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 4 9 5 221.00 0.04 2 4 10 6 235.44 1.48 3 5 9 4 279.21 2.00 4 5 43 38 69.05 0.70 5 6 9 3 292.15 0.60 6 6 10 4 285.54 1.50 7 6 43 37 69.05 0.70 8 7 10 3 281.43 0.97 9 7 15 8 189.02 5.74 10 7 43 36 69.07 0.70 11 7 44 37 69.06 0.70 12 7 71 64 69.06 0.70 13 7 75 68 66.00 0.58 14 7 82 75 28.69 0.61 15 7 83 76 28.57 0.60 16 7 84 77 28.54 0.61 17 8 82 74 28.86 0.57 18 8 83 75 28.58 0.60 19 8 84 76 28.53 0.62 20 9 43 34 122.63 0.19 21 9 84 75 28.62 0.65 22 10 14 4 250.46 6.50 23 10 15 5 222.47 1.88 24 10 39 29 122.77 0.20 25 10 43 33 122.73 0.20 26 10 83 73 28.72 0.64 27 10 84 74 28.66 0.64 28 11 14 3 275.88 0.43 29 11 15 4 259.79 2.44 30 11 83 72 28.77 0.65 31 11 84 73 28.68 0.63 32 11 85 74 28.67 0.63 33 12 16 4 274.48 0.12 34 12 68 56 79.05 1.21 35 12 72 60 71.80 0.45 36 12 83 71 28.93 0.59 37 13 16 3 283.07 0.08 38 13 17 4 283.06 0.10 39 14 17 3 285.56 1.16 40 14 18 4 285.56 1.16 41 15 18 3 284.79 1.55 42 15 19 4 283.60 2.14 43 15 40 25 136.47 2.33 44 15 43 28 136.43 2.31 45 15 44 29 136.05 2.13 46 15 68 53 104.93 1.19 47 15 71 56 103.59 0.52 48 15 83 68 28.78 0.65 49 16 19 3 283.56 0.94 50 16 20 4 282.38 0.58 51 16 64 48 104.99 1.18 52 16 65 49 104.96 1.18 53 16 68 52 104.91 1.21 54 17 20 3 284.22 0.34 55 17 21 4 284.21 0.34 56 18 21 3 284.22 0.34 57 18 22 4 284.22 0.34 58 18 36 18 136.62 2.31 59 18 39 21 136.50 2.33 60 18 40 22 136.49 2.33 61 19 22 3 284.22 0.34 62 19 23 4 281.81 0.30 63 19 40 21 136.48 2.33 64 19 53 34 128.94 2.49 65 19 64 45 105.14 1.13 66 19 67 48 105.14 1.14 67 19 68 49 105.00 1.22 68 20 23 3 282.86 0.85 69 20 24 4 274.19 0.15 70 20 25 5 269.03 2.43 71 20 64 44 105.14 1.14 72 21 25 4 250.71 3.70 73 21 26 5 216.92 3.58 74 21 27 6 216.91 3.58 75 21 33 12 146.66 1.93 76 21 36 15 142.06 0.35 77 22 25 3 252.51 3.71 78 22 33 11 141.75 0.20 79 22 36 14 141.75 0.20 80 22 37 15 141.75 0.20 81 23 53 30 131.83 3.92 82 23 62 39 105.55 0.97 83 23 64 41 105.51 0.97 84 23 67 44 105.51 0.97 85 24 64 40 105.52 0.97 86 25 33 8 167.44 4.65 87 26 33 7 234.77 2.73 88 27 32 5 261.05 2.71 89 27 33 6 240.02 5.36 90 27 36 9 204.63 12.11 91 29 32 3 292.51 0.22 92 29 33 4 285.52 3.71 93 30 33 3 279.32 0.60 94 30 34 4 277.12 0.49 95 31 34 3 282.58 0.56 96 31 35 4 277.14 0.51 97 32 35 3 278.60 0.21 98 32 36 4 276.99 0.50 99 33 36 3 279.64 0.83 100 33 37 4 280.33 2.18 101 34 37 3 283.39 0.65 102 34 38 4 280.22 2.24 103 35 38 3 293.58 3.53 104 35 39 4 279.47 2.62 105 36 39 3 286.65 0.07 106 36 40 4 279.48 2.62 107 37 40 3 279.47 2.60 108 37 41 4 283.11 0.77 109 37 50 13 134.55 5.08 110 37 53 16 134.43 5.15 111 37 54 17 134.42 5.15 112 38 41 3 284.85 0.10 113 38 42 4 283.11 0.77 114 39 42 3 286.74 0.88 115 39 43 4 274.74 0.57 116 40 43 3 278.68 1.45 117 40 44 4 274.58 0.60 118 40 46 6 260.61 5.55 119 40 49 9 139.68 7.63 120 40 52 12 134.63 5.11 121 40 71 31 104.97 1.17 122 41 45 4 255.66 3.93 123 41 49 8 134.65 5.12 124 41 50 9 134.66 5.11 125 43 75 32 103.40 0.55 126 44 71 27 104.96 1.18 127 44 74 30 103.50 0.51 128 44 75 31 103.06 0.46 129 45 74 29 104.90 1.18 130 46 49 3 273.06 1.25 131 46 52 6 252.81 4.72 132 46 70 24 105.43 1.00 133 46 74 28 103.64 0.57 134 47 74 27 105.11 1.07 135 48 51 3 278.12 1.27 136 48 52 4 273.28 1.36 137 48 55 7 208.80 7.96 138 49 52 3 292.14 0.91 139 50 53 3 292.14 0.91 140 50 54 4 274.32 3.17 141 51 54 3 274.33 3.17 142 51 55 4 254.43 6.00 143 52 55 3 288.39 0.97 144 52 67 15 105.48 0.99 145 52 70 18 105.47 0.98 146 53 56 3 303.88 1.95 147 53 67 14 105.51 0.97 148 56 61 5 159.06 1.59 149 56 62 6 105.72 0.93 150 57 60 3 269.04 1.25 151 61 66 5 241.94 1.89 152 62 67 5 256.76 1.98 153 63 66 3 285.12 1.42 154 63 67 4 281.32 0.48 155 64 67 3 287.32 0.32 156 64 68 4 281.32 0.48 157 65 68 3 281.32 0.47 158 65 69 4 279.29 0.54 159 66 69 3 279.32 0.53 160 66 70 4 279.30 0.51 161 67 70 3 284.14 2.92 162 67 71 4 280.13 0.93 163 68 71 3 281.62 0.18 164 68 72 4 279.31 0.51 165 69 72 3 281.62 0.18 166 69 73 4 281.62 0.18 167 70 73 3 283.76 0.76 168 70 74 4 275.49 1.43 169 71 74 3 275.26 1.54 170 71 75 4 275.26 1.54 171 71 83 12 178.86 3.48 172 72 83 11 178.85 3.49 173 73 76 3 278.62 0.15 174 73 77 4 279.81 0.45 175 74 77 3 283.13 1.79 176 74 78 4 279.81 0.45 177 74 80 6 257.80 6.64 178 75 78 3 279.85 0.43 179 75 79 4 269.74 0.67 180 75 80 5 244.17 13.45 181 75 81 6 244.11 13.42 182 75 82 7 208.25 4.22 183 76 79 3 270.95 0.06