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 7 22 15 262.59 0.21 2 7 181 174 264.83 0.17 3 9 13 4 286.07 0.30 4 9 15 6 264.50 0.01 5 10 13 3 295.74 0.81 6 11 67 56 393.67 0.27 7 13 88 75 292.10 1.01 8 13 89 76 295.85 0.84 9 13 90 77 307.67 0.38 10 13 163 150 388.54 1.38 11 14 17 3 273.50 4.39 12 14 18 4 264.81 0.08 13 14 88 74 284.37 0.54 14 14 163 149 302.71 0.85 15 15 18 3 275.64 1.56 16 15 19 4 264.79 0.10 17 15 88 73 264.95 0.15 18 16 19 3 264.93 0.18 19 16 20 4 264.79 0.11 20 16 34 18 375.17 9.56 21 16 201 185 206.12 0.01 22 17 20 3 263.91 0.11 23 17 21 4 392.67 1.06 24 17 163 146 278.64 0.49 25 17 166 149 390.49 1.49 26 17 167 150 392.53 0.87 27 17 196 179 262.81 0.28 28 17 201 184 206.12 0.01 29 18 86 68 262.75 0.23 30 18 88 70 264.25 0.08 31 18 161 143 264.81 0.10 32 18 166 148 299.38 2.55 33 18 174 156 394.44 0.53 34 19 37 18 262.72 0.23 35 19 38 19 262.72 0.23 36 19 41 22 262.40 0.24 37 19 42 23 262.55 0.23 38 19 43 24 262.52 0.24 39 19 65 46 262.00 0.01 40 20 31 11 267.48 2.58 41 20 37 17 262.19 0.10 42 20 201 181 206.12 0.01 43 21 170 149 371.22 11.04 44 21 174 153 393.25 1.01 45 22 41 19 262.66 0.21 46 22 63 41 262.52 0.21 47 22 174 152 394.22 0.64 48 23 31 8 350.87 16.30 49 23 36 13 263.10 0.38 50 23 40 17 262.69 0.20 51 23 41 18 262.68 0.20 52 24 28 4 392.82 1.23 53 24 29 5 391.68 1.02 54 24 31 7 269.81 2.61 55 25 28 3 393.37 0.18 56 26 63 37 262.63 0.20 57 30 195 165 262.75 0.27 58 30 200 170 230.57 1.85 59 31 36 5 353.44 0.33 60 31 37 6 309.25 11.61 61 33 213 180 104.27 1.91 62 34 201 167 206.16 0.00 63 34 204 170 182.37 1.09 64 34 205 171 182.33 1.07 65 34 208 174 149.15 4.63 66 34 214 180 102.86 1.24 67 34 215 181 99.59 0.38 68 34 216 182 99.35 0.26 69 35 208 173 149.15 4.63 70 35 213 178 102.90 1.24 71 37 201 164 206.13 0.01 72 61 181 120 262.92 0.17 73 61 183 122 262.86 0.19 74 63 181 118 264.11 0.15 75 63 183 120 262.95 0.21 76 84 180 96 264.69 0.14 77 84 181 97 262.91 0.23 78 84 182 98 264.29 0.06 79 85 180 95 264.86 0.18 80 86 177 91 264.64 0.12 81 86 180 94 264.89 0.17 82 86 181 95 264.86 0.18 83 89 266 158 29.80 0.57 84 89 268 160 29.50 0.70 85 90 268 159 29.50 0.70 86 91 268 158 29.50 0.70 87 92 249 138 47.13 0.08 88 92 259 148 41.12 0.12 89 92 268 157 29.53 0.70 90 93 236 124 66.76 0.60 91 93 237 125 61.59 1.95 92 93 238 126 60.98 1.70 93 93 249 137 47.13 0.07 94 96 249 134 47.16 0.07 95 97 236 120 66.81 0.59 96 97 237 121 66.72 0.58 97 102 216 114 99.53 0.09 98 110 241 112 62.76 1.29 99 120 259 120 46.60 0.04 100 121 248 108 47.34 0.00 101 121 249 109 47.19 0.07 102 121 252 112 46.97 0.01 103 124 252 109 46.42 0.18 104 124 257 114 45.62 0.44 105 124 259 116 41.25 0.01 106 138 259 102 41.08 0.10 107 138 262 105 40.34 0.03 108 138 263 106 40.31 0.04 109 138 268 111 29.79 0.57 110 139 258 100 41.10 0.10 111 139 259 101 41.08 0.10 112 139 262 104 40.31 0.04 113 142 262 101 40.31 0.04 114 143 258 96 41.11 0.10 115 143 261 99 40.59 0.01 116 143 262 100 40.31 0.04 117 147 262 96 40.31 0.04 118 157 180 23 264.81 0.18 119 158 180 22 264.86 0.18 120 159 176 17 264.92 0.15 121 159 177 18 264.82 0.18 122 159 180 21 264.87 0.18 123 160 266 87 29.52 0.70 124 161 173 12 264.93 0.13 125 161 177 16 264.97 0.16 126 162 266 85 29.53 0.70 127 162 268 87 29.50 0.70 128 164 268 85 29.52 0.70 129 165 173 8 394.50 0.07 130 166 173 7 394.18 0.04 131 166 174 8 391.78 1.17 132 167 198 31 262.19 0.07 133 170 193 23 341.55 25.73 134 171 186 15 394.47 0.50 135 171 189 18 393.05 0.12 136 171 190 19 392.09 0.60 137 171 193 22 345.38 23.95 138 174 189 15 394.21 0.61 139 174 192 18 394.20 0.60 140 174 193 19 389.13 3.08 141 175 189 14 394.22 0.60 142 194 200 6 223.25 0.73 143 195 200 5 207.43 0.57 144 196 200 4 206.32 0.03 145 196 201 5 206.13 0.01 146 197 200 3 206.37 0.04 147 197 201 4 206.32 0.02 148 198 201 3 210.51 2.11 149 198 202 4 206.31 0.01 150 199 202 3 212.68 1.50 151 199 203 4 206.30 0.01 152 200 203 3 206.15 0.01 153 200 204 4 205.31 0.01 154 201 204 3 202.13 3.90 155 201 205 4 196.36 5.45 156 202 205 3 208.55 0.69 157 202 206 4 207.24 0.03 158 203 206 3 217.59 0.42 159 203 207 4 207.28 0.01 160 204 207 3 222.38 2.81 161 204 208 4 208.81 0.32 162 205 208 3 213.97 1.29 163 205 209 4 208.38 0.54 164 205 215 10 107.48 1.14 165 205 216 11 104.19 2.41 166 206 209 3 206.88 1.29 167 206 210 4 206.84 1.29 168 207 210 3 211.78 0.92 169 207 211 4 205.93 0.84 170 208 211 3 206.85 1.30 171 208 212 4 205.93 0.84 172 208 213 5 177.59 3.00 173 209 212 3 207.74 0.06 174 209 213 4 183.24 0.17 175 209 215 6 134.20 10.88 176 238 242 4 169.61 3.82 177 238 246 8 108.84 0.72 178 239 242 3 181.62 2.79 179 239 246 7 122.89 3.42 180 241 245 4 197.74 3.32 181 242 245 3 201.86 3.52 182 242 246 4 185.59 0.05 183 243 246 3 208.34 0.41 184 243 247 4 200.03 4.42 185 244 247 3 200.03 4.42 186 244 248 4 199.79 4.30 187 245 248 3 211.78 1.66 188 245 249 4 211.75 1.68 189 246 249 3 211.78 1.66 190 246 250 4 211.75 1.68 191 247 250 3 212.57 1.27 192 247 251 4 193.28 3.68 193 248 251 3 202.72 3.92 194 248 252 4 187.82 0.95 195 249 252 3 193.31 0.78 196 249 253 4 188.85 0.40 197 249 259 10 142.88 2.57 198 250 253 3 202.23 2.60 199 250 254 4 188.82 0.38 200 251 254 3 208.27 0.42 201 251 255 4 188.80 0.36 202 252 255 3 203.32 2.36 203 252 257 5 179.02 2.50 204 252 259 7 147.78 0.12 205 252 260 8 142.83 2.54 206 253 259 6 143.13 2.44 207 253 260 7 142.65 2.56 208 253 263 10 142.66 2.56 209 253 268 15 107.47 1.27 210 254 260 6 142.88 2.56 211 254 264 10 142.81 2.54 212 255 260 5 164.72 5.18 213 255 264 9 147.92 0.06 214 257 260 3 200.96 3.64 215 257 261 4 189.08 0.80 216 258 261 3 191.52 2.02 217 258 262 4 192.18 0.76 218 259 262 3 211.38 2.31 219 259 263 4 192.42 0.63 220 260 263 3 200.35 3.15 221 260 264 4 190.39 0.14 222 261 264 3 211.18 0.29 223 261 265 4 200.16 3.25 224 262 265 3 202.71 4.52 225 262 266 4 200.16 3.25 226 263 266 3 208.44 5.41 227 263 267 4 187.28 0.35 228 263 268 5 148.56 0.15 229 263 269 6 133.79 6.94 230 264 267 3 200.40 3.37 231 264 269 5 110.13 0.06