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 10 7 187.29 0.33 2 3 18 15 92.66 9.75 3 3 40 37 92.55 9.75 4 4 9 5 202.83 7.86 5 4 10 6 187.30 0.33 6 4 14 10 187.19 0.38 7 4 40 36 93.20 10.03 8 4 44 40 93.22 10.04 9 5 40 35 93.24 10.03 10 5 44 39 93.23 10.04 11 6 9 3 293.76 1.30 12 6 10 4 279.51 0.65 13 6 44 38 93.23 10.04 14 7 10 3 294.75 6.46 15 7 15 8 216.54 1.12 16 7 44 37 93.28 10.03 17 7 45 38 93.25 10.05 18 7 72 65 75.65 1.27 19 7 76 69 71.02 0.12 20 7 82 75 38.15 0.16 21 7 83 76 37.73 0.19 22 7 84 77 37.28 0.10 23 8 82 74 38.06 0.12 24 8 83 75 37.90 0.06 25 8 84 76 37.30 0.11 26 8 85 77 35.84 0.18 27 9 14 5 278.75 0.43 28 9 85 76 37.11 0.20 29 10 14 4 278.75 0.43 30 10 15 5 271.56 1.21 31 10 40 30 114.65 12.12 32 10 44 34 107.27 13.62 33 10 84 74 37.58 0.19 34 10 85 75 37.26 0.12 35 11 14 3 286.31 1.00 36 11 15 4 282.10 2.10 37 11 84 73 37.70 0.20 38 11 85 74 37.56 0.20 39 11 87 76 35.68 0.20 40 12 15 3 288.69 1.20 41 12 16 4 282.08 2.08 42 12 69 57 85.11 2.48 43 12 73 61 80.08 0.01 44 12 84 72 37.73 0.19 45 13 16 3 288.69 1.20 46 13 17 4 283.49 1.40 47 14 17 3 288.62 1.16 48 14 18 4 288.60 1.16 49 15 18 3 288.60 1.17 50 15 19 4 288.04 0.88 51 15 41 26 114.82 12.16 52 15 44 29 115.05 12.04 53 15 45 30 115.03 12.04 54 15 69 54 85.48 2.66 55 15 72 57 85.26 2.59 56 15 84 69 37.72 0.20 57 16 19 3 288.12 0.85 58 16 20 4 288.10 0.85 59 16 65 49 85.70 2.69 60 16 69 53 85.50 2.65 61 17 20 3 292.18 2.89 62 17 21 4 288.09 0.85 63 18 21 3 292.17 2.89 64 18 22 4 291.16 2.38 65 18 44 26 115.64 12.17 66 19 22 3 297.03 0.46 67 19 23 4 291.16 2.39 68 19 41 22 116.20 11.88 69 19 54 35 115.03 11.87 70 19 65 46 85.89 2.70 71 19 68 49 85.81 2.74 72 19 69 50 85.80 2.75 73 20 23 3 290.23 2.85 74 20 24 4 288.00 3.97 75 20 65 45 85.96 2.68 76 21 24 3 287.52 0.04 77 21 25 4 287.07 0.05 78 21 37 16 116.45 11.87 79 22 25 3 292.38 1.91 80 22 26 4 287.06 0.05 81 22 34 12 116.51 11.84 82 22 37 15 116.49 11.85 83 22 38 16 116.45 11.86 84 22 41 19 116.42 11.88 85 22 54 32 116.04 11.79 86 23 26 3 292.38 1.91 87 23 27 4 291.61 2.29 88 23 65 42 86.68 2.94 89 24 27 3 299.94 3.11 90 24 28 4 291.61 2.29 91 25 28 3 285.31 0.85 92 25 33 8 116.66 11.88 93 25 34 9 116.62 11.87 94 25 37 12 116.62 11.87 95 26 34 8 116.66 11.87 96 26 55 29 116.35 11.79 97 31 34 3 275.94 1.33 98 31 35 4 269.62 6.57 99 32 36 4 292.75 1.32 100 33 36 3 292.75 1.33 101 33 37 4 290.83 2.98 102 34 37 3 296.11 0.35 103 34 38 4 292.75 1.34 104 34 55 21 160.81 8.38 105 35 38 3 292.75 1.34 106 35 39 4 292.75 1.34 107 36 39 3 293.14 1.14 108 36 40 4 285.70 2.58 109 37 40 3 293.14 1.14 110 37 41 4 279.44 1.91 111 38 41 3 282.88 0.18 112 38 42 4 281.33 1.24 113 38 51 13 161.16 8.50 114 38 54 16 161.54 8.67 115 38 55 17 161.28 8.46 116 39 42 3 290.47 0.51 117 39 43 4 281.33 1.24 118 40 43 3 287.35 2.06 119 40 44 4 281.06 1.10 120 41 44 3 293.11 1.83 121 41 45 4 277.95 2.66 122 41 50 9 167.79 5.62 123 41 53 12 161.78 8.62 124 41 54 13 161.77 8.62 125 41 68 27 129.16 24.43 126 41 72 31 128.79 24.46 127 42 46 4 277.95 2.66 128 42 50 8 161.71 8.62 129 42 51 9 161.71 8.61 130 43 46 3 285.98 1.91 131 45 72 27 128.08 24.95 132 45 75 30 126.99 25.50 133 45 76 31 126.28 25.84 134 46 75 29 127.80 25.12 135 46 76 30 126.69 25.64 136 46 81 35 77.83 18.46 137 47 50 3 294.69 0.44 138 47 53 6 261.93 4.23 139 47 71 24 129.09 24.49 140 47 75 28 127.01 25.50 141 48 75 27 128.94 24.55 142 49 52 3 292.49 0.70 143 49 53 4 282.48 2.04 144 50 53 3 305.79 4.45 145 51 54 3 294.05 0.28 146 51 55 4 286.41 1.91 147 52 55 3 290.93 0.35 148 52 56 4 263.88 3.20 149 52 57 5 263.88 3.20 150 53 61 8 189.58 1.83 151 53 68 15 129.27 24.38 152 53 71 18 129.08 24.47 153 53 72 19 129.07 24.48 154 54 57 3 300.54 1.32 155 54 68 14 129.28 24.37 156 57 61 4 293.86 0.54 157 57 63 6 172.74 2.87 158 58 61 3 300.97 1.46 159 58 71 13 165.37 6.35 160 61 67 6 187.34 4.30 161 61 68 7 193.14 1.40 162 61 70 9 173.75 2.50 163 61 71 10 173.74 2.50 164 62 67 5 190.81 5.91 165 64 67 3 284.48 0.45 166 64 68 4 288.05 1.29 167 65 68 3 289.56 0.54 168 65 69 4 288.07 1.29 169 66 69 3 289.56 0.55 170 66 70 4 288.06 1.29 171 67 70 3 291.89 1.70 172 67 71 4 293.38 2.60 173 68 71 3 293.38 2.60 174 68 72 4 293.38 2.60 175 69 72 3 289.44 0.61 176 69 73 4 285.87 1.16 177 69 84 15 38.23 0.22 178 70 73 3 295.53 2.43 179 70 74 4 285.88 1.16 180 71 74 3 288.28 0.00 181 71 75 4 287.01 0.63 182 72 75 3 293.52 0.91 183 72 76 4 278.81 3.46 184 72 84 12 38.40 0.28 185 73 76 3 295.06 3.18 186 73 77 4 284.67 1.79 187 73 84 11 68.28 15.22 188 74 77 3 292.91 1.13 189 74 78 4 284.89 1.74 190 75 78 3 286.81 2.69 191 75 79 4 286.81 2.69 192 76 79 3 292.88 0.34 193 76 80 4 284.42 1.50 194 76 81 5 208.84 4.45 195 76 82 6 211.17 3.29 196 76 83 7 129.24 15.24 197 77 80 3 292.87 0.34