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 44.33 0.43 2 16 140 119 43.88 0.13 3 16 142 121 57.77 1.26 4 16 143 122 64.64 0.27 5 16 144 123 65.16 0.07 6 16 156 135 64.09 0.18 7 16 157 136 59.92 0.01 8 16 158 137 58.12 0.89 9 16 189 170 62.54 0.56 10 16 190 171 43.72 0.16 11 16 194 175 43.67 0.18 12 17 143 121 65.17 0.07 13 17 144 122 65.17 0.07 14 17 145 123 65.30 0.07 15 17 146 124 65.31 0.06 16 17 188 167 65.30 0.06 17 17 188 168 65.26 0.07 18 17 189 169 65.11 0.05 19 17 191 171 65.12 0.04 20 17 220 195 65.19 0.05 21 17 221 196 65.19 0.05 22 18 158 135 65.89 0.23 23 18 188 166 65.31 0.07 24 18 188 167 65.27 0.07 25 19 157 133 65.89 0.23 26 19 158 134 65.89 0.23 27 20 137 112 79.93 0.10 28 20 156 131 89.25 0.20 29 20 157 132 76.31 1.15 30 20 158 133 190.71 4.26 31 20 159 134 275.62 1.71 32 21 154 128 148.59 5.45 33 21 155 129 146.97 6.28 34 21 156 130 133.58 12.96 35 22 26 4 166.46 2.10 36 22 27 5 148.72 5.79 37 22 139 112 135.84 0.83 38 22 155 128 161.08 0.66 39 22 156 129 200.53 0.65 40 23 26 3 182.02 0.27 41 24 71 44 140.06 0.10 42 25 28 3 177.96 2.19 43 25 69 41 140.66 0.24 44 25 79 51 156.71 0.60 45 25 117 89 144.00 1.91 46 27 30 3 217.37 22.16 47 27 137 105 144.04 1.89 48 27 139 107 152.72 0.60 49 28 116 85 156.53 0.79 50 28 117 86 156.22 0.63 51 28 118 87 153.66 0.95 52 28 119 88 150.20 0.57 53 29 45 14 149.62 0.30 54 29 46 15 146.58 0.62 55 29 119 87 155.15 0.96 56 29 120 88 148.62 0.21 57 29 121 89 147.00 1.00 58 29 137 103 156.87 0.64 59 29 198 166 156.16 0.45 60 29 200 168 156.62 0.68 61 30 43 11 156.91 0.65 62 30 44 12 156.84 0.62 63 30 139 104 156.92 0.65 64 30 140 105 157.03 0.70 65 30 141 106 158.87 0.47 66 30 155 120 178.09 2.23 67 30 198 165 156.50 0.61 68 31 43 10 157.38 0.88 69 31 44 11 156.91 0.64 70 31 45 12 156.88 0.63 71 31 46 13 156.86 0.62 72 31 52 19 156.91 0.65 73 31 65 32 159.66 0.06 74 31 65 33 159.66 0.07 75 31 66 34 158.78 0.51 76 31 141 105 159.40 0.21 77 32 40 6 159.90 0.04 78 32 42 8 159.66 0.07 79 32 65 31 159.71 0.06 80 32 65 32 159.72 0.05 81 32 73 38 159.81 0.06 82 32 141 104 159.40 0.21 83 33 40 5 159.98 0.01 84 33 41 6 159.90 0.04 85 33 42 7 159.67 0.07 86 33 43 8 159.66 0.07 87 33 52 17 159.69 0.06 88 33 54 19 159.68 0.07 89 33 58 23 159.90 0.04 90 33 63 28 159.84 0.06 91 33 64 29 159.83 0.07 92 33 65 30 159.73 0.05 93 33 104 68 159.74 0.04 94 33 106 70 159.72 0.05 95 34 39 3 167.34 2.35 96 34 40 4 159.99 0.01 97 34 41 5 159.98 0.01 98 34 63 27 159.87 0.07 99 34 64 28 159.86 0.07 100 34 65 30 159.85 0.07 101 37 41 4 171.90 0.57 102 37 60 23 168.63 0.20 103 37 62 25 160.03 0.03 104 45 121 75 220.54 5.51 105 46 120 73 254.22 3.83 106 46 121 74 234.16 0.29 107 47 120 72 286.42 0.92 108 47 121 73 258.02 5.40 109 47 123 75 203.53 1.30 110 47 238 186 55.33 0.24 111 47 242 190 31.32 0.47 112 48 242 189 31.37 0.49 113 51 242 186 31.30 0.46 114 51 245 189 20.93 0.02 115 71 153 80 157.83 0.51 116 71 154 81 156.72 0.61 117 71 155 82 154.62 0.70 118 72 153 79 157.38 0.73 119 72 154 80 157.12 0.75 120 73 153 78 157.50 0.68 121 74 153 77 157.49 0.68 122 87 245 154 25.91 1.57 123 89 237 144 76.15 2.27 124 89 241 148 41.09 4.44 125 89 245 152 21.41 0.21 126 91 234 139 104.89 0.62 127 91 237 142 82.59 0.79 128 92 237 141 100.06 0.42 129 98 180 80 214.14 27.23 130 99 180 79 213.99 27.19 131 100 177 75 213.96 27.20 132 100 179 77 213.74 27.31 133 100 180 78 213.73 27.30 134 101 179 76 155.92 0.88 135 101 234 129 112.67 1.36 136 102 229 123 156.51 0.67 137 103 229 122 156.43 0.64 138 103 234 127 98.92 0.24 139 103 237 130 73.66 0.24 140 103 238 131 70.58 0.91 141 105 237 128 70.95 0.89 142 105 238 129 54.91 0.45 143 105 241 132 31.38 0.48 144 105 242 133 31.30 0.47 145 107 245 134 19.48 0.68 146 121 209 84 287.38 0.43 147 122 204 82 286.26 0.12 148 122 209 83 272.00 0.20 149 123 204 81 232.63 1.79 150 123 209 82 199.34 3.35 151 123 231 104 259.19 9.50 152 123 235 108 71.42 0.49 153 123 238 111 62.07 3.60 154 123 239 112 55.32 0.25 155 124 204 80 193.99 2.06 156 124 209 81 176.62 3.14 157 124 210 82 169.46 0.30 158 124 232 104 194.37 41.85 159 124 235 107 80.90 0.04 160 127 210 80 158.42 1.44 161 128 210 79 155.09 1.26 162 129 134 4 167.13 0.82 163 129 162 32 136.78 0.14 164 129 210 78 156.67 0.65 165 130 134 3 179.93 0.52 166 130 162 31 137.25 0.36 167 132 162 30 137.31 0.40 168 132 163 31 137.74 0.19 169 132 164 32 137.79 0.18 170 133 161 28 137.47 0.28 171 133 162 29 137.78 0.21 172 134 161 27 137.88 0.14 173 134 162 28 137.90 0.14 174 135 160 25 137.90 0.14 175 135 161 26 137.90 0.14 176 136 159 23 137.52 0.27 177 136 160 24 137.82 0.14 178 136 162 26 144.62 0.00 179 137 157 20 137.03 0.33 180 137 158 21 137.52 0.27 181 137 159 22 137.78 0.13 182 138 157 19 135.80 0.84 183 138 158 20 137.09 0.36 184 138 160 22 138.81 0.53 185 138 183 45 158.33 0.76 186 138 228 88 156.66 0.64 187 139 155 16 138.00 0.12 188 139 156 17 137.66 0.21 189 139 157 18 135.84 0.83 190 140 155 15 138.00 0.12 191 140 156 16 137.84 0.12 192 141 151 10 157.55 0.96 193 141 152 11 156.97 0.68 194 141 153 12 156.84 0.62 195 141 154 13 151.75 0.92 196 141 155 14 138.05 0.10 197 142 151 9 157.62 0.92 198 142 152 10 157.30 0.83 199 143 148 5 159.91 0.05 200 143 149 6 159.00 0.30 201 143 150 7 158.19 0.69 202 143 151 8 157.62 0.92 203 143 191 50 208.74 4.96 204 144 150 6 158.76 0.42 205 144 152 8 158.16 0.70 206 144 156 12 143.16 2.44 207 145 148 3 167.83 1.94 208 145 149 4 159.89 0.04 209 145 150 5 159.83 0.02 210 146 220 71 157.28 0.87 211 146 221 72 157.28 0.87 212 146 221 73 157.28 0.87 213 152 156 4 166.39 2.15 214 158 184 27 149.28 5.54 215 158 188 32 137.92 0.14 216 158 189 33 137.87 0.15 217 159 184 26 149.33 5.53 218 160 184 24 149.30 5.54 219 160 184 25 149.31 5.54 220 161 183 22 173.83 0.21 221 161 184 23 149.48 5.62 222 161 184 24 150.14 5.13 223 162 181 19 262.43 8.26 224 162 182 20 192.59 4.85 225 162 183 21 174.26 0.35 226 162 201 41 147.07 0.48 227 163 182 19 235.00 11.78 228 163 183 20 179.16 1.81 229 163 184 21 179.16 1.82 230 163 185 23 178.19 2.30 231 163 225 60 151.30 0.29 232 171 223 50 157.49 0.93 233 171 224 51 157.47 0.92 234 171 225 52 157.46 0.91 235 172 215 41 160.05 0.03 236 172 216 42 160.02 0.04 237 172 217 43 159.94 0.02 238 172 224 50 157.55 0.94 239 172 225 51 157.52 0.93 240 172 227 53 156.85 0.65 241 175 215 38 160.07 0.04 242 176 215 37 160.08 0.04 243 176 227 49 157.50 0.94 244 178 230 50 157.31 0.90 245 178 233 53 155.62 0.55 246 179 229 48 157.35 0.91 247 179 230 49 156.92 0.70 248 179 233 52 151.31 0.59 249 179 234 53 149.78 1.35 250 180 215 33 159.59 0.24 251 180 227 45 157.47 0.93 252 180 228 46 157.34 0.89 253 180 230 48 156.69 0.67 254 181 199 20 157.97 0.90 255 181 210 27 157.70 0.90 256 181 211 28 157.71 0.91 257 181 227 44 157.35 0.88 258 181 228 45 156.94 0.69 259 181 229 46 156.85 0.65 260 181 230 47 156.68 0.67 261 182 225 41 157.50 0.92 262 182 226 42 157.35 0.88 263 182 227 43 156.84 0.65 264 183 225 40 157.50 0.93 265 183 226 41 157.46 0.94 266 183 228 43 157.08 0.77 267 184 188 5 273.67 5.33 268 185 222 34 158.29 0.77 269 185 223 35 157.93 0.86 270 185 225 37 157.66 0.92 271 186 222 33 158.30 0.77 272 187 221 30 158.44 0.80 273 187 221 31 158.41 0.79 274 187 222 32 158.33 0.76 275 188 221 29 158.56 0.84 276 188 221 28 164.22 1.98 277 189 221 27 195.50 13.66 278 189 226 33 156.68 0.67 279 190 228 34 156.61 0.62 280 199 228 25 156.72 0.68 281 209 231 22 118.30 1.54 282 210 230 20 156.50 0.68 283 210 231 21 122.72 0.14 284 210 232 22 111.51 1.26 285 211 228 17 156.76 0.68 286 211 229 18 156.51 0.67 287 211 231 20 117.95 1.36 288 212 228 16 156.63 0.63 289 212 229 17 156.41 0.72 290 212 231 19 117.95 1.36 291 213 228 15 156.60 0.62 292 214 227 13 156.93 0.70 293 214 228 14 156.60 0.63 294 214 229 15 156.45 0.70 295 215 226 11 157.55 0.95 296 215 227 12 156.94 0.70 297 217 224 7 187.56 0.68 298 221 224 3 286.74 0.26 299 229 234 5 286.63 0.29 300 231 234 3 287.79 0.56 301 231 235 4 269.08 4.67 302 231 238 7 69.19 0.04 303 232 235 3 86.23 1.78 304 234 237 3 72.38 0.02 305 234 238 4 70.75 0.82 306 235 238 3 70.66 0.75 307 235 239 4 68.26 0.43 308 236 239 3 71.29 0.51 309 236 240 4 61.09 3.14 310 237 240 3 60.61 3.30 311 237 241 4 53.13 0.35 312 238 241 3 51.88 8.28 313 238 242 4 31.33 0.46 314 239 242 3 54.70 9.40 315 239 243 4 31.32 0.46 316 240 243 3 31.80 0.28 317 240 244 4 31.32 0.46 318 241 244 3 53.34 10.65 319 241 245 4 30.70 0.17 320 242 245 3 50.53 9.38