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 43 41 172.19 1.35 2 2 47 45 139.84 0.12 3 3 39 36 175.44 0.76 4 3 40 37 175.22 0.68 5 4 8 4 328.18 0.78 6 4 40 36 175.59 0.69 7 5 33 28 182.81 2.62 8 5 37 32 178.06 1.02 9 5 40 35 177.05 1.35 10 5 95 90 17.98 0.01 11 6 10 4 327.47 1.05 12 6 11 5 306.73 0.15 13 6 14 8 306.63 0.21 14 6 37 31 178.12 1.04 15 7 10 3 331.35 0.81 16 7 11 4 327.08 1.25 17 7 95 88 21.21 0.01 18 8 11 3 335.62 1.17 19 8 12 4 331.36 0.81 20 8 40 32 178.16 1.10 21 8 47 39 174.84 0.61 22 8 50 42 174.52 0.51 23 8 51 43 174.50 0.52 24 8 54 46 174.22 0.64 25 9 12 3 335.66 1.19 26 9 13 4 335.53 1.25 27 9 58 49 154.84 7.07 28 9 60 51 141.67 0.50 29 9 61 52 141.65 0.51 30 10 13 3 335.55 1.26 31 10 14 4 335.53 1.25 32 10 90 80 42.04 2.11 33 10 91 81 38.74 0.58 34 10 93 83 38.74 0.58 35 11 14 3 343.99 1.44 36 11 15 4 334.22 1.89 37 11 29 18 183.77 2.48 38 11 32 21 183.71 2.50 39 11 33 22 183.63 2.47 40 11 47 36 174.90 0.61 41 11 51 40 174.77 0.65 42 12 15 3 331.95 0.76 43 12 16 4 331.94 0.76 44 12 29 17 183.69 2.51 45 12 51 39 174.81 0.65 46 12 55 43 174.22 0.65 47 12 61 49 141.55 0.46 48 12 77 65 122.45 0.51 49 13 16 3 340.07 0.64 50 13 17 4 327.13 1.08 51 13 18 5 327.13 1.08 52 13 60 47 141.66 0.49 53 13 61 48 141.62 0.49 54 13 79 66 110.61 0.29 55 13 87 74 51.97 0.26 56 13 88 75 48.51 1.62 57 13 91 78 42.07 2.10 58 14 17 3 337.52 0.64 59 14 18 4 327.06 1.07 60 14 32 18 183.73 2.50 61 14 91 77 42.11 2.12 62 15 18 3 337.52 0.64 63 15 19 4 324.52 0.18 64 15 24 9 221.84 0.51 65 15 29 14 183.73 2.50 66 15 32 17 183.73 2.50 67 16 19 3 328.82 1.97 68 16 22 6 251.22 6.79 69 16 23 7 221.84 0.51 70 16 24 8 221.83 0.51 71 16 61 45 141.59 0.48 72 16 77 61 122.48 0.52 73 16 78 62 118.83 0.29 74 16 79 63 115.59 0.07 75 17 22 5 256.28 4.25 76 17 79 62 118.78 0.27 77 17 84 67 73.89 0.36 78 19 23 4 330.51 0.09 79 19 24 5 292.39 5.48 80 20 23 3 372.16 1.06 81 20 24 4 346.08 3.33 82 22 78 56 122.24 0.63 83 22 79 57 121.79 0.85 84 22 81 59 118.78 0.27 85 23 76 53 122.56 0.53 86 23 77 54 122.49 0.52 87 23 78 55 120.57 0.15 88 24 28 4 297.17 2.77 89 24 29 5 287.23 2.21 90 24 76 52 122.53 0.53 91 24 77 53 122.48 0.52 92 25 28 3 330.99 0.54 93 25 76 51 122.53 0.53 94 25 77 52 122.50 0.52 95 26 30 4 341.01 1.19 96 26 52 26 175.89 0.95 97 26 76 50 122.51 0.52 98 26 77 51 122.50 0.52 99 27 30 3 341.00 1.19 100 28 31 3 339.45 0.42 101 28 32 4 335.04 1.79 102 29 32 3 335.04 1.79 103 29 33 4 335.03 1.79 104 29 47 18 176.63 0.91 105 29 51 22 175.78 1.05 106 30 34 4 320.01 0.99 107 30 47 17 176.63 0.91 108 30 48 18 176.49 0.96 109 30 51 21 176.22 1.01 110 30 52 22 176.34 0.95 111 31 34 3 338.96 0.22 112 31 35 4 319.05 0.49 113 32 35 3 335.76 1.37 114 32 36 4 328.28 5.11 115 33 36 3 335.49 2.64 116 33 37 4 318.32 0.75 117 33 40 7 245.08 4.83 118 33 47 14 176.59 0.93 119 34 37 3 337.62 1.57 120 34 40 6 222.01 0.71 121 34 47 13 178.71 0.12 122 37 40 3 336.03 1.60 123 38 41 3 332.87 0.48 124 39 43 4 319.37 2.36 125 40 47 7 233.31 10.73 126 44 47 3 353.07 0.51 127 44 48 4 319.80 0.18 128 46 49 3 351.21 1.01 129 46 50 4 335.45 1.03 130 47 50 3 334.51 0.59 131 47 51 4 334.53 0.58 132 48 51 3 343.00 0.42 133 48 52 4 340.18 0.40 134 49 52 3 338.33 1.32 135 49 53 4 338.33 1.32 136 50 53 3 344.07 1.56 137 50 54 4 331.56 1.95 138 51 54 3 336.10 2.42 139 51 55 4 334.42 1.52 140 51 77 26 122.45 0.51 141 52 55 3 341.20 0.13 142 53 56 3 339.46 0.98 143 53 57 4 339.23 0.87 144 54 57 3 336.36 0.56 145 54 58 4 314.45 3.17 146 55 58 3 334.48 1.10 147 55 61 6 201.23 0.46 148 55 77 22 122.43 0.53 149 58 61 3 335.45 1.53 150 60 79 19 114.62 0.13 151 60 80 20 110.51 0.25 152 60 83 23 86.72 0.76 153 60 87 27 67.47 2.29 154 61 77 16 122.47 0.52 155 61 78 17 119.34 0.48 156 61 79 18 114.58 0.15 157 61 80 19 113.06 0.91 158 62 77 15 122.48 0.52 159 62 78 16 122.45 0.52 160 62 80 18 118.81 0.29 161 63 76 13 122.63 0.54 162 63 77 14 122.50 0.51 163 64 75 11 122.68 0.53 164 64 76 12 122.64 0.54 165 64 77 13 122.61 0.53 166 64 78 14 122.61 0.53 167 65 71 6 213.21 6.17 168 65 78 13 122.67 0.54 169 70 74 4 344.88 3.12 170 71 78 7 218.00 2.90 171 79 84 5 279.50 8.87 172 79 87 8 256.81 2.60 173 80 83 3 326.25 5.63 174 80 84 4 320.44 8.54 175 81 84 3 344.35 2.42 176 83 86 3 347.44 0.87 177 83 87 4 322.31 4.28 178 84 87 3 330.23 2.50 179 84 88 4 312.70 0.04 180 85 88 3 334.81 0.29 181 85 89 4 323.57 3.66 182 86 89 3 345.15 4.03 183 87 91 4 328.07 1.41 184 88 91 3 317.25 4.01 185 88 92 4 317.25 4.01 186 89 93 4 317.25 4.01 187 90 93 3 325.76 0.24 188 96 100 4 313.19 0.09