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 59.06 1.34 2 16 140 119 58.99 1.36 3 16 142 121 59.04 1.42 4 16 143 122 63.02 2.33 5 16 144 123 63.67 2.07 6 16 156 135 61.15 2.10 7 16 157 136 59.97 1.73 8 16 158 137 59.95 1.74 9 16 189 170 60.15 0.95 10 16 190 171 58.83 1.41 11 16 194 175 58.91 1.37 12 17 143 121 63.88 2.05 13 17 144 122 63.77 2.10 14 17 145 123 65.08 1.54 15 17 146 124 65.17 1.51 16 17 188 167 68.53 0.19 17 17 188 168 65.04 1.54 18 17 189 169 63.40 2.16 19 17 191 171 63.59 2.09 20 17 220 195 65.09 1.53 21 17 221 196 65.14 1.50 22 18 158 135 69.23 0.18 23 18 188 166 68.55 0.18 24 18 188 167 65.08 1.53 25 19 157 133 69.22 0.18 26 19 158 134 66.77 1.41 27 20 137 112 83.39 0.60 28 20 156 131 86.36 0.03 29 20 157 132 74.80 0.70 30 20 158 133 212.59 2.10 31 20 159 134 277.77 0.77 32 21 154 128 137.35 0.04 33 21 155 129 148.60 5.96 34 21 156 130 110.31 0.49 35 22 26 4 170.15 0.14 36 22 27 5 149.72 8.36 37 22 139 112 135.62 0.83 38 22 155 128 165.38 0.01 39 22 156 129 201.36 3.02 40 23 26 3 178.27 0.43 41 24 71 44 139.95 0.90 42 25 28 3 171.18 0.52 43 25 69 41 141.67 1.76 44 25 79 51 160.47 1.42 45 25 117 89 141.06 0.21 46 27 30 3 175.39 1.58 47 27 137 105 139.82 0.77 48 27 139 107 148.62 1.78 49 27 157 125 282.27 2.13 50 28 116 85 157.06 0.18 51 28 117 86 156.84 0.07 52 28 118 87 153.81 0.27 53 28 119 88 151.33 0.10 54 29 45 14 147.22 0.73 55 29 46 15 146.94 0.88 56 29 119 87 153.81 0.27 57 29 120 88 151.32 0.09 58 29 121 89 146.94 0.88 59 29 137 103 157.53 0.27 60 29 198 166 157.21 0.16 61 29 200 168 157.10 0.22 62 30 43 11 158.76 0.59 63 30 44 12 157.55 0.26 64 30 139 104 157.56 0.26 65 30 140 105 157.65 0.29 66 30 141 106 160.83 1.25 67 30 155 120 207.27 17.36 68 30 198 165 157.25 0.14 69 31 43 10 158.86 0.65 70 31 44 11 157.56 0.26 71 31 45 12 157.56 0.26 72 31 46 13 157.52 0.24 73 31 52 19 157.56 0.26 74 31 65 32 165.24 1.75 75 31 66 33 165.25 1.74 76 31 67 34 165.24 1.75 77 31 141 105 161.06 1.28 78 32 40 6 165.34 2.00 79 32 42 8 161.09 1.28 80 32 65 31 165.31 1.72 81 32 66 32 165.28 1.73 82 32 73 38 165.89 1.74 83 32 141 104 161.06 1.28 84 33 40 5 165.60 1.89 85 33 41 6 163.33 0.99 86 33 42 7 162.50 0.59 87 33 43 8 161.32 1.18 88 33 54 19 161.97 0.77 89 33 58 23 165.12 1.74 90 33 63 28 165.85 1.84 91 33 64 29 165.71 1.90 92 33 65 30 165.33 1.71 93 33 104 68 165.03 1.80 94 33 106 70 163.59 1.03 95 34 39 3 172.19 0.26 96 34 40 4 165.81 1.78 97 34 41 5 165.81 1.78 98 34 63 27 165.88 1.84 99 34 64 28 165.78 1.85 100 34 66 30 165.85 1.82 101 37 41 4 172.22 0.26 102 37 60 23 175.78 0.02 103 37 62 25 166.06 1.85 104 45 121 75 213.80 0.42 105 46 120 73 259.36 6.96 106 46 121 74 236.26 0.80 107 47 121 73 259.06 1.34 108 47 123 75 211.11 1.40 109 47 238 186 56.05 5.25 110 47 242 190 30.29 0.48 111 48 242 189 30.41 0.42 112 51 242 186 30.27 0.48 113 51 245 189 21.41 0.21 114 71 153 80 163.37 1.50 115 71 154 81 161.08 0.74 116 71 155 82 158.04 0.65 117 72 153 79 162.07 0.94 118 72 154 80 161.63 1.02 119 73 153 78 162.18 0.89 120 74 153 77 162.18 0.89 121 87 245 154 24.18 0.21 122 89 237 144 78.62 2.06 123 89 241 148 31.75 0.14 124 89 245 152 24.16 0.20 125 91 234 139 118.35 6.34 126 91 237 142 79.45 1.73 127 92 237 141 103.73 1.30 128 98 180 80 208.37 18.12 129 99 180 79 207.73 18.39 130 100 177 75 171.81 0.43 131 100 179 77 190.74 9.91 132 100 180 78 171.91 0.51 133 101 179 76 171.87 0.51 134 101 234 129 120.70 5.17 135 102 229 123 154.29 1.07 136 103 229 122 154.28 1.06 137 103 234 127 103.59 1.34 138 103 237 130 77.50 2.55 139 103 238 131 68.84 0.90 140 105 237 128 71.03 0.03 141 105 238 129 56.05 5.26 142 105 241 132 30.97 0.14 143 105 242 133 30.27 0.48 144 107 245 134 20.88 0.06 145 122 204 82 281.44 0.69 146 122 209 83 262.70 7.41 147 123 204 81 229.94 3.71 148 123 209 82 198.50 1.50 149 123 231 104 226.75 3.35 150 123 235 108 74.06 0.48 151 123 238 111 56.38 5.32 152 124 204 80 187.63 1.27 153 124 209 81 178.07 6.04 154 124 210 82 161.62 1.58 155 124 232 104 114.16 3.42 156 124 235 107 77.64 0.12 157 127 210 80 157.10 0.21 158 128 210 79 152.56 0.27 159 129 134 4 164.71 0.25 160 129 162 32 137.35 0.05 161 129 210 78 154.89 0.77 162 130 134 3 182.52 1.76 163 130 162 31 137.65 0.08 164 132 162 30 137.80 0.07 165 132 163 31 138.24 0.12 166 132 164 32 138.28 0.12 167 133 161 28 137.97 0.01 168 133 162 29 138.27 0.12 169 134 161 27 138.27 0.12 170 134 162 28 138.31 0.13 171 135 160 25 138.25 0.12 172 135 161 26 138.28 0.14 173 136 159 23 138.04 0.04 174 136 160 24 138.10 0.07 175 136 162 26 139.80 0.76 176 137 157 20 137.53 0.07 177 137 158 21 137.91 0.08 178 137 159 22 138.04 0.04 179 138 157 19 137.35 0.06 180 138 158 20 137.38 0.04 181 138 160 22 138.38 0.14 182 138 228 88 155.21 0.91 183 139 155 16 138.33 0.12 184 139 156 17 138.00 0.02 185 139 157 18 135.52 0.89 186 140 155 15 138.33 0.12 187 140 156 16 138.00 0.02 188 141 151 10 157.95 0.36 189 141 152 11 157.58 0.25 190 141 153 12 157.53 0.27 191 141 154 13 150.54 0.92 192 141 155 14 138.34 0.12 193 142 151 9 159.83 1.29 194 142 152 10 157.96 0.36 195 143 148 5 164.16 0.97 196 143 149 6 160.72 1.32 197 143 150 7 160.10 1.22 198 143 151 8 159.88 1.28 199 143 191 50 205.38 5.33 200 144 150 6 160.73 1.32 201 144 152 8 160.04 1.24 202 144 156 12 138.28 0.11 203 145 148 3 169.10 0.39 204 145 150 5 160.85 1.27 205 146 220 71 157.94 0.35 206 146 221 72 157.93 0.35 207 146 221 73 157.91 0.36 208 151 192 43 159.75 1.22 209 152 156 4 165.40 0.41 210 158 184 27 138.37 0.15 211 158 188 32 138.33 0.14 212 158 189 33 138.31 0.14 213 159 184 26 138.44 0.18 214 160 184 24 138.28 0.12 215 160 184 25 138.38 0.15 216 161 183 22 159.27 10.33 217 161 184 23 138.33 0.14 218 161 184 24 138.60 0.16 219 162 181 19 219.86 0.48 220 162 182 20 213.46 1.28 221 162 183 21 159.27 10.33 222 162 201 41 150.25 0.80 223 163 182 19 213.47 1.28 224 163 183 20 195.49 7.71 225 163 184 21 170.39 4.84 226 163 185 23 166.85 6.54 227 163 225 60 151.66 0.01 228 171 223 50 160.20 1.46 229 171 224 51 160.06 1.51 230 171 225 52 160.06 1.51 231 172 215 41 171.57 0.40 232 172 216 42 166.31 0.12 233 172 217 43 164.10 0.02 234 172 224 50 160.29 1.46 235 172 225 51 160.30 1.45 236 172 227 53 159.93 1.47 237 175 215 38 171.67 0.41 238 176 215 37 171.71 0.40 239 176 227 49 160.06 1.45 240 178 230 50 157.20 0.25 241 178 233 53 154.36 0.03 242 179 229 48 157.20 0.24 243 179 230 49 156.69 0.46 244 179 233 52 151.76 0.14 245 179 234 53 149.21 1.13 246 180 215 33 171.84 0.43 247 180 227 45 157.75 0.35 248 180 228 46 157.20 0.24 249 180 230 48 156.45 0.35 250 181 199 20 160.85 1.22 251 181 210 27 160.40 1.22 252 181 211 28 160.41 1.22 253 181 227 44 157.25 0.23 254 181 228 45 157.16 0.23 255 181 229 46 157.13 0.23 256 181 230 47 156.13 0.45 257 182 225 41 157.75 0.35 258 182 226 42 157.25 0.23 259 182 227 43 157.10 0.21 260 183 225 40 157.75 0.32 261 183 226 41 157.68 0.32 262 183 228 43 157.16 0.23 263 184 188 5 265.56 6.45 264 185 222 34 161.06 1.21 265 185 223 35 160.80 1.28 266 185 225 37 160.72 1.25 267 186 222 33 161.74 1.20 268 187 221 30 167.76 1.48 269 187 221 31 165.80 0.83 270 187 222 32 161.72 1.18 271 188 221 29 167.97 1.41 272 188 221 28 169.39 0.70 273 189 221 27 237.69 8.14 274 189 226 33 154.94 0.84 275 190 228 34 155.08 0.70 276 199 228 25 155.63 0.70 277 209 231 22 118.66 0.13 278 210 230 20 154.25 1.08 279 210 231 21 122.48 1.78 280 210 232 22 111.62 2.16 281 211 228 17 155.63 0.70 282 211 229 18 154.74 0.84 283 211 231 20 113.86 1.45 284 212 228 16 154.86 0.83 285 212 229 17 153.16 0.53 286 212 231 19 125.81 3.71 287 213 228 15 153.91 0.36 288 214 227 13 156.47 0.28 289 214 228 14 154.44 0.52 290 214 229 15 154.41 0.53 291 215 226 11 157.15 0.23 292 215 227 12 156.51 0.38 293 217 224 7 167.91 5.41 294 221 224 3 266.98 3.54 295 231 235 4 280.87 0.96 296 231 238 7 56.45 5.46 297 232 235 3 86.95 3.85 298 234 237 3 71.05 0.26 299 234 238 4 69.01 0.82 300 235 238 3 68.85 0.90 301 235 239 4 68.84 0.90 302 236 239 3 71.68 0.35 303 236 240 4 68.84 0.90 304 237 240 3 56.16 5.32 305 237 241 4 54.26 6.16 306 238 241 3 47.59 7.78 307 238 242 4 30.75 0.28 308 239 242 3 35.07 1.00 309 239 243 4 30.72 0.27 310 240 243 3 34.51 1.28 311 240 244 4 33.62 1.73 312 241 244 3 48.23 9.05 313 241 245 4 29.82 0.61 314 242 245 3 48.27 9.24