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 3 7 4 343.42 5.78 2 3 8 5 343.41 5.78 3 3 55 52 117.56 2.88 4 3 77 74 103.02 2.05 5 3 78 75 102.03 1.67 6 4 7 3 355.20 0.12 7 4 8 4 344.45 5.26 8 4 78 74 103.07 2.07 9 5 8 3 359.11 0.22 10 5 9 4 343.42 5.78 11 5 74 69 103.63 1.88 12 5 89 84 67.54 0.40 13 6 9 3 344.45 5.26 14 6 10 4 333.47 0.80 15 6 11 5 333.47 0.81 16 7 11 4 325.32 4.88 17 7 12 5 331.99 1.55 18 8 12 4 331.98 1.55 19 8 70 62 107.51 0.30 20 8 74 66 107.12 0.15 21 8 77 69 105.09 1.10 22 8 78 70 105.09 1.10 23 9 13 4 346.60 0.68 24 9 27 18 166.92 1.30 25 9 29 20 166.41 1.06 26 9 70 61 108.94 1.02 27 10 13 3 357.10 3.90 28 10 14 4 352.11 1.87 29 11 14 3 364.86 0.35 30 11 15 4 354.24 2.69 31 12 15 3 361.20 0.79 32 12 16 4 354.31 2.68 33 12 47 35 164.30 1.15 34 12 51 39 163.69 0.93 35 13 16 3 364.76 5.72 36 13 17 4 364.76 5.71 37 13 24 11 205.36 10.15 38 13 27 14 166.78 1.23 39 14 17 3 357.48 1.10 40 14 18 4 356.51 1.59 41 14 24 10 212.09 6.84 42 15 18 3 357.48 1.10 43 15 19 4 356.50 1.59 44 15 47 32 164.35 1.15 45 15 50 35 164.34 1.15 46 15 51 36 164.34 1.14 47 15 54 39 164.19 1.20 48 16 19 3 360.29 0.35 49 16 20 4 345.17 1.81 50 16 21 5 335.58 0.68 51 16 22 6 276.07 10.10 52 16 27 11 218.68 3.48 53 16 37 21 166.39 1.04 54 16 44 28 165.17 1.06 55 16 47 31 164.35 1.15 56 17 21 4 335.58 0.68 57 17 22 5 296.41 20.26 58 17 23 6 255.84 0.01 59 18 21 3 348.49 2.05 60 19 43 24 165.27 1.06 61 19 46 27 165.19 1.06 62 19 47 28 165.18 1.07 63 19 50 31 165.02 0.99 64 20 39 19 165.96 1.01 65 20 43 23 165.27 1.06 66 20 47 27 165.19 1.07 67 22 26 4 353.53 3.77 68 22 27 5 336.07 2.35 69 22 37 15 166.49 1.07 70 23 26 3 349.89 2.04 71 23 27 4 343.40 1.29 72 24 27 3 359.36 0.85 73 26 31 5 356.25 1.02 74 27 31 4 353.25 0.34 75 27 37 10 198.75 1.47 76 28 31 3 371.75 0.65 77 28 70 42 159.42 2.81 78 29 70 41 159.37 2.81 79 30 100 70 30.05 2.12 80 31 36 5 253.39 7.21 81 31 37 6 247.31 4.16 82 31 69 38 159.78 2.96 83 31 70 39 159.59 2.88 84 32 35 3 344.69 2.42 85 32 36 4 320.91 9.47 86 32 68 36 159.82 2.96 87 32 69 37 159.78 2.96 88 33 37 4 320.91 9.47 89 33 44 11 199.00 4.08 90 33 64 31 160.75 2.54 91 33 67 34 160.16 2.79 92 33 68 35 159.80 2.96 93 33 73 40 159.78 2.96 94 34 37 3 353.18 0.55 95 34 38 4 248.93 3.35 96 34 40 6 228.46 0.59 97 37 44 7 288.41 2.10 98 39 43 4 340.23 0.12 99 39 44 5 349.28 1.79 100 40 44 4 355.66 1.33 101 41 44 3 355.67 1.33 102 41 45 4 354.04 0.52 103 42 45 3 370.69 1.54 104 42 46 4 355.75 1.28 105 43 46 3 369.83 1.11 106 43 47 4 354.13 0.48 107 44 47 3 357.85 0.38 108 44 48 4 353.51 0.18 109 45 48 3 359.62 1.26 110 45 49 4 349.50 1.80 111 46 49 3 352.64 0.24 112 46 50 4 354.46 1.14 113 47 50 3 361.08 0.53 114 47 51 4 350.64 3.05 115 48 51 3 359.31 0.36 116 48 52 4 340.83 0.38 117 48 64 16 160.74 2.53 118 49 53 4 344.56 0.93 119 50 53 3 344.56 0.93 120 50 54 4 334.39 4.16 121 51 54 3 349.49 1.53 122 51 55 4 327.84 0.88 123 51 56 5 307.95 2.71 124 51 57 6 303.73 1.38 125 52 56 4 290.81 5.09 126 52 57 5 289.16 5.91 127 52 59 7 277.56 0.46 128 53 56 3 323.96 1.72 129 57 77 20 147.87 0.79 130 58 80 22 147.87 0.79 131 59 63 4 299.58 0.64 132 59 64 5 282.00 2.88 133 59 67 8 266.35 10.62 134 59 73 14 197.27 3.09 135 59 76 17 157.37 2.77 136 59 77 18 157.38 2.75 137 60 63 3 348.72 5.80 138 60 64 4 343.15 4.90 139 61 64 3 337.80 7.58 140 61 65 4 329.25 11.85 141 63 66 3 356.58 1.81 142 63 67 4 341.65 5.66 143 63 76 13 216.88 7.71 144 64 67 3 350.80 1.26 145 66 72 6 326.78 3.42 146 66 76 10 285.72 6.34 147 67 72 5 326.78 3.42 148 67 73 6 285.74 6.36 149 67 76 9 285.75 6.36 150 68 72 4 344.92 3.64 151 69 72 3 352.62 0.21 152 69 73 4 344.99 3.61 153 69 100 31 30.79 1.76 154 70 73 3 351.82 0.21 155 70 74 4 345.00 3.61 156 71 74 3 358.44 0.14 157 71 75 4 348.50 1.86 158 71 88 17 69.95 0.29 159 72 75 3 358.43 0.15 160 72 76 4 347.75 1.19 161 73 77 4 360.26 1.20 162 74 77 3 360.80 0.93 163 74 78 4 348.50 1.06 164 74 89 15 69.89 0.32 165 75 78 3 360.24 1.20 166 75 79 4 348.40 1.02 167 75 80 5 348.56 1.09 168 75 87 12 77.61 4.05 169 75 88 13 69.94 0.30 170 76 79 3 364.56 0.96 171 76 80 4 350.82 0.04 172 77 80 3 364.48 1.00 173 77 81 4 359.87 3.30 174 78 81 3 361.94 2.27 175 78 82 4 348.48 1.12 176 78 83 5 344.56 3.00 177 78 89 11 202.19 1.39 178 79 84 5 320.23 3.12 179 79 87 8 202.21 1.39 180 79 88 9 202.19 1.40 181 84 87 3 391.23 1.04 182 86 91 5 338.51 2.28 183 86 95 9 182.25 6.90 184 87 91 4 338.28 2.16 185 87 95 8 182.26 6.90 186 88 91 3 374.33 5.61 187 90 100 10 33.92 0.19 188 91 95 4 323.80 3.93 189 91 98 7 109.20 34.76 190 92 102 10 36.77 1.20 191 93 97 4 328.65 2.79 192 94 97 3 354.47 1.39 193 94 98 4 328.54 0.01 194 95 98 3 359.51 1.14 195 99 102 3 380.50 1.81 196 99 103 4 365.84 0.70