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 6 4 250.72 1.21 2 3 6 3 263.01 4.94 3 3 7 4 254.06 0.45 4 3 50 47 57.54 7.19 5 3 72 69 29.12 0.33 6 3 73 70 25.68 0.42 7 4 7 3 258.94 0.42 8 4 8 4 250.72 1.22 9 4 69 65 31.71 0.70 10 5 8 3 256.25 1.38 11 5 9 4 250.69 1.25 12 6 9 3 260.57 0.40 13 6 10 4 250.02 3.57 14 6 49 43 60.44 6.81 15 6 50 44 59.02 7.52 16 7 10 3 263.81 3.33 17 7 11 4 236.56 5.80 18 7 46 39 60.86 6.60 19 7 50 43 60.70 6.71 20 7 69 62 36.01 0.18 21 7 72 65 36.10 0.13 22 8 11 3 263.81 3.33 23 8 12 4 236.53 5.80 24 9 13 4 236.80 5.84 25 10 13 3 255.93 1.55 26 10 14 4 238.05 5.76 27 10 42 32 70.17 8.79 28 10 46 36 61.48 6.33 29 10 49 39 61.50 6.33 30 11 14 3 253.97 2.20 31 11 15 4 237.19 5.34 32 11 16 5 200.87 6.45 33 11 22 11 139.60 0.56 34 11 28 17 96.36 9.94 35 11 42 31 71.27 8.22 36 11 65 54 50.02 0.57 37 12 16 4 191.78 1.94 38 12 17 5 200.88 6.45 39 12 19 7 157.84 1.43 40 12 22 10 150.29 4.80 41 14 17 3 274.28 0.17 42 14 42 28 71.78 8.15 43 14 45 31 71.80 8.15 44 15 21 6 177.41 4.61 45 15 28 13 96.37 9.94 46 15 32 17 94.29 11.02 47 15 34 19 90.38 12.69 48 15 38 23 76.46 10.23 49 15 39 24 76.26 10.33 50 15 42 27 75.77 10.13 51 16 19 3 241.47 7.45 52 16 20 4 206.69 6.29 53 16 21 5 175.72 5.45 54 16 22 6 155.46 2.98 55 17 21 4 231.15 8.21 56 20 23 3 316.36 2.16 57 21 32 11 97.42 11.21 58 22 32 10 111.82 11.10 59 23 26 3 250.04 1.80 60 23 28 5 168.96 1.90 61 23 31 8 148.05 1.17 62 23 32 9 141.44 2.13 63 24 64 40 54.87 1.25 64 24 66 42 52.23 2.06 65 24 69 45 54.54 1.19 66 25 64 39 54.91 1.24 67 26 31 5 216.07 10.87 68 26 32 6 172.48 1.30 69 26 64 38 56.10 1.83 70 27 30 3 273.26 0.79 71 27 31 4 243.75 2.42 72 28 32 4 243.19 2.70 73 28 34 6 153.09 3.58 74 28 39 11 108.17 11.88 75 28 42 14 141.37 2.16 76 28 65 37 62.54 5.00 77 29 33 4 166.78 3.25 78 29 34 5 165.84 2.83 79 34 39 5 237.00 0.74 80 35 38 3 262.91 2.60 81 35 39 4 244.62 4.54 82 36 39 3 258.74 2.52 83 36 40 4 255.34 0.82 84 37 40 3 263.01 0.38 85 37 41 4 252.44 2.27 86 38 41 3 255.37 0.83 87 38 42 4 254.59 1.23 88 39 42 3 264.98 0.89 89 39 43 4 256.39 2.12 90 39 65 26 93.78 20.62 91 40 43 3 256.74 1.97 92 40 44 4 260.48 3.83 93 40 56 16 112.64 11.40 94 40 59 19 102.23 16.41 95 40 60 20 102.34 16.47 96 41 44 3 262.32 2.92 97 41 45 4 261.88 3.14 98 42 45 3 262.32 2.92 99 42 46 4 260.48 3.83 100 43 46 3 266.56 0.79 101 43 47 4 264.68 1.73 102 43 54 11 132.11 2.60 103 43 59 16 102.52 16.45 104 43 65 22 93.16 21.02 105 43 68 25 90.16 22.50 106 44 47 3 260.82 0.20 107 44 48 4 257.99 1.62 108 44 56 12 130.57 2.87 109 45 48 3 260.83 0.20 110 45 49 4 257.47 1.88 111 46 49 3 264.35 1.56 112 46 50 4 257.22 2.00 113 46 54 8 153.10 0.96 114 46 68 22 90.20 22.53 115 46 72 26 88.60 23.28 116 47 51 4 231.50 1.18 117 47 52 5 172.60 1.42 118 47 53 6 175.99 1.70 119 47 54 7 149.29 2.86 120 48 51 3 236.41 4.84 121 50 72 22 86.26 24.48 122 52 71 19 89.36 22.94 123 52 72 20 89.34 22.93 124 52 75 23 86.17 24.43 125 54 58 4 245.72 0.39 126 54 59 5 245.78 0.35 127 55 58 3 258.26 1.64 128 55 59 4 255.59 2.97 129 56 60 4 247.40 1.15 130 57 60 3 261.44 0.04 131 57 61 4 247.38 1.14 132 58 61 3 260.67 0.14 133 58 62 4 245.39 0.18 134 58 71 13 151.81 0.08 135 59 62 3 260.65 0.73 136 62 65 3 284.52 0.18 137 62 67 5 251.00 0.23 138 62 68 6 235.22 4.84 139 62 71 9 222.53 1.51 140 63 67 4 252.91 1.12 141 64 67 3 267.50 1.24 142 64 68 4 254.84 1.29 143 65 68 3 262.89 0.89 144 65 69 4 255.33 1.54 145 66 69 3 259.75 0.68 146 66 70 4 257.45 0.12 147 67 70 3 258.67 0.72 148 67 71 4 255.28 1.20 149 68 71 3 257.48 0.10 150 68 72 4 258.21 0.16 151 69 72 3 264.91 0.04 152 69 73 4 263.30 0.77 153 70 73 3 267.36 1.94 154 70 74 4 260.14 0.81 155 71 74 3 260.29 0.77 156 71 75 4 260.25 0.76 157 72 75 3 262.12 0.14 158 72 76 4 260.14 0.82 159 73 76 3 259.70 1.03