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 44.55 0.82 2 16 140 119 44.70 0.73 3 16 142 121 44.70 0.73 4 16 143 122 58.49 2.79 5 16 144 123 58.91 2.58 6 16 156 135 53.99 3.02 7 16 157 136 53.91 3.06 8 16 158 137 53.25 2.71 9 16 189 170 57.85 2.72 10 16 190 171 44.54 0.81 11 16 191 172 44.54 0.81 12 16 194 175 44.54 0.81 13 17 143 121 58.95 2.60 14 17 144 122 58.94 2.60 15 17 145 123 59.83 2.18 16 17 146 124 61.42 1.49 17 17 188 167 59.89 2.04 18 17 188 168 59.54 2.17 19 17 189 169 58.70 2.48 20 17 191 171 58.79 2.52 21 17 220 195 59.65 2.22 22 17 221 196 59.55 2.16 23 18 158 135 63.95 0.07 24 18 188 166 59.90 2.04 25 18 188 167 59.55 2.17 26 19 157 133 63.80 0.14 27 19 158 134 62.08 1.01 28 20 137 112 88.53 0.70 29 20 156 131 93.49 1.41 30 20 157 132 77.16 0.09 31 20 158 133 197.62 4.11 32 20 159 134 279.62 1.83 33 21 154 128 148.81 4.30 34 21 155 129 158.64 0.54 35 21 156 130 147.93 4.71 36 22 26 4 169.67 0.03 37 22 27 5 164.48 1.63 38 22 139 112 139.06 0.54 39 22 155 128 166.70 1.25 40 22 156 129 199.40 0.27 41 23 26 3 180.44 1.14 42 24 71 44 142.91 0.92 43 24 117 90 141.19 0.21 44 25 69 41 140.72 0.18 45 25 79 51 156.33 0.51 46 25 117 89 140.71 0.18 47 27 30 3 175.50 0.43 48 27 139 107 145.40 0.56 49 28 116 85 156.43 0.55 50 28 117 86 156.41 0.55 51 28 118 87 156.18 0.57 52 28 119 88 150.34 0.42 53 29 45 14 151.16 1.70 54 29 46 15 146.95 0.38 55 29 119 87 156.19 0.57 56 29 120 88 148.68 0.45 57 29 121 89 146.96 0.38 58 29 198 166 156.31 0.62 59 29 200 168 156.28 0.57 60 30 43 11 156.90 0.42 61 30 44 12 156.55 0.52 62 30 139 104 156.90 0.42 63 30 140 105 157.05 0.47 64 30 141 106 158.81 0.58 65 30 155 120 201.90 12.12 66 30 197 164 156.50 0.53 67 30 198 165 156.44 0.57 68 31 43 10 156.93 0.42 69 31 44 11 156.68 0.54 70 31 45 12 156.62 0.56 71 31 46 13 156.90 0.42 72 31 52 19 156.63 0.56 73 31 65 32 158.86 0.62 74 31 65 33 158.86 0.62 75 31 66 34 157.72 0.39 76 31 141 105 158.87 0.58 77 32 40 6 159.35 0.77 78 32 42 8 158.81 0.59 79 32 65 31 158.93 0.64 80 32 65 32 158.91 0.65 81 32 73 38 159.31 0.74 82 32 141 104 158.86 0.59 83 33 40 5 159.38 0.77 84 33 41 6 159.35 0.77 85 33 42 7 158.93 0.64 86 33 43 8 158.84 0.58 87 33 52 17 158.87 0.60 88 33 54 19 158.86 0.60 89 33 58 23 159.30 0.81 90 33 63 28 159.32 0.80 91 33 64 29 159.34 0.78 92 33 65 30 159.23 0.77 93 33 106 70 159.22 0.78 94 34 39 3 166.03 0.39 95 34 40 4 159.38 0.77 96 34 41 5 159.59 0.67 97 34 63 27 159.35 0.78 98 34 64 28 159.34 0.78 99 34 65 30 159.33 0.75 100 37 41 4 167.31 0.46 101 37 60 23 167.17 0.40 102 45 121 75 214.33 0.79 103 46 120 73 251.31 4.48 104 46 121 74 230.81 1.54 105 47 120 72 284.51 2.06 106 47 121 73 256.55 7.09 107 47 123 75 203.34 1.52 108 47 238 186 62.30 3.23 109 47 242 190 31.64 0.14 110 48 242 189 31.70 0.17 111 51 242 186 31.64 0.14 112 51 245 189 19.62 0.70 113 71 153 80 157.03 0.48 114 71 154 81 156.23 0.54 115 71 155 82 155.94 0.59 116 72 153 79 156.99 0.51 117 72 154 80 156.58 0.57 118 73 153 78 157.04 0.48 119 74 153 77 157.18 0.51 120 87 245 154 24.69 0.47 121 89 237 144 76.73 1.24 122 89 241 148 50.31 0.88 123 89 245 152 25.31 1.00 124 91 234 139 104.84 0.38 125 91 237 142 82.02 0.56 126 92 237 141 93.09 0.77 127 98 180 80 213.34 23.31 128 99 180 79 168.99 1.16 129 100 177 75 168.93 1.17 130 100 179 77 168.97 1.15 131 100 180 78 168.93 1.17 132 101 179 76 168.87 1.19 133 101 234 129 115.34 4.84 134 102 229 123 157.08 0.39 135 103 229 122 157.01 0.39 136 103 234 127 95.36 1.84 137 103 237 130 76.03 0.58 138 103 238 131 72.48 0.55 139 104 237 129 74.93 0.36 140 105 237 128 74.92 0.36 141 105 238 129 61.90 3.42 142 105 241 132 40.91 3.82 143 105 242 133 31.68 0.16 144 107 245 134 17.88 0.18 145 122 204 82 277.78 3.32 146 122 209 83 265.26 2.77 147 123 204 81 247.47 11.67 148 123 209 82 201.27 1.15 149 123 231 104 220.42 24.71 150 123 235 108 75.03 0.07 151 123 238 111 69.00 0.21 152 123 239 112 61.95 3.40 153 124 204 80 198.92 0.20 154 124 209 81 182.03 1.49 155 124 210 82 171.75 3.64 156 124 232 104 107.14 1.55 157 124 235 107 77.97 0.69 158 127 210 80 158.78 0.49 159 128 210 79 157.18 0.41 160 129 134 4 173.96 1.07 161 129 162 32 138.77 0.56 162 129 210 78 158.47 0.63 163 130 134 3 183.05 0.24 164 130 162 31 140.06 0.07 165 132 162 30 140.06 0.07 166 132 163 31 140.15 0.06 167 132 164 32 140.24 0.07 168 132 165 33 140.41 0.04 169 133 161 28 140.09 0.06 170 133 162 29 140.19 0.05 171 134 161 27 140.21 0.07 172 134 162 28 140.27 0.07 173 135 159 24 140.13 0.07 174 135 160 25 140.25 0.06 175 135 161 26 140.26 0.06 176 136 158 22 140.12 0.07 177 136 159 23 140.12 0.07 178 136 160 24 140.23 0.07 179 136 162 26 140.44 0.06 180 137 157 20 139.59 0.20 181 137 158 21 139.85 0.18 182 137 159 22 140.07 0.07 183 138 157 19 139.71 0.22 184 138 158 20 139.71 0.22 185 138 160 22 140.34 0.07 186 138 228 88 158.59 0.59 187 139 155 16 140.33 0.07 188 139 156 17 139.82 0.21 189 139 157 18 139.06 0.54 190 140 155 15 140.33 0.07 191 140 156 16 140.00 0.10 192 141 151 10 157.06 0.45 193 141 152 11 156.56 0.54 194 141 153 12 156.42 0.52 195 141 154 13 148.44 0.42 196 141 155 14 140.33 0.07 197 142 151 9 157.08 0.45 198 142 152 10 157.05 0.47 199 143 148 5 159.62 0.66 200 143 149 6 158.37 0.82 201 143 150 7 158.24 0.85 202 143 151 8 157.06 0.45 203 143 191 50 204.29 0.86 204 144 150 6 158.41 0.84 205 144 152 8 157.84 0.84 206 144 156 12 139.91 0.18 207 145 148 3 177.79 0.08 208 145 149 4 159.35 0.79 209 145 150 5 159.10 0.69 210 145 191 48 184.33 0.45 211 146 220 71 157.45 0.69 212 146 221 72 157.78 0.84 213 151 192 43 158.02 0.74 214 152 156 4 169.75 0.83 215 158 188 32 139.97 0.20 216 158 189 33 139.66 0.25 217 159 184 26 140.34 0.08 218 160 184 24 140.04 0.12 219 160 184 25 140.33 0.08 220 161 183 22 181.74 1.73 221 161 184 23 173.37 1.43 222 161 184 24 173.37 1.43 223 162 181 19 244.75 1.33 224 162 182 20 190.47 0.45 225 162 183 21 185.14 0.03 226 162 201 41 141.53 0.38 227 163 182 19 223.13 10.53 228 163 183 20 188.31 1.49 229 163 184 21 188.31 1.49 230 163 185 23 185.07 0.07 231 163 225 60 151.56 1.01 232 167 185 19 280.95 0.11 233 171 223 50 158.25 0.50 234 171 224 51 158.52 0.58 235 171 225 52 158.55 0.58 236 172 215 41 168.72 1.23 237 172 216 42 168.62 1.22 238 172 217 43 167.96 0.89 239 172 224 50 158.59 0.59 240 172 225 51 158.59 0.59 241 172 227 53 158.03 0.35 242 175 215 38 168.94 1.14 243 176 215 37 168.94 1.14 244 176 227 49 158.53 0.60 245 178 230 50 158.38 0.53 246 178 233 53 156.69 0.51 247 179 229 48 158.38 0.53 248 179 230 49 157.20 0.43 249 179 233 52 146.81 0.06 250 179 234 53 146.07 0.38 251 180 215 33 168.95 1.14 252 180 227 45 158.58 0.59 253 180 228 46 158.50 0.59 254 180 230 48 157.10 0.47 255 181 210 27 158.71 0.56 256 181 211 28 158.71 0.56 257 181 227 44 158.52 0.57 258 181 228 45 157.90 0.30 259 181 229 46 157.20 0.43 260 181 230 47 157.01 0.46 261 182 225 41 158.59 0.59 262 182 226 42 158.55 0.58 263 182 227 43 157.24 0.43 264 183 225 40 158.61 0.58 265 183 226 41 158.58 0.58 266 183 228 43 157.68 0.21 267 184 225 39 158.62 0.58 268 184 188 5 279.62 0.85 269 185 222 34 159.01 0.49 270 185 223 35 158.77 0.53 271 185 225 37 158.67 0.55 272 186 222 33 159.11 0.44 273 187 221 30 159.33 0.48 274 187 221 31 159.24 0.45 275 187 222 32 159.15 0.43 276 188 221 29 165.21 2.45 277 188 221 28 167.97 1.50 278 189 220 26 285.80 0.04 279 189 221 27 167.98 1.49 280 189 226 33 157.94 0.28 281 190 228 34 157.30 0.41 282 199 228 25 158.56 0.59 283 209 231 22 116.92 2.23 284 210 229 19 158.59 0.59 285 210 230 20 157.22 0.39 286 210 231 21 122.18 0.41 287 211 228 17 158.57 0.59 288 211 229 18 157.96 0.35 289 211 231 20 112.41 0.74 290 212 228 16 158.50 0.58 291 212 229 17 157.19 0.43 292 212 231 19 110.41 0.23 293 213 228 15 157.34 0.36 294 214 227 13 158.57 0.60 295 214 228 14 158.52 0.62 296 214 229 15 157.34 0.37 297 215 226 11 158.59 0.59 298 215 227 12 158.56 0.60 299 216 226 10 158.59 0.59 300 217 224 7 167.44 4.96 301 221 224 3 285.53 0.53 302 231 235 4 276.31 3.03 303 231 238 7 72.53 0.10 304 232 235 3 84.10 0.29 305 234 237 3 75.09 0.10 306 234 238 4 72.60 0.09 307 235 238 3 74.75 0.28 308 235 239 4 71.33 0.52 309 236 239 3 73.28 0.46 310 236 240 4 71.07 0.65 311 237 240 3 70.56 0.91 312 237 241 4 59.86 4.38 313 238 241 3 53.62 7.79 314 238 242 4 32.66 0.31 315 239 242 3 55.07 5.15 316 239 243 4 32.84 0.74 317 240 243 3 53.13 9.92 318 240 244 4 32.84 0.74 319 241 244 3 39.55 2.62 320 241 245 4 29.47 0.12