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 37 36 101.12 0.32 2 3 10 7 206.06 3.58 3 3 18 15 117.64 2.22 4 3 37 34 106.61 2.69 5 3 40 37 107.20 2.98 6 4 9 5 217.04 5.61 7 4 10 6 209.53 1.85 8 4 14 10 195.71 1.17 9 4 40 36 125.83 1.50 10 4 44 40 126.12 1.36 11 5 9 4 293.81 0.91 12 5 43 38 126.12 1.36 13 5 44 39 126.12 1.36 14 6 9 3 295.33 1.65 15 6 10 4 293.81 0.91 16 6 44 38 126.14 1.35 17 7 10 3 293.88 0.86 18 7 15 8 240.36 6.10 19 7 44 37 126.25 1.36 20 7 45 38 126.25 1.36 21 7 76 69 72.53 0.22 22 7 83 76 31.07 0.07 23 7 84 77 29.37 0.27 24 8 82 74 32.77 0.34 25 8 83 75 31.11 0.08 26 8 85 77 29.34 0.28 27 9 14 5 286.08 2.94 28 9 85 76 28.43 0.46 29 10 14 4 286.06 2.94 30 10 15 5 279.42 0.09 31 10 40 30 158.84 0.21 32 10 44 34 158.78 0.22 33 10 84 74 30.05 0.07 34 10 85 75 28.30 0.41 35 11 14 3 290.45 0.80 36 11 15 4 291.12 0.42 37 11 84 73 30.09 0.06 38 11 85 74 28.43 0.46 39 11 87 76 26.25 0.43 40 12 15 3 292.60 0.26 41 12 16 4 290.41 0.78 42 12 69 57 80.98 0.60 43 12 73 61 80.95 0.61 44 12 84 72 30.56 0.18 45 13 16 3 291.05 1.01 46 13 17 4 290.51 0.72 47 14 17 3 289.52 0.23 48 14 18 4 289.51 0.23 49 15 18 3 292.39 0.04 50 15 19 4 289.51 0.23 51 15 41 26 167.31 1.38 52 15 44 29 167.31 1.38 53 15 45 30 166.78 1.23 54 15 69 54 81.00 0.61 55 15 72 57 80.99 0.60 56 15 84 69 30.09 0.06 57 16 19 3 290.39 0.67 58 16 20 4 290.39 0.67 59 16 65 49 81.50 0.56 60 16 69 53 81.10 0.59 61 17 20 3 290.35 0.69 62 17 21 4 288.15 1.79 63 18 21 3 293.40 0.89 64 18 22 4 284.50 0.04 65 18 37 19 167.94 1.60 66 18 40 22 167.91 1.60 67 18 41 23 167.62 1.48 68 18 44 26 167.61 1.47 69 19 22 3 290.69 0.47 70 19 23 4 282.18 1.18 71 19 41 22 167.78 1.55 72 19 54 35 165.88 1.50 73 19 65 46 81.54 0.57 74 19 68 49 81.53 0.58 75 19 69 50 81.48 0.56 76 20 23 3 282.44 1.19 77 20 24 4 282.31 1.25 78 20 65 45 81.56 0.58 79 21 24 3 291.31 1.10 80 21 25 4 287.50 0.79 81 21 37 16 168.22 1.69 82 22 25 3 293.93 0.18 83 22 26 4 291.35 1.11 84 22 34 12 168.44 1.61 85 22 37 15 168.22 1.69 86 22 38 16 168.21 1.69 87 22 41 19 168.21 1.69 88 22 54 32 166.38 1.25 89 22 55 33 166.34 1.28 90 23 26 3 293.93 0.18 91 23 27 4 293.04 0.27 92 23 65 42 81.61 0.58 93 24 27 3 300.09 0.64 94 24 28 4 293.04 0.27 95 25 28 3 291.35 1.10 96 25 33 8 168.70 1.56 97 25 34 9 168.65 1.57 98 25 37 12 168.66 1.57 99 26 34 8 168.71 1.57 100 26 55 29 166.49 1.28 101 31 34 3 287.66 0.70 102 31 35 4 283.92 0.82 103 32 35 3 300.71 0.57 104 32 36 4 289.98 1.86 105 33 36 3 298.90 2.00 106 33 37 4 287.13 1.02 107 34 37 3 294.30 0.30 108 34 38 4 285.37 0.13 109 34 55 21 166.63 1.21 110 35 38 3 291.91 1.50 111 35 39 4 285.30 0.09 112 36 39 3 288.01 0.60 113 36 40 4 287.18 1.02 114 37 40 3 288.13 0.54 115 37 41 4 288.13 0.54 116 38 41 3 288.14 0.55 117 38 42 4 287.12 1.05 118 38 51 13 166.81 1.29 119 38 54 16 166.65 1.22 120 38 55 17 166.63 1.21 121 39 42 3 293.35 0.78 122 39 43 4 284.63 2.08 123 40 43 3 291.91 1.50 124 40 44 4 286.24 1.27 125 41 44 3 299.45 2.27 126 41 45 4 288.65 0.07 127 41 50 9 166.82 1.29 128 41 51 10 166.81 1.29 129 41 53 12 166.81 1.29 130 41 54 13 166.63 1.22 131 41 68 27 81.42 0.52 132 41 72 31 80.74 0.49 133 42 45 3 301.30 1.71 134 42 46 4 286.30 1.25 135 42 50 8 166.81 1.29 136 42 51 9 166.81 1.29 137 43 46 3 294.72 2.67 138 44 76 32 72.95 0.39 139 45 72 27 80.23 0.47 140 45 75 30 77.89 0.54 141 45 76 31 72.95 0.38 142 46 75 29 78.33 0.41 143 46 76 30 77.80 0.58 144 46 81 35 47.46 1.48 145 47 50 3 286.26 1.25 146 47 53 6 194.87 2.21 147 47 75 28 78.23 0.45 148 48 75 27 79.51 0.09 149 49 52 3 292.67 2.54 150 50 53 3 310.65 0.34 151 51 54 3 303.75 2.19 152 51 55 4 288.39 0.74 153 52 55 3 294.12 0.37 154 52 56 4 250.24 3.17 155 52 57 5 250.24 3.17 156 53 61 8 187.45 1.60 157 53 68 15 81.43 0.52 158 53 71 18 81.42 0.52 159 53 72 19 81.35 0.49 160 54 57 3 306.41 1.23 161 54 68 14 81.53 0.57 162 57 61 4 289.90 2.06 163 57 63 6 83.42 1.40 164 58 61 3 300.68 1.30 165 61 67 6 129.40 21.34 166 61 68 7 198.77 0.59 167 61 71 10 84.61 2.00 168 62 67 5 174.46 1.20 169 64 67 3 282.21 1.28 170 64 68 4 280.94 0.63 171 65 68 3 286.77 1.94 172 65 69 4 285.19 2.73 173 66 69 3 286.78 1.94 174 66 70 4 285.20 2.72 175 67 70 3 292.56 0.73 176 67 71 4 281.50 0.36 177 68 71 3 292.56 0.73 178 68 72 4 282.60 0.20 179 69 72 3 286.82 1.92 180 69 73 4 282.56 0.21 181 69 84 15 31.12 0.07 182 70 73 3 295.96 3.32 183 70 74 4 282.68 0.15 184 71 74 3 289.28 0.80 185 71 75 4 282.68 0.14 186 72 75 3 292.85 0.71 187 72 76 4 284.28 0.67 188 72 84 12 31.17 0.09 189 73 76 3 288.22 0.30 190 73 77 4 284.12 0.81 191 73 84 11 31.17 0.09 192 74 77 3 295.09 3.13 193 74 78 4 284.12 0.81 194 75 78 3 287.80 1.02 195 75 79 4 284.12 0.81 196 75 81 6 274.06 5.83 197 76 79 3 287.20 0.81 198 76 80 4 284.12 0.81 199 76 81 5 260.25 0.17 200 76 82 6 251.18 4.70 201 77 80 3 285.67 0.04