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 6 4 295.64 1.57 2 2 74 72 31.87 2.56 3 3 6 3 295.66 1.57 4 3 7 4 295.65 1.57 5 3 77 74 35.53 0.39 6 3 81 78 30.61 2.00 7 4 7 3 295.81 1.66 8 4 8 4 276.47 2.12 9 5 8 3 286.75 1.61 10 5 9 4 285.45 2.27 11 5 70 65 49.11 0.85 12 5 71 66 49.08 0.86 13 5 74 69 48.55 1.12 14 6 9 3 290.24 1.56 15 6 10 4 284.72 1.20 16 6 74 68 48.45 1.17 17 6 75 69 47.43 0.69 18 6 78 72 47.33 0.74 19 7 10 3 292.57 0.26 20 7 11 4 287.89 2.53 21 7 78 71 47.77 0.83 22 8 11 3 293.96 0.69 23 8 12 4 291.48 0.74 24 9 12 3 299.35 2.99 25 9 13 4 287.90 2.52 26 9 67 58 52.13 0.18 27 9 71 62 49.14 0.86 28 9 75 66 48.61 1.10 29 10 13 3 299.35 3.00 30 10 14 4 272.27 3.64 31 10 15 5 272.27 3.64 32 10 18 8 212.16 3.35 33 10 31 21 70.78 0.11 34 10 75 65 48.62 1.11 35 10 78 68 48.58 1.11 36 10 79 69 48.59 1.10 37 10 88 78 33.02 0.06 38 11 15 4 243.06 5.34 39 13 63 50 52.41 0.11 40 13 67 54 52.37 0.12 41 14 17 3 303.61 1.49 42 14 18 4 258.75 5.02 43 14 75 61 51.46 0.19 44 15 18 3 279.16 0.90 45 15 19 4 226.63 5.98 46 17 22 5 211.19 0.27 47 17 23 6 180.91 1.01 48 17 24 7 178.45 0.21 49 17 25 8 178.44 0.21 50 18 21 3 287.85 1.88 51 18 22 4 200.66 4.39 52 18 23 5 188.13 2.60 53 18 31 13 75.23 0.32 54 19 22 3 297.20 1.78 55 20 88 68 33.11 0.10 56 20 89 69 32.29 0.41 57 21 30 9 76.17 0.78 58 21 31 10 75.22 0.32 59 21 88 67 33.36 0.23 60 22 30 8 76.17 0.79 61 23 26 3 296.36 1.94 62 23 27 4 182.33 2.35 63 23 29 6 84.66 1.47 64 23 30 7 76.18 0.79 65 25 59 34 70.15 0.01 66 26 29 3 292.49 3.78 67 28 35 7 214.27 1.76 68 28 39 11 132.20 18.00 69 29 39 10 132.38 20.37 70 30 35 5 236.27 3.54 71 30 36 6 243.59 2.83 72 31 36 5 286.08 0.41 73 31 79 48 58.88 3.21 74 31 83 52 58.88 3.21 75 31 88 57 53.09 5.78 76 32 35 3 300.48 2.07 77 32 36 4 290.48 0.58 78 32 83 51 58.89 3.21 79 32 88 56 53.14 5.80 80 33 36 3 297.36 3.15 81 33 37 4 290.49 0.58 82 33 44 11 162.99 1.49 83 33 83 50 58.90 3.22 84 34 37 3 298.74 0.80 85 34 38 4 290.50 0.59 86 35 38 3 298.53 1.56 87 35 39 4 290.47 0.60 88 36 39 3 298.03 1.84 89 36 40 4 273.19 2.50 90 36 44 8 163.06 1.52 91 36 49 13 162.83 1.46 92 36 79 43 64.22 5.42 93 36 83 47 59.38 3.06 94 37 44 7 163.07 1.52 95 40 43 3 280.17 0.36 96 40 48 8 184.28 1.74 97 40 49 9 184.28 1.74 98 40 52 12 163.05 1.52 99 41 48 7 184.34 1.72 100 41 57 16 162.25 1.09 101 42 45 3 354.44 0.41 102 42 48 6 205.33 4.83 103 43 48 5 283.40 1.49 104 44 80 36 160.34 1.38 105 44 83 39 159.07 1.54 106 44 84 40 158.85 1.50 107 45 48 3 298.24 1.38 108 45 49 4 290.53 1.95 109 45 80 35 160.34 1.38 110 46 49 3 292.81 1.33 111 46 50 4 288.60 1.04 112 46 76 30 160.51 1.42 113 46 77 31 160.50 1.42 114 46 80 34 160.34 1.38 115 47 50 3 299.36 2.29 116 47 51 4 288.61 1.04 117 48 51 3 301.74 0.96 118 48 52 4 288.60 1.05 119 49 52 3 299.21 2.23 120 49 53 4 288.58 1.05 121 49 76 27 160.50 1.41 122 49 79 30 160.38 1.38 123 49 80 31 160.34 1.38 124 50 53 3 292.49 0.84 125 50 54 4 289.83 0.42 126 50 72 22 160.68 1.39 127 50 73 23 160.67 1.39 128 50 76 26 160.53 1.41 129 51 54 3 292.24 0.72 130 51 55 4 288.38 1.08 131 52 55 3 292.12 0.78 132 52 56 4 281.49 0.22 133 52 57 5 269.25 5.90 134 52 60 8 204.55 1.92 135 53 60 7 204.49 1.95 136 53 62 9 162.49 0.77 137 53 63 10 162.44 0.77 138 53 67 14 162.12 0.88 139 53 72 19 160.72 1.39 140 53 75 22 160.58 1.39 141 54 62 8 162.49 0.77 142 54 64 10 162.28 0.82 143 54 72 18 160.77 1.40 144 55 62 7 163.86 1.45 145 56 60 4 204.58 1.89 146 56 61 5 167.05 0.10 147 56 62 6 163.89 1.46 148 57 60 3 289.80 2.30 149 63 66 3 291.31 0.24 150 63 67 4 260.75 11.39 151 63 72 9 200.34 0.34 152 64 67 3 308.99 0.97 153 64 72 8 215.04 7.67 154 67 71 4 288.91 2.05 155 67 72 5 283.38 0.68 156 68 71 3 295.31 1.78 157 68 72 4 289.36 1.82 158 69 72 3 296.69 1.37 159 69 73 4 291.96 0.54 160 70 73 3 295.16 2.13 161 70 74 4 290.14 1.44 162 71 74 3 294.06 2.68 163 71 75 4 287.32 0.03 164 72 75 3 298.02 0.64 165 72 76 4 291.73 2.52 166 73 76 3 298.03 0.63 167 73 77 4 291.73 2.52 168 74 77 3 295.66 0.55 169 74 78 4 289.42 0.32 170 75 78 3 295.78 0.49 171 75 79 4 289.41 0.33 172 76 79 3 299.32 1.46 173 76 80 4 287.19 1.43 174 77 80 3 294.23 4.00 175 77 81 4 287.01 1.53 176 78 81 3 290.05 2.54 177 78 82 4 287.04 1.52 178 78 88 10 231.77 2.42 179 79 82 3 306.28 4.50 180 79 83 4 287.22 1.44 181 79 88 9 220.51 8.04 182 80 83 3 297.74 0.23 183 80 84 4 288.21 1.60 184 81 84 3 293.42 3.04 185 81 85 4 288.21 1.60 186 82 85 3 292.72 3.40 187 82 86 4 279.29 2.35 188 82 87 5 239.51 1.46 189 82 88 6 231.77 2.42 190 83 86 3 282.72 0.63 191 83 88 5 260.15 3.70