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 3 256.35 2.49 2 2 6 4 247.66 1.84 3 3 6 3 261.94 3.46 4 3 7 4 255.16 2.95 5 3 72 69 31.91 0.45 6 3 73 70 27.61 0.75 7 3 76 73 19.02 1.02 8 4 7 3 261.32 0.12 9 4 8 4 256.47 2.56 10 4 24 20 82.60 14.92 11 4 69 65 32.59 0.40 12 5 8 3 261.33 0.13 13 5 9 4 256.47 2.56 14 6 9 3 255.73 2.93 15 6 10 4 246.55 1.36 16 6 49 43 76.42 9.05 17 6 50 44 76.35 9.03 18 7 10 3 261.44 0.08 19 7 11 4 246.64 1.30 20 7 46 39 76.70 9.19 21 7 50 43 76.36 9.02 22 7 68 61 54.44 0.93 23 7 69 62 54.26 0.97 24 7 72 65 47.13 0.26 25 8 11 3 252.03 1.76 26 8 12 4 243.88 0.08 27 8 22 14 87.69 12.59 28 8 23 15 87.59 12.58 29 8 24 16 87.53 12.57 30 8 65 57 60.73 0.76 31 8 69 61 58.36 0.08 32 9 12 3 259.22 1.23 33 9 13 4 247.33 1.65 34 10 13 3 261.68 0.01 35 10 14 4 252.85 4.41 36 10 42 32 79.03 8.17 37 10 45 35 78.94 8.13 38 10 46 36 78.86 8.15 39 10 49 39 78.60 8.03 40 11 14 3 257.25 2.21 41 11 15 4 252.93 4.37 42 11 22 11 87.91 12.51 43 11 28 17 87.48 12.46 44 11 32 21 87.73 12.38 45 11 42 31 79.01 8.17 46 11 65 54 67.59 2.53 47 11 68 57 60.87 0.83 48 12 15 3 258.05 1.81 49 12 16 4 243.40 0.01 50 12 17 5 213.84 6.08 51 12 22 10 87.90 12.51 52 13 16 3 257.24 2.21 53 14 41 27 79.18 8.14 54 14 42 28 79.06 8.20 55 14 45 31 79.03 8.18 56 15 28 13 87.75 12.35 57 15 32 17 87.98 12.38 58 15 34 19 87.62 12.29 59 15 38 23 80.72 8.88 60 15 42 27 79.19 8.14 61 17 21 4 258.09 1.07 62 17 22 5 250.62 2.56 63 17 32 15 93.77 9.73 64 18 21 3 271.58 1.11 65 18 22 4 262.39 0.52 66 19 22 3 265.85 0.45 67 20 23 3 292.18 1.02 68 21 26 5 212.83 10.69 69 21 32 11 118.66 1.35 70 22 32 10 139.07 0.70 71 22 65 43 86.36 2.36 72 23 26 3 245.16 1.24 73 23 65 42 86.47 2.35 74 24 65 41 86.44 2.33 75 24 66 42 86.42 2.33 76 24 69 45 86.42 2.32 77 26 31 5 157.78 1.50 78 26 32 6 157.77 1.49 79 26 64 38 101.46 4.81 80 26 65 39 101.38 4.80 81 27 30 3 240.90 4.54 82 27 31 4 190.56 0.68 83 27 32 5 161.08 3.14 84 27 63 36 101.55 4.82 85 27 64 37 101.45 4.81 86 28 32 4 178.72 5.25 87 28 33 5 164.91 1.66 88 28 34 6 157.71 1.48 89 28 39 11 156.28 1.01 90 28 42 14 147.56 0.28 91 28 62 34 101.62 4.84 92 28 63 35 101.57 4.84 93 28 64 36 101.54 4.86 94 28 65 37 101.51 4.88 95 28 68 40 99.17 6.06 96 29 33 4 164.48 1.44 97 29 34 5 157.72 1.49 98 29 39 10 157.19 1.41 99 32 65 33 101.59 4.86 100 34 38 4 246.84 2.46 101 34 39 5 246.83 2.46 102 35 38 3 261.88 0.77 103 35 39 4 251.58 0.76 104 36 39 3 257.65 1.35 105 36 40 4 250.96 0.42 106 37 40 3 262.62 0.40 107 37 41 4 250.96 0.43 108 38 41 3 260.14 0.84 109 38 42 4 251.22 0.57 110 39 42 3 256.08 2.44 111 39 43 4 251.49 0.17 112 40 43 3 258.06 0.26 113 40 44 4 253.66 1.23 114 41 44 3 257.34 0.62 115 41 45 4 253.17 1.48 116 42 45 3 255.55 0.29 117 42 46 4 253.18 1.49 118 43 46 3 261.26 2.56 119 43 47 4 253.18 1.49 120 43 54 11 126.33 1.49 121 43 59 16 103.39 5.69 122 44 47 3 255.56 0.29 123 44 48 4 253.15 1.50 124 45 48 3 268.70 4.65 125 45 49 4 253.09 1.47 126 46 49 3 268.97 4.52 127 46 50 4 251.09 0.76 128 46 54 8 149.96 2.42 129 46 68 22 89.77 12.63 130 46 72 26 84.45 15.20 131 47 50 3 269.20 4.40 132 47 51 4 244.69 0.18 133 47 52 5 203.05 13.18 134 47 53 6 156.82 5.85 135 47 54 7 151.71 3.29 136 48 51 3 248.68 1.02 137 50 72 22 84.52 15.26 138 50 77 27 68.46 21.45 139 51 77 26 74.44 18.45 140 52 71 19 91.45 13.01 141 52 72 20 87.27 14.04 142 53 71 18 91.50 13.03 143 54 59 5 206.29 8.52 144 54 62 8 174.24 3.99 145 54 71 17 91.48 13.03 146 55 58 3 261.67 1.17 147 55 59 4 252.68 2.35 148 55 71 16 123.40 2.02 149 56 59 3 254.94 1.21 150 57 61 4 258.64 0.60 151 58 61 3 270.03 2.06 152 58 62 4 258.64 0.60 153 58 71 13 124.36 1.05 154 58 75 17 118.67 0.35 155 59 62 3 265.89 0.29 156 60 63 3 306.43 1.06 157 61 67 6 213.92 5.00 158 62 67 5 213.91 5.00 159 62 68 6 189.81 5.33 160 62 71 9 179.66 0.27 161 63 67 4 252.34 1.25 162 64 67 3 258.25 0.04 163 64 68 4 253.18 1.66 164 65 68 3 259.72 1.60 165 65 69 4 253.17 1.67 166 66 69 3 261.69 0.61 167 66 70 4 251.36 1.73 168 67 70 3 263.05 2.24 169 67 71 4 258.19 1.13 170 68 71 3 259.51 0.47 171 68 72 4 258.71 0.87 172 69 72 3 260.04 1.23 173 69 73 4 254.02 3.21 174 70 73 3 259.00 0.86 175 70 74 4 258.19 1.14 176 71 74 3 259.24 0.74 177 71 75 4 258.50 0.97 178 72 75 3 267.74 1.62 179 72 76 4 258.50 0.97 180 73 76 3 267.75 1.62