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 1 147 152 5 150.73 0.60 2 147 155 8 142.51 1.82 3 147 176 29 35.37 0.72 4 147 181 34 29.39 0.35 5 147 184 37 27.09 1.50 6 148 151 3 154.16 1.68 7 148 152 4 153.44 1.31 8 149 152 3 156.87 0.32 9 149 153 4 153.45 1.31 10 150 153 3 156.19 0.02 11 150 154 4 153.46 1.30 12 151 154 3 156.36 0.14 13 151 155 4 152.43 0.79 14 151 176 25 42.72 1.18 15 152 155 3 154.75 0.34 16 152 156 4 153.64 0.19 17 152 184 32 32.11 0.35 18 152 189 37 28.71 0.18 19 153 156 3 153.65 0.20 20 153 157 4 153.27 0.38 21 154 157 3 156.18 1.07 22 154 158 4 151.60 0.46 23 154 173 19 47.10 0.53 24 155 158 3 156.16 1.81 25 155 159 4 152.60 0.04 26 155 169 14 48.02 1.08 27 155 173 18 47.12 0.53 28 155 181 26 39.12 0.85 29 155 185 30 32.06 0.36 30 156 159 3 152.70 0.09 31 156 160 4 152.61 0.04 32 156 185 29 33.56 0.06 33 157 160 3 155.65 0.76 34 157 161 4 152.40 0.86 35 158 161 3 155.65 0.76 36 158 162 4 149.88 0.34 37 158 169 11 59.11 0.52 38 159 162 3 155.63 0.77 39 159 163 4 128.25 7.33 40 159 164 5 139.28 1.81 41 159 166 7 102.79 2.70 42 159 169 10 68.80 1.05 43 159 185 26 42.16 1.54 44 159 192 33 26.87 0.73 45 160 193 33 23.32 0.48 46 162 165 3 161.66 0.98 47 162 168 6 107.97 0.11 48 162 169 7 98.84 4.67 49 164 192 28 32.23 0.30 50 165 168 3 156.10 1.75 51 165 169 4 147.62 1.72 52 166 169 3 151.34 0.48 53 166 170 4 146.20 1.50 54 166 178 12 53.28 2.14 55 166 181 15 53.27 2.14 56 166 182 16 53.23 2.12 57 166 185 19 53.24 2.12 58 166 186 20 53.25 2.12 59 167 171 4 152.95 1.28 60 168 171 3 156.52 1.54 61 168 172 4 154.48 0.52 62 169 172 3 158.94 0.33 63 169 173 4 154.48 0.52 64 169 181 12 64.98 2.27 65 170 173 3 152.38 1.55 66 170 174 4 150.28 0.58 67 170 176 6 82.88 2.08 68 170 177 7 65.91 2.60 69 170 178 8 65.15 2.23 70 170 181 11 65.08 2.26 71 171 174 3 159.31 2.25 72 173 176 3 155.87 1.55 73 176 180 4 150.81 1.38 74 176 181 5 134.69 3.23 75 177 180 3 158.48 0.64 76 177 181 4 150.82 1.39 77 178 181 3 159.03 0.36 78 178 182 4 150.83 1.39 79 179 182 3 151.97 0.86 80 179 183 4 150.87 1.42 81 180 183 3 157.75 0.41 82 180 184 4 152.53 0.60 83 181 184 3 157.75 0.41 84 181 185 4 152.59 0.64 85 182 185 3 158.83 0.13 86 182 186 4 152.59 0.64 87 183 186 3 156.53 1.81 88 183 187 4 153.08 0.38 89 184 187 3 156.48 1.31 90 184 188 4 149.78 2.03 91 184 189 5 149.77 2.03 92 185 188 3 162.14 0.97 93 185 189 4 149.77 2.03 94 185 190 5 149.74 2.04 95 185 191 6 149.73 2.04 96 185 192 7 149.72 2.05 97 186 190 4 149.72 2.04 98 186 192 6 149.71 2.04 99 187 190 3 162.47 1.11