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 1 149 175 26 39.14 0.45 2 150 153 3 162.75 0.49 3 150 168 18 37.80 0.91 4 150 171 21 38.99 0.52 5 150 172 22 38.97 0.51 6 150 175 25 39.15 0.45 7 150 185 35 37.92 0.69 8 150 189 39 37.43 0.80 9 150 193 43 32.49 1.71 10 151 189 38 37.48 0.78 11 151 193 42 33.56 1.18 12 153 164 11 61.34 2.45 13 153 167 14 47.31 3.36 14 153 168 15 40.81 0.26 15 153 171 18 40.94 0.28 16 153 193 40 39.02 0.53 17 154 164 10 62.61 1.83 18 154 167 13 56.23 0.10 19 154 193 39 39.16 0.46 20 155 159 4 109.50 1.47 21 155 160 5 107.40 2.52 22 155 161 6 90.84 4.55 23 155 164 9 64.10 1.08 24 155 193 38 39.20 0.48 25 155 194 39 39.16 0.47 26 155 195 40 39.16 0.47 27 155 198 43 38.99 0.52 28 156 159 3 130.63 12.04 29 156 195 39 39.20 0.48 30 159 163 4 156.94 0.39 31 159 164 5 152.53 1.80 32 159 167 8 148.98 0.29 33 160 163 3 159.19 1.52 34 160 164 4 156.94 0.39 35 161 164 3 158.43 1.13 36 161 165 4 156.14 0.01 37 161 190 29 50.70 0.72 38 161 198 37 39.36 0.51 39 161 202 41 39.99 0.79 40 161 214 53 39.42 0.50 41 161 215 54 39.42 0.50 42 161 218 57 35.15 0.70 43 162 165 3 160.08 0.34 44 162 166 4 158.20 0.21 45 162 215 53 39.45 0.48 46 163 166 3 161.96 1.21 47 163 167 4 158.28 0.18 48 164 167 3 164.38 2.48 49 164 168 4 158.29 0.18 50 164 189 25 52.38 1.23 51 164 190 26 49.98 0.36 52 164 193 29 50.72 0.69 53 164 194 30 49.12 0.07 54 165 168 3 166.10 1.96 55 165 169 4 158.30 0.18 56 165 190 25 51.02 0.73 57 165 211 46 49.26 0.02 58 165 215 50 44.16 2.56 59 166 169 3 169.83 0.10 60 166 170 4 158.83 0.44 61 167 170 3 167.19 0.12 62 167 171 4 156.65 0.36 63 168 171 3 163.52 0.32 64 168 172 4 158.97 1.36 65 168 185 17 52.62 1.18 66 168 189 21 52.43 1.23 67 168 190 22 51.23 0.99 68 169 172 3 162.93 0.61 69 169 173 4 158.87 1.42 70 169 182 13 58.83 1.59 71 169 186 17 52.57 1.20 72 169 190 21 52.42 1.23 73 169 211 42 52.41 1.23 74 170 173 3 158.60 1.28 75 170 174 4 158.20 1.08 76 171 174 3 166.61 1.23 77 171 175 4 159.91 0.22 78 172 175 3 159.91 0.21 79 172 176 4 155.88 0.44 80 172 177 5 127.19 2.96 81 172 182 10 69.45 2.09 82 172 185 13 60.05 1.05 83 173 176 3 155.84 0.43 84 177 181 4 158.92 0.48 85 177 182 5 155.72 1.13 86 178 181 3 159.03 0.53 87 178 182 4 158.94 0.48 88 179 182 3 159.00 0.51 89 179 183 4 159.06 0.51 90 180 183 3 162.32 0.37 91 180 184 4 161.66 0.04 92 181 184 3 165.53 0.01 93 181 185 4 161.66 0.04 94 182 185 3 169.74 2.12 95 182 186 4 163.62 0.94 96 183 186 3 171.59 2.58 97 183 187 4 164.66 0.42 98 184 187 3 163.22 0.30 99 184 188 4 157.91 1.55 100 185 188 3 160.91 0.83 101 185 189 4 149.03 0.26 102 185 190 5 140.08 4.21 103 186 190 4 140.02 4.21 104 186 191 5 140.02 4.21 105 186 211 25 130.58 1.49 106 186 214 28 130.59 1.50 107 187 208 21 133.96 3.58 108 188 191 3 162.11 0.10 109 188 192 4 156.53 2.61 110 189 192 3 162.12 0.18 111 189 193 4 155.08 3.33 112 190 193 3 169.50 3.60 113 190 194 4 161.23 0.27 114 190 211 21 137.68 3.35 115 190 214 24 137.68 3.34 116 191 194 3 171.00 2.85 117 191 199 8 137.77 3.29 118 191 202 11 137.74 3.31 119 191 203 12 137.76 3.31 120 191 214 23 137.68 3.34 121 192 199 7 139.00 2.73 122 194 198 4 161.19 1.00 123 194 199 5 167.02 0.49 124 194 202 8 226.87 19.04 125 195 198 3 170.38 0.95 126 195 199 4 224.46 5.77