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 8 136.81 1.36 2 3 6 3 149.94 1.55 3 3 7 4 145.47 1.61 4 4 7 3 146.70 1.00 5 4 8 4 147.25 0.72 6 4 118 114 22.48 0.66 7 5 8 3 151.72 1.51 8 5 9 4 147.56 0.57 9 5 116 111 26.74 0.44 10 5 117 112 22.63 0.61 11 5 118 113 22.63 0.61 12 6 9 3 152.33 2.06 13 6 10 4 145.94 0.24 14 7 10 3 149.75 0.77 15 7 11 4 145.93 0.24 16 8 11 3 151.53 2.33 17 8 12 4 144.37 1.02 18 8 13 5 144.25 1.06 19 8 54 46 79.81 0.76 20 8 108 100 33.62 0.03 21 8 117 109 33.74 0.03 22 8 118 110 33.62 0.04 23 8 119 111 33.58 0.01 24 8 120 112 33.51 0.02 25 9 12 3 153.44 1.48 26 9 13 4 140.25 0.12 27 9 33 24 118.85 1.03 28 9 51 42 87.52 1.66 29 10 33 23 118.78 1.03 30 10 34 24 119.05 1.14 31 10 35 25 119.03 1.13 32 11 35 24 119.03 1.13 33 11 44 33 117.63 1.34 34 11 46 35 114.34 0.85 35 12 44 32 118.52 1.24 36 12 45 33 116.81 1.43 37 12 46 34 114.34 0.85 38 12 47 35 114.33 0.85 39 12 120 108 33.83 0.07 40 13 33 20 119.38 1.23 41 13 47 34 114.36 0.86 42 13 49 36 114.33 0.85 43 13 50 37 114.31 0.84 44 13 51 38 111.64 0.53 45 13 54 41 99.38 0.26 46 14 17 3 163.09 1.26 47 14 25 11 118.98 1.03 48 14 29 15 119.31 1.20 49 14 33 19 119.40 1.23 50 14 46 32 118.55 1.22 51 14 47 33 116.81 1.44 52 14 48 34 114.39 0.84 53 15 49 34 114.36 0.86 54 15 50 35 114.33 0.85 55 15 51 36 114.33 0.85 56 17 48 31 119.09 1.16 57 18 48 30 119.09 1.16 58 18 80 62 119.09 1.16 59 19 48 29 119.10 1.16 60 19 80 61 119.09 1.16 61 19 101 82 119.11 1.15 62 20 25 5 119.45 1.21 63 20 48 28 119.33 1.24 64 20 82 62 119.35 1.24 65 20 99 79 125.30 4.15 66 20 101 81 119.19 1.18 67 22 25 3 161.90 4.58 68 22 99 77 150.13 0.82 69 23 99 76 150.14 0.83 70 25 46 21 187.24 4.98 71 25 48 23 165.86 1.71 72 25 82 57 167.60 0.85 73 25 99 74 186.44 0.30 74 26 82 56 235.28 0.45 75 26 97 71 217.02 0.12 76 26 98 72 217.01 0.12 77 26 99 73 203.37 1.43 78 27 96 69 232.81 0.56 79 27 97 70 229.56 2.04 80 29 46 17 232.83 0.55 81 30 35 5 335.37 1.64 82 30 36 6 324.81 0.98 83 30 41 11 233.50 0.44 84 30 44 14 233.36 0.49 85 30 46 16 233.28 0.48 86 30 97 67 233.09 0.43 87 31 36 5 327.97 2.56 88 33 46 13 233.40 0.46 89 35 41 6 253.58 1.75 90 35 44 9 233.51 0.42 91 35 46 11 233.50 0.42 92 36 40 4 336.54 0.12 93 36 95 59 336.81 0.35 94 36 97 61 336.72 0.30 95 40 86 46 233.47 0.46 96 41 86 45 233.49 0.43 97 42 85 43 233.39 0.45 98 42 86 44 233.40 0.45 99 43 84 41 233.36 0.45 100 43 85 42 233.38 0.45 101 44 83 39 233.37 0.45 102 44 84 40 233.26 0.45 103 45 81 36 233.39 0.45 104 45 82 37 233.34 0.46 105 45 83 38 233.24 0.45 106 45 120 75 37.19 0.64 107 46 81 35 233.34 0.46 108 46 82 36 233.30 0.46 109 46 84 38 233.24 0.45 110 47 79 32 233.41 0.46 111 47 80 33 233.35 0.46 112 47 81 34 233.24 0.45 113 47 106 59 235.40 36.82 114 47 120 73 37.41 0.71 115 48 80 32 233.30 0.46 116 48 81 33 233.24 0.45 117 48 82 34 233.24 0.45 118 49 79 30 233.31 0.45 119 49 80 31 233.26 0.45 120 53 79 26 232.99 0.46 121 54 79 25 227.51 1.58 122 54 117 63 60.92 2.31 123 55 116 61 62.16 2.78 124 55 117 62 62.16 2.78 125 57 73 16 233.05 0.46 126 57 74 17 233.03 0.46 127 57 75 18 222.61 1.66 128 57 79 22 209.72 0.47 129 58 73 15 233.03 0.46 130 58 115 57 64.45 2.03 131 58 116 58 64.09 2.21 132 58 117 59 64.04 2.23 133 60 73 13 233.27 0.45 134 60 74 14 233.16 0.47 135 60 75 15 232.46 0.39 136 60 76 16 225.33 1.68 137 61 73 12 233.29 0.45 138 61 74 13 233.17 0.47 139 61 76 15 232.66 0.29 140 62 70 8 260.76 0.69 141 62 71 9 233.37 0.45 142 62 72 10 233.34 0.46 143 62 73 11 233.30 0.45 144 63 72 9 233.41 0.47 145 63 73 10 233.33 0.45 146 63 74 11 233.33 0.45 147 63 107 44 233.45 0.45 148 64 72 8 242.10 1.09 149 65 109 44 233.02 0.46 150 65 121 56 62.45 2.73 151 66 121 55 62.77 2.60 152 66 122 56 62.76 2.60 153 71 109 38 233.11 0.44 154 71 110 39 233.08 0.43 155 71 111 40 233.02 0.46 156 71 115 44 173.37 2.22 157 72 107 35 233.26 0.45 158 72 108 36 233.11 0.44 159 72 109 37 233.00 0.46 160 72 121 49 62.44 2.70 161 73 107 34 233.16 0.46 162 73 108 35 233.09 0.43 163 73 110 37 232.50 0.48 164 73 115 42 106.17 7.10 165 74 105 31 233.28 0.45 166 74 106 32 233.16 0.46 167 74 107 33 232.63 0.58 168 74 124 50 39.05 0.67 169 75 79 4 216.99 0.12 170 75 105 30 233.12 0.44 171 75 106 31 233.10 0.43 172 76 105 29 233.12 0.45 173 77 105 28 232.68 0.49 174 78 103 25 233.10 0.44 175 78 104 26 220.36 1.03 176 78 105 27 216.98 0.13 177 79 103 24 225.27 1.71 178 79 104 25 217.74 0.09 179 79 106 27 212.91 2.04 180 80 101 21 233.12 0.44 181 80 102 22 231.88 0.79 182 80 103 23 216.93 0.15 183 81 101 20 217.90 0.16 184 81 102 21 217.58 0.16 185 81 104 23 208.74 0.01 186 81 106 25 168.44 0.10 187 81 123 42 37.27 0.61 188 82 99 17 233.11 0.44 189 82 100 18 217.91 0.15 190 82 101 19 216.84 0.21 191 83 98 15 233.12 0.44 192 83 99 16 218.57 0.16 193 83 100 17 216.99 0.13 194 84 97 13 233.09 0.45 195 84 98 14 217.75 0.10 196 85 97 12 233.12 0.44 197 85 98 13 232.66 0.47 198 86 95 9 233.41 0.46 199 86 96 10 233.28 0.45 200 86 97 11 233.20 0.48 201 87 96 9 233.38 0.45 202 87 97 10 233.32 0.46 203 87 98 11 233.27 0.45 204 90 94 4 293.82 5.55 205 90 95 5 233.54 0.44 206 90 96 6 233.53 0.44 207 104 123 19 37.64 0.63 208 104 124 20 37.40 0.68 209 105 123 18 37.77 0.69 210 105 124 19 37.40 0.68 211 106 120 14 59.12 1.20 212 106 122 16 39.77 0.38 213 106 123 17 37.86 0.65 214 107 120 13 59.19 1.17 215 107 121 14 58.11 0.72 216 107 122 15 41.08 0.40 217 107 124 17 39.05 0.67 218 108 117 9 63.95 2.17 219 108 119 11 62.41 2.72 220 108 120 12 59.28 1.22 221 108 121 13 58.77 1.03 222 109 117 8 63.99 2.17 223 109 118 9 63.94 2.18 224 109 119 10 63.04 2.50 225 110 115 5 67.88 0.48 226 110 116 6 64.26 2.13 227 110 117 7 64.00 2.17 228 110 118 8 63.95 2.18 229 111 115 4 93.73 12.46 230 111 116 5 67.86 0.47 231 111 118 7 67.27 0.53 232 112 115 3 151.64 0.01