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 2 207 205 160.91 0.85 2 4 207 203 166.07 0.61 3 8 207 199 182.16 0.81 4 9 157 148 176.81 1.71 5 10 137 127 180.87 1.40 6 10 157 147 176.82 1.71 7 10 159 149 178.19 1.51 8 10 207 197 187.76 0.32 9 14 157 143 191.94 3.45 10 14 158 144 184.90 0.08 11 14 159 145 182.79 1.17 12 14 188 174 179.44 2.23 13 15 135 120 204.90 1.65 14 15 159 144 183.22 0.96 15 15 188 173 179.34 2.23 16 16 187 171 179.97 2.53 17 16 188 172 179.78 2.44 18 17 145 128 208.77 3.76 19 17 187 170 179.98 2.52 20 17 222 205 120.35 1.69 21 18 144 126 179.99 2.52 22 18 188 170 179.98 2.52 23 18 189 171 179.98 2.52 24 18 222 204 118.67 0.58 25 19 157 138 204.53 3.43 26 19 158 139 199.56 0.95 27 19 188 169 180.00 2.52 28 20 156 136 213.56 1.03 29 20 157 137 213.44 1.02 30 21 154 133 228.08 3.17 31 21 155 134 218.76 1.48 32 21 156 135 213.62 1.01 33 22 155 133 231.48 3.24 34 22 156 134 224.41 1.32 35 22 157 135 218.78 1.47 36 27 137 110 235.74 4.11 37 27 139 112 236.07 4.28 38 27 155 128 236.85 4.33 39 27 157 130 236.34 4.15 40 27 200 173 208.92 0.82 41 27 207 180 208.66 0.69 42 29 198 169 208.59 0.82 43 29 200 171 209.72 1.22 44 29 207 178 209.73 1.21 45 30 139 109 235.96 4.21 46 30 141 111 236.98 4.33 47 30 155 125 236.97 4.32 48 30 198 168 208.11 1.05 49 32 141 109 237.04 4.35 50 40 141 101 237.51 4.25 51 40 193 153 199.90 2.62 52 42 195 153 201.56 2.19 53 43 195 152 201.52 2.20 54 43 196 153 203.00 1.48 55 43 197 154 207.14 1.33 56 44 196 152 202.69 1.60 57 44 197 153 206.86 1.19 58 45 198 153 208.56 0.83 59 45 209 164 209.08 0.90 60 47 209 162 208.73 0.92 61 47 238 191 37.33 0.60 62 47 242 195 31.14 1.34 63 51 241 190 35.99 0.52 64 51 242 191 33.90 0.07 65 51 245 194 25.36 0.48 66 53 209 156 209.16 0.92 67 53 212 159 208.54 0.83 68 54 196 142 203.05 1.47 69 54 212 158 208.58 0.84 70 55 196 141 207.14 1.33 71 55 212 157 208.69 0.84 72 55 213 158 208.57 0.85 73 57 195 138 208.62 0.80 74 57 214 157 208.58 0.79 75 58 195 137 207.48 1.16 76 70 141 71 237.53 4.19 77 71 141 70 237.53 4.20 78 71 153 82 237.56 4.20 79 71 154 83 237.30 4.19 80 71 155 84 237.11 4.26 81 72 153 81 237.55 4.20 82 72 154 82 237.34 4.21 83 73 141 68 237.56 4.20 84 73 153 80 237.59 4.21 85 74 153 79 237.60 4.20 86 89 237 148 57.44 0.95 87 89 241 152 36.55 0.40 88 89 245 156 34.97 0.21 89 90 237 147 59.69 0.69 90 91 237 146 59.80 0.74 91 98 177 79 231.75 2.62 92 98 180 82 231.84 2.64 93 99 180 81 231.80 2.64 94 99 214 115 208.99 0.86 95 99 215 116 208.84 0.85 96 100 177 77 231.68 2.64 97 100 179 79 231.72 2.62 98 100 180 80 231.72 2.64 99 101 179 78 231.30 2.46 100 101 234 133 68.42 0.10 101 102 214 112 208.08 1.05 102 102 229 127 89.34 0.40 103 103 212 109 208.70 0.84 104 103 234 131 68.06 0.01 105 103 237 134 57.45 0.96 106 103 238 135 56.03 0.85 107 104 237 133 57.44 0.95 108 105 237 132 56.23 0.76 109 105 238 133 50.68 1.50 110 105 241 136 36.45 0.36 111 105 242 137 35.73 0.55 112 121 200 79 162.52 0.06 113 121 207 86 162.87 0.18 114 121 209 88 162.51 0.05 115 122 206 84 162.90 0.18 116 122 207 85 162.52 0.04 117 122 208 86 162.01 0.09 118 122 209 87 162.22 0.20 119 123 208 85 162.83 0.20 120 123 209 86 162.24 0.18 121 123 231 108 68.19 0.06 122 123 235 112 53.47 0.36 123 123 238 115 36.83 0.42 124 123 239 116 36.49 0.26 125 124 128 4 168.28 1.92 126 124 130 6 172.18 3.86 127 124 203 79 169.28 1.34 128 124 208 84 162.91 0.19 129 124 209 85 162.75 0.12 130 124 231 107 68.23 0.04 131 124 232 108 68.09 0.01 132 124 235 111 53.99 0.61 133 125 128 3 181.41 2.37 134 125 232 107 68.17 0.05 135 125 235 110 55.04 0.39 136 126 232 106 68.17 0.05 137 126 235 109 56.65 0.59 138 126 236 110 54.51 0.86 139 128 203 75 186.58 0.24 140 128 232 104 68.23 0.04 141 130 162 32 180.06 1.82 142 130 201 71 182.48 0.95 143 130 203 73 192.91 0.54 144 130 208 78 187.63 0.29 145 130 210 80 179.69 1.99 146 130 232 102 68.25 0.04 147 131 134 3 193.21 0.59 148 131 162 31 181.00 1.39 149 132 162 30 180.97 1.38 150 132 163 31 180.06 1.82 151 132 164 32 180.06 1.82 152 133 161 28 229.94 2.89 153 133 162 29 226.31 1.14 154 134 161 27 230.09 2.92 155 134 162 28 230.08 2.92 156 135 159 24 304.24 2.72 157 135 160 25 237.76 4.21 158 135 161 26 230.33 2.79 159 136 159 23 311.35 0.82 160 136 160 24 294.26 1.67 161 136 162 26 234.24 2.58 162 136 199 63 208.90 0.81 163 136 200 64 262.86 2.90 164 137 198 61 209.06 0.89 165 137 199 62 209.24 0.80 166 138 190 52 175.15 4.70 167 138 198 60 208.95 0.83 168 138 199 61 298.81 6.31 169 138 213 75 202.51 1.46 170 138 228 90 91.53 0.26 171 139 198 59 309.98 0.60 172 140 194 54 200.55 2.44 173 141 193 52 200.52 2.46 174 141 194 53 200.82 2.54 175 142 191 49 188.85 0.73 176 142 192 50 200.50 2.48 177 142 193 51 200.59 2.44 178 142 194 52 200.84 2.54 179 143 191 48 200.50 2.48 180 143 192 49 200.82 2.54 181 146 191 45 201.53 2.21 182 146 218 72 200.84 2.55 183 146 219 73 200.47 2.46 184 146 220 74 200.53 2.43 185 151 192 41 200.80 2.54 186 151 193 42 200.81 2.54 187 158 188 30 199.51 2.18 188 159 188 29 248.84 26.63 189 160 186 26 309.94 0.85 190 160 188 28 199.75 2.08 191 160 228 68 93.66 0.44 192 162 201 39 311.96 1.11 193 163 225 62 95.42 0.07 194 165 230 65 93.51 0.42 195 168 225 57 104.38 0.68 196 171 223 52 127.30 0.56 197 171 224 53 113.40 0.29 198 171 225 54 113.39 0.29 199 172 224 52 117.57 0.07 200 172 225 53 113.32 0.33 201 172 227 55 113.09 0.39 202 176 227 51 94.15 0.24 203 178 230 52 91.52 0.42 204 179 229 50 91.32 0.50 205 179 230 51 89.34 0.40 206 179 233 54 68.50 0.07 207 179 234 55 68.47 0.08 208 180 227 47 93.95 0.28 209 180 228 48 93.52 0.42 210 180 230 50 89.28 0.37 211 181 227 46 93.65 0.43 212 181 228 47 93.37 0.49 213 181 230 49 89.10 0.29 214 182 225 43 95.28 0.01 215 182 226 44 94.50 0.40 216 182 227 45 93.49 0.41 217 183 225 42 94.51 0.40 218 183 226 43 94.22 0.40 219 183 228 45 93.57 0.40 220 184 225 41 95.27 0.02 221 185 222 37 115.38 0.90 222 185 223 38 113.16 0.25 223 185 224 39 112.92 0.25 224 185 225 40 97.27 0.96 225 186 222 36 116.27 0.08 226 187 222 35 113.81 0.07 227 188 222 34 113.78 0.09 228 189 220 31 309.12 0.17 229 189 221 32 306.24 0.21 230 189 222 33 113.74 0.10 231 190 194 4 265.04 5.08 232 190 213 23 206.34 3.52 233 190 228 38 94.13 0.35 234 191 194 3 190.75 1.58 235 194 197 3 201.47 2.00 236 199 211 12 240.66 2.74 237 199 228 29 89.36 0.41 238 201 210 9 223.51 2.66 239 209 231 22 68.22 0.05 240 210 231 21 68.29 0.07 241 211 228 17 89.28 0.38 242 211 229 18 88.78 0.18 243 211 231 20 68.33 0.09 244 212 228 16 89.37 0.41 245 212 229 17 88.87 0.18 246 212 231 19 70.61 1.22 247 213 228 15 89.84 0.34 248 214 227 13 93.67 0.44 249 214 228 14 93.11 0.45 250 214 229 15 92.78 0.29 251 215 227 12 94.03 0.30 252 216 226 10 94.47 0.38 253 216 227 11 94.42 0.35 254 217 220 3 293.88 1.55 255 217 221 4 205.80 4.67 256 217 224 7 113.38 0.28 257 221 224 3 113.39 0.29 258 229 234 5 68.38 0.04 259 230 233 3 106.07 3.93 260 230 234 4 82.31 6.98 261 231 234 3 98.58 0.29 262 231 235 4 61.87 3.21 263 232 235 3 99.24 0.62 264 234 237 3 109.36 5.71 265 234 238 4 97.83 1.33 266 235 238 3 97.55 1.48 267 235 239 4 75.16 12.67 268 236 239 3 77.21 11.64 269 236 240 4 98.63 0.94 270 237 240 3 98.56 0.31 271 237 241 4 97.35 0.29 272 238 241 3 118.16 1.37 273 238 242 4 97.32 0.28 274 239 242 3 105.64 1.33 275 239 243 4 97.32 0.28 276 240 243 3 97.89 0.73 277 240 244 4 95.83 0.04 278 241 244 3 102.98 1.81 279 241 245 4 36.48 1.65 280 242 245 3 103.88 1.36