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 4 207 203 160.20 0.69 2 8 207 199 186.35 0.42 3 9 157 148 163.84 0.36 4 10 137 127 184.69 0.75 5 10 157 147 175.84 2.05 6 14 157 143 186.43 0.44 7 14 158 144 186.40 0.42 8 14 159 145 186.43 0.44 9 14 188 174 186.16 0.35 10 15 159 144 186.47 0.42 11 15 188 173 186.15 0.34 12 16 187 171 186.18 0.33 13 16 188 172 186.18 0.33 14 17 187 170 186.25 0.30 15 17 188 171 186.19 0.33 16 17 189 172 186.19 0.33 17 17 222 205 123.23 0.38 18 18 143 125 199.35 6.91 19 18 188 170 186.23 0.32 20 18 189 171 186.18 0.32 21 18 191 173 186.16 0.32 22 18 192 174 186.16 0.32 23 18 220 202 184.81 0.06 24 19 157 138 188.81 0.98 25 19 158 139 188.38 0.83 26 19 188 169 186.59 0.45 27 19 192 173 186.16 0.31 28 20 156 136 199.97 6.55 29 20 157 137 188.85 0.99 30 21 154 133 201.77 7.45 31 21 155 134 200.16 6.63 32 21 156 135 200.02 6.57 33 22 155 133 217.72 0.62 34 22 157 135 200.00 6.58 35 27 137 110 217.25 0.66 36 27 139 112 218.31 0.91 37 27 155 128 219.25 1.33 38 27 157 130 219.09 1.27 39 27 200 173 211.69 0.91 40 27 207 180 211.58 0.97 41 29 198 169 209.47 0.80 42 29 200 171 212.16 0.74 43 29 207 178 213.12 1.35 44 30 139 109 217.93 0.69 45 30 141 111 219.62 1.34 46 30 155 125 219.59 1.35 47 30 198 168 209.41 0.77 48 32 141 109 219.66 1.35 49 40 141 101 219.87 1.39 50 40 194 154 208.50 1.12 51 42 194 152 207.31 0.64 52 42 195 153 208.46 1.07 53 43 194 151 204.57 0.31 54 43 195 152 208.41 1.03 55 43 196 153 208.62 1.11 56 43 197 154 208.87 1.02 57 44 196 152 208.54 1.10 58 44 197 153 208.88 1.00 59 45 198 153 209.81 0.63 60 45 209 164 211.52 0.67 61 47 238 191 41.71 1.01 62 47 242 195 34.27 0.73 63 48 242 194 34.27 0.73 64 51 241 190 36.68 0.30 65 51 242 191 35.48 0.14 66 51 245 194 26.75 0.27 67 53 209 156 212.02 0.91 68 53 212 159 210.22 0.84 69 54 196 142 208.42 1.04 70 54 212 158 210.17 0.82 71 55 196 141 208.60 1.14 72 55 212 157 211.30 0.70 73 55 213 158 210.24 0.84 74 57 195 138 210.08 0.79 75 57 213 156 211.37 0.70 76 57 214 157 210.07 0.83 77 58 195 137 208.63 1.15 78 58 196 138 208.91 1.02 79 70 141 71 219.76 1.41 80 71 141 70 219.80 1.42 81 71 154 83 219.67 1.45 82 71 155 84 219.49 1.42 83 72 153 81 219.73 1.46 84 72 154 82 219.63 1.44 85 73 141 68 219.85 1.43 86 73 144 71 220.06 1.47 87 73 153 80 219.75 1.46 88 74 153 79 219.76 1.47 89 89 237 148 56.84 0.59 90 89 241 152 38.30 0.32 91 89 245 156 34.45 0.66 92 90 237 147 61.11 2.71 93 91 234 143 67.87 0.56 94 91 237 146 61.11 2.71 95 98 177 79 216.38 0.43 96 98 180 82 216.50 0.38 97 99 180 81 216.28 0.37 98 99 214 115 211.38 0.70 99 99 215 116 211.35 0.70 100 100 177 77 216.12 0.39 101 100 179 79 216.18 0.40 102 100 180 80 216.13 0.39 103 101 179 78 216.12 0.38 104 101 234 133 71.27 1.06 105 102 214 112 210.07 0.77 106 102 229 127 88.51 1.02 107 103 212 109 211.30 0.70 108 103 234 131 67.67 0.64 109 103 237 134 61.05 2.68 110 103 238 135 56.56 0.57 111 104 237 133 56.86 0.59 112 105 237 132 56.37 0.48 113 105 238 133 48.29 1.40 114 105 241 136 37.36 0.11 115 105 242 137 36.54 0.37 116 107 245 138 32.47 0.83 117 121 200 79 159.26 0.36 118 121 207 86 159.43 0.43 119 121 208 87 159.42 0.43 120 121 209 88 159.05 0.48 121 122 206 84 159.42 0.43 122 122 207 85 159.16 0.53 123 122 208 86 158.75 0.36 124 122 209 87 158.15 0.67 125 123 208 85 159.20 0.55 126 123 209 86 158.98 0.48 127 123 231 108 67.81 0.56 128 123 235 112 53.80 0.20 129 123 238 115 38.68 0.51 130 123 239 116 37.40 0.01 131 124 128 4 161.59 1.21 132 124 130 6 159.46 0.45 133 124 208 84 159.54 0.41 134 124 209 85 159.53 0.41 135 124 231 107 67.84 0.55 136 124 232 108 67.42 0.41 137 124 235 111 55.18 0.12 138 125 128 3 180.69 4.14 139 125 232 107 67.52 0.41 140 125 235 110 56.38 0.48 141 126 232 106 67.52 0.40 142 126 235 109 56.39 0.48 143 126 236 110 55.18 0.12 144 128 203 75 186.38 0.42 145 128 232 104 67.55 0.42 146 130 162 32 182.97 0.60 147 130 201 71 186.40 0.42 148 130 203 73 188.20 0.97 149 130 208 78 188.04 1.01 150 130 210 80 182.97 1.16 151 131 134 3 188.43 0.70 152 131 162 31 185.00 0.28 153 132 162 30 184.91 0.32 154 132 163 31 183.06 0.61 155 132 164 32 182.80 0.48 156 133 161 28 186.39 0.41 157 133 162 29 186.39 0.41 158 134 161 27 201.41 7.70 159 134 162 28 201.19 7.62 160 135 159 24 305.14 2.87 161 135 160 25 304.06 2.70 162 135 161 26 201.53 7.75 163 136 159 23 311.06 0.06 164 136 160 24 305.13 2.87 165 136 162 26 218.90 0.88 166 136 199 63 215.28 1.24 167 136 200 64 272.81 0.96 168 137 159 22 311.89 0.30 169 137 160 23 311.49 0.15 170 137 199 62 239.94 4.32 171 138 192 54 189.55 1.36 172 138 193 55 193.28 0.30 173 138 198 60 242.33 3.12 174 138 228 90 95.34 0.02 175 139 193 54 195.06 0.42 176 140 192 52 194.17 0.03 177 140 193 53 198.27 1.97 178 140 194 54 204.06 0.54 179 141 192 51 201.57 0.29 180 141 194 53 205.82 0.15 181 142 191 49 201.57 0.29 182 142 192 50 202.12 0.36 183 142 193 51 204.62 0.45 184 142 194 52 207.21 0.70 185 143 191 48 204.12 0.56 186 143 192 49 204.12 0.56 187 143 220 77 203.99 0.50 188 145 191 46 207.46 0.59 189 145 193 48 288.81 2.92 190 145 194 49 288.82 2.92 191 146 191 45 208.39 0.88 192 146 218 72 208.28 0.83 193 146 219 73 207.47 0.55 194 146 220 74 207.47 0.55 195 156 192 36 193.44 0.22 196 158 188 30 201.96 0.14 197 158 192 34 192.97 0.65 198 159 188 29 227.56 12.22 199 160 188 28 218.96 8.62 200 160 190 30 197.51 2.14 201 160 228 68 95.76 0.12 202 162 201 39 311.46 0.14 203 163 225 62 96.28 0.34 204 165 230 65 95.62 0.16 205 168 225 57 106.32 0.51 206 171 223 52 159.66 17.24 207 171 224 53 112.66 1.59 208 171 225 54 110.39 0.48 209 172 224 52 115.07 1.71 210 172 225 53 112.52 1.54 211 172 227 55 109.22 0.83 212 176 227 51 95.72 0.13 213 178 230 52 95.20 0.32 214 179 229 50 94.66 0.04 215 179 230 51 90.81 0.33 216 179 233 54 71.31 1.05 217 180 227 47 95.69 0.14 218 180 228 48 95.58 0.17 219 180 230 50 88.49 1.02 220 181 227 46 95.70 0.14 221 181 228 47 95.28 0.01 222 181 230 49 88.17 0.94 223 182 225 43 96.27 0.34 224 182 226 44 96.21 0.35 225 182 227 45 95.69 0.14 226 182 228 46 95.69 0.14 227 183 225 42 96.27 0.34 228 183 226 43 95.94 0.21 229 183 228 45 95.70 0.14 230 184 225 41 96.27 0.33 231 185 222 37 113.48 0.94 232 185 223 38 109.97 0.46 233 185 224 39 109.36 0.73 234 185 225 40 97.97 0.51 235 186 222 36 116.38 1.53 236 187 222 35 113.50 0.95 237 188 222 34 111.81 0.12 238 189 220 31 311.70 0.23 239 189 221 32 217.03 11.55 240 189 222 33 111.79 0.12 241 190 226 36 96.27 0.33 242 190 228 38 96.27 0.33 243 193 213 20 312.12 0.35 244 194 197 3 207.05 0.76 245 199 211 12 258.14 5.23 246 199 228 29 88.52 1.02 247 201 210 9 259.02 0.55 248 209 231 22 67.83 0.56 249 210 230 20 68.00 0.56 250 210 231 21 67.83 0.56 251 211 228 17 88.50 1.01 252 211 229 18 86.47 0.27 253 211 231 20 67.91 0.55 254 212 228 16 88.52 1.02 255 212 229 17 86.50 0.26 256 212 231 19 70.09 0.04 257 213 228 15 91.37 0.58 258 214 227 13 95.70 0.14 259 214 228 14 93.17 0.52 260 214 229 15 93.45 0.37 261 215 227 12 95.74 0.12 262 217 221 4 244.66 13.54 263 221 224 3 114.27 0.06 264 229 234 5 82.33 6.66 265 230 233 3 105.87 2.16 266 230 234 4 82.33 6.66 267 231 234 3 99.34 0.69 268 231 235 4 65.56 3.92 269 232 235 3 106.66 2.94 270 234 237 3 112.86 4.10 271 234 238 4 78.91 10.93 272 235 238 3 105.09 4.25 273 235 239 4 108.06 5.73 274 236 239 3 110.18 4.67 275 236 240 4 99.32 0.76 276 237 240 3 112.73 3.40 277 237 241 4 99.32 0.75 278 238 241 3 110.84 4.34 279 238 242 4 99.31 0.75 280 239 242 3 100.39 0.89 281 239 243 4 97.03 0.57 282 240 243 3 100.62 1.00 283 240 244 4 100.20 1.21 284 241 244 3 112.52 0.09 285 241 245 4 98.89 0.75 286 242 245 3 111.25 4.32