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 1 29 28 36.76 0.77 2 1 30 29 36.48 0.64 3 1 77 76 36.77 0.75 4 2 25 23 46.74 0.14 5 2 30 28 37.24 0.80 6 2 83 81 30.26 0.53 7 3 84 81 31.18 0.07 8 3 85 82 27.41 0.60 9 4 22 18 46.80 0.14 10 4 23 19 46.81 0.15 11 4 24 20 46.78 0.16 12 4 25 21 46.80 0.15 13 4 30 26 46.04 0.21 14 4 33 29 39.77 0.16 15 4 73 69 33.97 0.48 16 4 75 71 37.27 0.77 17 4 85 81 31.77 0.36 18 5 22 17 46.81 0.14 19 5 23 18 46.81 0.15 20 6 20 14 50.62 0.01 21 6 21 15 50.41 0.02 22 6 22 16 46.82 0.14 23 6 73 67 37.31 0.76 24 6 85 79 37.31 0.76 25 6 87 81 36.53 0.61 26 7 20 13 50.68 0.02 27 7 21 14 50.65 0.02 28 7 23 16 50.69 0.05 29 8 18 10 80.00 0.14 30 8 88 80 37.15 0.72 31 8 89 81 31.18 0.93 32 8 90 82 31.18 0.93 33 9 18 9 80.02 0.14 34 9 19 10 79.87 0.19 35 9 20 11 64.39 6.76 36 9 21 12 64.36 6.74 37 10 18 8 80.02 0.14 38 10 19 9 79.95 0.14 39 10 90 80 37.26 0.75 40 10 91 81 36.53 0.61 41 10 92 82 32.45 0.18 42 11 19 8 80.00 0.15 43 13 17 4 292.47 2.29 44 13 19 6 255.51 0.49 45 14 17 3 292.48 2.29 46 15 65 50 50.52 0.06 47 15 91 76 37.45 0.70 48 15 92 77 37.24 0.76 49 15 93 78 36.53 0.60 50 16 61 45 54.96 1.27 51 16 62 46 54.95 1.28 52 16 63 47 53.30 1.09 53 17 59 42 60.35 1.09 54 17 60 43 60.20 1.02 55 17 61 44 54.87 1.23 56 18 59 41 60.36 1.09 57 18 60 42 60.15 1.05 58 18 63 45 60.14 1.05 59 18 89 71 45.25 3.56 60 18 90 72 37.37 0.74 61 18 91 73 35.12 0.06 62 19 58 39 71.06 0.19 63 19 59 40 60.41 1.12 64 20 35 15 71.09 0.18 65 20 57 37 71.45 0.30 66 20 58 38 71.11 0.17 67 20 87 67 65.27 1.34 68 21 56 35 71.85 0.21 69 21 57 36 71.51 0.34 70 22 33 11 72.08 0.09 71 22 35 13 71.73 0.07 72 22 51 29 72.22 0.12 73 22 55 33 72.17 0.15 74 22 56 34 71.94 0.19 75 22 57 35 71.86 0.20 76 22 58 36 71.94 0.17 77 22 73 51 71.61 0.09 78 24 33 9 72.25 0.07 79 25 30 5 261.56 2.05 80 28 78 50 162.28 0.43 81 29 77 48 160.63 0.07 82 29 78 49 162.24 0.42 83 30 33 3 427.40 0.15 84 30 75 45 139.22 0.04 85 30 76 46 161.74 0.50 86 30 77 47 161.88 0.58 87 31 53 22 199.07 1.05 88 31 76 45 162.53 0.38 89 31 77 46 162.50 0.38 90 31 78 47 162.50 0.39 91 32 50 18 216.30 1.43 92 32 75 43 162.61 0.40 93 32 76 44 162.53 0.38 94 33 50 17 216.30 1.43 95 33 51 18 216.22 1.45 96 33 52 19 216.18 1.44 97 33 53 20 212.66 0.27 98 33 55 22 209.61 0.13 99 33 73 40 162.75 0.42 100 33 74 41 162.65 0.38 101 33 75 42 162.61 0.40 102 34 48 14 217.50 0.98 103 34 49 15 217.41 0.98 104 34 50 16 216.29 1.44 105 34 51 17 216.29 1.44 106 34 73 39 162.78 0.41 107 34 74 40 162.66 0.38 108 34 76 42 162.64 0.39 109 35 48 13 217.51 0.99 110 35 49 14 217.47 0.98 111 35 51 16 217.38 0.97 112 35 58 23 199.11 1.02 113 35 60 25 189.25 0.58 114 35 72 37 162.84 0.42 115 35 73 38 162.78 0.41 116 35 87 52 162.48 0.41 117 36 46 10 217.93 1.01 118 36 47 11 217.75 0.99 119 36 48 12 217.51 0.99 120 36 71 35 164.07 1.01 121 36 72 36 162.96 0.47 122 36 74 38 162.84 0.41 123 37 46 9 217.94 1.00 124 37 47 10 217.86 1.02 125 37 48 11 217.84 1.01 126 37 49 12 217.85 1.02 127 37 60 23 190.60 0.10 128 37 63 26 183.22 0.65 129 37 69 32 178.52 0.58 130 37 70 33 175.56 1.27 131 37 71 34 167.86 1.37 132 37 89 52 162.43 0.40 133 38 42 4 311.31 1.62 134 38 43 5 272.66 0.92 135 38 44 6 258.36 1.84 136 38 46 8 217.94 1.00 137 38 69 31 178.53 0.58 138 38 70 32 178.04 0.35 139 39 42 3 329.26 0.76 140 39 64 25 183.06 0.58 141 39 67 28 182.46 0.57 142 39 68 29 180.12 0.18 143 39 69 30 178.53 0.58 144 40 68 28 180.71 0.11 145 40 69 29 178.57 0.57 146 40 70 30 178.56 0.58 147 41 67 26 182.77 0.67 148 43 70 27 178.97 0.72 149 46 72 26 177.61 0.58 150 49 58 9 220.31 1.78 151 51 55 4 282.31 0.57 152 51 58 7 221.94 0.96 153 52 55 3 305.69 4.55 154 60 63 3 339.87 0.57 155 60 89 29 162.49 0.42 156 63 69 6 272.87 0.44 157 63 89 26 162.54 0.42 158 63 91 28 159.68 0.41 159 64 67 3 308.55 0.77 160 64 69 5 295.86 1.24 161 64 91 27 162.07 0.55 162 65 93 28 158.89 0.23 163 66 91 25 162.41 0.44 164 66 92 26 160.61 0.47 165 67 90 23 162.45 0.43 166 67 91 24 162.41 0.42 167 68 88 20 162.54 0.40 168 68 89 21 162.50 0.40 169 68 90 22 162.37 0.40 170 69 88 19 162.51 0.40 171 69 89 20 162.48 0.40 172 69 91 22 162.26 0.36 173 70 87 17 162.52 0.40 174 70 88 18 162.41 0.39 175 71 86 15 162.52 0.40 176 71 87 16 162.47 0.40 177 71 88 17 162.42 0.39 178 71 89 18 162.39 0.38 179 72 84 12 162.55 0.40 180 72 85 13 162.52 0.40 181 72 86 14 162.47 0.40 182 72 87 15 162.45 0.39 183 73 85 12 162.50 0.40 184 73 87 14 162.45 0.39 185 74 82 8 244.49 3.96 186 74 83 9 194.25 16.26 187 74 84 10 191.46 14.88 188 75 82 7 244.49 3.96 189 75 83 8 231.50 2.37 190 76 81 5 255.07 1.20 191 76 82 6 244.50 3.96 192 77 81 4 264.58 3.56 193 77 82 5 255.06 1.20 194 77 83 6 255.06 1.20