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 40.09 0.96 2 16 140 119 40.22 1.02 3 16 142 121 40.48 0.86 4 16 143 122 48.24 0.64 5 16 144 123 48.30 0.61 6 16 156 134 42.40 0.50 7 16 157 135 43.55 0.02 8 16 158 136 41.73 0.89 9 16 189 169 47.25 0.84 10 16 190 170 40.52 1.23 11 16 194 174 39.98 0.96 12 17 143 121 48.77 0.62 13 17 144 122 48.59 0.71 14 17 145 123 50.01 0.50 15 17 158 135 49.48 0.78 16 17 188 166 49.41 0.75 17 17 1188 167 49.38 0.74 18 17 189 168 48.30 0.60 19 17 191 170 48.41 0.55 20 17 220 194 48.61 0.47 21 17 221 195 49.23 0.77 22 18 158 134 50.00 0.80 23 18 188 165 49.61 0.84 24 18 1188 166 49.39 0.74 25 19 157 132 50.82 0.39 26 19 158 133 49.95 0.77 27 20 156 130 89.17 1.03 28 20 157 131 62.06 1.19 29 20 158 132 182.46 0.65 30 20 159 133 273.56 0.91 31 21 71 47 134.89 0.16 32 21 154 127 141.91 0.17 33 21 155 128 144.91 0.72 34 21 156 129 142.23 0.28 35 22 26 4 170.34 2.92 36 22 27 5 158.74 1.89 37 22 71 46 134.97 0.20 38 22 139 112 134.05 0.04 39 22 155 127 153.45 0.12 40 22 156 128 185.30 0.98 41 23 26 3 192.59 4.64 42 24 71 44 137.96 1.35 43 25 28 3 179.16 4.54 44 25 69 41 137.69 0.81 45 25 71 43 139.60 0.77 46 25 77 49 141.41 0.15 47 25 79 51 140.00 0.72 48 25 117 89 135.28 0.28 49 27 30 3 222.30 18.09 50 27 137 105 137.78 1.53 51 27 139 107 137.97 0.81 52 27 157 124 274.64 0.27 53 28 117 86 140.00 0.72 54 28 118 87 139.50 0.62 55 28 119 88 138.62 0.99 56 29 45 14 138.40 1.10 57 29 46 15 138.16 1.12 58 29 119 87 139.71 0.72 59 29 120 88 138.53 1.07 60 29 121 89 137.31 1.02 61 29 198 165 139.71 0.72 62 29 200 167 139.81 0.67 63 30 43 11 140.15 0.78 64 30 44 12 140.09 0.77 65 30 139 104 140.12 0.79 66 30 141 106 143.63 0.49 67 30 155 119 261.49 0.37 68 30 198 164 140.09 0.78 69 31 43 10 140.75 0.64 70 31 44 11 140.13 0.78 71 31 45 12 140.13 0.77 72 31 46 13 140.15 0.76 73 31 52 19 140.13 0.77 74 31 65 32 143.65 0.48 75 31 66 33 143.52 0.53 76 31 67 34 142.44 0.68 77 31 141 105 143.66 0.48 78 32 40 6 147.09 0.01 79 32 42 8 144.87 1.03 80 32 65 31 143.86 0.43 81 32 66 32 143.66 0.49 82 32 73 38 146.81 0.14 83 32 141 104 143.67 0.48 84 33 40 5 147.31 0.01 85 33 41 6 147.30 0.00 86 33 42 7 144.97 0.99 87 33 43 8 144.78 1.03 88 33 54 19 144.84 1.01 89 33 58 23 147.19 0.05 90 33 63 28 145.21 0.97 91 33 64 29 145.13 0.97 92 33 65 30 145.06 0.96 93 33 104 68 147.09 0.03 94 33 106 70 145.06 0.99 95 34 39 3 190.80 9.48 96 34 40 4 147.31 0.00 97 34 41 5 147.34 0.01 98 34 64 28 145.15 0.97 99 34 66 30 145.18 0.95 100 37 41 4 190.03 8.53 101 37 60 23 268.40 1.61 102 45 121 75 225.80 1.49 103 46 120 73 274.48 0.30 104 46 121 74 268.93 2.96 105 47 121 73 274.48 0.27 106 47 123 75 198.66 1.98 107 47 242 189 25.10 0.45 108 48 242 188 25.11 0.45 109 51 241 184 44.18 1.11 110 51 242 185 24.89 0.55 111 53 238 179 59.30 0.89 112 71 153 79 140.53 0.54 113 71 154 80 139.64 0.76 114 71 155 81 138.97 1.07 115 72 153 78 140.41 0.59 116 72 154 79 139.80 0.78 117 73 153 77 140.55 0.54 118 74 153 76 140.74 0.62 119 89 237 143 69.98 0.14 120 89 241 147 38.08 6.92 121 90 237 142 72.24 1.27 122 91 234 138 104.28 1.03 123 91 237 141 69.98 0.14 124 92 237 140 87.31 1.57 125 98 180 79 202.99 1.83 126 99 180 78 186.62 8.38 127 100 177 74 147.18 0.25 128 100 179 76 146.81 0.41 129 100 180 77 146.80 0.42 130 101 179 75 146.21 0.35 131 101 234 128 117.25 3.08 132 102 229 122 141.69 0.68 133 103 231 123 139.28 0.38 134 103 234 126 92.08 0.76 135 103 237 129 69.96 0.15 136 103 238 130 67.95 0.03 137 104 237 128 68.83 0.42 138 105 237 127 68.03 0.04 139 105 238 128 61.30 0.12 140 105 241 131 28.37 2.06 141 105 242 132 24.91 0.55 142 122 209 82 271.06 2.12 143 123 204 80 253.58 0.61 144 123 209 81 186.94 2.85 145 123 231 103 245.71 7.94 146 123 235 107 68.50 0.27 147 123 238 110 62.28 2.36 148 123 239 111 59.29 0.89 149 123 242 114 28.95 1.41 150 124 204 79 180.27 0.62 151 124 209 80 164.97 0.51 152 124 210 81 159.14 1.37 153 124 231 102 269.82 3.00 154 124 232 103 96.33 2.31 155 124 235 106 71.33 1.10 156 125 204 78 181.22 0.15 157 127 210 79 146.40 1.99 158 128 210 78 142.81 0.69 159 129 134 4 148.72 0.77 160 129 162 31 134.43 0.18 161 129 210 77 143.00 0.72 162 130 134 3 175.43 2.73 163 130 162 30 134.59 0.15 164 132 162 29 134.69 0.10 165 132 163 30 134.91 0.19 166 132 164 31 134.96 0.20 167 133 162 28 134.94 0.18 168 134 161 26 134.99 0.20 169 134 162 27 134.99 0.20 170 135 159 23 134.92 0.20 171 135 160 24 134.99 0.20 172 135 161 25 134.99 0.20 173 136 159 22 134.75 0.11 174 136 160 23 134.96 0.21 175 136 162 25 135.19 0.23 176 137 157 19 134.46 0.17 177 137 158 20 134.69 0.10 178 137 159 21 134.73 0.12 179 138 157 18 134.02 0.05 180 138 158 19 134.49 0.18 181 138 160 21 135.07 0.20 182 138 228 87 143.07 0.72 183 139 155 15 135.00 0.21 184 139 156 16 134.73 0.10 185 139 157 17 134.04 0.04 186 140 155 14 134.95 0.18 187 140 156 15 134.82 0.17 188 141 152 10 139.49 0.71 189 141 153 11 139.16 0.86 190 141 154 12 138.41 1.06 191 141 155 13 134.99 0.20 192 142 152 9 139.74 0.81 193 142 194 53 274.62 0.88 194 143 191 49 230.42 4.46 195 143 192 50 275.22 0.58 196 144 149 5 142.34 0.01 197 144 152 7 139.90 0.82 198 144 156 11 135.02 0.19 199 145 220 71 152.03 0.87 200 146 149 3 158.97 2.04 201 150 154 3 161.72 0.69 202 150 156 5 146.89 0.06 203 158 1188 32 134.59 0.17 204 158 189 33 134.49 0.17 205 159 1184 26 161.62 0.62 206 160 183 23 180.49 2.57 207 160 184 24 161.62 0.62 208 160 1184 25 161.50 0.56 209 160 228 66 134.75 0.09 210 161 183 22 202.91 3.43 211 161 184 23 174.62 2.62 212 161 1184 24 168.25 2.69 213 162 181 19 274.73 0.82 214 162 182 20 271.45 2.24 215 162 183 21 202.91 3.43 216 162 201 41 137.10 1.18 217 163 182 19 271.45 2.25 218 163 183 20 257.81 9.06 219 163 184 21 271.20 2.36 220 163 185 23 208.15 0.81 221 163 225 60 138.55 1.09 222 167 185 19 275.29 0.43 223 171 185 15 275.45 0.52 224 171 223 50 142.43 0.86 225 171 225 52 142.72 0.72 226 172 215 41 149.77 0.61 227 172 216 42 149.37 0.48 228 172 217 43 149.44 0.45 229 172 224 50 142.91 0.62 230 172 225 51 143.08 0.70 231 172 227 53 142.63 0.69 232 175 215 38 149.75 0.59 233 175 217 40 149.78 0.61 234 176 215 37 149.47 0.47 235 176 227 49 142.90 0.65 236 178 230 50 142.50 0.68 237 178 233 53 140.24 0.73 238 179 229 48 142.61 0.71 239 179 230 49 142.24 0.80 240 179 233 52 139.69 0.70 241 179 234 53 136.36 0.13 242 180 215 33 146.67 0.48 243 180 227 45 142.87 0.67 244 180 228 46 142.62 0.71 245 180 230 48 142.21 0.79 246 181 199 20 143.18 0.55 247 181 210 27 142.91 0.58 248 181 211 28 142.96 0.58 249 181 227 44 142.67 0.73 250 181 228 45 142.53 0.71 251 181 229 46 142.45 0.74 252 181 230 47 141.41 0.42 253 182 225 41 142.90 0.65 254 182 226 42 142.84 0.67 255 182 227 43 142.52 0.76 256 183 226 41 142.87 0.62 257 183 228 43 142.74 0.65 258 1184 1188 5 273.98 0.26 259 185 222 34 144.91 0.14 260 185 223 35 143.59 0.43 261 185 225 37 143.23 0.62 262 186 222 33 144.91 0.15 263 187 221 30 145.10 0.11 264 187 1221 31 145.06 0.12 265 187 222 32 145.02 0.11 266 188 221 29 145.14 0.12 267 1188 221 28 145.47 0.03 268 189 221 27 264.94 0.90 269 189 226 33 143.05 0.76 270 190 228 34 143.00 0.76 271 199 228 25 143.08 0.73 272 209 231 22 124.59 9.38 273 210 230 20 142.87 0.70 274 210 231 21 141.74 0.81 275 210 232 22 98.83 1.25 276 211 228 17 143.03 0.71 277 211 229 18 142.84 0.68 278 211 231 20 104.95 0.44 279 212 228 16 142.82 0.68 280 212 229 17 142.43 0.80 281 212 231 19 110.74 0.18 282 213 228 15 142.81 0.69 283 214 227 13 143.05 0.72 284 214 228 14 142.88 0.69 285 214 229 15 142.84 0.67 286 215 226 11 143.12 0.71 287 215 227 12 143.05 0.72 288 216 227 11 143.07 0.73 289 217 224 7 186.09 4.82 290 1221 224 3 274.88 0.08 291 230 234 4 273.44 0.81 292 231 234 3 273.55 0.85 293 231 235 4 272.77 0.99 294 231 238 7 66.72 0.40 295 232 235 3 77.90 2.14 296 234 237 3 68.54 0.25 297 234 238 4 67.98 0.01 298 235 238 3 68.00 0.02 299 235 239 4 67.51 0.01 300 236 239 3 67.72 0.01 301 236 240 4 67.50 0.01 302 237 240 3 59.60 0.73 303 237 241 4 57.55 0.08 304 238 241 3 53.16 0.03 305 238 242 4 25.13 0.45 306 239 242 3 27.36 1.18 307 239 243 4 25.13 0.45 308 240 243 3 35.62 1.55