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 1 268 271 3 127.43 0.52 2 268 272 4 119.25 1.09 3 269 272 3 119.67 0.89 4 269 273 4 119.06 1.19 5 269 302 33 15.41 0.04 6 270 273 3 126.50 0.83 7 270 274 4 122.62 1.09 8 271 274 3 126.50 0.83 9 271 275 4 123.45 0.68 10 272 275 3 126.45 0.80 11 272 276 4 121.78 0.16 12 273 276 3 128.77 1.29 13 273 277 4 120.96 0.24 14 273 299 26 27.66 1.15 15 274 277 3 123.67 1.07 16 274 278 4 123.70 1.05 17 275 278 3 128.19 1.19 18 275 279 4 121.42 0.09 19 276 279 3 125.98 1.90 20 276 280 4 121.41 0.09 21 276 295 19 42.70 0.61 22 276 299 23 37.84 0.64 23 276 302 26 29.52 0.92 24 277 280 3 124.24 1.32 25 277 281 4 120.92 0.33 26 278 281 3 126.41 0.24 27 278 282 4 119.70 0.29 28 279 282 3 125.84 1.78 29 279 283 4 121.12 0.45 30 279 295 16 43.21 0.38 31 280 283 3 124.82 0.03 32 280 284 4 118.50 0.64 33 280 292 12 43.21 0.37 34 280 295 15 43.20 0.37 35 280 296 16 43.19 0.38 36 280 299 19 43.19 0.38 37 281 284 3 122.70 1.03 38 281 285 4 119.36 0.20 39 282 285 3 134.31 1.82 40 282 286 4 111.59 3.68 41 283 286 3 124.86 0.99 42 283 288 5 58.84 1.17 43 283 289 6 58.86 1.17 44 283 291 8 52.49 1.96 45 283 292 9 46.85 0.29 46 284 289 5 58.86 1.17 47 284 292 8 46.84 0.30 48 288 291 3 134.25 0.46 49 289 292 3 121.52 0.61 50 289 293 4 119.75 0.83 51 290 293 3 130.21 0.11 52 290 294 4 122.61 0.45 53 291 294 3 124.62 0.42 54 291 295 4 120.27 0.85 55 292 295 3 123.10 0.33 56 292 296 4 120.14 0.79 57 293 296 3 123.09 0.33 58 293 297 4 121.78 0.04 59 294 297 3 123.89 0.07 60 294 298 4 122.80 0.44 61 295 298 3 123.88 0.09 62 295 299 4 122.78 0.45 63 296 299 3 123.66 0.01 64 296 300 4 122.78 0.45 65 297 300 3 123.66 0.01 66 297 301 4 122.78 0.45 67 298 301 3 121.14 0.48 68 298 302 4 117.56 0.83 69 299 302 3 118.74 0.24