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 42.75 0.45 2 16 140 119 53.94 5.14 3 16 142 121 53.94 5.14 4 16 143 122 63.54 1.45 5 16 144 123 63.90 1.56 6 16 156 135 58.78 3.83 7 16 158 137 56.33 4.46 8 16 189 170 61.36 1.53 9 16 190 171 40.34 0.76 10 16 194 175 40.84 0.58 11 17 143 121 63.93 1.57 12 17 144 122 63.91 1.56 13 17 145 123 64.65 1.88 14 17 146 124 64.64 1.88 15 17 188 167 63.93 1.57 16 17 188 168 63.90 1.56 17 17 189 169 63.62 1.44 18 17 191 171 63.81 1.53 19 17 220 195 63.86 1.54 20 17 221 196 63.92 1.57 21 18 158 135 63.98 1.54 22 18 188 166 64.52 1.86 23 18 188 167 63.91 1.56 24 19 157 133 64.77 1.79 25 19 158 134 63.98 1.54 26 20 137 112 86.04 3.42 27 20 156 131 119.95 18.10 28 20 157 132 115.03 20.56 29 20 158 133 138.31 32.17 30 21 71 47 138.34 0.92 31 21 154 128 155.24 0.46 32 21 155 129 156.98 0.11 33 21 156 130 155.25 0.45 34 22 26 4 167.56 1.45 35 22 27 5 158.21 0.58 36 22 71 46 138.42 0.92 37 22 155 128 161.71 0.38 38 22 156 129 197.17 0.24 39 23 26 3 170.97 3.05 40 24 71 44 142.77 0.96 41 25 69 41 143.47 0.62 42 25 71 43 147.50 1.98 43 25 117 89 140.41 0.10 44 27 30 3 174.56 1.30 45 27 137 105 140.56 0.95 46 27 139 107 146.15 1.78 47 28 116 85 149.09 1.20 48 28 117 86 149.00 1.24 49 28 118 87 145.55 0.96 50 28 119 88 144.62 0.56 51 29 45 14 144.44 0.66 52 29 46 15 144.54 0.53 53 29 119 87 147.31 1.08 54 29 120 88 144.62 0.57 55 29 121 89 143.79 0.57 56 29 198 166 148.90 1.29 57 29 200 168 148.72 1.28 58 30 43 11 149.34 1.22 59 30 44 12 149.15 1.21 60 30 139 104 149.22 1.23 61 30 141 106 155.17 0.49 62 30 155 120 208.42 21.37 63 30 198 165 148.90 1.30 64 31 43 10 154.12 0.58 65 31 44 11 149.19 1.23 66 31 45 12 149.18 1.22 67 31 46 13 149.27 1.18 68 31 52 19 149.19 1.22 69 31 65 32 155.18 0.48 70 31 66 33 154.95 0.41 71 31 67 34 154.41 0.38 72 31 141 105 155.23 0.47 73 32 40 6 157.61 0.41 74 32 42 8 156.99 0.11 75 32 43 9 154.74 0.53 76 32 65 31 156.55 0.18 77 32 66 32 155.22 0.48 78 32 73 38 156.68 0.13 79 32 141 104 155.24 0.47 80 33 40 5 157.67 0.40 81 33 41 6 157.65 0.40 82 33 42 7 157.49 0.35 83 33 43 8 156.56 0.19 84 33 52 17 156.60 0.22 85 33 54 19 157.16 0.50 86 33 58 23 157.65 0.42 87 33 63 28 157.59 0.40 88 33 64 29 157.57 0.40 89 33 65 30 157.19 0.48 90 33 104 68 157.63 0.42 91 33 106 70 157.47 0.36 92 34 39 3 162.38 0.10 93 34 40 4 157.75 0.43 94 34 41 5 157.75 0.43 95 34 63 27 157.68 0.43 96 34 64 28 157.59 0.39 97 34 66 30 157.50 0.35 98 37 41 4 167.72 1.68 99 37 60 23 184.12 9.96 100 37 62 25 166.72 1.17 101 45 121 75 229.38 3.18 102 46 120 73 286.33 0.23 103 46 121 74 249.46 6.08 104 47 121 73 274.69 4.62 105 47 123 75 204.87 0.15 106 47 238 186 60.38 1.93 107 51 242 186 29.58 0.30 108 51 245 189 20.62 0.32 109 71 153 80 149.47 1.16 110 71 154 81 149.08 1.21 111 71 155 82 147.19 0.83 112 72 153 79 149.46 1.16 113 72 154 80 149.12 1.21 114 73 153 78 149.47 1.16 115 74 153 77 150.19 0.82 116 87 245 154 20.61 0.31 117 89 237 144 78.48 0.13 118 89 241 148 32.31 0.35 119 89 245 152 20.96 0.21 120 91 234 139 107.72 0.85 121 91 237 142 82.48 1.86 122 92 237 141 93.20 1.04 123 98 180 80 260.68 7.79 124 99 180 79 260.51 7.82 125 100 177 75 168.04 1.67 126 100 179 77 168.08 1.68 127 100 180 78 168.07 1.68 128 101 179 76 168.06 1.67 129 101 234 129 119.69 5.29 130 102 229 123 149.34 1.16 131 103 229 122 149.28 1.05 132 103 234 127 97.23 0.08 133 103 237 130 77.83 0.38 134 103 238 131 61.52 2.50 135 105 237 128 69.78 3.62 136 105 238 129 56.72 0.10 137 105 241 132 32.20 0.41 138 105 242 133 29.79 0.21 139 107 245 134 19.97 0.64 140 122 209 83 279.38 4.59 141 123 204 81 248.09 1.16 142 123 209 82 199.96 1.65 143 123 231 104 141.96 4.88 144 123 235 108 74.42 2.15 145 123 238 111 61.36 2.42 146 124 204 80 196.94 1.69 147 124 209 81 183.69 2.19 148 124 210 82 177.95 1.60 149 124 231 103 269.68 0.84 150 124 232 104 108.68 1.02 151 124 235 107 78.92 1.10 152 125 204 79 197.58 1.46 153 127 210 80 155.00 0.04 154 128 210 79 149.27 1.04 155 129 134 4 165.81 0.06 156 129 162 32 137.65 0.85 157 129 210 78 153.80 0.52 158 130 134 3 182.88 0.92 159 130 162 31 138.12 1.02 160 132 162 30 138.07 1.04 161 132 163 31 138.31 0.94 162 132 164 32 138.41 0.98 163 133 161 28 138.15 1.02 164 133 162 29 138.43 0.98 165 134 161 27 138.43 0.98 166 134 162 28 138.45 0.98 167 135 159 24 138.37 0.97 168 135 160 25 138.41 0.98 169 135 161 26 138.44 0.97 170 136 159 23 138.27 1.02 171 136 160 24 138.40 0.98 172 136 162 26 140.85 1.18 173 137 157 20 137.94 1.01 174 137 158 21 138.18 1.00 175 137 159 22 138.27 1.02 176 138 157 19 137.70 0.90 177 138 158 20 137.81 0.94 178 138 160 22 138.62 0.94 179 138 183 45 155.15 0.32 180 138 228 88 154.29 0.31 181 139 155 16 138.53 0.97 182 139 156 17 138.06 1.06 183 139 157 18 137.75 0.91 184 140 155 15 138.55 0.96 185 140 156 16 138.05 1.04 186 141 152 11 149.18 1.25 187 141 153 12 149.14 1.24 188 141 154 13 145.22 1.07 189 141 155 14 138.52 0.99 190 142 151 9 154.40 0.64 191 142 152 10 151.66 0.26 192 142 194 54 286.19 0.63 193 143 148 5 160.22 1.68 194 143 149 6 154.81 0.55 195 143 150 7 154.79 0.56 196 143 151 8 154.68 0.51 197 143 191 50 195.80 5.08 198 143 192 51 285.35 1.75 199 144 150 6 154.81 0.56 200 144 152 8 154.69 0.51 201 144 156 12 138.44 0.98 202 145 148 3 172.66 0.92 203 145 150 5 156.34 0.21 204 146 220 71 154.79 0.54 205 146 221 72 154.60 0.45 206 146 221 73 154.59 0.45 207 151 192 43 154.69 0.51 208 152 156 4 164.28 1.89 209 158 188 32 138.33 0.99 210 158 189 33 138.10 1.07 211 159 184 26 147.15 5.23 212 160 183 23 146.97 5.44 213 160 184 24 147.03 5.28 214 160 184 25 147.15 5.23 215 161 183 22 147.27 5.33 216 161 184 23 147.24 5.31 217 161 184 24 149.42 4.21 218 162 181 19 207.40 1.71 219 162 182 20 197.65 6.58 220 162 183 21 147.28 5.33 221 163 182 19 197.66 6.58 222 163 183 20 197.60 6.58 223 163 184 21 172.99 7.38 224 163 185 23 163.91 2.88 225 163 225 60 146.31 1.75 226 167 185 19 278.05 0.45 227 171 223 50 154.44 0.39 228 171 224 51 154.17 0.52 229 171 225 52 154.17 0.52 230 172 215 41 167.93 1.64 231 172 216 42 167.92 1.64 232 172 217 43 164.62 0.00 233 172 224 50 154.47 0.40 234 172 225 51 154.48 0.40 235 172 227 53 153.47 0.89 236 175 215 38 168.05 1.69 237 176 215 37 168.09 1.68 238 176 227 49 154.34 0.45 239 178 230 50 153.38 0.77 240 178 233 53 149.03 1.28 241 179 229 48 153.53 0.71 242 179 230 49 151.59 0.06 243 179 233 52 147.85 0.99 244 179 234 53 146.59 1.56 245 180 215 33 168.09 1.67 246 180 227 45 154.12 0.55 247 180 228 46 153.93 0.55 248 180 230 48 149.91 0.90 249 181 210 27 154.19 0.80 250 181 227 44 153.74 0.67 251 181 228 45 153.47 0.68 252 181 230 47 149.34 1.18 253 182 225 41 154.20 0.51 254 182 226 42 154.07 0.56 255 182 227 43 152.66 0.28 256 183 199 18 155.14 0.32 257 183 226 41 154.16 0.52 258 183 228 43 153.83 0.52 259 184 225 39 154.24 0.50 260 184 188 5 272.81 5.68 261 185 222 34 155.38 0.46 262 185 223 35 154.90 0.52 263 185 225 37 154.75 0.51 264 186 222 33 157.47 1.48 265 187 221 30 161.46 0.48 266 187 221 31 157.58 1.43 267 187 222 32 155.58 0.49 268 188 221 29 161.51 0.49 269 188 221 28 166.77 1.05 270 189 221 27 228.12 15.94 271 189 226 33 151.21 0.82 272 190 228 34 151.56 0.03 273 199 228 25 154.25 0.33 274 209 231 22 138.19 4.41 275 210 230 20 153.66 0.45 276 210 231 21 138.21 4.41 277 210 232 22 110.00 1.41 278 211 228 17 153.89 0.48 279 211 229 18 153.81 0.48 280 211 231 20 116.70 1.90 281 212 228 16 153.60 0.42 282 212 229 17 149.35 1.09 283 212 231 19 117.44 1.49 284 213 228 15 151.56 0.03 285 214 227 13 154.10 0.36 286 214 228 14 152.34 0.36 287 214 229 15 151.54 0.03 288 215 226 11 154.23 0.34 289 215 227 12 153.91 0.40 290 217 224 7 174.83 1.14 291 221 224 3 283.26 1.22 292 231 235 4 286.60 0.22 293 232 235 3 127.23 22.67 294 234 237 3 67.89 2.81 295 234 238 4 61.86 2.67 296 235 238 3 65.02 4.25 297 235 239 4 61.50 2.49 298 236 239 3 65.02 4.24 299 236 240 4 61.40 2.44 300 237 240 3 60.36 2.10 301 237 241 4 52.70 0.21 302 238 241 3 54.70 5.09 303 238 242 4 31.92 0.55 304 239 242 3 45.41 2.12 305 239 243 4 31.73 0.65 306 240 243 3 31.96 0.53 307 240 244 4 31.73 0.65 308 241 244 3 63.45 3.98 309 241 245 4 30.07 0.18 310 242 245 3 48.33 3.59