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 23 28 5 243.60 1.65 2 23 29 6 225.86 0.46 3 23 32 9 232.31 2.98 4 23 53 30 102.28 31.12 5 23 64 41 78.50 23.24 6 24 29 5 260.29 0.70 7 24 64 40 80.14 22.55 8 24 97 73 16.88 0.18 9 25 28 3 263.22 0.35 10 25 29 4 260.30 0.70 11 26 29 3 261.41 1.26 12 26 30 4 265.84 2.08 13 26 48 22 114.22 30.77 14 26 49 23 112.86 31.44 15 27 30 3 266.94 1.53 16 27 31 4 266.95 1.53 17 28 31 3 267.98 1.02 18 28 32 4 266.95 1.53 19 29 32 3 267.99 1.02 20 29 33 4 267.98 1.02 21 29 48 19 118.12 29.03 22 29 49 20 118.12 29.03 23 29 51 22 118.02 29.00 24 29 52 23 118.01 29.00 25 29 53 24 118.00 29.00 26 29 64 35 97.95 18.98 27 29 92 63 55.69 2.17 28 30 33 3 271.34 0.66 29 30 44 14 126.86 24.95 30 30 45 15 122.11 27.23 31 30 48 18 118.02 29.00 32 32 53 21 128.41 23.81 33 32 54 22 128.54 23.73 34 33 36 3 259.37 1.01 35 33 44 11 128.94 23.91 36 33 47 14 128.95 23.92 37 33 48 15 128.93 23.91 38 33 52 19 128.82 23.86 39 33 53 20 128.64 23.77 40 33 54 21 128.57 23.74 41 33 61 28 115.86 17.34 42 34 54 20 128.83 23.68 43 35 54 19 128.97 23.63 44 36 40 4 266.86 2.00 45 36 42 6 242.88 3.90 46 36 44 8 129.31 23.80 47 36 47 11 129.33 23.80 48 36 54 18 129.11 23.70 49 36 59 23 128.53 23.34 50 36 61 25 128.36 23.26 51 37 40 3 263.79 0.47 52 37 54 17 129.29 23.70 53 37 58 21 134.31 20.52 54 37 59 22 128.62 23.34 55 41 73 32 119.42 7.53 56 41 74 33 119.40 7.52 57 41 75 34 121.56 2.48 58 42 47 5 257.22 2.94 59 42 73 31 119.42 7.53 60 42 77 35 106.85 6.58 61 43 46 3 262.34 0.38 62 43 47 4 261.47 0.82 63 44 47 3 269.50 1.54 64 44 48 4 261.47 0.83 65 45 48 3 269.50 1.54 66 45 49 4 259.81 1.69 67 46 49 3 264.82 0.81 68 46 50 4 260.37 1.42 69 46 79 33 110.59 8.51 70 47 50 3 264.81 0.81 71 47 51 4 264.81 0.81 72 47 52 5 254.41 4.31 73 47 61 14 153.60 8.47 74 47 73 26 131.16 1.66 75 47 79 32 110.58 8.51 76 48 51 3 261.74 0.72 77 48 52 4 251.32 2.60 78 49 92 43 76.56 12.60 79 50 79 29 110.62 8.52 80 50 80 30 110.59 8.53 81 50 83 33 110.59 8.53 82 50 92 42 76.58 12.58 83 50 93 43 76.54 12.60 84 51 63 12 157.30 10.45 85 51 64 13 157.30 10.46 86 51 92 41 76.55 12.60 87 52 61 9 157.45 10.40 88 52 62 10 157.41 10.43 89 52 63 11 157.31 10.46 90 52 70 18 156.72 10.63 91 52 73 21 156.62 10.60 92 52 79 27 110.70 8.55 93 52 83 31 110.66 8.56 94 53 61 8 157.52 10.43 95 53 62 9 157.41 10.43 96 53 64 11 157.31 10.47 97 54 57 3 336.19 2.03 98 54 58 4 284.69 1.25 99 54 59 5 232.81 2.19 100 54 60 6 197.98 2.10 101 54 61 7 157.52 10.44 102 55 60 5 207.85 2.65 103 55 61 6 177.93 0.29 104 55 62 7 177.87 0.26 105 57 60 3 273.34 0.94 106 59 71 12 156.68 10.64 107 59 72 13 156.68 10.64 108 59 73 14 156.65 10.65 109 60 69 9 156.93 10.68 110 60 70 10 156.79 10.68 111 60 71 11 156.69 10.63 112 61 69 8 156.84 10.69 113 61 70 9 156.71 10.63 114 61 73 12 156.66 10.64 115 62 67 5 185.47 1.59 116 62 68 6 156.98 10.69 117 62 69 7 156.72 10.63 118 63 66 3 262.39 3.18 119 63 67 4 206.18 6.07 120 63 68 5 182.61 1.78 121 63 83 20 110.73 8.58 122 63 90 27 85.80 17.16 123 64 67 3 261.17 2.56 124 64 92 28 77.78 13.16 125 64 97 33 74.98 13.04 126 65 90 25 91.84 17.12 127 65 91 26 85.75 17.14 128 65 92 27 77.80 13.17 129 65 97 32 75.10 12.98 130 66 83 17 110.75 8.58 131 66 87 21 110.16 8.78 132 66 90 24 88.79 18.65 133 68 86 18 110.31 8.79 134 68 87 19 110.19 8.78 135 69 86 17 110.34 8.79 136 70 73 3 348.74 0.47 137 70 82 12 110.77 8.58 138 70 86 16 110.62 8.63 139 73 77 4 250.23 2.06 140 73 79 6 212.80 0.89 141 73 82 9 193.03 0.14 142 74 77 3 265.05 2.02 143 77 82 5 253.55 1.23 144 78 81 3 260.63 2.31 145 78 82 4 257.78 0.79 146 79 82 3 269.27 1.01 147 79 83 4 257.79 0.78 148 80 83 3 269.27 1.01 149 80 84 4 256.66 0.21 150 80 93 13 89.91 19.25 151 81 84 3 267.34 0.01 152 81 85 4 257.72 0.73 153 82 85 3 266.55 2.39 154 82 86 4 257.72 0.74 155 83 86 3 266.81 0.80 156 83 87 4 256.61 0.24 157 83 90 7 221.38 2.06 158 83 93 10 184.35 1.83 159 84 87 3 258.76 1.32 160 84 88 4 243.12 4.53 161 84 93 9 184.35 1.83 162 85 88 3 270.71 0.78 163 87 90 3 271.87 0.20 164 90 93 3 262.69 1.25 165 90 94 4 253.34 0.41 166 91 94 3 259.97 2.61 167 91 95 4 253.34 0.41 168 91 96 5 212.72 0.26 169 91 97 6 212.74 0.26 170 92 95 3 263.48 0.85 171 92 97 5 229.80 7.81 172 95 98 3 260.93 3.10