73 1.76 13 17 144 122 62.68 1.79 14 17 145 123 63.02 1.75 15 17 146 124 63.88 1.31 16 17 188 167 67.67 0.61 17 17 188 168 62.79 1.74 18 17 189 169 62.29 1.82 19 17 191 171 62.29 1.82 20 17 220 195 62.77 1.73 21 17 221 196 62.77 1.73 22 18 158 135 67.71 0.58 23 18 188 166 67.67 0.61 24 18 188 167 62.91 1.69 25 19 157 133 67.88 0.48 26 19 158 134 64.59 0.97 27 20 137 112 86.64 1.02 28 20 156 131 120.79 17.16 29 20 157 132 120.61 18.66 30 20 158 133 197.84 5.28 31 20 159 134 276.21 4.09 32 21 154 128 146.32 4.39 33 21 155 129 145.91 4.59 34 21 156 130 133.99 10.96 35 22 26 4 160.97 0.96 36 22 27 5 158.09 0.35 37 22 139 112 135.99 1.04 38 22 155 128 162.00 1.02 39 22 156 129 195.69 0.20 40 23 26 3 176.99 0.59 41 24 71 44 141.22 0.42 42 25 28 3 171.80 1.83 43 25 69 41 140.87 0.72 44 25 79 51 151.75 2.08 45 25 117 89 138.87 0.12 46 27 30 3 185.60 1.39 47 27 137 105 139.93 0.71 48 27 139 107 145.19 0.06 49 28 116 85 151.97 1.98 50 28 117 86 151.56 2.00 51 28 118 87 149.18 1.12 52 28 119 88 147.53 0.56 53 29 45 14 147.18 0.74 54 29 46 15 145.15 0.27 55 29 119 87 149.94 1.25 56 29 120 88 147.22 0.72 57 29 121 89 144.98 0.18 58 29 137 103 151.99 1.99 59 29 198 166 151.59 2.02 60 29 200 168 151.62 2.02 61 30 43 11 152.69 2.29 62 30 44 12 151.97 1.97 63 30 139 104 152.16 2.04 64 30 140 105 155.87 0.87 65 30 141 106 156.71 0.75 66 30 155 120 204.67 18.66 67 30 198 165 151.63 2.01 68 31 43 10 156.06 0.94 69 31 44 11 152.34 2.15 70 31 46 13 152.00 1.98 71 31 52 19 152.00 1.98 72 31 65 32 156.60 0.80 73 31 66 33 156.60 0.80 74 31 67 34 156.09 0.88 75 31 141 105 156.75 0.76 76 32 40 6 157.21 0.65 77 32 42 8 156.78 0.73 78 32 65 31 156.75 0.76 79 32 66 32 156.69 0.78 80 32 73 38 156.89 0.77 81 32 141 104 156.75 0.75 82 33 40 5 157.33 0.64 83 33 41 6 157.16 0.61 84 33 42 7 156.81 0.73 85 33 43 8 156.76 0.75 86 33 54 19 156.76 0.75 87 33 58 23 157.14 0.60 88 33 63 28 157.25 0.67 89 33 64 29 157.19 0.68 90 33 65 30 156.81 0.75 91 33 104 68 157.09 0.59 92 33 106 70 157.08 0.59 93 34 39 3 161.73 0.68 94 34 40 4 157.38 0.61 95 34 41 5 157.37 0.61 96 34 63 27 157.28 0.68 97 34 64 28 157.24 0.68 98 34 66 30 157.19 0.65 99 37 41 4 171.46 0.62 100 37 60 23 173.97 8.83 101 37 62 25 160.07 0.69 102 40 73 32 286.51 0.71 103 45 121 75 216.12 0.68 104 46 120 73 254.06 0.01 105 46 121 74 236.27 0.80 106 47 121 73 257.87 0.74 107 47 123 75 204.05 2.14 108 47 238 186 56.77 4.90 109 47 242 190 30.49 0.38 110 48 242 189 30.50 0.38 111 51 242 186 30.48 0.38 112 51 245 189 24.25 0.33 113 71 153 80 154.15 1.08 114 71 154 81 151.90 1.97 115 71 155 82 150.20 1.71 116 72 153 79 154.13 1.08 117 72 154 80 152.02 2.04 118 73 153 78 154.20 1.06 119 74 153 77 154.78 0.79 120 87 245 154 23.78 0.04 121 89 237 144 78.62 2.06 122 89 241 148 32.77 0.64 123 89 245 152 23.80 0.02 124 91 234 139 118.35 6.34 125 91 237 142 82.22 0.35 126 92 237 141 103.49 1.42 127 98 180 80 219.89 12.31 128 99 180 79 155.70 1.23 129 100 177 75 154.34 0.91 130 100 179 77 154.44 0.88 131 100 180 78 155.21 1.26 132 101 179 76 154.34 0.91 133 101 234 129 118.29 2.44 134 102 229 123 153.38 0.63 135 103 229 122 153.34 0.65 136 103 234 127 103.50 1.41 137 103 237 130 77.49 2.55 138 103 238 131 69.09 0.84 139 105 237 128 69.83 0.91 140 105 238 129 56.52 5.15 141 105 241 132 32.48 0.90 142 105 242 133 30.48 0.37 143 107 245 134 22.18 0.71 144 122 204 82 282.55 0.14 145 122 209 83 273.72 2.39 146 123 204 81 263.03 2.63 147 123 209 82 199.63 0.92 148 123 231 104 149.28 1.60 149 123 235 108 73.68 0.70 150 123 238 111 57.61 4.89 151 123 239 112 56.76 4.91 152 124 204 80 189.34 3.09 153 124 209 81 175.97 3.27 154 124 210 82 166.81 0.42 155 124 231 103 286.20 1.42 156 124 232 104 132.65 8.29 157 124 235 107 74.95 0.07 158 127 210 80 159.92 1.20 159 128 210 79 152.25 0.01 160 129 134 4 166.62 0.79 161 129 162 32 137.40 0.33 162 129 210 78 154.72 0.69 163 130 134 3 185.05 1.60 164 130 162 31 138.47 0.10 165 132 162 30 138.54 0.14 166 132 163 31 138.72 0.21 167 132 164 32 138.75 0.21 168 133 161 28 138.61 0.17 169 133 162 29 138.75 0.21 170 134 161 27 138.75 0.21 171 134 162 28 138.78 0.21 172 135 159 24 138.66 0.18 173 135 160 25 138.78 0.21 174 135 161 26 138.78 0.21 175 136 159 23 138.67 0.18 176 136 160 24 138.78 0.21 177 136 162 26 139.97 0.68 178 137 157 20 137.97 0.14 179 137 158 21 138.63 0.19 180 137 159 22 138.66 0.18 181 138 157 19 137.27 0.10 182 138 158 20 137.78 0.14 183 138 160 22 138.85 0.21 184 138 228 88 154.91 0.71 185 139 155 16 138.78 0.22 186 139 156 17 138.31 0.04 187 139 157 18 135.97 1.03 188 140 155 15 138.77 0.23 189 140 156 16 138.44 0.13 190 141 151 10 156.18 0.91 191 141 152 11 154.27 1.20 192 141 153 12 153.91 1.07 193 141 154 13 147.44 0.60 194 141 155 14 138.77 0.22 195 142 151 9 156.22 0.93 196 142 152 10 156.21 0.94 197 143 148 5 157.01 0.71 198 143 149 6 156.46 0.89 199 143 150 7 156.34 0.90 200 143 151 8 156.22 0.93 201 143 191 50 198.25 0.43 202 143 192 51 286.23 1.08 203 144 150 6 156.38 0.92 204 144 152 8 156.22 0.92 205 144 156 12 138.75 0.21 206 145 148 3 165.02 0.14 207 145 150 5 156.47 0.90 208 146 220 71 155.90 1.09 209 146 221 72 155.88 1.10 210 146 221 73 155.88 1.09 211 151 192 43 156.23 0.94 212 151 193 44 156.22 0.93 213 152 156 4 162.88 0.60 214 158 184 27 138.75 0.23 215 158 188 32 138.72 0.22 216 158 189 33 138.30 0.02 217 159 184 26 138.82 0.21 218 160 184 24 138.73 0.24 219 160 184 25 138.81 0.21 220 161 183 22 150.57 6.15 221 161 184 23 150.40 6.05 222 161 184 24 150.44 6.00 223 162 181 19 250.43 9.05 224 162 182 20 164.70 13.21 225 162 183 21 150.59 6.15 226 162 201 41 147.15 0.75 227 163 182 19 202.49 9.16 228 163 183 20 164.71 13.16 229 163 184 21 171.36 9.83 230 163 185 23 159.56 1.66 231 163 225 60 148.07 0.29 232 171 223 50 156.06 0.85 233 171 224 51 156.06 0.85 234 171 225 52 156.06 0.85 235 172 215 41 155.84 1.04 236 172 216 42 155.81 1.03 237 172 217 43 155.65 1.05 238 172 224 50 156.13 0.88 239 172 225 51 156.13 0.88 240 172 227 53 155.29 0.59 241 175 215 38 155.72 1.10 242 176 215 37 155.84 1.16 243 176 227 49 156.03 0.92 244 178 230 50 154.99 0.77 245 178 233 53 153.28 0.58 246 179 229 48 155.69 0.88 247 179 230 49 154.81 0.69 248 179 233 52 149.53 0.97 249 179 234 53 149.09 1.07 250 180 215 33 156.48 0.86 251 180 227 45 156.04 0.91 252 180 228 46 155.59 0.99 253 180 230 48 154.77 0.68 254 181 199 20 156.61 0.85 255 181 210 27 156.15 0.92 256 181 211 28 156.37 0.81 257 181 227 44 155.96 0.89 258 181 228 45 155.52 1.02 259 181 229 46 154.88 0.72 260 181 230 47 154.68 0.72 261 182 225 41 156.08 0.87 262 182 226 42 155.97 0.89 263 182 227 43 154.90 0.72 264 183 225 40 156.13 0.89 265 183 226 41 156.06 0.86 266 183 228 43 155.72 0.91 267 184 188 5 286.41 0.42 268 185 222 34 156.47 0.92 269 185 223 35 156.29 0.92 270 185 225 37 156.21 0.89 271 186 222 33 156.85 0.73 272 187 221 30 156.96 0.73 273 187 221 31 156.94 0.74 274 187 222 32 156.91 0.75 275 188 221 29 156.97 0.73 276 188 221 28 183.42 8.62 277 189 221 27 216.16 7.71 278 189 226 33 154.66 0.77 279 190 228 34 154.38 0.56 280 199 228 25 154.85 0.70 281 209 231 22 135.60 6.62 282 210 230 20 154.08 0.60 283 210 231 21 139.00 6.17 284 210 232 22 132.28 8.18 285 211 228 17 154.85 0.70 286 211 229 18 154.15 0.67 287 211 231 20 132.28 8.18 288 212 228 16 154.77 0.71 289 212 229 17 153.34 0.55 290 212 231 19 114.78 1.92 291 213 228 15 153.69 0.69 292 214 227 13 154.98 0.74 293 214 228 14 154.44 0.58 294 214 229 15 153.38 0.54 295 215 226 11 155.64 1.06 296 215 227 12 155.53 1.01 297 217 224 7 189.59 2.48 298 221 224 3 286.75 1.04 299 231 235 4 286.34 1.59 300 231 238 7 69.41 1.01 301 232 235 3 83.83 0.62 302 234 237 3 72.32 0.04 303 234 238 4 69.42 1.01 304 235 238 3 69.75 1.18 305 235 239 4 69.42 1.02 306 236 239 3 72.17 0.11 307 236 240 4 69.23 1.09 308 237 240 3 56.52 5.14 309 237 241 4 55.84 5.00 310 238 241 3 67.83 0.68 311 238 242 4 32.48 0.90 312 239 242 3 49.25 9.28 313 239 243 4 30.50 0.38 314 240 243 3 33.10 0.58 315 240 244 4 30.62 0.43 316 241 244 3 52.09 10.84 317 241 245 4 29.89 0.52 318 242 245 3 48.27 9.24