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 36.84 3.25 2 16 140 119 36.84 3.25 3 16 142 121 53.16 4.88 4 16 143 122 57.93 4.54 5 16 144 123 60.17 3.66 6 16 156 135 53.81 4.55 7 16 158 137 51.28 3.87 8 16 189 170 59.08 3.35 9 16 190 171 36.83 3.25 10 16 194 175 36.83 3.25 11 17 143 121 60.61 3.46 12 17 144 122 60.31 3.60 13 17 145 123 61.45 3.29 14 17 146 124 63.75 2.18 15 17 188 167 61.60 3.23 16 17 188 168 61.25 3.39 17 17 189 169 60.29 3.60 18 17 191 171 60.30 3.58 19 17 220 195 60.77 3.64 20 17 221 196 60.84 3.59 21 18 158 135 64.88 2.41 22 18 188 166 61.63 3.23 23 18 188 167 61.28 3.38 24 19 157 133 65.78 1.13 25 19 158 134 64.05 1.99 26 20 137 112 85.05 1.09 27 20 156 131 156.84 0.77 28 20 157 132 75.44 0.97 29 20 158 133 197.62 4.11 30 20 159 134 225.05 6.10 31 21 154 128 156.94 0.76 32 21 155 129 159.17 0.26 33 21 156 130 156.94 0.76 34 22 26 4 166.16 1.56 35 22 27 5 159.53 1.56 36 22 139 112 137.95 0.03 37 22 155 128 164.63 1.79 38 22 156 129 195.94 0.98 39 23 26 3 177.74 0.04 40 24 71 44 142.60 0.42 41 25 69 41 141.17 0.20 42 25 79 51 153.70 0.81 43 25 117 89 141.17 0.20 44 27 30 3 235.62 3.85 45 27 137 105 140.91 0.36 46 27 139 107 144.54 1.66 47 28 116 85 153.28 1.02 48 28 117 86 153.28 1.02 49 28 118 87 152.42 0.60 50 28 119 88 148.60 0.42 51 29 45 14 148.50 0.37 52 29 46 15 146.97 0.39 53 29 119 87 153.12 0.96 54 29 120 88 148.60 0.42 55 29 121 89 144.71 0.74 56 29 137 103 153.81 0.83 57 29 198 166 153.28 1.02 58 29 200 168 153.28 1.02 59 30 43 11 154.46 0.82 60 30 44 12 153.81 0.83 61 30 139 104 154.00 0.74 62 30 140 105 154.46 0.83 63 30 141 106 156.61 0.90 64 30 155 120 200.28 13.83 65 30 198 165 153.43 0.95 66 31 43 10 155.03 0.69 67 31 44 11 153.91 0.79 68 31 45 12 153.91 0.79 69 31 46 13 153.91 0.78 70 31 52 19 153.91 0.79 71 31 65 32 156.66 0.88 72 31 66 33 156.50 0.95 73 31 67 34 155.93 0.70 74 31 141 105 156.75 0.83 75 32 40 6 157.43 0.79 76 32 42 8 156.73 0.84 77 32 43 9 156.21 1.01 78 32 65 31 156.94 0.74 79 32 66 32 156.66 0.88 80 32 73 38 157.41 0.79 81 32 141 104 156.62 0.90 82 33 40 5 157.53 0.77 83 33 41 6 157.49 0.75 84 33 42 7 156.85 0.79 85 33 43 8 156.73 0.85 86 33 52 17 156.71 0.86 87 33 54 19 156.72 0.85 88 33 58 23 157.40 0.79 89 33 63 28 157.41 0.81 90 33 64 29 157.40 0.81 91 33 65 30 157.05 0.80 92 33 104 68 157.16 0.75 93 33 106 70 157.05 0.80 94 34 39 3 164.08 2.64 95 34 40 4 157.54 0.77 96 34 41 5 157.54 0.76 97 34 63 27 157.41 0.82 98 34 64 28 157.40 0.81 99 34 66 30 157.40 0.81 100 37 41 4 165.56 1.33 101 37 60 23 166.24 0.86 102 45 121 75 210.16 1.53 103 46 120 73 262.94 1.71 104 46 121 74 218.82 1.98 105 47 120 72 282.05 2.71 106 47 121 73 240.38 3.30 107 47 123 75 197.81 1.05 108 47 238 186 59.09 1.68 109 48 242 189 37.74 3.19 110 51 242 186 36.91 2.77 111 51 245 189 27.54 3.56 112 53 238 180 58.77 1.84 113 67 118 50 286.98 0.32 114 69 118 49 287.10 0.39 115 71 153 80 154.52 0.92 116 71 154 81 154.08 0.99 117 71 155 82 152.99 0.89 118 72 153 79 154.52 0.92 119 72 154 80 154.31 0.88 120 73 153 78 154.53 0.93 121 74 153 77 154.52 0.94 122 87 245 154 28.75 2.80 123 89 237 144 81.09 0.94 124 89 241 148 50.44 0.83 125 89 245 152 29.07 2.84 126 91 234 139 104.84 0.38 127 91 237 142 77.64 0.86 128 92 237 141 92.84 0.90 129 98 180 80 214.68 21.66 130 99 180 79 214.61 21.64 131 100 177 75 166.91 2.16 132 100 179 77 166.93 2.18 133 100 180 78 166.94 2.17 134 101 179 76 166.81 2.19 135 101 234 129 112.12 0.62 136 102 229 123 153.20 0.42 137 103 229 122 153.19 0.42 138 103 234 127 96.74 2.54 139 103 237 130 74.66 0.25 140 103 238 131 63.24 3.98 141 105 237 128 73.28 0.94 142 105 238 129 58.77 1.83 143 105 241 132 40.02 4.28 144 105 242 133 37.50 3.07 145 107 245 134 26.32 4.01 146 122 204 82 262.99 1.68 147 122 209 83 235.20 0.61 148 123 204 81 235.19 0.61 149 123 209 82 194.34 3.00 150 123 231 104 259.30 3.89 151 123 235 108 73.22 0.97 152 123 238 111 59.09 1.69 153 123 239 112 58.86 1.80 154 124 204 80 187.96 1.33 155 124 209 81 182.37 0.52 156 124 210 82 165.78 0.77 157 124 232 104 179.00 36.26 158 124 235 107 77.97 0.69 159 127 210 80 155.94 0.67 160 128 210 79 152.62 0.29 161 129 134 4 172.25 0.22 162 129 162 32 138.21 0.85 163 129 210 78 154.97 0.43 164 130 134 3 180.89 1.04 165 130 162 31 140.67 0.36 166 132 162 30 140.68 0.37 167 132 163 31 140.72 0.38 168 132 164 32 140.79 0.35 169 133 161 28 140.68 0.37 170 133 162 29 140.79 0.36 171 134 161 27 140.83 0.35 172 134 162 28 140.84 0.35 173 135 159 24 140.72 0.39 174 135 160 25 140.83 0.35 175 135 161 26 140.84 0.35 176 136 158 22 140.73 0.39 177 136 159 23 140.73 0.39 178 136 160 24 140.84 0.35 179 136 162 26 141.00 0.35 180 137 157 20 140.10 0.34 181 137 158 21 140.66 0.41 182 137 159 22 140.69 0.40 183 138 157 19 138.91 0.48 184 138 158 20 139.14 0.52 185 138 160 22 140.91 0.39 186 138 183 45 156.87 0.89 187 138 228 88 155.93 0.65 188 139 155 16 140.84 0.36 189 139 156 17 140.63 0.42 190 139 157 18 137.94 0.03 191 140 155 15 140.79 0.39 192 140 156 16 140.63 0.41 193 141 152 11 153.88 0.80 194 141 153 12 153.33 1.03 195 141 154 13 149.28 0.63 196 141 155 14 140.75 0.42 197 142 151 9 155.11 0.70 198 142 152 10 154.48 0.93 199 143 148 5 159.00 0.10 200 143 149 6 155.46 0.64 201 143 150 7 155.38 0.65 202 143 151 8 155.16 0.68 203 143 191 50 217.85 9.51 204 143 192 51 286.87 1.55 205 144 150 6 155.46 0.64 206 144 152 8 155.23 0.71 207 144 156 12 140.56 0.51 208 145 148 3 176.69 0.95 209 146 220 71 154.16 0.97 210 146 221 72 154.37 0.86 211 151 192 43 155.40 0.65 212 152 156 4 169.81 0.79 213 158 188 32 140.22 0.29 214 158 189 33 140.16 0.29 215 159 184 26 140.88 0.37 216 160 184 24 140.44 0.31 217 160 184 25 140.84 0.39 218 161 183 22 180.15 2.54 219 161 184 23 158.30 8.37 220 161 184 24 140.91 0.38 221 162 181 19 242.96 5.86 222 162 182 20 242.84 5.80 223 162 183 21 180.21 2.52 224 162 201 41 144.40 1.80 225 163 182 19 242.85 5.80 226 163 183 20 190.30 2.51 227 163 184 21 183.35 0.96 228 163 185 23 180.19 2.52 229 163 225 60 149.80 0.97 230 167 185 19 242.36 9.78 231 171 223 50 155.85 0.64 232 171 224 51 155.94 0.68 233 171 225 52 155.94 0.69 234 172 215 41 166.66 2.25 235 172 216 42 165.66 1.92 236 172 217 43 164.09 1.32 237 172 224 50 155.96 0.68 238 172 225 51 155.96 0.68 239 172 227 53 155.26 0.62 240 175 215 38 166.74 2.23 241 176 215 37 166.74 2.23 242 176 227 49 155.72 0.79 243 178 230 50 154.77 0.89 244 178 233 53 152.67 0.23 245 179 229 48 155.56 0.83 246 179 230 49 154.47 0.80 247 179 233 52 151.37 0.13 248 179 234 53 148.06 0.57 249 180 215 33 166.76 2.23 250 180 227 45 155.73 0.80 251 180 228 46 155.58 0.85 252 180 230 48 154.22 0.69 253 181 199 20 156.72 0.85 254 181 210 27 155.71 0.84 255 181 211 28 155.71 0.85 256 181 227 44 155.69 0.80 257 181 228 45 155.24 0.70 258 181 229 46 154.69 0.83 259 181 230 47 154.21 0.69 260 182 225 41 155.95 0.69 261 182 226 42 155.93 0.69 262 182 227 43 154.59 0.88 263 183 225 40 156.00 0.69 264 183 226 41 155.96 0.70 265 183 228 43 155.33 0.65 266 184 225 39 155.98 0.70 267 184 188 5 281.12 0.10 268 185 222 34 157.37 0.58 269 185 223 35 156.67 0.85 270 185 225 37 156.04 0.68 271 186 222 33 157.56 0.54 272 187 221 30 165.82 2.16 273 187 221 31 163.30 1.00 274 187 222 32 160.22 0.67 275 188 221 29 165.85 2.17 276 188 221 28 170.75 0.28 277 189 221 27 173.16 1.48 278 189 226 33 154.22 1.01 279 190 228 34 153.12 0.37 280 199 228 25 155.91 0.62 281 209 231 22 116.27 1.30 282 210 229 19 155.97 0.66 283 210 230 20 153.66 0.23 284 210 231 21 119.01 0.07 285 210 232 22 109.76 1.81 286 211 228 17 155.96 0.66 287 211 229 18 154.05 0.24 288 211 231 20 115.56 1.54 289 212 228 16 154.19 0.41 290 212 229 17 152.91 0.28 291 212 231 19 114.18 0.28 292 213 228 15 153.74 0.13 293 214 227 13 155.93 0.69 294 214 228 14 155.00 0.42 295 214 229 15 154.31 0.17 296 215 226 11 156.00 0.69 297 215 227 12 155.71 0.72 298 217 224 7 167.37 4.99 299 231 235 4 282.87 2.27 300 231 238 7 60.31 2.31 301 232 235 3 84.08 0.30 302 234 237 3 73.18 0.99 303 234 238 4 62.69 3.50 304 235 238 3 62.78 3.53 305 235 239 4 59.00 1.86 306 236 239 3 69.60 0.12 307 236 240 4 58.88 1.79 308 237 240 3 61.16 3.05 309 237 241 4 61.04 3.12 310 238 241 3 43.21 2.68 311 238 242 4 37.50 3.07 312 239 242 3 40.02 4.28 313 239 243 4 37.49 3.06 314 240 243 3 39.96 4.30 315 240 244 4 39.96 4.30 316 241 244 3 37.34 3.00 317 241 245 4 36.49 2.83 318 242 245 3 33.34 4.76