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 3 27 24 308.06 0.03 2 4 24 20 308.92 0.45 3 4 27 23 308.42 0.18 4 4 92 87 308.33 0.32 5 4 94 89 307.97 0.01 6 4 107 98 307.90 0.03 7 4 109 100 307.46 0.14 8 5 23 18 308.94 0.47 9 5 24 19 308.96 0.46 10 5 92 86 308.92 0.47 11 5 110 100 307.63 0.06 12 6 21 15 309.65 0.29 13 6 22 16 309.54 0.34 14 6 23 17 308.96 0.46 15 6 34 28 309.24 0.32 16 6 90 83 309.00 0.61 17 6 92 85 308.94 0.47 18 6 110 99 307.81 0.04 19 6 111 100 307.68 0.07 20 6 112 101 307.36 0.18 21 7 20 13 309.90 0.36 22 7 21 14 309.65 0.29 23 7 22 15 309.56 0.33 24 7 112 100 307.78 0.03 25 8 22 14 309.75 0.33 26 9 20 11 310.04 0.35 27 10 113 98 307.93 0.02 28 11 114 98 307.92 0.02 29 12 114 97 307.93 0.02 30 12 115 98 307.92 0.03 31 13 17 4 324.90 3.95 32 13 18 5 324.90 3.95 33 13 114 96 307.94 0.02 34 13 115 97 307.91 0.02 35 13 116 98 307.81 0.04 36 13 116 99 307.82 0.04 37 14 17 3 347.76 4.48 38 14 116 97 307.85 0.05 39 14 116 98 307.83 0.04 40 15 116 96 307.88 0.04 41 15 116 97 307.83 0.04 42 16 81 64 390.82 3.25 43 16 82 65 406.20 3.96 44 16 116 95 307.88 0.04 45 18 79 60 535.99 2.52 46 19 90 70 449.72 1.04 47 19 114 90 307.85 0.04 48 21 112 86 307.83 0.03 49 27 107 75 308.08 0.03 50 29 107 73 308.17 0.06 51 31 97 65 536.15 1.99 52 31 402 205 45.80 0.92 53 33 402 203 45.99 1.01 54 35 106 66 308.38 0.01 55 35 404 203 45.88 1.05 56 37 337 140 44.32 1.20 57 37 340 143 44.41 1.21 58 39 411 206 43.64 0.97 59 40 408 202 44.72 1.23 60 41 389 187 45.42 1.27 61 41 406 199 45.48 1.28 62 41 408 201 44.04 1.11 63 42 336 134 45.01 1.22 64 42 389 186 44.72 1.18 65 42 408 200 44.04 1.11 66 43 336 133 44.55 1.14 67 43 389 185 44.77 1.12 68 43 406 197 45.38 1.26 69 44 406 196 45.40 1.27 70 45 406 195 45.41 1.27 71 48 402 188 46.01 1.02 72 48 403 189 46.01 1.02 73 48 404 190 46.01 1.02 74 50 402 186 45.91 0.96 75 82 116 30 307.82 0.03 76 83 116 29 307.89 0.04 77 84 116 28 307.90 0.03 78 84 116 29 307.75 0.00 79 84 217 46 52.95 0.12 80 87 114 23 308.11 0.02 81 87 115 24 307.88 0.01 82 87 116 25 307.75 0.01 83 88 113 21 308.11 0.03 84 88 114 22 307.98 0.01 85 89 112 19 308.12 0.03 86 89 113 20 307.87 0.01 87 90 111 17 308.12 0.03 88 90 112 18 307.94 0.01 89 90 114 20 307.87 0.01 90 91 108 13 308.18 0.03 91 91 111 16 307.88 0.01 92 91 341 91 44.08 1.23 93 91 343 93 43.89 1.26 94 93 106 9 308.26 0.07 95 93 108 11 308.13 0.04 96 94 107 9 308.18 0.06 97 96 104 4 348.06 2.33 98 98 331 74 45.46 0.83 99 99 348 90 44.18 1.25 100 104 345 86 43.38 1.53 101 105 345 85 43.29 1.54 102 106 335 74 43.29 1.54 103 106 345 84 43.29 1.54 104 108 343 80 43.27 1.54 105 113 341 73 44.03 1.20 106 203 206 3 365.24 0.81 107 301 406 99 180.80 1.40 108 301 407 100 170.12 1.54 109 302 323 21 187.52 3.85 110 302 324 22 187.27 3.75 111 302 325 23 187.26 3.75 112 302 405 97 181.72 1.61 113 303 322 19 187.52 3.85 114 303 323 20 187.52 3.85 115 303 324 21 187.34 3.76 116 303 390 86 185.19 3.60 117 303 391 87 181.44 1.67 118 303 405 96 181.76 1.63 119 303 406 97 181.28 1.59 120 303 407 98 177.68 1.66 121 304 322 18 187.57 3.86 122 304 323 19 187.58 3.86 123 304 325 21 187.71 3.86 124 305 320 15 187.68 3.88 125 305 321 16 187.63 3.88 126 305 322 17 187.58 3.86 127 305 334 29 187.57 3.87 128 305 390 84 187.56 3.87 129 305 408 97 181.81 1.61 130 305 409 98 181.06 1.50 131 305 410 99 179.91 1.21 132 306 321 15 187.66 3.89 133 306 410 98 181.30 1.58 134 309 410 95 182.00 1.65 135 309 411 96 181.86 1.60 136 310 318 8 318.46 1.58 137 310 412 96 181.92 1.62 138 310 413 97 181.84 1.59 139 311 413 96 181.61 1.71 140 311 414 97 181.41 1.65 141 311 415 98 181.28 1.60 142 312 316 4 364.35 4.30 143 312 318 6 327.37 3.20 144 312 413 95 181.93 1.62 145 312 414 96 181.38 1.62 146 312 415 97 181.37 1.62 147 313 316 3 391.62 0.65 148 313 415 96 181.36 1.62 149 313 417 98 181.24 1.62 150 314 414 94 181.94 1.62 151 315 380 64 502.63 4.22 152 315 381 65 502.63 4.22 153 315 414 93 182.03 1.67 154 318 412 88 181.97 1.66 155 320 412 86 181.12 1.52 156 333 404 65 191.23 2.48 157 381 414 28 182.06 1.67 158 382 414 27 182.05 1.67 159 384 412 23 182.18 1.64 160 384 413 24 182.06 1.67 161 384 414 25 182.06 1.67 162 385 412 22 182.13 1.66 163 385 413 23 182.06 1.67 164 385 414 24 182.05 1.67 165 386 412 21 182.06 1.68 166 387 410 18 182.18 1.64 167 387 411 19 182.05 1.67 168 388 409 16 182.14 1.65 169 388 410 17 182.07 1.68 170 389 408 14 182.15 1.65 171 389 409 15 181.95 1.67 172 391 405 9 185.86 0.10 173 391 406 10 182.14 1.65 174 392 403 6 210.69 3.79 175 392 404 7 190.98 2.62 176 392 405 8 187.49 0.87 177 393 403 5 208.14 5.07 178 393 404 6 193.81 4.03 179 400 403 3 390.42 2.93