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 10 8 173.50 2.44 2 6 10 4 243.71 1.25 3 7 10 3 253.66 3.73 4 7 11 4 197.20 5.23 5 8 49 41 96.37 0.96 6 8 50 42 96.17 0.93 7 9 12 3 259.87 0.62 8 9 13 4 244.71 1.60 9 9 50 41 96.19 0.92 10 9 53 44 96.16 0.93 11 10 13 3 259.86 0.62 12 10 14 4 248.75 0.41 13 11 14 3 254.18 2.22 14 11 15 4 248.62 0.26 15 12 15 3 253.89 2.89 16 12 16 4 248.62 0.26 17 12 43 31 111.11 3.03 18 12 50 38 96.62 1.08 19 12 54 42 96.48 1.08 20 13 16 3 255.36 2.15 21 13 17 4 248.62 0.26 22 13 53 40 96.52 1.06 23 13 54 41 96.50 1.07 24 13 58 45 94.89 1.07 25 13 59 46 94.73 0.99 26 13 62 49 83.64 1.18 27 14 17 3 256.83 0.18 28 14 18 4 248.56 0.24 29 15 18 3 253.12 2.04 30 15 19 4 241.63 1.00 31 15 41 26 112.47 3.45 32 15 42 27 112.55 3.41 33 15 43 28 112.50 3.41 34 16 19 3 252.37 0.60 35 16 20 4 243.06 0.28 36 16 37 21 112.31 3.40 37 16 41 25 112.45 3.44 38 16 43 27 112.52 3.40 39 16 54 38 99.70 2.29 40 16 59 43 95.02 1.13 41 17 20 3 258.61 2.34 42 17 21 4 241.92 0.82 43 17 62 45 89.62 0.09 44 17 65 48 70.47 0.49 45 18 21 3 253.07 2.75 46 18 22 4 245.28 1.15 47 19 22 3 256.94 3.17 48 19 23 4 247.66 0.09 49 19 32 13 130.65 1.88 50 19 37 18 112.73 3.46 51 19 40 21 112.73 3.46 52 19 41 22 112.71 3.45 53 20 23 3 258.43 0.07 54 20 24 4 242.38 0.41 55 20 37 17 112.73 3.46 56 20 65 45 78.42 3.78 57 20 72 52 69.14 0.80 58 20 73 53 66.56 0.54 59 20 74 54 65.42 0.12 60 21 24 3 250.32 1.19 61 21 25 4 242.43 0.39 62 21 74 53 65.75 0.24 63 22 25 3 253.15 0.22 64 22 26 4 247.18 2.77 65 23 26 3 258.56 2.33 66 23 27 4 248.88 0.59 67 23 28 5 235.65 2.92 68 23 30 7 229.99 0.10 69 23 32 9 174.68 2.25 70 23 40 17 112.91 3.43 71 24 27 3 253.16 0.23 72 24 28 4 235.65 2.92 73 24 29 5 193.99 7.36 74 24 74 50 66.08 0.15 75 24 76 52 65.71 0.20 76 31 68 37 70.45 0.51 77 31 71 40 69.41 0.80 78 31 72 41 69.28 0.80 79 31 73 42 68.94 0.81 80 32 36 4 251.22 1.27 81 32 37 5 250.04 1.62 82 32 71 39 69.27 0.79 83 32 72 40 69.27 0.80 84 33 36 3 252.87 0.44 85 33 37 4 253.66 0.82 86 33 71 38 69.25 0.79 87 34 37 3 255.08 0.11 88 34 38 4 252.94 0.45 89 34 51 17 112.90 3.27 90 34 54 20 112.84 3.23 91 34 55 21 112.82 3.23 92 34 59 25 112.12 3.20 93 34 72 38 69.03 0.79 94 35 38 3 253.66 0.81 95 35 39 4 252.94 0.45 96 36 39 3 264.68 3.35 97 36 40 4 252.94 0.45 98 37 40 3 258.43 0.53 99 37 41 4 252.91 0.43 100 37 59 22 112.31 3.08 101 37 72 35 69.20 0.76 102 38 41 3 253.06 1.10 103 38 42 4 251.18 1.21 104 38 43 5 195.24 10.48 105 38 44 6 165.94 1.91 106 38 46 8 165.94 1.91 107 38 51 13 144.56 2.68 108 38 54 16 131.31 1.62 109 39 42 3 250.34 1.73 110 39 44 5 203.82 14.20 111 43 46 3 239.55 2.88 112 44 51 7 238.96 1.88 113 46 50 4 251.15 0.17 114 46 51 5 246.87 2.07 115 46 54 8 236.66 0.57 116 47 50 3 263.16 0.84 117 47 51 4 249.06 0.97 118 48 51 3 252.11 0.65 119 48 52 4 249.06 0.97 120 49 52 3 258.25 3.31 121 49 53 4 251.82 2.33 122 50 53 3 252.13 2.21 123 50 54 4 251.87 2.33 124 51 54 3 252.16 2.19 125 51 55 4 252.15 2.19 126 52 55 3 252.15 2.19 127 52 56 4 252.14 2.19 128 53 56 3 263.62 3.56 129 53 57 4 242.62 2.30 130 53 58 5 230.21 2.83 131 54 58 4 220.48 1.34 132 54 59 5 208.43 4.68 133 55 60 5 226.69 4.46 134 55 72 17 68.95 0.82 135 56 60 4 242.22 0.33 136 57 60 3 257.64 0.61 137 57 61 4 239.25 1.81 138 58 61 3 260.71 0.59 139 58 62 4 236.16 0.28 140 59 65 6 104.03 16.25 141 59 67 8 103.98 16.26 142 59 72 13 68.60 0.83 143 62 65 3 245.85 1.49 144 63 75 12 65.71 0.31 145 64 74 10 95.94 14.70 146 64 75 11 65.36 0.15 147 64 79 15 44.45 0.42 148 64 80 16 44.44 0.42 149 65 72 7 145.84 2.73 150 65 73 8 131.62 2.73 151 66 72 6 150.61 5.08 152 66 73 7 135.43 2.41 153 66 75 9 102.18 16.89 154 67 70 3 261.96 2.13 155 67 71 4 213.78 1.55 156 67 72 5 154.24 3.28 157 68 71 3 264.42 1.43 158 68 73 5 164.74 1.98 159 74 80 6 241.91 2.60 160 75 78 3 362.69 1.84 161 76 79 3 267.46 1.09 162 76 80 4 231.32 2.96