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 8 140.12 1.16 2 3 6 3 153.30 2.73 3 3 7 4 153.31 2.73 4 4 7 3 153.31 2.73 5 4 8 4 153.31 2.73 6 4 118 114 23.86 0.53 7 5 8 3 153.32 2.73 8 5 9 4 153.32 2.73 9 5 116 111 24.08 0.58 10 5 117 112 23.94 0.52 11 5 118 113 23.93 0.51 12 6 9 3 153.33 2.73 13 6 10 4 153.32 2.73 14 7 10 3 151.33 1.55 15 7 11 4 148.97 1.90 16 8 11 3 151.20 1.65 17 8 12 4 146.88 2.93 18 8 13 5 140.62 0.89 19 8 54 46 55.70 8.50 20 8 108 100 35.42 0.14 21 8 117 109 35.65 0.06 22 8 118 110 35.62 0.04 23 8 119 111 35.41 0.14 24 8 120 112 35.41 0.14 25 9 12 3 152.88 1.30 26 9 13 4 139.72 1.27 27 9 33 24 118.00 1.01 28 9 51 42 86.09 1.39 29 10 33 23 117.95 1.02 30 10 34 24 118.22 0.91 31 11 35 24 118.23 0.89 32 11 41 30 118.76 0.62 33 11 44 33 115.12 0.78 34 11 46 35 114.00 0.27 35 12 44 32 117.53 0.85 36 12 45 33 114.12 0.28 37 12 46 34 114.00 0.27 38 12 47 35 114.00 0.27 39 12 120 108 35.98 0.22 40 13 33 20 120.75 0.14 41 13 47 34 114.02 0.26 42 13 49 36 114.00 0.27 43 13 50 37 113.91 0.22 44 13 51 38 108.92 0.18 45 13 54 41 97.44 2.32 46 14 17 3 164.44 0.32 47 14 25 11 120.55 0.07 48 14 29 15 120.70 0.14 49 14 33 19 120.77 0.14 50 14 46 32 117.59 0.83 51 14 47 33 116.26 0.24 52 14 48 34 114.00 0.26 53 15 49 34 114.03 0.25 54 15 50 35 113.92 0.24 55 15 51 36 113.92 0.24 56 17 48 31 120.27 0.14 57 18 48 30 120.31 0.12 58 18 80 62 120.34 0.12 59 19 48 29 120.56 0.20 60 19 80 61 120.56 0.19 61 19 101 82 120.71 0.18 62 20 25 5 120.83 0.17 63 20 48 28 120.64 0.20 64 20 82 62 120.73 0.18 65 20 99 79 120.80 0.15 66 20 101 81 120.73 0.18 67 22 25 3 153.88 2.26 68 22 99 77 151.56 0.76 69 23 99 76 148.81 2.13 70 24 28 4 336.80 0.60 71 25 46 21 178.59 2.10 72 25 48 23 163.93 0.56 73 25 82 57 170.88 0.27 74 25 99 74 182.19 0.14 75 26 30 4 336.14 0.28 76 26 82 56 191.50 4.95 77 26 97 71 216.78 0.01 78 26 98 72 216.77 0.01 79 26 99 73 201.53 0.72 80 27 96 69 232.00 0.86 81 27 97 70 231.06 0.86 82 29 46 17 232.59 1.03 83 30 35 5 336.10 0.92 84 30 36 6 314.59 0.64 85 30 41 11 232.90 0.99 86 30 44 14 232.84 0.96 87 30 46 16 232.69 0.98 88 30 97 67 232.63 0.98 89 31 36 5 325.55 5.65 90 33 46 13 232.72 0.99 91 35 41 6 284.63 16.16 92 35 44 9 232.96 0.98 93 35 46 11 232.94 0.98 94 36 95 59 335.12 0.14 95 36 97 61 334.57 0.41 96 40 86 46 232.87 1.00 97 40 90 50 336.61 0.68 98 42 85 43 232.84 0.98 99 42 86 44 232.85 0.97 100 43 84 41 232.81 0.98 101 43 85 42 232.82 0.98 102 44 83 39 232.82 0.98 103 44 84 40 232.78 0.99 104 45 81 36 232.85 0.97 105 45 82 37 232.81 0.98 106 45 83 38 232.75 0.99 107 45 120 75 36.62 0.35 108 46 81 35 232.80 0.99 109 46 82 36 232.77 0.98 110 46 84 38 232.74 0.97 111 47 54 7 336.70 0.40 112 47 79 32 232.86 0.97 113 47 80 33 232.80 0.99 114 47 81 34 232.75 0.98 115 47 106 59 246.65 42.84 116 47 120 73 36.94 0.23 117 48 80 32 232.78 0.99 118 48 81 33 232.75 0.98 119 48 82 34 232.74 0.97 120 49 79 30 232.80 0.98 121 49 80 31 232.77 0.98 122 53 79 26 232.56 0.99 123 54 79 25 229.86 1.03 124 54 117 63 69.58 1.54 125 55 116 61 71.59 1.15 126 55 117 62 70.03 1.77 127 57 73 16 232.65 1.01 128 57 74 17 232.61 1.01 129 57 75 18 217.61 0.27 130 57 79 22 212.66 1.86 131 58 73 15 232.59 1.01 132 58 115 57 72.95 1.58 133 58 116 58 72.61 1.44 134 58 117 59 72.53 1.40 135 60 73 13 232.72 0.98 136 60 74 14 232.66 1.02 137 60 75 15 230.80 0.89 138 60 76 16 225.75 0.97 139 61 73 12 232.74 1.00 140 61 74 13 232.68 1.00 141 61 76 15 231.09 1.07 142 62 70 8 246.82 1.50 143 62 72 10 232.84 0.99 144 62 73 11 232.78 0.98 145 63 72 9 232.85 0.99 146 63 73 10 232.84 0.99 147 63 74 11 232.83 0.99 148 63 107 44 233.53 1.32 149 64 70 6 336.35 0.26 150 64 72 8 248.11 0.85 151 65 109 44 232.58 1.02 152 65 121 56 69.81 1.52 153 66 121 55 69.86 1.54 154 66 122 56 69.83 1.52 155 71 109 38 232.63 1.02 156 71 110 39 232.61 1.01 157 71 111 40 232.58 1.02 158 71 115 44 163.00 5.24 159 72 107 35 232.72 0.99 160 72 108 36 232.62 1.01 161 72 109 37 232.55 1.02 162 72 121 49 68.98 1.26 163 73 107 34 232.67 0.99 164 73 108 35 232.62 1.00 165 73 110 37 232.09 0.81 166 73 115 42 131.73 3.38 167 74 105 31 232.75 0.99 168 74 106 32 232.69 0.99 169 74 107 33 231.61 1.05 170 74 124 50 38.19 0.37 171 75 79 4 216.75 0.01 172 75 105 30 232.67 0.99 173 75 106 31 232.62 1.00 174 76 105 29 232.65 0.99 175 77 105 28 230.74 1.48 176 78 103 25 232.62 0.99 177 78 104 26 217.59 0.25 178 78 105 27 216.75 0.02 179 79 103 24 221.87 0.56 180 79 104 25 216.96 0.06 181 79 106 27 207.09 0.58 182 80 101 21 232.67 0.99 183 80 102 22 231.53 1.29 184 80 103 23 216.72 0.01 185 81 101 20 222.59 0.18 186 81 102 21 216.81 0.01 187 81 104 23 207.78 0.90 188 81 106 25 168.87 0.07 189 81 123 42 36.68 0.29 190 82 99 17 232.65 0.99 191 82 100 18 219.37 0.66 192 82 101 19 216.69 0.04 193 83 98 15 232.68 1.00 194 83 99 16 223.73 1.41 195 83 100 17 216.77 0.01 196 84 97 13 232.61 0.99 197 84 98 14 217.56 0.26 198 85 97 12 232.63 0.99 199 85 98 13 232.23 0.98 200 86 90 4 275.55 0.27 201 86 96 10 232.78 0.98 202 86 97 11 232.68 1.01 203 87 90 3 336.39 0.14 204 87 96 9 232.80 0.98 205 87 97 10 232.78 0.98 206 87 98 11 232.75 0.98 207 90 94 4 330.74 0.99 208 90 95 5 232.93 0.99 209 90 96 6 232.91 1.00 210 104 123 19 36.93 0.19 211 104 124 20 36.73 0.18 212 105 123 18 37.26 0.24 213 105 124 19 36.85 0.21 214 106 120 14 66.74 0.86 215 106 122 16 39.23 0.63 216 106 123 17 37.04 0.14 217 107 120 13 66.80 0.89 218 107 121 14 65.42 0.64 219 107 122 15 41.69 0.48 220 107 124 17 38.50 0.27 221 108 117 9 72.49 1.42 222 108 119 11 69.10 1.32 223 108 120 12 67.30 0.98 224 108 121 13 66.54 0.96 225 109 117 8 72.57 1.42 226 109 118 9 72.50 1.41 227 109 119 10 70.01 1.64 228 110 115 5 124.42 0.28 229 110 116 6 73.04 1.52 230 110 117 7 72.56 1.42 231 110 118 8 72.56 1.41 232 111 115 4 131.74 3.38 233 111 116 5 100.31 11.79 234 111 118 7 72.66 1.43 235 112 115 3 146.56 0.55