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 5 3 258.84 0.20 2 2 6 4 256.56 0.86 3 3 6 3 256.70 0.88 4 3 7 4 256.62 0.83 5 3 50 47 83.25 0.81 6 3 69 66 33.32 0.36 7 3 72 69 33.22 0.41 8 3 73 70 32.08 0.18 9 3 76 73 19.98 0.76 10 4 7 3 262.22 1.97 11 4 8 4 256.52 0.88 12 4 24 20 119.80 1.69 13 4 69 65 33.40 0.40 14 5 8 3 262.21 1.97 15 5 9 4 254.78 0.07 16 6 9 3 256.61 0.82 17 6 10 4 253.58 0.70 18 6 49 43 84.73 0.25 19 6 50 44 84.73 0.25 20 7 10 3 260.88 1.31 21 7 11 4 252.70 1.11 22 7 46 39 84.72 0.26 23 7 50 43 84.75 0.24 24 7 68 61 43.64 1.02 25 7 69 62 43.25 0.82 26 7 72 65 42.20 0.85 27 8 11 3 255.69 0.38 28 8 12 4 252.47 1.23 29 8 19 11 125.02 0.52 30 8 22 14 120.61 1.61 31 8 23 15 120.62 1.62 32 8 24 16 120.25 1.47 33 8 65 57 59.34 0.58 34 9 12 3 264.45 1.04 35 9 13 4 252.50 1.22 36 9 19 10 125.02 0.52 37 10 13 3 264.45 1.04 38 10 14 4 252.37 1.14 39 10 42 32 84.77 0.25 40 10 45 35 84.77 0.24 41 10 46 36 84.75 0.25 42 10 49 39 84.77 0.24 43 10 50 40 84.80 0.24 44 11 14 3 258.06 0.52 45 11 15 4 252.37 1.15 46 11 22 11 125.22 0.84 47 11 28 17 119.67 1.61 48 11 32 21 119.67 1.60 49 11 42 31 84.77 0.25 50 11 65 54 64.50 1.99 51 12 15 3 256.69 1.00 52 12 16 4 248.78 0.49 53 12 17 5 191.06 0.84 54 12 22 10 125.22 0.84 55 13 16 3 260.21 0.77 56 14 41 27 85.02 0.18 57 14 42 28 84.92 0.23 58 14 45 31 84.97 0.21 59 15 28 13 120.00 1.45 60 15 32 17 119.67 1.60 61 15 34 19 116.78 0.42 62 15 38 23 95.74 0.32 63 17 22 5 241.96 2.39 64 17 32 15 119.74 1.59 65 18 21 3 262.89 0.95 66 18 22 4 261.19 3.24 67 19 22 3 264.67 1.51 68 20 23 3 284.11 1.13 69 21 26 5 225.04 10.79 70 21 32 11 133.88 1.94 71 22 32 10 133.88 1.94 72 22 65 43 81.76 0.11 73 23 26 3 245.90 0.36 74 23 65 42 81.78 0.11 75 24 65 41 81.78 0.11 76 24 66 42 81.67 0.12 77 24 69 45 81.70 0.09 78 25 64 39 82.83 0.34 79 26 31 5 159.75 0.12 80 26 32 6 159.74 0.12 81 26 64 38 82.84 0.34 82 26 65 39 82.82 0.35 83 27 30 3 263.82 6.16 84 27 31 4 162.10 1.05 85 27 32 5 162.58 1.54 86 27 63 36 82.91 0.33 87 27 64 37 82.84 0.34 88 28 32 4 159.77 0.12 89 28 33 5 162.60 1.53 90 28 34 6 159.63 0.07 91 28 42 14 108.93 5.80 92 28 62 34 83.03 0.36 93 28 63 35 82.92 0.33 94 28 64 36 82.88 0.33 95 28 65 37 82.84 0.34 96 28 68 40 82.24 0.18 97 29 33 4 162.60 1.53 98 29 34 5 159.72 0.10 99 32 65 33 82.84 0.34 100 34 38 4 252.76 2.38 101 35 38 3 257.30 0.12 102 35 39 4 257.30 0.12 103 36 39 3 260.62 0.30 104 36 40 4 257.30 0.12 105 37 40 3 261.04 0.29 106 37 41 4 256.50 0.52 107 38 41 3 259.35 1.14 108 38 42 4 253.14 0.25 109 39 42 3 258.13 0.67 110 39 43 4 253.15 0.26 111 40 43 3 261.88 0.65 112 40 44 4 256.97 1.80 113 41 44 3 260.44 0.48 114 41 45 4 255.23 0.93 115 42 45 3 260.02 0.27 116 42 46 4 256.98 1.79 117 43 46 3 258.12 0.52 118 43 47 4 252.08 0.66 119 43 54 11 127.53 0.06 120 43 59 16 83.03 0.36 121 44 47 3 257.12 1.72 122 44 48 4 256.90 1.82 123 45 48 3 257.12 1.71 124 45 49 4 252.59 0.40 125 46 49 3 255.17 0.96 126 46 50 4 251.97 0.62 127 46 68 22 59.42 0.55 128 46 72 26 44.26 0.37 129 47 51 4 216.15 1.11 130 47 52 5 171.30 3.91 131 47 53 6 154.12 4.81 132 47 54 7 154.14 4.83 133 48 51 3 239.76 1.45 134 50 72 22 44.30 0.38 135 50 76 26 21.20 0.68 136 52 71 19 59.86 0.33 137 52 75 23 42.65 0.51 138 52 76 24 41.69 0.62 139 54 58 4 251.81 1.10 140 54 59 5 247.73 0.91 141 54 62 8 242.15 1.97 142 54 71 17 66.34 2.16 143 55 58 3 257.50 1.74 144 55 59 4 257.10 1.49 145 55 71 16 108.69 9.81 146 56 59 3 257.12 1.48 147 56 60 4 257.10 1.49 148 57 60 3 257.20 1.44 149 57 61 4 259.94 0.07 150 58 61 3 266.94 1.88 151 58 62 4 261.62 0.78 152 58 71 13 118.75 4.94 153 59 62 3 261.63 0.78 154 60 63 3 295.29 1.47 155 62 67 5 209.15 12.05 156 62 68 6 186.96 6.48 157 62 71 9 176.33 1.16 158 64 67 3 262.28 4.21 159 64 68 4 253.43 0.20 160 65 68 3 263.11 3.80 161 65 69 4 253.43 0.20 162 66 69 3 254.28 0.61 163 66 70 4 253.44 0.19 164 67 70 3 254.70 0.43 165 67 71 4 253.44 0.19 166 68 71 3 260.85 1.21 167 68 72 4 253.28 0.11 168 69 72 3 256.02 0.25 169 69 73 4 254.52 0.51 170 70 73 3 254.92 0.31 171 70 74 4 253.02 1.26 172 71 74 3 252.28 1.02 173 71 75 4 247.34 1.45 174 72 75 3 253.54 0.38 175 72 76 4 235.84 7.20