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 2 17 15 35.83 0.42 2 2 20 18 31.36 0.45 3 2 21 19 30.80 0.17 4 2 49 44 33.28 0.74 5 2 50 45 32.02 0.11 6 2 51 46 37.90 0.49 7 3 51 45 38.00 0.54 8 4 9 5 62.79 0.07 9 4 13 9 46.13 0.25 10 4 14 10 41.73 1.02 11 4 17 13 38.90 0.21 12 4 51 44 39.04 0.15 13 4 52 45 40.70 0.93 14 4 187 172 63.28 0.04 15 5 8 3 81.73 2.17 16 5 9 4 63.08 0.07 17 6 9 3 74.87 5.60 18 6 52 43 49.91 0.61 19 6 137 124 63.55 0.06 20 6 138 125 63.66 0.07 21 6 141 128 66.23 0.26 22 7 54 43 66.41 0.36 23 7 55 44 71.59 1.69 24 7 138 124 66.78 0.45 25 9 13 4 73.05 0.95 26 9 187 167 81.30 0.62 27 10 13 3 75.28 0.39 28 10 14 4 74.97 0.26 29 10 187 166 81.34 0.64 30 11 14 3 80.09 2.02 31 11 15 4 79.50 0.12 32 11 187 165 81.89 0.51 33 12 15 3 82.57 0.78 34 12 16 4 82.67 0.72 35 13 16 3 88.72 2.04 36 13 17 4 82.73 0.70 37 14 17 3 83.32 0.66 38 14 18 4 83.01 0.82 39 14 169 147 88.36 0.78 40 14 173 151 83.92 0.36 41 14 183 159 91.34 1.55 42 14 187 162 98.78 0.86 43 15 18 3 85.98 0.83 44 15 19 4 90.44 0.04 45 15 180 156 87.09 1.15 46 16 19 3 92.25 0.62 47 16 20 4 92.72 0.84 48 17 20 3 96.94 0.30 49 17 21 4 93.03 0.98 50 17 50 30 104.95 0.21 51 17 170 145 100.41 0.67 52 18 21 3 98.62 0.80 53 18 22 4 96.69 0.17 54 18 169 143 102.01 0.27 55 18 170 144 101.62 0.07 56 18 173 147 99.21 0.58 57 18 174 148 93.69 1.33 58 18 180 153 99.61 0.71 59 19 22 3 104.89 0.24 60 19 23 4 104.86 0.14 61 20 23 3 104.98 0.20 62 20 24 4 104.97 0.20 63 21 24 3 106.30 0.66 64 21 25 4 104.98 0.20 65 21 48 24 138.62 0.59 66 21 50 26 139.31 0.71 67 21 63 38 136.16 1.70 68 21 170 141 117.14 4.79 69 21 174 145 104.98 0.21 70 22 25 3 106.28 0.67 71 22 36 12 104.93 0.21 72 22 173 143 124.31 1.22 73 22 174 144 107.03 0.96 74 22 180 149 134.19 0.34 75 22 252 216 104.95 0.20 76 22 253 217 104.93 0.21 77 24 48 21 146.53 3.60 78 24 65 37 139.56 0.77 79 25 38 11 131.27 0.89 80 25 39 12 138.89 0.46 81 25 48 20 182.87 14.35 82 25 65 36 138.68 0.58 83 25 68 39 138.91 0.47 84 25 253 214 138.57 0.58 85 27 37 9 139.49 0.76 86 27 38 10 139.44 0.71 87 27 39 11 139.53 0.76 88 27 256 216 138.91 0.47 89 31 262 219 51.40 0.99 90 32 261 217 85.15 8.68 91 32 262 218 30.21 5.67 92 33 261 216 85.11 8.65 93 33 262 217 54.20 0.44 94 34 262 216 48.31 3.39