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 3 257.06 0.17 2 2 6 4 257.05 0.17 3 3 6 3 257.63 0.46 4 3 7 4 254.80 0.82 5 3 50 47 77.97 1.93 6 3 72 69 31.77 0.33 7 3 73 70 30.15 0.28 8 4 7 3 263.51 2.04 9 4 8 4 255.42 0.50 10 4 24 20 119.48 2.21 11 4 69 65 32.81 0.04 12 5 8 3 267.70 0.05 13 5 9 4 254.04 1.53 14 6 9 3 257.35 0.12 15 6 10 4 257.35 0.12 16 6 49 43 85.04 0.56 17 6 50 44 85.02 0.57 18 7 10 3 257.99 0.43 19 7 11 4 252.69 2.21 20 7 46 39 85.00 0.56 21 7 50 43 85.02 0.57 22 7 68 61 58.30 0.39 23 7 69 62 55.27 0.59 24 7 72 65 46.66 0.56 25 8 11 3 261.12 2.00 26 8 12 4 254.56 1.28 27 8 19 11 139.25 4.53 28 8 22 14 121.92 1.54 29 8 23 15 121.89 1.56 30 8 24 16 121.67 1.62 31 8 65 57 67.95 1.52 32 8 69 61 60.26 1.14 33 9 12 3 256.23 1.49 34 9 13 4 256.05 1.41 35 9 19 10 140.58 3.87 36 10 13 3 256.68 1.27 37 10 14 4 256.00 1.44 38 10 42 32 85.78 0.46 39 10 45 35 85.08 0.56 40 10 46 36 85.08 0.55 41 10 49 39 85.06 0.56 42 11 14 3 262.69 0.15 43 11 15 4 255.78 1.46 44 11 22 11 122.25 1.42 45 11 28 17 119.38 2.25 46 11 32 21 119.25 2.31 47 11 42 31 85.72 0.46 48 11 65 54 68.12 1.59 49 11 68 57 61.98 1.47 50 12 15 3 260.11 0.62 51 12 16 4 252.62 3.04 52 12 17 5 208.50 7.77 53 12 19 7 152.91 2.29 54 12 22 10 122.23 1.43 55 13 16 3 256.46 1.17 56 14 41 27 86.08 0.36 57 14 42 28 85.84 0.48 58 14 45 31 85.84 0.48 59 15 28 13 119.94 2.51 60 15 32 17 119.28 2.32 61 15 34 19 119.04 2.31 62 15 38 23 98.62 1.90 63 15 42 27 88.49 1.54 64 17 21 4 256.12 0.83 65 17 22 5 251.14 2.60 66 17 32 15 119.23 2.33 67 18 21 3 261.06 0.88 68 18 22 4 258.54 0.38 69 19 22 3 264.05 0.61 70 20 23 3 277.11 0.76 71 21 32 11 119.53 2.23 72 22 32 10 122.17 0.91 73 22 65 43 80.39 1.70 74 23 26 3 255.27 2.02 75 23 65 42 80.86 1.46 76 24 65 41 80.86 1.46 77 24 66 42 79.85 1.44 78 24 69 45 79.82 1.46 79 25 64 39 81.31 1.48 80 26 31 5 149.94 1.71 81 26 32 6 149.94 1.71 82 26 64 38 81.33 1.48 83 26 65 39 81.31 1.48 84 27 30 3 233.53 2.97 85 27 31 4 155.13 0.88 86 27 32 5 150.18 1.82 87 27 63 36 81.42 1.50 88 27 64 37 81.33 1.48 89 28 32 4 150.18 1.82 90 28 33 5 150.18 1.82 91 28 34 6 149.91 1.71 92 28 42 14 139.39 1.42 93 28 62 34 81.50 1.51 94 28 63 35 81.42 1.50 95 28 64 36 81.34 1.47 96 28 65 37 81.34 1.47 97 28 68 40 80.57 1.83 98 29 34 5 149.91 1.71 99 29 39 10 148.27 2.42 100 32 65 33 81.32 1.48 101 34 38 4 254.58 0.61 102 34 39 5 254.56 0.60 103 35 38 3 258.77 2.60 104 35 39 4 260.92 1.53 105 36 39 3 264.77 0.40 106 36 40 4 264.77 0.40 107 37 40 3 265.12 0.22 108 37 41 4 259.18 1.66 109 38 41 3 260.78 0.86 110 38 42 4 254.71 0.58 111 39 42 3 262.92 1.30 112 39 43 4 256.31 0.21 113 40 43 3 259.91 1.14 114 40 44 4 256.04 2.13 115 41 44 3 260.75 0.22 116 41 45 4 250.97 0.40 117 42 45 3 261.75 2.51 118 42 46 4 250.95 0.40 119 43 46 3 259.37 0.66 120 43 47 4 253.34 1.56 121 43 54 11 131.13 2.17 122 43 59 16 81.62 1.59 123 44 47 3 259.61 3.10 124 44 48 4 253.34 1.57 125 45 48 3 259.76 3.48 126 45 49 4 250.66 2.91 127 46 49 3 260.24 3.23 128 46 50 4 248.93 2.46 129 46 54 8 149.34 0.93 130 46 68 22 62.13 1.40 131 46 72 26 54.23 0.48 132 47 50 3 263.10 2.83 133 47 51 4 236.15 1.75 134 47 52 5 197.05 0.49 135 47 53 6 159.07 0.40 136 47 54 7 151.77 3.24 137 48 51 3 252.14 8.30 138 50 72 22 54.77 0.29 139 50 77 27 37.11 0.55 140 51 77 26 37.26 0.53 141 52 71 19 62.21 1.41 142 52 72 20 60.25 0.70 143 52 75 23 46.87 0.45 144 53 71 18 62.25 1.39 145 54 58 4 256.42 1.16 146 54 59 5 241.30 1.07 147 54 62 8 204.86 4.11 148 54 71 17 62.25 1.39 149 55 58 3 258.75 2.32 150 55 59 4 256.43 1.16 151 55 71 16 72.84 0.42 152 56 59 3 256.44 1.16 153 56 60 4 256.42 1.17 154 57 60 3 257.29 0.73 155 58 61 3 260.05 2.27 156 58 62 4 255.06 1.85 157 58 71 13 103.17 15.12 158 59 62 3 255.96 1.68 159 60 63 3 293.09 1.58 160 62 67 5 231.15 0.48 161 62 68 6 221.83 4.18 162 62 71 9 195.03 1.85 163 63 67 4 246.41 2.54 164 64 67 3 251.83 2.03 165 64 68 4 255.78 1.72 166 65 68 3 257.56 0.84 167 65 69 4 255.35 1.94 168 66 69 3 255.91 1.67 169 66 70 4 253.44 0.99 170 67 70 3 261.94 0.41 171 67 71 4 253.35 1.03 172 68 71 3 261.94 0.41 173 68 72 4 245.78 2.91 174 69 72 3 260.00 0.71 175 69 73 4 245.67 2.93 176 70 73 3 257.93 1.75 177 70 74 4 244.67 3.42 178 71 74 3 257.79 1.68 179 71 75 4 250.94 3.64 180 72 75 3 265.12 1.99 181 72 76 4 254.52 1.85 182 73 76 3 267.47 0.81