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 1 145 188 43 13.89 1.07 2 146 176 30 40.76 0.90 3 147 151 4 160.98 1.57 4 147 155 8 149.55 1.54 5 147 176 29 41.58 0.48 6 147 180 33 38.12 0.88 7 147 181 34 37.70 0.67 8 147 184 37 32.48 1.82 9 148 151 3 161.80 1.17 10 148 152 4 161.80 1.16 11 149 152 3 161.81 1.17 12 149 153 4 161.80 1.16 13 150 153 3 162.22 0.96 14 150 154 4 161.80 1.16 15 151 154 3 163.39 1.19 16 151 155 4 158.17 0.18 17 151 173 22 49.27 0.57 18 151 176 25 48.41 0.90 19 152 155 3 161.55 1.87 20 152 156 4 158.18 0.18 21 152 184 32 39.59 0.18 22 152 189 37 38.06 0.94 23 153 156 3 167.70 2.50 24 153 157 4 159.41 0.44 25 154 157 3 160.85 0.12 26 154 158 4 158.63 0.99 27 154 173 19 51.24 0.41 28 155 158 3 165.00 2.12 29 155 159 4 159.56 0.54 30 155 166 11 92.42 4.37 31 155 169 14 69.23 0.91 32 155 173 18 52.23 0.09 33 155 181 26 43.50 0.41 34 155 184 29 42.10 1.10 35 155 185 30 39.61 0.22 36 156 159 3 161.96 1.31 37 156 160 4 161.53 1.53 38 156 185 29 39.87 0.30 39 156 189 33 38.68 0.64 40 157 160 3 167.46 0.94 41 157 161 4 159.30 0.41 42 158 161 3 163.88 0.85 43 158 162 4 154.24 1.21 44 158 163 5 151.28 0.27 45 158 169 11 75.12 2.04 46 159 163 4 150.18 0.82 47 159 164 5 117.16 3.03 48 159 166 7 109.20 4.00 49 159 169 10 92.45 4.36 50 159 185 26 43.59 0.45 51 162 165 3 176.24 1.14 52 162 169 7 109.97 4.38 53 163 169 6 141.90 3.05 54 165 168 3 161.68 1.50 55 165 169 4 158.97 2.85 56 166 169 3 161.65 1.52 57 166 170 4 159.03 2.82 58 166 181 15 48.55 0.90 59 166 182 16 48.54 0.90 60 166 185 19 48.54 0.90 61 167 170 3 169.18 0.65 62 168 171 3 164.13 0.12 63 169 172 3 172.67 3.98 64 169 173 4 156.82 1.89 65 170 173 3 156.82 1.89 66 170 174 4 140.01 6.51 67 170 176 6 96.79 1.64 68 170 181 11 59.13 0.38 69 173 176 3 167.00 0.94 70 176 181 5 142.04 2.08 71 177 180 3 155.83 0.24 72 177 181 4 155.85 0.23 73 178 181 3 161.28 0.63 74 178 182 4 155.88 0.22 75 179 182 3 164.72 0.35 76 179 183 4 155.88 0.22 77 180 183 3 158.10 0.88 78 180 184 4 155.90 0.21 79 181 184 3 163.00 1.21 80 181 185 4 157.20 0.92 81 182 185 3 156.29 0.47 82 182 186 4 155.41 0.03 83 183 186 3 160.59 0.01 84 183 187 4 155.03 0.17 85 184 187 3 155.30 0.04 86 184 188 4 155.00 0.17 87 184 189 5 155.00 0.17 88 185 189 4 146.58 4.21 89 185 190 5 146.56 4.21 90 186 190 4 122.42 1.33 91 186 191 5 119.94 0.09 92 187 191 4 122.17 1.47 93 188 191 3 164.55 1.22 94 190 193 3 171.94 0.21