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 19 23 4 160.27 0.26 2 21 27 6 169.66 0.57 3 21 137 112 72.36 0.01 4 22 137 111 97.40 0.10 5 22 188 162 137.65 0.65 6 25 71 44 142.16 1.26 7 26 117 89 138.22 0.63 8 27 139 108 138.04 0.64 9 28 116 86 138.49 0.58 10 28 117 87 138.40 0.61 11 28 118 88 138.22 0.63 12 28 119 89 138.13 0.62 13 29 45 15 138.13 0.62 14 29 46 16 138.12 0.61 15 29 119 88 138.22 0.64 16 29 120 89 138.13 0.62 17 29 121 90 138.00 0.67 18 29 137 104 138.49 0.59 19 29 139 106 138.50 0.58 20 29 198 165 138.33 0.60 21 29 200 167 138.40 0.61 22 30 44 13 138.46 0.59 23 30 139 105 138.49 0.59 24 30 141 107 143.02 0.14 25 30 198 164 138.43 0.58 26 31 43 11 140.11 0.83 27 31 44 12 138.48 0.58 28 31 45 13 138.49 0.58 29 31 52 20 138.48 0.58 30 31 66 33 145.15 1.27 31 31 67 34 145.03 1.32 32 31 68 35 144.94 1.35 33 31 141 106 143.03 0.15 34 32 40 7 145.34 1.25 35 32 42 9 143.76 0.53 36 32 66 32 145.19 1.28 37 32 67 33 145.14 1.27 38 32 73 39 145.56 1.35 39 32 141 105 143.03 0.15 40 33 40 6 146.92 2.00 41 33 41 7 145.01 1.12 42 33 42 8 144.00 0.64 43 33 43 9 143.43 0.35 44 33 44 10 142.99 0.15 45 33 52 18 143.83 0.58 46 33 54 20 143.60 0.47 47 33 58 24 145.27 1.28 48 33 65 30 145.27 1.25 49 33 66 31 145.24 1.27 50 33 106 71 145.09 1.22 51 34 39 4 262.27 1.00 52 34 40 5 146.92 2.00 53 34 64 28 145.49 1.31 54 34 65 29 145.31 1.24 55 34 67 31 145.53 1.32 56 35 41 5 245.46 0.76 57 35 60 24 257.45 1.43 58 35 61 25 267.35 0.58 59 35 64 27 150.28 1.07 60 40 153 108 139.10 0.29 61 45 121 75 245.72 0.29 62 46 120 73 266.37 1.57 63 46 121 74 266.00 1.39 64 47 121 73 265.93 1.53 65 47 123 75 245.38 0.43 66 47 238 185 50.81 0.36 67 47 242 189 37.23 0.78 68 48 242 188 37.23 0.78 69 51 241 184 42.59 1.06 70 51 242 185 37.23 0.78 71 53 123 69 200.18 4.71 72 53 231 172 119.34 1.78 73 53 238 179 50.84 0.35 74 69 117 48 267.99 0.52 75 69 118 49 264.15 2.43 76 70 155 81 142.12 1.26 77 71 154 79 142.16 1.26 78 72 152 76 143.38 1.30 79 72 153 77 143.31 1.33 80 72 154 78 142.19 1.25 81 73 152 75 143.40 1.29 82 73 153 76 143.27 1.34 83 74 152 74 143.38 1.28 84 89 237 143 65.64 0.47 85 89 241 147 45.42 1.71 86 90 237 142 68.72 1.71 87 91 234 138 118.62 2.10 88 91 237 141 67.78 1.25 89 92 237 140 88.67 0.04 90 98 180 78 140.98 0.48 91 99 180 77 139.34 0.14 92 100 177 73 138.20 0.66 93 100 179 75 138.34 0.61 94 100 180 76 139.31 0.14 95 101 179 74 137.84 0.51 96 101 234 128 120.52 3.06 97 102 229 122 138.41 0.61 98 103 229 121 138.31 0.67 99 103 234 126 88.75 0.06 100 103 237 129 64.30 1.11 101 103 238 130 59.00 0.58 102 105 237 127 63.81 1.31 103 105 238 128 51.14 0.21 104 105 241 131 42.59 1.06 105 122 208 80 267.24 0.81 106 122 209 81 266.05 1.37 107 123 208 79 249.59 0.57 108 123 209 80 188.55 6.82 109 123 231 103 114.68 0.13 110 123 238 110 51.12 0.21 111 124 208 78 193.27 0.10 112 124 209 79 164.09 0.70 113 124 210 80 155.12 0.10 114 124 232 103 89.00 0.04 115 124 235 106 64.37 1.28 116 125 235 105 69.53 1.67 117 129 210 77 140.94 0.18 118 131 210 75 159.77 1.36 119 133 162 27 137.19 0.49 120 133 201 68 202.57 0.18 121 134 161 25 136.15 0.14 122 134 162 26 136.18 0.14 123 135 161 24 136.18 0.14 124 136 159 21 135.30 0.26 125 136 160 22 136.15 0.14 126 136 162 24 137.99 0.61 127 137 157 18 134.82 0.48 128 137 158 19 135.26 0.27 129 137 159 20 136.12 0.15 130 138 157 17 125.37 4.25 131 138 158 18 134.97 0.12 132 138 159 19 137.09 0.59 133 138 160 20 137.90 0.64 134 138 228 87 141.85 0.56 135 139 155 14 137.30 0.49 136 139 156 15 135.27 0.27 137 139 157 16 118.15 0.42 138 140 155 13 137.34 0.48 139 140 156 14 135.24 0.25 140 141 154 11 138.00 0.61 141 141 155 12 137.33 0.48 142 142 153 9 138.21 0.64 143 142 154 10 138.19 0.65 144 142 156 12 137.25 0.52 145 143 150 5 143.68 0.47 146 143 151 6 142.50 0.12 147 143 152 7 140.41 0.91 148 143 153 8 138.31 0.60 149 144 151 5 144.16 0.71 150 144 156 10 137.90 0.61 151 144 192 48 236.84 1.53 152 145 151 4 148.74 0.45 153 145 192 47 183.42 0.30 154 156 190 36 137.39 0.52 155 156 192 38 136.70 0.43 156 156 193 39 135.19 0.30 157 158 188 32 137.69 0.62 158 158 191 35 136.80 0.22 159 158 220 60 135.24 0.23 160 159 188 30 137.88 0.65 161 159 188 31 137.87 0.64 162 160 183 23 218.66 2.43 163 160 184 24 156.50 0.17 164 160 185 25 141.93 1.51 165 160 188 29 137.90 0.64 166 160 199 41 137.84 0.64 167 160 220 58 137.34 0.49 168 160 228 67 136.58 0.33 169 161 183 22 264.87 1.44 170 161 184 23 181.21 3.30 171 161 185 24 159.73 1.03 172 162 183 21 267.24 0.28 173 162 199 39 138.17 0.61 174 162 201 41 137.97 0.61 175 162 210 46 137.84 0.64 176 163 183 20 267.99 0.43 177 163 184 21 267.99 0.43 178 163 225 61 138.02 0.64 179 165 230 64 137.95 0.62 180 167 222 54 141.31 0.35 181 171 223 51 141.40 0.36 182 171 225 53 141.44 0.38 183 172 215 41 141.15 0.60 184 172 216 42 140.95 0.54 185 172 217 43 141.52 0.42 186 172 224 51 141.46 0.39 187 172 225 52 141.50 0.40 188 172 227 54 141.10 0.49 189 175 215 38 140.96 0.51 190 176 215 37 141.06 0.52 191 176 227 50 141.05 0.51 192 178 230 51 140.99 0.54 193 178 233 54 139.26 0.19 194 179 229 49 141.00 0.53 195 179 230 50 140.24 0.30 196 179 233 53 125.09 0.18 197 179 234 54 120.49 0.41 198 180 215 33 141.23 0.55 199 180 227 46 141.18 0.52 200 180 228 47 141.00 0.53 201 180 229 48 140.81 0.59 202 180 230 49 139.83 0.27 203 181 199 20 142.06 0.35 204 181 210 27 141.22 0.48 205 181 227 45 141.16 0.51 206 181 228 46 140.98 0.54 207 181 230 48 138.46 0.57 208 182 225 42 141.53 0.45 209 182 226 43 141.16 0.48 210 182 227 44 140.78 0.49 211 182 228 45 140.53 0.38 212 183 199 18 142.09 0.34 213 183 225 41 141.57 0.44 214 183 226 42 141.56 0.45 215 183 228 44 140.91 0.58 216 184 221 35 141.87 0.43 217 184 222 36 141.91 0.49 218 185 221 34 142.21 0.39 219 185 222 35 141.97 0.48 220 188 220 30 142.44 0.39 221 188 222 32 142.23 0.39 222 188 191 4 267.52 0.99 223 188 220 29 142.43 0.39 224 199 228 26 141.87 0.55 225 209 231 23 97.73 0.12 226 210 231 22 118.83 10.20 227 210 232 23 90.09 0.57 228 211 228 18 141.86 0.56 229 211 229 19 140.90 0.24 230 211 231 21 90.98 0.17 231 212 228 17 140.89 0.24 232 212 229 18 140.73 0.28 233 212 231 20 91.86 0.79 234 213 228 16 140.76 0.28 235 214 227 14 141.81 0.52 236 214 228 15 141.16 0.23 237 214 229 16 141.03 0.17 238 215 227 13 141.91 0.55 239 216 227 12 141.93 0.55 240 217 224 8 212.44 9.69 241 217 225 9 142.10 0.48 242 217 226 10 141.83 0.51 243 218 226 9 141.78 0.52 244 218 227 10 141.78 0.52 245 219 228 10 141.75 0.53 246 221 224 4 239.19 7.59 247 221 225 5 141.91 0.46 248 221 226 6 141.78 0.53 249 222 224 3 265.50 0.70 250 222 225 4 176.65 11.43 251 222 225 3 265.68 0.79 252 229 234 5 263.06 0.18 253 231 235 4 262.43 0.13 254 232 235 3 72.39 2.52 255 234 237 3 61.84 0.42 256 234 238 4 56.41 0.38 257 235 238 3 59.00 0.57 258 235 239 4 56.20 0.48 259 236 239 3 57.91 0.43 260 236 240 4 54.03 0.61 261 237 240 3 51.12 0.21 262 237 241 4 50.80 0.36 263 238 241 3 47.48 0.80 264 238 242 4 43.28 0.90 265 239 242 3 43.41 0.84 266 239 243 4 42.93 1.07 267 240 243 3 43.29 0.90 268 240 244 4 40.16 0.31 269 241 244 3 45.34 3.54