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 5 27 22 208.34 43.34 2 5 28 23 208.38 43.34 3 5 29 24 208.38 43.34 4 6 25 19 208.31 43.36 5 6 26 20 208.34 43.34 6 6 27 21 208.37 43.34 7 6 93 87 207.38 43.16 8 6 94 88 208.22 43.40 9 6 95 89 208.31 43.36 10 6 104 98 208.32 43.35 11 6 105 99 208.04 43.37 12 6 106 100 204.37 41.95 13 7 25 18 208.37 43.33 14 7 26 19 208.37 43.33 15 8 24 16 208.37 43.33 16 8 25 17 208.37 43.33 17 8 36 28 208.34 43.34 18 8 91 83 208.30 43.36 19 8 92 84 208.31 43.36 20 8 93 85 208.32 43.35 21 8 106 98 208.33 43.34 22 8 107 99 208.27 43.34 23 8 108 100 207.81 43.30 24 8 109 101 207.28 43.17 25 9 13 4 349.50 3.03 26 9 23 14 208.37 43.34 27 9 24 15 208.38 43.34 28 9 109 100 207.78 43.30 29 10 13 3 377.76 1.32 30 10 109 99 207.94 43.33 31 10 215 205 35.90 1.27 32 11 108 97 208.35 43.33 33 11 109 98 207.90 43.31 34 11 110 99 207.90 43.30 35 11 156 145 33.70 0.53 36 11 215 204 39.71 0.41 37 12 110 98 207.91 43.30 38 12 153 141 47.40 0.19 39 12 154 142 42.16 0.07 40 12 155 143 42.29 0.45 41 12 215 203 39.71 0.41 42 13 21 8 288.72 4.55 43 13 23 10 208.97 43.32 44 13 109 96 208.37 43.32 45 13 110 97 208.22 43.30 46 13 111 98 207.77 43.27 47 13 112 99 207.75 43.27 48 14 111 97 208.03 43.38 49 14 112 98 207.81 43.27 50 14 114 100 207.62 43.25 51 14 117 103 155.99 41.86 52 14 120 106 50.50 0.06 53 14 152 138 51.61 0.60 54 14 154 140 48.80 0.01 55 14 215 201 48.44 0.10 56 14 216 202 48.33 0.08 57 14 217 203 48.36 0.14 58 15 18 3 493.28 3.72 59 15 19 4 341.71 0.52 60 15 21 6 300.38 1.28 61 15 80 65 312.12 2.16 62 15 81 66 341.82 0.47 63 15 82 67 343.78 1.43 64 15 84 69 344.95 1.70 65 15 111 96 208.35 43.31 66 15 112 97 207.91 43.36 67 15 113 98 207.47 43.16 68 15 114 99 207.44 43.15 69 16 19 3 353.72 1.24 70 16 114 98 207.26 43.06 71 16 115 99 203.50 41.23 72 16 117 101 198.52 43.72 73 17 115 98 203.21 41.38 74 18 82 64 391.89 2.85 75 19 82 63 435.68 2.25 76 20 80 60 465.92 1.90 77 20 81 61 465.85 1.92 78 20 82 62 460.79 0.69 79 21 79 58 495.28 7.93 80 21 80 59 486.64 12.26 81 22 77 55 499.29 6.43 82 22 78 56 508.68 1.65 83 22 79 57 495.31 7.95 84 23 36 13 481.19 3.14 85 23 77 54 511.32 0.58 86 23 78 55 509.00 1.74 87 23 109 86 208.78 43.01 88 29 104 75 287.58 4.89 89 31 104 73 220.75 38.28 90 32 98 66 514.99 0.26 91 33 98 65 439.35 2.83 92 35 103 68 219.33 38.91 93 37 103 66 219.31 38.91 94 37 105 68 217.45 39.62 95 45 105 60 219.00 38.88 96 53 98 45 514.96 0.27 97 80 111 31 208.40 43.27 98 86 113 27 208.43 43.27 99 87 113 26 208.42 43.27 100 88 110 22 209.36 43.25 101 88 111 23 209.16 43.22 102 88 112 24 208.88 43.12 103 88 113 25 208.66 43.01 104 89 110 21 209.36 43.25 105 89 111 22 209.31 43.27 106 90 108 18 209.41 43.23 107 90 109 19 209.40 43.24 108 90 110 20 209.31 43.23 109 91 108 17 209.38 43.23 110 91 109 18 209.37 43.23 111 91 111 20 208.95 43.09 112 92 105 13 216.39 40.13 113 92 106 14 216.08 40.20 114 92 108 16 209.37 43.24 115 93 105 12 216.33 40.11 116 93 106 13 215.99 39.95 117 94 103 9 219.31 38.91 118 94 104 10 218.91 38.92 119 94 105 11 216.33 40.11 120 95 103 8 220.25 38.45 121 95 104 9 219.21 38.90 122 96 100 4 378.78 1.02 123 96 101 5 317.73 0.85 124 96 102 6 283.19 7.06 125 96 103 7 220.68 38.29 126 97 101 4 339.03 0.34 127 98 101 3 354.82 3.43 128 112 154 42 48.52 0.13 129 114 117 3 412.88 2.33 130 116 119 3 389.79 2.12 131 117 120 3 356.80 5.72 132 117 217 100 167.40 29.48 133 117 223 106 181.42 29.59 134 118 121 3 512.08 0.24 135 118 225 107 181.63 29.59 136 118 227 109 181.97 29.74 137 119 151 32 212.32 14.57 138 119 185 66 216.06 15.24 139 120 151 31 212.35 14.59 140 120 152 32 212.34 14.58 141 120 214 94 191.04 25.21 142 120 227 107 182.41 29.76 143 120 230 110 181.93 29.75 144 121 149 28 216.49 15.04 145 121 150 29 215.27 15.17 146 121 151 30 213.25 14.26 147 121 187 66 216.50 15.04 148 121 214 93 191.03 25.22 149 121 227 106 182.42 29.76 150 121 230 109 181.99 29.74 151 122 149 27 223.24 18.14 152 122 150 28 216.01 15.21 153 122 214 92 191.01 25.21 154 122 230 108 182.09 29.79 155 122 233 111 181.93 29.75 156 123 147 24 226.21 19.49 157 123 148 25 223.36 18.19 158 123 150 27 216.01 15.21 159 123 155 32 215.62 15.39 160 123 212 89 201.16 22.62 161 123 214 91 191.59 25.12 162 123 235 112 179.44 29.96 163 124 146 22 227.56 19.94 164 124 147 23 226.31 19.50 165 124 148 24 226.30 19.50 166 124 235 111 181.89 29.74 167 125 145 20 227.59 19.94 168 125 146 21 227.55 19.94 169 125 147 22 226.35 19.48 170 125 210 85 224.04 20.93 171 125 212 87 209.56 24.99 172 125 235 110 181.97 29.73 173 125 236 111 181.46 29.73 174 125 237 112 178.45 29.54 175 126 145 19 227.63 19.93 176 126 146 20 227.58 19.93 177 126 237 111 180.72 30.09 178 127 143 16 227.85 20.01 179 127 144 17 227.83 20.01 180 127 145 18 227.66 19.94 181 127 159 32 227.67 19.93 182 127 210 83 227.65 19.93 183 127 237 110 181.97 29.73 184 127 239 112 179.96 30.27 185 128 143 15 227.91 20.04 186 128 144 16 227.90 20.04 187 128 146 18 227.85 20.01 188 129 143 14 227.93 20.04 189 129 201 72 241.70 21.43 190 129 242 113 178.00 29.30 191 130 134 4 341.95 1.64 192 130 135 5 335.50 1.58 193 130 141 11 228.38 20.14 194 130 142 12 228.31 20.12 195 130 143 13 228.30 20.12 196 130 201 71 243.77 22.39 197 131 134 3 353.82 1.74 198 131 135 4 341.96 1.64 199 132 135 3 351.33 0.63 200 132 136 4 341.96 1.64 201 133 136 3 356.27 1.83 202 133 137 4 345.64 3.48 203 134 137 3 348.42 1.59 204 134 138 4 335.38 1.57 205 134 139 5 332.69 0.40 206 134 140 6 329.25 2.04 207 134 141 7 329.14 2.10 208 134 142 8 319.62 1.94 209 135 139 4 329.29 2.04 210 135 140 5 329.28 2.04 211 135 141 6 329.22 2.06 212 135 198 63 330.77 1.29 213 135 201 66 329.31 2.04 214 135 202 67 332.36 0.93 215 136 139 3 334.45 2.12 216 143 239 96 182.20 29.82 217 157 172 15 514.97 0.01 218 157 192 35 514.48 0.24 219 159 194 35 483.88 5.21 220 201 240 39 182.24 29.80 221 201 241 40 181.66 29.84 222 201 242 41 181.51 29.76 223 202 242 40 181.87 29.74 224 202 243 41 180.91 30.01 225 202 244 42 181.10 29.92 226 203 241 38 182.24 29.80 227 204 240 36 182.35 29.79 228 204 241 37 182.22 29.81 229 204 243 39 182.20 29.82 230 206 240 34 182.23 29.80 231 206 241 35 182.16 29.80 232 207 238 31 182.38 29.78 233 207 239 32 182.25 29.80 234 207 240 33 181.97 29.73 235 208 238 30 182.25 29.80 236 208 239 31 182.21 29.82 237 208 240 32 181.97 29.73 238 208 241 33 181.97 29.73 239 209 236 27 182.37 29.79 240 209 237 28 182.25 29.80 241 209 238 29 181.97 29.73 242 210 236 26 182.25 29.80 243 210 237 27 182.21 29.82 244 211 234 23 182.37 29.79 245 211 235 24 182.31 29.78 246 211 236 25 182.17 29.80 247 212 234 22 182.31 29.77 248 212 235 23 182.25 29.80 249 213 232 19 182.44 29.79 250 213 233 20 182.33 29.78 251 213 234 21 182.23 29.80 252 214 230 16 182.75 29.74 253 214 231 17 182.68 29.75 254 214 232 18 182.37 29.79 255 214 233 19 182.31 29.78 256 215 232 17 182.38 29.78 257 216 230 14 182.77 29.73 258 216 231 15 182.71 29.76 259 216 232 16 182.40 29.79 260 217 221 4 255.66 29.16 261 217 223 6 198.64 37.26 262 217 230 13 182.78 29.73 263 217 231 14 182.72 29.75 264 217 232 15 182.71 29.76 265 218 221 3 326.74 3.70 266 218 229 11 183.63 29.80 267 219 229 10 183.47 29.93 268 221 229 8 183.78 29.86 269 223 227 4 374.50 0.64 270 223 228 5 301.41 0.41 271 223 229 6 183.79 29.86 272 223 230 7 185.87 30.90