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 10 8 141.53 1.42 2 3 6 3 153.17 4.10 3 3 7 4 157.12 2.12 4 3 113 110 24.23 0.93 5 4 7 3 157.48 1.75 6 4 8 4 154.28 0.71 7 5 8 3 159.21 1.08 8 5 9 4 154.30 0.70 9 5 113 108 28.28 2.33 10 6 9 3 159.88 0.75 11 6 10 4 153.19 0.16 12 7 10 3 156.91 0.73 13 7 11 4 151.64 0.61 14 8 11 3 159.81 0.71 15 8 12 4 145.36 0.16 16 8 13 5 144.58 0.23 17 8 54 46 68.30 0.78 18 8 108 100 52.56 1.35 19 9 12 3 158.39 2.48 20 9 13 4 143.56 0.09 21 9 33 24 121.52 1.34 22 9 51 42 93.42 1.73 23 10 33 23 121.42 1.39 24 10 34 24 121.57 1.32 25 10 35 25 121.57 1.32 26 10 46 36 120.67 1.36 27 11 35 24 121.67 1.27 28 11 41 30 121.88 1.37 29 11 44 33 120.76 1.36 30 11 46 35 120.71 1.34 31 12 41 29 122.12 1.34 32 12 44 32 120.78 1.37 33 12 45 33 120.69 1.36 34 12 46 34 120.68 1.36 35 12 47 35 120.67 1.36 36 13 33 20 122.93 1.15 37 13 47 34 120.73 1.34 38 13 49 36 120.72 1.34 39 13 50 37 120.58 1.28 40 13 51 38 115.55 0.79 41 13 54 41 103.59 1.08 42 14 17 3 173.94 0.47 43 14 25 11 123.19 1.04 44 14 29 15 123.01 1.11 45 14 46 32 121.09 1.46 46 14 47 33 120.81 1.36 47 14 48 34 120.73 1.34 48 15 49 34 120.73 1.33 49 15 50 35 120.63 1.30 50 15 51 36 120.67 1.32 51 17 48 31 121.63 1.27 52 18 48 30 122.14 1.15 53 18 80 62 122.31 1.17 54 19 48 29 122.31 1.17 55 19 80 61 122.39 1.20 56 19 101 82 123.31 1.03 57 20 25 5 123.36 1.02 58 20 48 28 123.24 0.99 59 20 82 62 123.31 1.02 60 20 99 79 123.34 1.02 61 20 101 81 123.32 1.02 62 21 25 4 133.57 4.01 63 22 25 3 157.88 2.96 64 22 99 77 154.51 1.20 65 23 99 76 154.51 1.20 66 25 46 21 193.65 0.94 67 25 48 23 169.49 0.23 68 25 82 57 174.13 1.00 69 25 99 74 192.58 0.40 70 26 82 56 244.62 1.02 71 26 97 71 222.68 0.29 72 26 98 72 222.49 0.21 73 26 99 73 200.76 1.18 74 27 96 69 233.17 0.75 75 27 97 70 231.86 0.91 76 29 46 17 233.52 0.61 77 30 35 5 341.83 0.91 78 30 36 6 336.73 3.47 79 30 41 11 233.91 0.65 80 30 44 14 233.84 0.62 81 30 46 16 233.69 0.63 82 30 97 67 233.34 0.73 83 31 36 5 336.73 3.48 84 33 46 13 233.59 0.58 85 35 41 6 233.95 0.65 86 35 44 9 233.91 0.66 87 35 46 11 233.88 0.65 88 36 97 61 321.81 6.46 89 40 86 46 233.95 0.59 90 42 85 43 233.90 0.61 91 42 86 44 233.92 0.62 92 43 84 41 233.84 0.62 93 43 85 42 233.85 0.62 94 44 83 39 233.84 0.62 95 44 84 40 233.75 0.62 96 45 81 36 233.86 0.62 97 45 82 37 233.82 0.62 98 45 83 38 233.75 0.60 99 46 81 35 233.81 0.61 100 46 82 36 233.78 0.61 101 46 84 38 233.73 0.64 102 47 54 7 341.55 0.26 103 47 79 32 233.88 0.62 104 47 80 33 233.82 0.61 105 47 81 34 233.72 0.63 106 47 106 59 282.20 0.46 107 48 80 32 233.79 0.61 108 48 81 33 233.71 0.62 109 48 82 34 233.71 0.62 110 49 79 30 233.80 0.61 111 49 80 31 233.75 0.61 112 53 79 26 233.46 0.67 113 54 79 25 231.88 0.74 114 57 73 16 233.49 0.66 115 57 74 17 233.46 0.67 116 57 75 18 224.65 0.48 117 57 79 22 218.55 0.42 118 58 73 15 233.46 0.67 119 60 73 13 233.66 0.64 120 60 74 14 233.52 0.67 121 60 75 15 233.38 0.69 122 60 76 16 227.51 1.87 123 61 73 12 233.71 0.62 124 61 74 13 233.52 0.67 125 61 76 15 233.37 0.70 126 62 70 8 241.96 1.47 127 62 72 10 233.84 0.62 128 62 73 11 233.72 0.62 129 63 72 9 233.88 0.61 130 63 73 10 233.84 0.62 131 63 74 11 233.79 0.60 132 63 107 44 233.97 0.60 133 64 72 8 243.60 0.66 134 65 109 44 233.50 0.67 135 71 109 38 233.51 0.67 136 71 110 39 233.49 0.68 137 71 111 40 233.46 0.67 138 72 107 35 233.68 0.64 139 72 108 36 233.52 0.67 140 72 109 37 233.44 0.67 141 73 107 34 233.52 0.67 142 73 108 35 233.49 0.68 143 73 110 37 233.21 0.77 144 74 105 31 233.69 0.64 145 74 106 32 233.52 0.67 146 74 107 33 233.23 0.77 147 75 79 4 227.72 2.41 148 75 105 30 233.50 0.68 149 75 106 31 233.48 0.68 150 76 105 29 233.50 0.68 151 77 105 28 232.56 0.69 152 78 103 25 233.47 0.68 153 78 104 26 222.50 0.21 154 78 105 27 221.39 0.28 155 79 103 24 228.25 0.89 156 79 104 25 222.49 0.23 157 79 106 27 212.70 0.18 158 80 101 21 233.59 0.62 159 80 102 22 232.55 0.57 160 80 103 23 221.33 0.31 161 81 101 20 230.06 1.80 162 81 102 21 222.50 0.22 163 81 104 23 214.13 0.50 164 81 106 25 173.22 0.53 165 82 99 17 233.48 0.68 166 82 100 18 224.86 0.80 167 82 101 19 220.81 0.57 168 83 99 16 232.55 0.57 169 83 100 17 221.40 0.29 170 84 97 13 233.46 0.69 171 84 98 14 231.67 1.01 172 85 97 12 233.48 0.68 173 85 98 13 233.33 0.67 174 86 90 4 290.44 11.02 175 86 96 10 233.75 0.61 176 86 97 11 233.50 0.67 177 87 90 3 342.56 0.14 178 87 96 9 233.80 0.60 179 87 97 10 233.72 0.60 180 87 98 11 233.67 0.60 181 90 94 4 341.07 0.11 182 90 95 5 234.01 0.60 183 90 96 6 234.00 0.60 184 111 115 4 153.29 1.41 185 112 115 3 164.61 0.48