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 44.63 0.66 2 16 140 119 44.63 0.66 3 16 142 121 44.64 0.65 4 16 143 122 51.51 0.69 5 16 144 123 52.73 1.26 6 16 156 135 45.45 0.98 7 16 157 136 44.72 0.61 8 16 158 137 44.71 0.61 9 16 189 170 50.38 0.21 10 16 190 171 44.63 0.66 11 16 194 175 44.58 0.63 12 17 143 121 53.02 1.40 13 17 144 122 53.02 1.40 14 17 145 123 53.27 1.48 15 17 146 124 58.13 0.96 16 17 188 167 53.56 1.29 17 17 188 168 52.91 1.34 18 17 189 169 52.70 1.27 19 17 191 171 52.05 0.93 20 17 220 195 53.05 1.40 21 17 221 196 53.08 1.41 22 18 158 135 61.09 2.68 23 18 188 166 61.68 2.76 24 18 188 167 53.04 1.40 25 19 157 133 64.92 0.77 26 19 158 134 61.06 2.69 27 20 137 112 81.13 0.61 28 20 156 131 152.12 0.59 29 20 157 132 164.76 3.31 30 20 158 133 264.55 5.71 31 20 159 134 279.67 1.22 32 21 154 128 152.24 0.56 33 21 155 129 155.43 2.14 34 21 156 130 159.03 3.85 35 22 26 4 169.24 0.18 36 22 27 5 148.07 5.79 37 22 139 112 136.96 0.14 38 22 155 128 224.81 3.24 39 23 26 3 212.57 0.90 40 24 71 44 142.94 0.01 41 25 28 3 189.17 4.66 42 25 69 41 143.00 0.06 43 25 79 51 150.24 0.66 44 25 117 89 142.75 0.09 45 27 30 3 215.37 12.63 46 27 137 105 142.92 0.01 47 27 139 107 148.11 0.94 48 27 157 125 283.53 0.01 49 28 117 86 150.09 0.57 50 28 118 87 148.07 0.01 51 28 119 88 145.63 0.53 52 29 45 14 145.82 0.43 53 29 46 15 144.83 0.93 54 29 119 87 150.09 0.59 55 29 120 88 147.03 0.46 56 29 121 89 145.55 0.57 57 29 137 103 150.33 0.66 58 29 198 166 150.11 0.60 59 29 200 168 149.82 0.72 60 30 43 11 150.41 0.65 61 30 44 12 150.33 0.68 62 30 139 104 150.36 0.67 63 30 140 105 150.66 0.62 64 30 141 106 152.46 0.53 65 30 155 120 147.26 4.17 66 30 198 165 150.25 0.65 67 31 43 10 150.53 0.60 68 31 44 11 150.35 0.67 69 31 45 12 150.37 0.67 70 31 46 13 150.50 0.60 71 31 52 19 150.35 0.67 72 31 65 32 152.24 0.48 73 31 66 33 152.27 0.46 74 31 67 34 151.35 0.44 75 31 141 105 152.49 0.53 76 32 40 6 152.75 0.47 77 32 42 8 152.46 0.53 78 32 65 31 152.50 0.53 79 32 66 32 152.41 0.48 80 32 73 38 152.83 0.43 81 32 141 104 152.49 0.53 82 33 40 5 152.81 0.46 83 33 41 6 152.66 0.51 84 33 42 7 152.49 0.52 85 33 43 8 152.46 0.52 86 33 54 19 152.39 0.49 87 33 58 23 152.52 0.53 88 33 63 28 152.74 0.43 89 33 64 29 152.74 0.42 90 33 65 30 152.51 0.52 91 33 104 68 152.46 0.53 92 33 106 70 152.40 0.49 93 34 39 3 170.09 0.11 94 34 40 4 152.81 0.46 95 34 41 5 152.80 0.46 96 34 63 27 152.78 0.43 97 34 64 28 152.77 0.42 98 34 66 30 152.75 0.42 99 37 41 4 174.89 0.13 100 37 60 23 171.15 0.64 101 37 62 25 162.68 0.30 102 40 193 152 285.44 0.21 103 42 193 150 285.45 0.21 104 45 121 75 252.55 0.07 105 46 121 74 283.26 1.07 106 47 121 73 284.86 0.22 107 47 123 75 212.62 0.29 108 47 238 186 65.30 0.68 109 47 242 190 31.55 0.18 110 51 242 186 31.53 0.17 111 51 245 189 21.12 0.70 112 53 238 180 65.06 0.55 113 71 153 80 150.47 0.61 114 71 154 81 149.81 0.88 115 71 155 82 144.02 0.51 116 72 153 79 150.33 0.68 117 72 154 80 150.02 0.78 118 73 153 78 150.32 0.68 119 74 153 77 150.34 0.69 120 87 245 154 24.98 0.75 121 89 237 144 78.51 1.07 122 89 241 148 60.63 1.35 123 89 245 152 27.28 0.61 124 91 234 139 102.54 1.77 125 91 237 142 78.59 0.78 126 92 237 141 97.75 0.54 127 98 180 80 219.26 25.40 128 99 180 79 168.97 3.25 129 100 177 75 155.81 3.21 130 100 179 77 155.91 3.16 131 100 180 78 155.96 3.12 132 101 179 76 155.80 3.19 133 101 234 129 117.81 2.10 134 102 229 123 155.60 2.08 135 103 229 122 156.44 2.50 136 103 234 127 96.85 1.05 137 103 237 130 77.98 1.08 138 103 238 131 69.81 0.07 139 105 237 128 74.76 2.29 140 105 238 129 65.24 0.64 141 105 241 132 45.01 4.38 142 105 242 133 31.85 0.30 143 107 245 134 21.12 0.70 144 123 204 81 284.33 0.20 145 123 209 82 202.67 3.58 146 123 231 104 146.66 7.62 147 123 235 108 76.86 1.64 148 123 238 111 69.67 0.09 149 123 239 112 65.31 0.68 150 124 204 80 193.08 1.23 151 124 209 81 186.13 4.70 152 124 210 82 169.15 0.18 153 124 231 103 282.33 0.98 154 124 232 104 132.75 14.33 155 124 235 107 81.81 0.83 156 127 210 80 159.97 1.02 157 128 210 79 156.93 2.25 158 129 134 4 163.02 0.40 159 129 162 32 136.56 0.32 160 129 210 78 157.24 2.34 161 130 134 3 178.08 0.68 162 130 162 31 137.82 0.47 163 132 162 30 137.84 0.46 164 132 163 31 138.05 0.42 165 132 164 32 138.12 0.43 166 133 161 28 137.90 0.48 167 133 162 29 138.06 0.42 168 134 161 27 138.06 0.42 169 134 162 28 138.14 0.42 170 135 160 25 138.12 0.43 171 135 161 26 138.13 0.42 172 136 159 23 138.00 0.43 173 136 160 24 138.12 0.43 174 136 162 26 143.62 0.34 175 137 157 20 137.38 0.36 176 137 158 21 137.99 0.43 177 137 159 22 138.01 0.43 178 138 157 19 136.18 0.15 179 138 158 20 136.66 0.38 180 138 160 22 138.44 0.55 181 138 228 88 157.25 2.33 182 139 155 16 138.03 0.42 183 139 156 17 137.49 0.42 184 139 157 18 136.56 0.34 185 140 155 15 137.98 0.42 186 140 156 16 137.77 0.46 187 141 152 11 150.24 0.67 188 141 153 12 149.69 0.80 189 141 154 13 141.58 0.66 190 141 155 14 138.03 0.44 191 142 151 9 150.34 0.67 192 142 152 10 150.34 0.67 193 142 192 52 284.94 0.45 194 142 193 53 285.41 0.21 195 142 194 54 275.89 4.77 196 143 148 5 152.52 0.58 197 143 149 6 151.02 0.56 198 143 150 7 150.88 0.53 199 143 151 8 150.66 0.51 200 143 191 50 189.85 0.14 201 143 192 51 272.02 4.86 202 144 150 6 151.02 0.56 203 144 152 8 150.74 0.48 204 144 156 12 137.96 0.49 205 145 148 3 165.67 0.04 206 145 150 5 151.74 0.21 207 146 220 71 150.96 0.52 208 146 221 72 150.99 0.49 209 146 221 73 151.00 0.48 210 152 156 4 156.78 2.60 211 158 188 32 137.81 0.33 212 158 189 33 137.52 0.42 213 159 184 26 162.60 1.65 214 160 184 24 148.97 5.17 215 160 184 25 149.40 4.95 216 161 183 22 175.57 3.12 217 161 184 23 164.53 2.31 218 161 184 24 164.53 2.31 219 162 181 19 236.93 19.43 220 162 182 20 193.85 2.09 221 162 183 21 185.60 1.89 222 162 201 41 143.65 0.33 223 163 182 19 220.33 7.96 224 163 183 20 193.81 2.10 225 163 184 21 190.19 0.28 226 163 185 23 184.13 2.62 227 163 225 60 147.88 0.12 228 171 223 50 152.10 0.26 229 171 224 51 152.06 0.24 230 171 225 52 152.09 0.26 231 172 215 41 152.22 0.38 232 172 216 42 152.31 0.39 233 172 217 43 152.34 0.38 234 172 224 50 152.17 0.27 235 172 225 51 152.17 0.27 236 172 227 53 151.66 0.30 237 175 215 38 156.69 2.55 238 176 215 37 156.69 2.55 239 176 227 49 152.09 0.25 240 178 230 50 151.30 0.40 241 178 233 53 148.78 0.29 242 179 229 48 151.30 0.40 243 179 230 49 151.15 0.42 244 179 233 52 148.55 0.18 245 179 234 53 147.18 0.84 246 180 215 33 152.41 0.41 247 180 227 45 152.07 0.23 248 180 228 46 151.77 0.36 249 180 230 48 151.09 0.43 250 181 199 20 152.43 0.38 251 181 210 27 152.00 0.27 252 181 211 28 152.03 0.26 253 181 227 44 152.03 0.25 254 181 228 45 151.40 0.45 255 181 229 46 151.31 0.41 256 181 230 47 150.97 0.42 257 182 225 41 152.10 0.24 258 182 226 42 152.07 0.24 259 182 227 43 151.46 0.41 260 183 225 40 152.13 0.24 261 183 226 41 152.12 0.24 262 183 228 43 151.58 0.43 263 184 188 5 282.88 1.30 264 185 222 34 157.28 1.99 265 185 223 35 155.31 1.02 266 185 225 37 152.50 0.18 267 186 222 33 157.44 2.06 268 187 221 30 157.82 2.10 269 187 221 31 157.66 2.02 270 187 222 32 157.47 2.04 271 188 221 29 157.88 2.08 272 188 221 28 199.83 8.04 273 189 221 27 283.03 1.22 274 189 226 33 156.72 2.43 275 190 228 34 156.75 2.42 276 199 228 25 157.24 2.33 277 209 231 22 138.79 11.32 278 210 230 20 157.18 2.35 279 210 231 21 141.54 9.94 280 210 232 22 136.07 11.19 281 211 228 17 157.24 2.33 282 211 229 18 157.15 2.31 283 211 231 20 136.07 11.19 284 212 228 16 157.21 2.35 285 212 229 17 157.02 2.29 286 212 231 19 136.90 10.38 287 213 228 15 157.04 2.30 288 214 227 13 157.24 2.33 289 214 228 14 157.14 2.29 290 214 229 15 157.03 2.29 291 215 226 11 157.41 2.29 292 215 227 12 157.25 2.33 293 216 227 11 157.24 2.35 294 217 224 7 219.62 13.82 295 221 224 3 284.60 0.23 296 231 235 4 284.36 0.29 297 231 238 7 69.99 0.07 298 232 235 3 86.09 1.30 299 234 237 3 72.11 0.83 300 234 238 4 70.23 0.04 301 235 238 3 72.00 0.89 302 235 239 4 70.09 0.00 303 236 239 3 70.32 0.04 304 236 240 4 69.95 0.06 305 237 240 3 68.26 0.48 306 237 241 4 64.93 0.50 307 238 241 3 65.56 1.26 308 238 242 4 31.87 0.29 309 239 242 3 63.72 5.08 310 239 243 4 31.87 0.29 311 240 243 3 42.66 5.54 312 240 244 4 31.87 0.29 313 241 244 3 31.54 0.15 314 241 245 4 31.38 0.10 315 242 245 3 27.07 1.91