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 58.27 1.46 2 16 140 119 58.36 1.42 3 16 142 121 58.45 1.47 4 16 143 122 59.01 1.57 5 16 144 123 59.87 1.19 6 16 156 135 58.60 1.39 7 16 157 136 58.80 1.40 8 16 158 137 58.80 1.40 9 16 189 170 58.94 1.39 10 16 190 171 58.34 1.52 11 16 194 175 57.76 1.20 12 17 143 121 60.07 1.10 13 17 144 122 60.07 1.10 14 17 145 123 60.30 1.08 15 17 146 124 62.62 1.42 16 17 188 167 60.32 1.02 17 17 188 168 60.20 1.03 18 17 189 169 59.73 1.26 19 17 191 171 60.00 1.10 20 17 221 196 60.22 1.05 21 18 188 166 61.81 0.28 22 18 188 167 60.22 1.04 23 19 157 133 65.75 1.39 24 19 158 134 60.23 1.04 25 20 137 112 79.69 1.83 26 20 156 131 90.55 2.98 27 20 157 132 71.84 0.87 28 20 158 133 120.48 23.46 29 20 159 134 244.36 5.58 30 21 71 47 140.08 0.29 31 21 154 128 152.12 0.88 32 21 155 129 152.22 0.92 33 21 156 130 152.06 0.93 34 22 26 4 159.60 3.46 35 22 27 5 148.17 4.87 36 22 71 46 142.69 0.85 37 22 155 128 169.24 0.96 38 22 156 129 198.86 1.17 39 23 26 3 243.59 14.04 40 24 71 44 148.12 0.94 41 25 28 3 191.08 7.29 42 25 71 43 148.84 0.62 43 25 79 51 149.12 0.70 44 25 117 89 144.87 0.15 45 27 30 3 176.33 0.07 46 27 137 105 144.85 0.17 47 27 139 107 147.87 1.06 48 28 116 85 148.93 0.64 49 28 117 86 148.91 0.65 50 28 118 87 148.81 0.64 51 28 119 88 148.35 0.82 52 29 45 14 148.37 0.81 53 29 46 15 148.19 0.74 54 29 119 87 148.85 0.64 55 29 120 88 148.35 0.82 56 29 121 89 147.88 0.90 57 29 137 103 149.01 0.61 58 29 198 166 148.81 0.64 59 29 200 168 148.84 0.64 60 30 44 12 148.91 0.62 61 30 45 13 148.85 0.64 62 30 139 104 149.25 0.63 63 30 140 105 149.35 0.59 64 30 141 106 152.10 0.99 65 30 155 120 272.45 5.67 66 30 198 165 148.88 0.62 67 31 43 10 150.27 0.20 68 31 44 11 149.15 0.70 69 31 45 12 149.16 0.69 70 31 46 13 149.15 0.70 71 31 52 19 149.14 0.70 72 31 65 32 152.22 1.02 73 31 65 33 152.22 1.02 74 31 66 34 152.01 1.01 75 31 141 105 152.16 1.02 76 32 40 6 152.66 1.03 77 32 42 8 152.19 1.03 78 32 43 9 151.55 0.74 79 32 65 31 152.37 0.97 80 32 65 32 152.25 1.03 81 32 73 38 152.66 0.96 82 32 141 104 152.16 1.02 83 33 40 5 152.69 1.02 84 33 41 6 152.64 1.03 85 33 42 7 152.20 1.02 86 33 52 17 152.25 1.02 87 33 54 19 152.20 1.01 88 33 63 28 152.60 1.01 89 33 64 29 152.60 1.01 90 33 65 30 152.41 0.99 91 33 104 68 152.22 1.01 92 33 106 70 152.38 0.98 93 34 39 3 177.24 2.27 94 34 40 4 152.72 1.01 95 34 41 5 152.71 1.01 96 34 63 27 152.66 1.02 97 34 64 28 152.61 1.01 98 34 65 30 152.62 1.00 99 37 41 4 164.71 0.18 100 37 60 23 156.56 2.96 101 45 121 75 206.22 1.45 102 46 120 73 236.88 5.33 103 46 121 74 226.91 1.83 104 47 120 72 286.66 0.84 105 47 121 73 240.12 2.73 106 47 123 75 201.24 0.07 107 51 241 185 39.36 2.28 108 51 242 186 32.23 1.02 109 51 245 189 21.72 0.60 110 66 118 50 286.69 0.84 111 69 118 49 282.73 2.69 112 71 153 80 149.79 0.89 113 71 154 81 149.07 0.71 114 71 155 82 148.78 0.63 115 72 153 79 149.79 0.89 116 72 154 80 149.52 0.83 117 73 152 77 150.91 0.58 118 73 153 78 149.75 0.92 119 74 153 77 149.88 0.94 120 87 245 154 21.91 0.51 121 89 237 144 77.32 0.70 122 89 241 148 33.85 0.22 123 89 245 152 20.38 0.39 124 91 234 139 105.90 0.19 125 91 237 142 79.70 0.29 126 92 237 141 95.59 2.13 127 98 180 80 151.53 0.84 128 99 180 79 151.13 1.03 129 100 177 75 149.66 0.38 130 100 179 77 149.99 0.53 131 100 180 78 149.99 0.54 132 101 179 76 149.73 0.44 133 101 234 129 128.87 4.13 134 102 229 123 156.64 1.85 135 103 229 122 156.68 1.89 136 103 234 127 99.61 0.12 137 103 237 130 76.72 1.11 138 103 238 131 72.25 0.59 139 104 237 129 76.61 1.05 140 105 237 128 75.89 1.02 141 105 238 129 66.10 1.91 142 105 241 132 32.93 0.68 143 105 242 133 30.83 0.14 144 107 245 134 19.50 0.02 145 121 209 84 286.68 0.83 146 122 204 82 278.21 5.07 147 122 209 83 252.24 2.35 148 123 209 82 190.66 0.29 149 123 235 108 77.85 0.02 150 123 238 111 69.59 0.98 151 123 239 112 66.95 0.19 152 124 204 80 181.96 1.02 153 124 209 81 178.02 1.63 154 124 210 82 173.39 0.68 155 124 232 104 268.75 7.61 156 124 235 107 81.59 0.52 157 125 204 79 182.02 1.02 158 127 210 80 159.81 1.63 159 128 210 79 157.25 2.00 160 129 134 4 170.60 0.49 161 129 162 32 137.80 0.27 162 129 210 78 158.03 1.79 163 130 134 3 185.57 1.44 164 132 162 30 139.16 0.35 165 132 163 31 140.34 0.24 166 132 164 32 140.43 0.21 167 133 162 29 140.39 0.23 168 134 160 26 140.35 0.25 169 134 161 27 140.33 0.26 170 134 162 28 140.44 0.21 171 135 159 24 140.31 0.26 172 135 160 25 140.35 0.25 173 135 161 26 140.40 0.23 174 136 159 23 140.32 0.26 175 136 160 24 140.34 0.26 176 136 162 26 147.20 0.73 177 137 157 20 138.69 0.11 178 137 158 21 140.20 0.21 179 137 159 22 140.28 0.24 180 138 157 19 136.53 0.90 181 138 158 20 138.78 0.15 182 138 160 22 144.81 0.15 183 138 183 45 152.05 1.06 184 138 228 88 158.22 1.84 185 139 155 16 143.60 0.12 186 139 156 17 139.99 0.27 187 139 157 18 138.54 0.06 188 140 155 15 143.40 0.12 189 140 156 16 140.25 0.20 190 141 152 11 149.01 0.72 191 141 153 12 148.91 0.74 192 141 154 13 148.66 0.69 193 141 155 14 142.02 0.35 194 142 152 10 149.31 0.58 195 142 194 54 284.14 0.51 196 143 148 5 154.24 1.84 197 143 149 6 151.43 0.65 198 143 150 7 151.37 0.68 199 143 152 9 150.12 0.18 200 143 191 50 218.55 1.29 201 144 150 6 151.56 0.70 202 144 152 8 151.24 0.70 203 145 149 4 152.35 0.86 204 145 150 5 152.11 0.98 205 146 220 71 151.31 0.65 206 146 221 72 151.34 0.63 207 152 156 4 173.37 0.33 208 158 184 27 153.63 5.42 209 158 188 32 140.24 0.17 210 158 189 33 140.00 0.06 211 159 184 26 155.31 5.30 212 160 183 23 177.02 2.90 213 160 184 24 152.84 5.82 214 160 184 25 154.58 4.94 215 161 183 22 178.11 2.37 216 161 184 23 173.65 1.22 217 161 184 24 173.64 1.22 218 162 181 19 277.23 2.85 219 162 182 20 231.26 12.63 220 162 183 21 183.56 0.36 221 162 199 39 147.77 0.96 222 162 201 41 147.50 0.85 223 163 182 19 277.23 2.85 224 163 183 20 208.53 1.28 225 163 184 21 208.52 1.28 226 163 185 23 174.75 1.16 227 163 225 60 148.55 0.62 228 167 185 19 278.05 0.45 229 171 223 50 152.37 0.81 230 171 225 52 152.18 0.91 231 172 215 41 152.41 0.83 232 172 216 42 152.40 0.82 233 172 217 43 152.38 0.81 234 172 224 50 152.41 0.83 235 172 225 51 152.41 0.83 236 172 227 53 151.87 1.02 237 175 215 38 152.41 0.84 238 175 217 40 152.46 0.85 239 176 215 37 152.40 0.85 240 176 227 49 151.96 1.05 241 178 230 50 151.50 0.88 242 178 233 53 149.20 0.65 243 179 229 48 151.49 0.86 244 179 230 49 151.15 0.95 245 179 233 52 148.17 0.76 246 179 234 53 146.56 1.55 247 180 215 33 151.99 1.04 248 180 227 45 151.60 0.88 249 180 228 46 151.25 0.98 250 180 229 47 151.12 0.94 251 180 230 48 151.06 0.91 252 181 227 44 151.59 0.88 253 181 228 45 151.18 0.96 254 181 230 47 149.80 0.42 255 182 225 41 151.74 0.91 256 182 226 42 151.58 0.86 257 182 227 43 151.15 0.95 258 183 199 18 151.86 0.99 259 183 226 41 151.58 0.85 260 183 228 43 151.09 1.00 261 184 188 5 262.48 3.98 262 185 222 34 157.33 1.49 263 185 223 35 152.12 1.09 264 185 225 37 151.52 0.83 265 186 222 33 157.32 1.49 266 187 221 30 157.66 1.46 267 187 221 31 157.53 1.43 268 187 222 32 157.33 1.50 269 188 221 29 157.84 1.53 270 188 221 28 158.98 1.85 271 189 221 27 193.84 3.25 272 189 226 33 157.44 1.54 273 189 228 35 157.44 1.54 274 190 228 34 157.41 1.55 275 199 228 25 158.28 1.81 276 209 231 22 137.74 11.34 277 210 230 20 158.04 1.89 278 210 231 21 142.08 9.22 279 210 232 22 133.71 13.18 280 211 228 17 158.19 1.83 281 211 229 18 158.06 1.89 282 211 231 20 135.41 12.33 283 212 228 16 158.06 1.89 284 212 229 17 157.22 2.00 285 212 231 19 137.62 10.85 286 213 228 15 157.69 1.75 287 214 227 13 158.25 1.81 288 214 228 14 158.10 1.81 289 214 229 15 157.94 1.82 290 215 226 11 158.28 1.81 291 215 227 12 158.27 1.81 292 216 226 10 158.28 1.81 293 216 227 11 158.28 1.81 294 217 224 7 181.88 1.37 295 221 224 3 285.25 2.02 296 231 235 4 276.13 6.41 297 231 238 7 71.33 0.41 298 232 235 3 84.15 0.61 299 234 237 3 78.22 0.90 300 234 238 4 73.38 0.48 301 235 238 3 74.17 0.71 302 235 239 4 71.91 0.25 303 236 239 3 74.00 0.79 304 236 240 4 72.00 0.20 305 237 240 3 69.50 1.10 306 237 241 4 50.79 4.91 307 238 241 3 34.64 1.02 308 238 242 4 33.41 0.43 309 239 242 3 34.62 1.03 310 239 243 4 33.41 0.44 311 240 243 3 33.42 0.43 312 240 244 4 33.41 0.43 313 241 244 3 33.41 1.21 314 241 245 4 28.84 0.97 315 242 245 3 35.51 2.25