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 10 8 139.55 0.42 2 3 6 3 146.42 1.63 3 3 7 4 143.03 0.62 4 4 7 3 150.31 0.14 5 4 8 4 148.56 0.79 6 4 118 114 24.24 0.36 7 5 8 3 150.20 0.04 8 5 9 4 146.04 0.48 9 5 116 111 24.75 0.56 10 5 117 112 24.34 0.36 11 5 118 113 24.30 0.39 12 6 9 3 151.62 2.41 13 6 10 4 146.48 0.70 14 7 10 3 148.80 0.45 15 7 11 4 146.47 0.70 16 8 11 3 147.16 0.38 17 8 12 4 145.77 1.05 18 8 13 5 143.47 0.10 19 8 54 46 79.72 0.71 20 8 108 100 34.04 0.24 21 8 117 109 34.22 0.17 22 8 118 110 34.04 0.24 23 8 119 111 34.01 0.23 24 8 120 112 33.91 0.19 25 9 12 3 147.16 0.38 26 9 13 4 141.25 0.43 27 9 33 24 119.09 0.91 28 9 51 42 84.36 2.17 29 10 33 23 118.59 1.12 30 10 34 24 119.25 0.97 31 10 35 25 119.51 1.10 32 11 35 24 119.52 1.11 33 11 41 30 119.58 1.12 34 11 44 33 115.98 0.35 35 11 46 35 115.09 0.77 36 12 44 32 118.72 0.88 37 12 45 33 115.81 0.43 38 12 46 34 115.08 0.77 39 12 47 35 115.06 0.78 40 12 120 108 35.36 0.39 41 13 33 20 120.06 1.29 42 13 47 34 115.12 0.75 43 13 49 36 115.06 0.78 44 13 50 37 114.94 0.79 45 13 51 38 107.41 0.56 46 13 54 41 90.07 3.79 47 14 17 3 179.38 0.68 48 14 25 11 119.50 1.11 49 14 29 15 119.52 1.11 50 14 33 19 120.08 1.29 51 14 46 32 119.03 0.97 52 14 47 33 116.96 0.99 53 14 48 34 115.12 0.75 54 15 48 33 115.23 0.72 55 15 49 34 115.14 0.74 56 15 50 35 115.11 0.74 57 17 48 31 119.52 1.11 58 18 48 30 119.42 1.04 59 18 80 62 119.72 1.19 60 19 48 29 120.01 1.28 61 19 80 61 119.76 1.18 62 19 101 82 119.88 1.22 63 20 25 5 120.16 1.28 64 20 48 28 120.05 1.29 65 20 82 62 120.05 1.29 66 20 99 79 120.11 1.27 67 20 101 81 119.99 1.28 68 22 25 3 164.66 0.18 69 23 99 76 149.79 0.14 70 25 46 21 189.17 4.01 71 25 48 23 166.75 1.14 72 25 82 57 171.12 2.33 73 25 99 74 187.69 1.28 74 26 30 4 336.07 0.96 75 26 82 56 242.71 1.38 76 26 97 71 214.34 0.46 77 26 98 72 214.33 0.47 78 26 99 73 202.34 1.94 79 27 96 69 231.03 0.06 80 27 97 70 225.25 0.58 81 29 46 17 233.17 0.74 82 30 35 5 336.81 0.01 83 30 36 6 336.08 0.17 84 30 41 11 233.59 0.66 85 30 44 14 233.43 0.71 86 30 46 16 233.31 0.71 87 30 97 67 233.06 0.80 88 31 36 5 333.72 1.79 89 33 46 13 233.19 0.66 90 35 41 6 261.14 13.04 91 35 44 9 233.61 0.69 92 35 46 11 233.49 0.74 93 36 40 4 333.54 1.28 94 36 95 59 333.75 1.20 95 36 97 61 333.74 1.20 96 40 86 46 233.55 0.69 97 42 85 43 233.50 0.71 98 42 86 44 233.52 0.71 99 43 84 41 233.44 0.70 100 43 85 42 233.46 0.70 101 44 83 39 233.45 0.70 102 44 84 40 233.38 0.70 103 45 81 36 233.47 0.70 104 45 82 37 233.44 0.71 105 45 83 38 233.34 0.70 106 45 120 75 36.47 0.35 107 46 81 35 233.43 0.70 108 46 82 36 233.38 0.70 109 46 84 38 233.34 0.71 110 47 54 7 336.43 0.99 111 47 79 32 233.49 0.70 112 47 80 33 233.44 0.70 113 47 81 34 233.37 0.70 114 47 106 59 165.48 3.83 115 47 120 73 37.04 0.07 116 48 80 32 233.39 0.71 117 48 81 33 233.36 0.70 118 48 82 34 233.34 0.71 119 49 79 30 233.41 0.70 120 49 80 31 233.38 0.71 121 53 79 26 233.05 0.78 122 54 79 25 225.21 2.23 123 54 117 63 59.34 0.87 124 55 117 62 59.34 0.87 125 57 73 16 233.11 0.80 126 57 74 17 233.09 0.80 127 57 75 18 222.22 1.67 128 57 79 22 209.39 1.55 129 58 73 15 233.08 0.79 130 58 115 57 65.86 0.93 131 58 116 58 61.80 0.88 132 58 117 59 61.77 0.88 133 60 73 13 233.34 0.71 134 60 74 14 233.19 0.73 135 60 75 15 232.67 0.56 136 60 76 16 221.30 1.21 137 61 73 12 233.37 0.70 138 61 74 13 233.20 0.72 139 61 76 15 233.11 0.73 140 62 70 8 241.88 2.12 141 62 72 10 233.45 0.69 142 62 73 11 233.37 0.70 143 63 72 9 233.47 0.69 144 63 73 10 233.46 0.69 145 63 74 11 233.44 0.70 146 63 107 44 233.52 0.70 147 64 72 8 255.41 0.93 148 65 109 44 233.14 0.76 149 65 121 56 59.86 0.95 150 66 121 55 59.89 0.96 151 66 122 56 59.88 0.96 152 71 109 38 233.13 0.78 153 71 110 39 233.12 0.78 154 71 111 40 233.09 0.78 155 71 115 44 153.77 0.42 156 72 107 35 233.36 0.70 157 72 108 36 233.15 0.77 158 72 109 37 232.97 0.83 159 72 121 49 59.59 0.96 160 73 107 34 233.21 0.74 161 73 108 35 233.12 0.77 162 73 110 37 232.32 0.67 163 73 115 42 100.86 10.15 164 74 105 31 233.36 0.70 165 74 106 32 233.23 0.75 166 74 107 33 232.88 0.79 167 74 124 50 40.88 0.19 168 75 79 4 214.27 0.50 169 75 105 30 233.20 0.74 170 75 106 31 233.16 0.75 171 76 105 29 233.18 0.75 172 77 105 28 230.92 0.18 173 78 103 25 233.11 0.77 174 78 104 26 219.68 0.42 175 78 105 27 214.30 0.47 176 79 103 24 221.96 0.48 177 79 104 25 214.40 0.48 178 79 106 27 205.77 1.14 179 80 101 21 233.20 0.74 180 80 102 22 231.58 0.95 181 80 103 23 214.30 0.48 182 81 101 20 217.40 0.95 183 81 102 21 214.39 0.48 184 81 104 23 207.67 0.77 185 81 106 25 164.83 1.97 186 81 123 42 36.74 0.24 187 82 99 17 233.18 0.75 188 82 100 18 216.65 0.64 189 82 101 19 213.53 0.08 190 83 98 15 233.21 0.75 191 83 99 16 218.06 1.35 192 83 100 17 214.34 0.47 193 84 97 13 233.13 0.76 194 84 98 14 216.63 0.65 195 85 97 12 233.19 0.75 196 85 98 13 232.75 0.65 197 86 90 4 297.19 2.89 198 86 96 10 233.38 0.71 199 86 97 11 233.22 0.74 200 87 90 3 330.24 1.16 201 87 96 9 233.45 0.70 202 87 97 10 233.40 0.70 203 87 98 11 233.37 0.70 204 90 95 5 233.61 0.69 205 90 96 6 233.59 0.69 206 104 123 19 37.78 0.50 207 104 124 20 36.99 0.12 208 105 123 18 38.12 0.64 209 105 124 19 36.99 0.12 210 106 120 14 58.66 0.55 211 106 122 16 46.58 3.02 212 106 123 17 37.77 0.51 213 107 120 13 58.70 0.57 214 107 121 14 56.28 1.40 215 107 122 15 46.58 3.02 216 107 124 17 40.86 0.18 217 108 117 9 61.77 0.86 218 108 119 11 59.56 0.98 219 108 120 12 58.97 0.70 220 108 121 13 58.63 0.56 221 109 117 8 61.80 0.87 222 109 118 9 61.77 0.86 223 109 119 10 60.38 0.67 224 110 115 5 68.61 0.60 225 110 116 6 62.05 0.96 226 110 117 7 61.80 0.88 227 110 118 8 61.79 0.87 228 111 115 4 126.83 2.86 229 111 116 5 66.02 0.90 230 111 118 7 61.90 0.90 231 112 115 3 147.64 1.19