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 5 9 4 344.18 0.83 2 5 22 17 126.30 6.79 3 7 21 14 126.64 6.90 4 7 22 15 127.42 6.27 5 7 23 16 126.41 6.79 6 8 19 11 140.50 0.54 7 8 20 12 140.47 0.53 8 8 21 13 128.25 6.59 9 9 19 10 140.56 0.56 10 9 20 11 140.47 0.53 11 9 22 13 140.52 0.55 12 10 17 7 142.16 0.10 13 10 18 8 141.69 0.04 14 10 19 9 140.68 0.50 15 11 17 6 158.78 8.21 16 11 18 7 142.16 0.10 17 11 20 9 141.62 0.07 18 11 65 54 53.61 0.84 19 11 69 58 40.27 6.95 20 12 17 5 158.78 8.21 21 13 47 34 53.66 0.84 22 13 55 42 56.59 0.62 23 13 65 52 53.64 0.85 24 14 17 3 354.55 0.12 25 14 65 51 53.65 0.84 26 16 106 90 9.57 1.30 27 18 105 87 9.34 1.20 28 18 106 88 9.29 1.22 29 20 25 5 341.60 1.61 30 21 24 3 359.61 2.00 31 21 25 4 341.60 1.61 32 22 25 3 349.40 2.29 33 22 26 4 340.64 1.15 34 22 34 12 233.24 10.22 35 23 26 3 349.52 2.35 36 25 28 3 344.53 2.38 37 25 83 58 14.16 0.96 38 28 32 4 339.44 1.69 39 28 33 5 325.61 5.09 40 29 32 3 351.45 0.55 41 30 33 3 359.62 4.88 42 30 34 4 332.90 1.39 43 30 43 13 156.09 1.17 44 31 34 3 338.61 1.26 45 31 35 4 321.19 4.46 46 31 36 5 321.19 4.46 47 31 41 10 174.44 7.73 48 32 76 44 43.75 0.24 49 34 41 7 181.02 4.46 50 34 42 8 171.81 9.05 51 34 43 9 156.34 1.41 52 35 41 6 181.03 4.47 53 35 42 7 181.02 4.46 54 35 52 17 153.19 0.42 55 35 76 41 51.95 1.78 56 36 39 3 339.33 1.81 57 36 40 4 278.83 1.63 58 36 41 5 181.03 4.47 59 36 76 40 53.40 2.10 60 37 40 3 339.00 1.30 61 37 42 5 249.63 20.79 62 44 48 4 325.12 4.15 63 45 48 3 354.67 0.77 64 46 51 5 281.44 5.23 65 46 52 6 266.13 4.26 66 46 65 19 239.25 1.94 67 46 69 23 239.08 1.97 68 47 52 5 266.13 4.27 69 47 53 6 259.09 0.75 70 47 55 8 259.09 0.76 71 47 65 18 239.29 1.91 72 48 51 3 341.67 0.98 73 48 53 5 304.12 6.37 74 49 53 4 328.94 7.34 75 50 53 3 362.68 0.66 76 50 63 13 253.65 1.92 77 51 63 12 253.75 1.86 78 52 55 3 455.91 0.94 79 52 62 10 253.80 1.86 80 52 63 11 253.66 1.92 81 52 64 12 253.66 1.92 82 52 65 13 253.36 1.86 83 52 68 16 253.62 1.93 84 53 63 10 253.85 1.85 85 54 59 5 269.49 2.93 86 54 63 9 253.89 1.87 87 54 64 10 253.85 1.89 88 54 65 11 253.85 1.89 89 55 65 10 253.87 1.88 90 56 59 3 342.91 2.81 91 57 66 9 253.89 1.89 92 59 64 5 254.00 1.88 93 59 67 8 253.94 1.90 94 60 67 7 253.97 1.88 95 60 71 11 253.91 1.90 96 61 64 3 341.18 1.98 97 61 67 6 295.83 0.35 98 64 67 3 339.80 2.17 99 64 68 4 337.72 1.09 100 65 68 3 344.16 0.09 101 65 69 4 337.73 1.09 102 66 69 3 342.92 2.16 103 66 70 4 337.73 1.09 104 67 70 3 347.60 1.64 105 67 71 4 334.90 0.30 106 67 74 7 298.22 0.20 107 68 78 10 122.78 3.10 108 69 78 9 122.80 3.09 109 69 79 10 122.78 3.09 110 69 80 11 122.78 3.10 111 70 78 8 147.99 4.99 112 70 80 10 122.68 3.16 113 70 106 36 46.81 3.98 114 71 74 3 377.31 2.94 115 71 78 7 174.34 1.71 116 72 84 12 143.47 7.23 117 74 77 3 358.30 3.66 118 74 78 4 343.94 2.63 119 77 82 5 327.24 2.03 120 77 85 8 322.27 3.38 121 78 81 3 343.55 1.49 122 78 82 4 337.51 2.52 123 79 82 3 350.50 0.60 124 79 83 4 344.64 1.04 125 80 83 3 346.00 1.65 126 80 84 4 344.62 1.04 127 80 98 18 166.97 0.17 128 81 84 3 346.74 2.09 129 81 85 4 344.63 1.05 130 82 85 3 357.43 0.34 131 82 86 4 344.38 1.18 132 83 86 3 344.36 1.16 133 83 87 4 341.63 2.52 134 83 97 14 167.46 0.04 135 83 98 15 177.60 5.01 136 84 87 3 344.36 1.17 137 84 88 4 341.62 2.53 138 84 98 14 177.88 5.15 139 85 88 3 343.58 2.89 140 86 97 11 236.99 11.90 141 87 90 3 350.45 1.93 142 87 93 6 265.23 0.36 143 87 94 7 265.29 2.00 144 87 97 10 236.99 11.90 145 88 94 6 324.88 1.18 146 89 94 5 335.41 1.03 147 90 93 3 347.49 0.14 148 90 94 4 347.49 0.14 149 91 94 3 347.50 0.14 150 91 95 4 344.08 1.56 151 92 95 3 347.70 0.24 152 92 96 4 338.51 1.21 153 93 96 3 348.53 1.19 154 93 97 4 338.51 1.21 155 94 97 3 346.68 0.26 156 94 98 4 324.31 3.40 157 94 99 5 317.70 1.99 158 95 99 4 310.68 4.44 159 95 101 6 310.68 4.44 160 95 102 7 272.00 2.10 161 95 103 8 205.15 3.88 162 96 103 7 205.13 3.89 163 96 104 8 205.13 3.88 164 97 104 7 205.15 3.87 165 99 103 4 212.72 0.10 166 100 106 6 226.09 14.36 167 101 106 5 213.38 0.25 168 101 107 6 205.10 3.88 169 102 106 4 307.14 4.03 170 102 107 5 204.78 3.90 171 103 106 3 329.63 2.54