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 2 206 198 160.78 1.28 2 2 207 199 159.59 1.14 3 3 206 197 160.84 1.26 4 4 7 3 307.94 0.11 5 4 8 4 303.83 0.12 6 4 26 19 160.90 1.23 7 4 28 21 160.98 1.23 8 4 29 22 160.92 1.20 9 4 207 197 161.34 1.07 10 6 23 14 168.83 2.64 11 6 24 15 178.32 2.11 12 6 25 16 168.46 2.29 13 6 26 17 167.16 2.75 14 7 26 16 168.58 2.29 15 8 26 15 178.25 2.15 16 8 27 16 178.25 2.15 17 8 207 193 182.47 0.53 18 9 23 11 191.91 1.48 19 9 157 142 184.45 0.35 20 10 20 7 189.85 2.52 21 10 137 124 183.15 0.30 22 10 157 141 184.75 0.20 23 10 159 143 179.68 0.65 24 10 207 191 184.70 0.21 25 11 20 6 278.87 4.50 26 16 189 170 172.39 3.33 27 16 190 171 171.97 3.31 28 16 194 175 172.72 3.22 29 17 188 168 172.75 3.27 30 17 189 169 172.47 3.33 31 17 191 171 172.28 3.31 32 17 220 200 163.77 4.96 33 17 222 202 116.34 1.02 34 18 187 166 172.76 3.27 35 18 188 167 172.55 3.37 36 25 117 92 166.60 2.81 37 27 200 170 195.66 0.38 38 27 207 177 195.69 0.39 39 28 117 89 162.22 0.62 40 28 118 90 161.16 1.14 41 28 119 91 161.00 1.21 42 29 119 90 160.92 1.21 43 29 120 91 160.53 1.05 44 29 121 92 158.44 1.11 45 29 198 166 190.47 0.07 46 29 200 168 195.61 0.35 47 29 207 175 195.72 0.33 48 30 198 165 189.15 0.88 49 40 193 150 179.00 0.31 50 42 195 150 184.16 0.10 51 43 195 149 184.01 0.16 52 43 196 150 186.22 0.91 53 43 197 151 188.24 1.15 54 44 196 149 184.15 0.10 55 44 197 150 187.63 1.45 56 45 121 76 158.35 0.96 57 45 198 150 189.16 0.88 58 45 209 161 194.72 0.04 59 46 118 72 162.44 0.74 60 46 119 73 160.99 1.22 61 46 120 74 160.14 0.85 62 46 121 75 159.39 0.64 63 47 120 73 160.83 1.20 64 47 121 74 160.58 1.08 65 47 123 76 160.92 1.20 66 47 238 188 42.34 0.40 67 47 242 192 29.43 0.95 68 48 120 72 161.01 1.15 69 48 242 191 29.21 0.84 70 51 241 187 33.97 0.35 71 51 242 188 29.45 0.94 72 51 245 191 22.32 0.42 73 53 209 153 194.84 0.01 74 53 212 156 189.21 0.74 75 54 196 139 184.12 0.09 76 54 212 155 189.55 0.85 77 55 196 138 188.22 1.15 78 55 212 154 193.30 0.07 79 55 213 155 192.22 0.43 80 57 195 135 189.60 0.85 81 57 214 154 190.99 0.18 82 58 195 134 189.25 0.88 83 58 196 135 189.47 0.82 84 68 118 50 160.96 1.19 85 69 117 48 162.18 0.63 86 69 118 49 160.92 1.21 87 81 118 37 301.77 1.90 88 89 237 145 58.44 1.57 89 89 241 149 36.73 0.16 90 89 245 153 29.80 0.97 91 90 237 144 61.98 0.10 92 91 234 140 69.53 0.46 93 91 237 143 61.98 0.10 94 98 177 76 195.24 0.13 95 98 180 79 195.66 0.09 96 99 180 78 195.21 0.09 97 99 214 112 194.70 0.07 98 99 215 113 194.44 0.17 99 100 177 74 195.00 0.10 100 100 179 76 195.06 0.10 101 100 180 77 195.04 0.10 102 101 179 75 195.02 0.10 103 101 234 130 69.80 0.49 104 102 214 109 192.21 0.40 105 102 229 124 89.05 0.70 106 103 212 106 193.87 0.21 107 103 234 128 69.45 0.47 108 103 237 131 58.45 1.57 109 103 238 132 52.05 0.93 110 104 237 130 58.43 1.56 111 105 237 129 55.61 0.86 112 105 238 130 45.06 0.36 113 105 241 133 35.84 0.32 114 107 245 135 25.98 0.70 115 121 200 76 159.65 1.10 116 121 207 83 160.78 1.28 117 121 208 84 160.44 1.11 118 121 209 85 159.38 0.64 119 122 206 81 160.88 1.24 120 122 207 82 160.78 1.28 121 122 208 83 159.65 1.10 122 122 209 84 158.94 0.86 123 123 208 82 160.81 1.26 124 123 209 83 160.46 1.13 125 123 231 105 69.52 0.45 126 123 235 109 51.61 0.80 127 123 238 112 38.38 1.57 128 124 128 4 183.63 0.86 129 124 130 6 167.51 4.07 130 124 208 81 161.16 1.12 131 124 209 82 160.89 1.23 132 124 231 104 69.53 0.46 133 124 232 105 69.39 0.47 134 124 235 108 51.64 0.79 135 125 128 3 189.05 1.79 136 125 232 104 69.53 0.46 137 126 232 103 69.52 0.45 138 126 235 106 57.88 1.82 139 126 236 107 52.16 1.03 140 128 203 72 185.24 0.06 141 128 232 101 69.54 0.43 142 129 203 71 185.62 0.03 143 130 162 29 175.36 1.45 144 130 201 68 184.42 0.34 145 130 203 70 189.31 0.89 146 130 208 75 184.91 0.21 147 130 210 77 175.08 1.58 148 130 232 99 69.53 0.44 149 131 134 3 193.94 0.39 150 131 162 28 179.19 0.32 151 132 162 27 179.05 0.30 152 132 163 28 175.41 1.44 153 132 164 29 175.47 1.41 154 133 161 25 185.37 0.04 155 133 162 26 180.44 0.06 156 134 161 24 194.06 0.23 157 134 162 25 189.81 2.25 158 135 161 23 194.53 0.24 159 136 199 60 200.28 0.10 160 136 200 61 267.04 6.04 161 137 199 59 197.59 1.32 162 137 200 60 280.43 5.94 163 138 198 57 195.36 0.35 164 138 199 58 195.36 0.36 165 138 213 72 188.30 1.07 166 139 198 56 194.53 0.04 167 140 194 51 172.57 3.25 168 141 194 50 172.72 3.22 169 142 192 47 172.31 3.36 170 142 193 48 172.36 3.36 171 142 194 49 172.77 3.24 172 143 191 45 172.11 3.27 173 143 192 46 172.59 3.25 174 146 218 69 175.93 1.70 175 146 219 70 172.56 3.24 176 158 188 30 172.48 3.40 177 159 188 29 172.50 3.39 178 160 183 23 215.43 0.80 179 160 184 24 194.75 0.18 180 160 188 28 172.47 3.41 181 160 228 68 91.88 0.09 182 161 183 22 278.18 0.68 183 161 184 23 219.94 1.51 184 161 186 25 194.41 0.08 185 162 183 21 304.78 2.77 186 163 225 62 94.64 1.40 187 165 230 65 91.36 0.00 188 168 225 57 101.84 1.72 189 171 223 52 122.33 0.03 190 171 225 54 105.97 0.19 191 172 217 45 299.88 4.80 192 172 224 52 115.77 1.45 193 172 225 53 110.14 0.94 194 172 227 55 103.84 0.69 195 176 227 51 91.56 0.07 196 178 230 52 90.97 0.12 197 179 229 50 90.53 0.10 198 179 230 51 88.98 0.67 199 179 233 54 69.92 0.42 200 180 227 47 91.44 0.04 201 180 228 48 91.34 0.00 202 180 229 49 90.42 0.04 203 180 230 50 88.98 0.68 204 181 227 46 91.44 0.04 205 181 228 47 91.37 0.01 206 181 230 49 88.71 0.72 207 182 225 43 92.08 0.12 208 182 226 44 91.59 0.07 209 182 227 45 91.52 0.07 210 183 225 42 92.08 0.12 211 183 226 43 91.75 0.01 212 183 228 45 91.44 0.03 213 184 225 41 92.06 0.11 214 185 222 37 109.87 1.73 215 185 223 38 104.29 0.54 216 185 224 39 103.18 1.05 217 185 225 40 94.64 1.40 218 186 222 36 112.28 0.56 219 187 222 35 109.92 1.74 220 188 222 34 106.58 0.12 221 189 221 32 304.50 0.84 222 189 222 33 107.52 0.35 223 190 194 4 265.56 0.30 224 190 213 23 200.39 1.85 225 190 228 38 91.83 0.03 226 191 194 3 184.51 3.23 227 194 197 3 189.30 0.84 228 199 211 12 290.60 2.35 229 199 228 29 89.00 0.67 230 201 210 9 277.32 0.42 231 209 231 22 69.52 0.45 232 210 230 20 69.81 0.43 233 210 231 21 69.53 0.46 234 211 228 17 89.00 0.67 235 211 229 18 86.27 0.28 236 211 231 20 69.55 0.45 237 212 228 16 89.00 0.67 238 212 229 17 88.24 0.96 239 212 231 19 70.21 0.21 240 213 228 15 90.42 0.02 241 214 227 13 91.53 0.09 242 214 228 14 91.01 0.15 243 214 229 15 90.59 0.07 244 215 227 12 91.55 0.09 245 217 220 3 211.44 3.85 246 217 221 4 192.05 6.52 247 217 224 7 107.45 0.39 248 221 224 3 107.87 0.18 249 229 234 5 102.06 1.54 250 230 233 3 112.98 0.17 251 230 234 4 103.05 2.02 252 231 234 3 102.53 1.77 253 231 235 4 102.06 1.53 254 232 235 3 112.94 0.02 255 234 237 3 112.40 1.13 256 234 238 4 104.34 1.08 257 235 238 3 103.57 0.69 258 235 239 4 101.34 1.24 259 236 239 3 109.38 0.09 260 236 240 4 106.51 1.34 261 237 240 3 109.37 0.09 262 237 241 4 106.56 1.32 263 238 241 3 110.86 0.83 264 238 242 4 106.56 1.32 265 239 242 3 106.95 1.12 266 239 243 4 106.25 1.17 267 240 243 3 111.34 1.37 268 240 244 4 111.34 1.37 269 241 244 3 111.34 1.37 270 241 245 4 107.73 0.43 271 242 245 3 111.34 1.38