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 1 82 81 11.92 0.27 2 2 81 79 18.96 0.69 3 3 7 4 266.71 2.40 4 3 8 5 264.96 1.53 5 3 55 52 53.69 13.45 6 3 78 75 31.97 1.16 7 3 81 78 25.01 1.02 8 4 7 3 286.76 0.57 9 4 8 4 284.54 0.54 10 4 78 74 35.60 0.66 11 5 8 3 288.19 0.14 12 5 9 4 278.63 0.30 13 5 29 24 129.90 0.10 14 5 78 73 41.02 0.73 15 6 9 3 286.76 0.57 16 6 10 4 282.66 1.48 17 7 10 3 294.59 0.88 18 7 11 4 284.87 1.81 19 7 55 48 106.05 2.98 20 8 11 3 281.78 0.26 21 8 12 4 281.61 0.34 22 8 55 47 106.03 2.98 23 8 74 66 61.78 0.24 24 8 77 69 58.40 0.09 25 8 78 70 56.59 0.04 26 9 12 3 285.30 2.95 27 9 13 4 279.32 0.04 28 9 27 18 130.07 0.11 29 9 29 20 130.12 0.10 30 9 74 65 62.10 0.07 31 10 13 3 291.38 0.09 32 10 14 4 278.36 0.53 33 11 14 3 290.31 0.45 34 11 15 4 282.00 1.20 35 11 54 43 116.34 1.09 36 11 55 44 115.12 1.40 37 12 15 3 291.32 0.86 38 12 16 4 280.19 1.45 39 12 33 21 130.38 0.21 40 12 48 36 117.31 1.40 41 12 51 39 116.56 1.09 42 12 70 58 72.09 1.35 43 12 77 65 62.62 1.03 44 13 16 3 286.77 1.42 45 13 17 4 279.86 1.61 46 13 24 11 130.46 0.34 47 13 27 14 130.14 0.09 48 14 17 3 289.28 0.28 49 14 24 10 133.47 0.86 50 14 54 40 117.38 1.44 51 15 18 3 283.73 0.32 52 15 19 4 283.73 0.31 53 15 47 32 117.47 1.42 54 15 48 33 117.44 1.41 55 15 50 35 117.48 1.42 56 15 51 36 117.35 1.38 57 15 54 39 117.42 1.42 58 16 19 3 280.58 1.24 59 16 20 4 278.72 1.12 60 16 33 17 130.40 0.21 61 16 37 21 130.49 0.24 62 16 48 32 117.45 1.41 63 17 21 4 235.74 6.42 64 17 22 5 222.44 0.23 65 18 47 29 122.06 2.56 66 19 39 20 130.37 0.23 67 19 43 24 127.67 0.62 68 19 44 25 127.32 0.81 69 19 47 28 122.12 2.54 70 19 48 29 125.85 0.69 71 20 37 17 130.58 0.20 72 22 26 4 281.38 2.03 73 22 27 5 272.75 1.02 74 22 31 9 163.59 0.00 75 22 36 14 141.97 0.96 76 22 37 15 131.25 0.10 77 23 26 3 286.07 0.31 78 23 27 4 282.23 1.61 79 24 27 3 293.91 0.90 80 25 28 3 368.43 2.31 81 26 31 5 278.72 0.37 82 27 31 4 280.31 1.89 83 27 70 43 94.81 2.38 84 28 31 3 290.05 2.93 85 28 70 42 94.89 2.41 86 28 71 43 94.81 2.38 87 29 71 42 94.77 2.40 88 29 74 45 94.78 2.37 89 29 75 46 94.78 2.37 90 31 36 5 249.86 12.98 91 31 37 6 249.88 12.98 92 31 69 38 95.05 2.41 93 31 70 39 95.02 2.40 94 32 35 3 274.08 0.90 95 32 36 4 249.89 12.98 96 32 37 5 249.89 12.97 97 32 68 36 95.21 2.33 98 32 69 37 95.02 2.39 99 33 37 4 249.90 12.98 100 33 38 5 249.89 12.97 101 33 39 6 206.52 8.69 102 33 44 11 195.16 3.59 103 33 48 15 176.91 2.94 104 33 67 34 101.78 2.95 105 33 68 35 95.24 2.34 106 33 69 36 95.17 2.31 107 33 70 37 95.09 2.29 108 33 73 40 94.73 2.31 109 34 38 4 249.90 12.98 110 34 39 5 206.53 8.68 111 34 44 10 206.06 8.53 112 34 68 34 96.17 2.12 113 35 38 3 272.87 1.50 114 37 70 33 95.10 2.27 115 39 43 4 273.48 1.01 116 39 44 5 271.20 2.13 117 40 43 3 281.66 3.08 118 40 44 4 275.57 0.04 119 41 44 3 287.63 0.12 120 41 45 4 285.24 1.31 121 41 65 24 103.81 3.68 122 42 45 3 288.62 2.25 123 42 46 4 282.74 2.56 124 43 46 3 288.63 2.25 125 43 47 4 287.32 1.60 126 44 47 3 294.85 0.25 127 44 48 4 269.12 0.01 128 44 64 20 103.62 3.78 129 44 65 21 103.58 3.79 130 44 67 23 103.32 3.71 131 45 49 4 263.19 2.92 132 45 61 16 104.43 3.59 133 45 62 17 104.37 3.57 134 45 64 19 103.63 3.78 135 45 65 20 103.82 3.69 136 46 49 3 285.91 0.76 137 46 50 4 278.82 2.79 138 47 50 3 282.76 0.83 139 47 51 4 278.81 2.79 140 48 51 3 277.00 2.48 141 48 52 4 276.99 2.48 142 48 64 16 103.62 3.78 143 49 52 3 277.00 2.48 144 49 53 4 276.99 2.48 145 49 61 12 123.12 5.75 146 49 64 15 104.06 3.57 147 50 54 4 276.98 2.48 148 51 54 3 284.22 0.25 149 51 55 4 287.00 1.65 150 52 55 3 295.10 1.18 151 52 56 4 276.95 2.51 152 52 57 5 257.70 1.09 153 52 59 7 195.12 0.71 154 52 77 25 68.25 1.78 155 53 56 3 277.22 0.81 156 53 57 4 275.37 1.73 157 56 82 26 53.25 0.59 158 57 77 20 71.40 0.42 159 57 80 23 58.93 0.28 160 57 81 24 55.08 0.14 161 57 82 25 54.07 0.20 162 58 80 22 60.44 0.36 163 59 63 4 281.98 0.83 164 59 64 5 281.76 0.72 165 59 67 8 255.52 4.33 166 59 76 17 73.92 0.62 167 59 77 18 73.76 0.56 168 60 63 3 285.95 1.16 169 60 76 16 79.50 1.85 170 61 64 3 301.71 2.49 171 62 65 3 301.70 2.49 172 63 66 3 289.26 0.53 173 63 67 4 289.27 0.53 174 63 76 13 139.97 2.54 175 64 67 3 291.82 0.75 176 65 68 3 321.80 1.28 177 67 72 5 245.09 1.08 178 67 73 6 225.86 8.53 179 69 72 3 288.24 0.89 180 69 73 4 287.55 1.23 181 70 73 3 290.86 0.42 182 70 74 4 287.55 1.23 183 71 74 3 287.54 1.23 184 71 75 4 287.53 1.24 185 72 75 3 290.91 0.45 186 72 76 4 287.53 1.23 187 73 76 3 285.92 2.12 188 73 77 4 279.31 1.67 189 74 77 3 277.50 2.57 190 74 78 4 277.38 2.63 191 75 78 3 277.40 2.63 192 75 79 4 276.41 2.14 193 76 79 3 282.27 0.74 194 76 80 4 276.41 2.14 195 77 80 3 280.44 0.18 196 77 81 4 272.50 0.20 197 78 81 3 280.97 0.45