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 3 33 30 50.06 0.14 2 3 84 81 51.87 0.69 3 3 85 82 49.74 0.07 4 4 31 27 50.05 0.14 5 4 32 28 52.86 0.23 6 4 83 79 52.58 0.35 7 4 85 81 52.77 0.27 8 5 83 78 53.01 0.39 9 5 85 80 52.91 0.31 10 5 86 81 50.41 0.04 11 6 29 23 53.26 0.42 12 6 30 24 53.78 0.27 13 6 31 25 53.70 0.21 14 6 35 29 52.84 0.34 15 6 81 75 50.11 0.12 16 6 82 76 53.20 0.41 17 6 83 77 53.30 0.38 18 6 86 80 53.33 0.24 19 6 87 81 52.84 0.33 20 6 88 82 49.97 0.18 21 7 29 22 53.87 0.27 22 7 30 23 53.87 0.28 23 7 88 81 52.92 0.30 24 8 11 3 232.48 2.19 25 8 27 19 53.65 0.29 26 8 28 20 53.88 0.28 27 8 29 21 53.88 0.28 28 8 88 80 53.83 0.24 29 8 89 81 53.56 0.32 30 8 90 82 52.87 0.29 31 9 28 19 53.99 0.25 32 9 30 21 54.06 0.27 33 10 27 17 53.98 0.26 34 10 28 18 54.01 0.24 35 11 90 79 53.93 0.25 36 12 26 14 54.02 0.24 37 12 27 15 54.08 0.27 38 12 39 27 54.02 0.25 39 12 77 65 53.93 0.24 40 12 78 66 54.00 0.24 41 12 79 67 54.02 0.25 42 12 90 78 54.02 0.25 43 12 91 79 53.98 0.25 44 12 92 80 53.85 0.24 45 13 25 12 54.06 0.26 46 13 92 79 53.95 0.24 47 14 25 11 54.21 0.32 48 14 92 78 53.97 0.24 49 14 93 79 53.84 0.24 50 15 24 9 54.22 0.32 51 15 25 10 54.23 0.32 52 15 93 78 54.01 0.25 53 15 94 79 53.85 0.24 54 15 95 80 53.85 0.24 55 16 95 79 53.85 0.24 56 16 97 81 53.84 0.24 57 17 21 4 200.48 3.31 58 17 22 5 189.15 1.01 59 17 23 6 130.65 18.94 60 17 69 52 86.44 16.46 61 17 94 77 54.07 0.26 62 17 95 78 53.98 0.26 63 17 96 79 53.84 0.24 64 17 97 80 53.84 0.24 65 18 21 3 211.97 1.23 66 18 69 51 93.21 19.82 67 18 97 79 53.86 0.24 68 19 69 50 96.11 21.27 69 19 70 51 90.56 18.50 70 19 96 77 54.05 0.25 71 19 97 78 53.90 0.22 72 19 98 79 53.48 0.30 73 20 68 48 101.56 22.75 74 20 69 49 100.32 23.38 75 21 68 47 101.63 22.78 76 21 69 48 101.63 22.78 77 22 65 43 106.89 20.37 78 22 66 44 105.89 20.86 79 22 67 45 103.00 22.20 80 22 68 46 102.46 22.46 81 22 69 47 102.44 22.47 82 23 65 42 106.89 20.37 83 23 66 43 106.17 20.72 84 23 69 46 106.12 20.70 85 23 94 71 54.34 0.14 86 24 63 39 110.08 20.94 87 24 64 40 107.87 20.00 88 24 65 41 106.92 20.36 89 25 39 14 158.80 1.18 90 25 63 38 150.29 1.07 91 25 64 39 109.94 20.99 92 25 77 52 106.02 20.52 93 25 92 67 62.70 1.15 94 25 93 68 62.70 1.15 95 25 94 69 61.44 1.66 96 26 39 13 161.23 2.37 97 26 57 31 162.77 2.54 98 26 61 35 161.27 2.36 99 26 62 36 160.78 2.14 100 26 63 37 150.41 1.05 101 27 39 12 161.25 2.36 102 27 61 34 162.66 2.60 103 27 62 35 161.24 2.36 104 27 79 52 112.89 17.08 105 28 58 30 164.65 1.73 106 28 60 32 164.56 1.69 107 28 61 33 162.03 2.19 108 29 35 6 182.63 2.32 109 29 56 27 165.96 1.08 110 29 60 31 164.67 1.72 111 29 81 52 120.56 13.21 112 29 88 59 85.00 4.56 113 30 35 5 188.40 5.17 114 30 60 30 173.06 2.46 115 31 34 3 220.99 1.78 116 31 35 4 194.81 1.97 117 31 83 52 138.66 4.17 118 32 83 51 144.22 1.40 119 33 83 50 144.22 1.39 120 33 84 51 144.21 1.39 121 35 81 46 144.22 1.39 122 35 82 47 144.18 1.36 123 35 83 48 143.49 1.02 124 36 81 45 144.24 1.38 125 36 82 46 143.77 1.16 126 37 54 17 266.27 2.06 127 37 79 42 144.34 1.37 128 37 80 43 144.26 1.36 129 38 79 41 144.34 1.36 130 38 80 42 144.30 1.38 131 39 54 15 360.34 0.08 132 39 64 25 259.99 0.79 133 39 77 38 145.94 0.60 134 39 78 39 144.66 1.20 135 39 79 40 144.57 1.24 136 40 77 37 145.98 0.55 137 40 78 38 144.66 1.20 138 40 80 40 144.65 1.20 139 41 66 25 358.46 1.76 140 41 72 31 175.76 1.45 141 41 73 32 167.53 3.02 142 41 75 34 146.41 0.55 143 41 76 35 146.38 0.55 144 41 77 36 146.12 0.53 145 42 74 32 167.53 3.02 146 42 75 33 146.41 0.55 147 42 76 34 146.38 0.55 148 51 73 22 197.38 2.84 149 64 77 13 146.02 0.53 150 66 69 3 236.37 0.84 151 66 73 7 173.15 0.33 152 66 77 11 146.16 0.43 153 66 94 28 99.02 21.08 154 69 73 4 197.84 3.06 155 69 94 25 99.09 21.11 156 69 96 27 97.50 21.46 157 70 73 3 210.11 0.80 158 70 96 26 97.92 21.63 159 71 74 3 218.79 3.54 160 71 96 25 97.95 21.62 161 73 94 21 100.75 20.30 162 73 96 23 98.80 20.98 163 74 94 20 100.88 20.24 164 74 95 21 99.05 21.09 165 74 96 22 98.95 21.05 166 75 93 18 100.91 20.24 167 75 94 19 100.79 20.25 168 76 92 16 100.95 20.25 169 76 93 17 100.86 20.21 170 77 91 14 100.98 20.23 171 77 92 15 100.92 20.23 172 77 93 16 100.86 20.21 173 77 94 17 100.83 20.21 174 78 89 11 104.53 18.48 175 78 90 12 103.90 18.78 176 78 91 13 100.90 20.19 177 79 89 10 104.19 18.63 178 79 90 11 103.90 18.75 179 80 87 7 108.09 17.68 180 80 88 8 106.42 17.75 181 80 89 9 103.99 18.70 182 81 87 6 108.48 17.87 183 81 88 7 108.00 17.72 184 82 86 4 186.04 1.55 185 82 87 5 108.48 17.87 186 83 86 3 215.58 0.47