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 21 24 3 97.15 0.04 2 21 25 4 91.78 1.67 3 21 105 84 62.04 0.48 4 22 25 3 94.59 0.29 5 22 26 4 88.36 0.85 6 22 269 232 34.78 0.24 7 22 274 237 13.19 0.35 8 23 26 3 110.19 3.81 9 23 44 21 62.02 0.48 10 23 100 77 65.59 1.52 11 23 102 79 62.01 0.47 12 23 103 80 64.44 1.68 13 23 104 81 62.04 0.48 14 23 261 223 62.04 0.48 15 23 265 227 61.52 0.32 16 23 268 230 47.16 0.60 17 23 269 231 39.84 1.02 18 23 274 236 13.84 0.07 19 24 66 42 85.25 0.22 20 24 100 76 65.60 1.52 21 24 105 81 65.56 1.54 22 24 106 82 65.58 1.53 23 24 107 83 65.61 1.52 24 25 66 41 85.74 0.38 25 26 30 4 135.40 1.23 26 26 66 40 85.75 0.38 27 26 101 75 83.02 0.03 28 26 102 76 73.92 2.02 29 26 274 233 17.11 0.79 30 27 66 39 85.75 0.38 31 27 101 74 85.53 0.36 32 28 101 73 85.66 0.34 33 29 48 19 85.80 0.35 34 29 69 40 86.31 0.38 35 29 101 72 85.67 0.34 36 30 46 16 85.64 0.33 37 30 47 17 86.28 0.16 38 30 102 72 85.69 0.33 39 30 273 228 26.23 1.22 40 30 274 229 24.70 0.92 41 31 46 15 86.47 0.26 42 32 46 14 93.94 1.27 43 32 47 15 103.09 0.01 44 33 46 13 114.80 0.09 45 34 46 12 115.88 0.16 46 34 47 13 115.89 0.15 47 34 71 37 118.95 0.66 48 34 72 38 121.43 1.51 49 35 45 10 115.93 0.17 50 35 46 11 115.92 0.17 51 35 220 185 214.27 9.77 52 36 44 8 115.95 0.17 53 36 45 9 115.95 0.17 54 36 71 35 122.49 1.36 55 36 115 79 115.95 0.17 56 36 117 81 122.72 1.47 57 36 217 181 217.52 8.14 58 36 220 184 225.93 10.09 59 36 223 187 244.78 0.69 60 37 43 6 119.09 0.67 61 37 44 7 116.00 0.19 62 37 46 9 122.30 1.26 63 37 115 78 122.06 1.15 64 37 262 210 115.95 0.18 65 37 264 212 115.94 0.18 66 37 265 213 115.88 0.15 67 38 42 4 122.92 0.73 68 38 43 5 119.19 0.62 69 38 115 77 133.31 1.76 70 38 262 209 115.94 0.18 71 39 42 3 132.62 1.33 72 39 43 4 122.95 0.76 73 39 115 76 247.12 0.49 74 43 265 207 196.02 1.20 75 44 268 209 114.86 4.54 76 46 268 207 245.09 1.56 77 102 274 157 20.41 1.99 78 222 264 27 247.84 0.23 79 261 269 8 248.12 1.17 80 265 268 3 114.86 4.54 81 265 269 4 97.17 0.72 82 266 269 3 113.87 4.50 83 266 270 4 95.86 0.07 84 267 270 3 94.94 0.58 85 267 271 4 94.82 0.53 86 268 271 3 96.14 1.19 87 268 272 4 80.85 5.24 88 268 273 5 38.84 2.63 89 268 274 6 31.88 0.67 90 269 272 3 96.14 1.19 91 269 274 5 28.07 2.10