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 3 256.32 1.53 2 2 6 4 246.97 1.15 3 3 6 3 254.78 0.76 4 3 7 4 246.97 1.15 5 3 50 47 84.70 0.86 6 3 72 69 29.40 0.41 7 3 73 70 27.16 0.51 8 4 7 3 260.43 0.21 9 4 8 4 250.25 0.33 10 4 69 65 38.23 1.51 11 4 73 69 30.45 0.11 12 5 8 3 256.42 1.18 13 5 9 4 250.25 0.33 14 6 9 3 253.24 1.81 15 6 10 4 246.40 1.60 16 6 49 43 86.55 0.85 17 6 50 44 86.54 0.85 18 7 10 3 256.88 3.64 19 7 11 4 246.47 1.55 20 7 46 39 86.58 0.87 21 7 50 43 86.97 0.67 22 7 68 61 51.27 1.44 23 7 69 62 51.19 1.40 24 7 72 65 40.38 1.22 25 8 11 3 251.44 4.00 26 8 12 4 245.72 1.17 27 8 19 11 138.77 8.92 28 8 22 14 111.27 2.31 29 8 24 16 110.03 2.93 30 8 65 57 63.47 0.34 31 8 69 61 57.81 0.38 32 9 12 3 247.64 0.21 33 9 13 4 245.74 1.16 34 9 19 10 135.05 3.62 35 10 13 3 261.69 1.25 36 10 14 4 245.73 1.16 37 10 42 32 87.28 0.62 38 10 45 35 87.20 0.58 39 10 46 36 87.16 0.59 40 10 49 39 87.03 0.66 41 10 50 40 87.06 0.65 42 11 14 3 256.98 3.58 43 11 15 4 245.72 1.16 44 11 22 11 115.38 2.71 45 11 28 17 100.47 1.72 46 11 32 21 100.52 1.71 47 11 42 31 87.28 0.62 48 11 65 54 63.66 0.33 49 11 68 57 63.33 0.18 50 12 15 3 261.95 1.09 51 12 16 4 239.85 0.04 52 12 17 5 208.71 4.21 53 12 19 7 146.82 4.96 54 12 22 10 115.39 2.71 55 13 16 3 249.11 0.48 56 14 41 27 87.55 0.65 57 14 42 28 87.47 0.67 58 14 45 31 87.42 0.67 59 15 28 13 100.87 1.53 60 15 32 17 100.53 1.71 61 15 34 19 100.25 1.66 62 15 38 23 97.25 0.42 63 15 42 27 87.54 0.64 64 17 21 4 254.74 0.10 65 17 22 5 246.04 1.75 66 17 32 15 100.64 1.66 67 18 21 3 267.61 3.43 68 18 22 4 265.10 4.69 69 19 22 3 266.60 3.93 70 20 23 3 280.24 2.27 71 21 26 5 239.81 3.35 72 21 32 11 117.03 1.64 73 22 65 43 80.29 1.69 74 23 26 3 246.66 3.54 75 23 65 42 80.64 1.75 76 24 65 41 80.50 1.62 77 24 66 42 79.43 1.27 78 24 69 45 77.08 1.04 79 25 64 39 81.47 1.52 80 26 31 5 152.81 0.72 81 26 32 6 152.81 0.72 82 26 64 38 81.48 1.52 83 26 65 39 81.45 1.52 84 27 30 3 257.85 2.69 85 27 31 4 153.27 0.51 86 27 32 5 152.84 0.72 87 27 63 36 81.50 1.52 88 27 64 37 81.48 1.52 89 28 32 4 182.19 13.95 90 28 33 5 152.84 0.72 91 28 34 6 152.79 0.73 92 28 39 11 145.46 2.65 93 28 42 14 140.71 0.28 94 28 62 34 81.52 1.51 95 28 63 35 81.48 1.51 96 28 64 36 81.47 1.52 97 28 65 37 81.45 1.51 98 28 68 40 80.36 1.01 99 29 33 4 152.84 0.71 100 29 34 5 152.78 0.72 101 29 39 10 152.49 0.78 102 32 65 33 81.45 1.52 103 34 38 4 233.54 2.62 104 34 39 5 235.83 1.48 105 35 38 3 250.80 1.03 106 35 39 4 249.03 1.79 107 36 39 3 260.92 1.20 108 36 40 4 249.04 1.80 109 37 40 3 249.58 1.64 110 37 41 4 249.01 1.82 111 38 41 3 268.63 3.03 112 38 42 4 249.11 1.88 113 39 42 3 261.32 0.62 114 39 43 4 249.06 1.86 115 40 43 3 257.02 0.17 116 40 44 4 250.94 0.96 117 41 44 3 253.99 0.56 118 41 45 4 250.94 0.96 119 42 45 3 250.94 0.96 120 42 46 4 250.94 0.96 121 43 46 3 251.86 1.42 122 43 47 4 250.94 0.96 123 43 54 11 130.29 5.40 124 43 59 16 81.52 1.50 125 44 47 3 258.27 1.25 126 44 48 4 244.34 2.61 127 45 48 3 258.52 0.74 128 45 49 4 243.58 2.68 129 46 49 3 257.34 1.14 130 46 50 4 241.21 1.50 131 46 54 8 181.55 15.96 132 46 62 16 96.42 5.96 133 46 68 22 63.51 0.27 134 47 50 3 260.63 0.52 135 47 51 4 237.47 1.42 136 47 52 5 203.98 4.74 137 47 53 6 174.56 9.97 138 47 54 7 152.12 1.24 139 48 51 3 239.41 2.40 140 50 72 22 48.97 0.18 141 53 71 18 88.25 11.55 142 54 58 4 254.12 0.38 143 54 59 5 242.25 1.37 144 54 62 8 226.28 1.98 145 54 71 17 87.79 11.78 146 55 58 3 254.61 0.14 147 55 59 4 254.34 0.48 148 55 71 16 105.50 2.97 149 56 59 3 255.67 0.52 150 56 60 4 254.36 0.47 151 57 60 3 260.46 0.55 152 57 61 4 260.46 0.55 153 58 61 3 261.83 0.14 154 58 62 4 260.45 0.55 155 58 71 13 114.69 1.54 156 58 75 17 105.50 2.98 157 59 62 3 262.22 0.34 158 60 63 3 283.68 2.83 159 61 67 6 195.27 6.96 160 62 67 5 192.88 4.33 161 62 68 6 159.01 1.30 162 62 71 9 159.00 1.31 163 63 67 4 252.27 2.77 164 64 67 3 252.28 2.77 165 64 68 4 254.43 1.69 166 65 68 3 252.39 0.66 167 65 69 4 252.40 0.66 168 66 69 3 254.53 0.41 169 66 70 4 252.39 0.66 170 67 70 3 258.27 1.46 171 67 71 4 252.39 0.66 172 68 71 3 258.97 1.35 173 68 72 4 249.71 3.10 174 69 72 3 258.79 1.44 175 69 73 4 247.30 4.31 176 70 73 3 254.37 0.78 177 70 74 4 247.30 4.31 178 71 74 3 254.62 0.66 179 71 75 4 255.81 0.06 180 72 75 3 254.50 0.59 181 72 76 4 255.30 0.20 182 73 76 3 259.09 1.70