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 37 34 110.18 7.65 2 3 40 37 112.60 8.96 3 4 9 5 253.49 0.54 4 4 10 6 237.41 0.69 5 4 14 10 232.44 3.18 6 4 40 36 117.31 11.13 7 5 9 4 311.60 0.92 8 5 40 35 117.33 11.14 9 5 44 39 117.32 11.15 10 6 9 3 331.17 4.70 11 6 10 4 315.79 0.89 12 6 44 38 118.86 11.91 13 7 10 3 316.52 0.52 14 7 15 8 266.88 6.09 15 7 44 37 118.87 11.91 16 7 45 38 118.87 11.91 17 7 76 69 94.48 0.16 18 7 83 76 55.52 0.56 19 7 84 77 55.23 0.53 20 8 82 74 58.00 0.40 21 8 83 75 57.72 0.53 22 8 85 77 55.09 0.59 23 9 14 5 310.38 0.30 24 9 85 76 54.99 0.64 25 10 14 4 305.37 2.20 26 10 15 5 304.67 2.39 27 10 18 8 297.36 0.41 28 10 40 30 139.10 11.79 29 10 44 34 136.83 12.50 30 10 84 74 55.23 0.53 31 10 85 75 54.98 0.64 32 11 14 3 316.42 1.59 33 11 15 4 310.42 0.32 34 11 84 73 55.32 0.51 35 11 85 74 55.00 0.64 36 12 15 3 313.72 1.33 37 12 16 4 311.98 0.47 38 12 69 57 107.78 4.48 39 12 73 61 105.26 3.29 40 12 84 72 55.37 0.50 41 13 16 3 319.18 0.35 42 13 17 4 312.63 0.80 43 14 17 3 316.35 1.06 44 14 18 4 312.66 0.81 45 15 18 3 315.25 0.49 46 15 19 4 315.25 0.49 47 15 41 26 147.32 10.97 48 15 44 29 147.66 11.20 49 15 45 30 147.24 11.02 50 15 69 54 111.97 6.57 51 15 72 57 111.60 6.45 52 15 84 69 55.37 0.50 53 16 19 3 315.95 0.15 54 16 20 4 315.26 0.50 55 16 65 49 112.34 6.41 56 16 69 53 112.12 6.49 57 17 20 3 317.01 0.38 58 17 21 4 308.75 0.07 59 18 21 3 317.01 0.38 60 18 22 4 310.69 0.89 61 18 40 22 148.25 10.96 62 18 44 26 148.24 10.96 63 19 22 3 314.87 0.12 64 19 23 4 313.79 0.66 65 19 41 22 148.19 10.93 66 19 54 35 147.34 10.86 67 19 65 46 112.52 6.49 68 19 68 49 112.56 6.54 69 19 69 50 112.45 6.50 70 20 23 3 313.78 2.39 71 20 24 4 310.74 0.86 72 20 65 45 112.61 6.53 73 21 24 3 317.01 0.77 74 21 25 4 310.74 0.86 75 21 37 16 148.84 10.75 76 22 25 3 317.11 0.14 77 22 26 4 313.96 0.77 78 22 34 12 148.87 10.75 79 22 37 15 148.83 10.75 80 22 38 16 148.83 10.75 81 22 41 19 148.78 10.76 82 22 54 32 148.23 10.48 83 22 55 33 148.38 10.53 84 23 26 3 311.79 1.85 85 23 27 4 311.07 2.21 86 23 65 42 113.59 6.81 87 24 27 3 319.89 0.35 88 24 28 4 307.39 0.38 89 25 28 3 306.31 0.17 90 25 33 8 148.94 10.73 91 25 34 9 148.92 10.73 92 25 37 12 148.92 10.73 93 26 34 8 148.93 10.73 94 26 55 29 148.53 10.54 95 31 34 3 297.53 2.36 96 31 35 4 296.07 1.63 97 32 36 4 313.27 1.28 98 33 36 3 317.22 0.69 99 33 37 4 312.66 1.58 100 34 37 3 313.28 1.28 101 34 38 4 312.67 1.58 102 34 55 21 178.13 0.66 103 35 38 3 313.42 2.63 104 35 39 4 308.80 0.35 105 36 39 3 319.53 0.18 106 36 40 4 308.85 0.32 107 37 40 3 315.34 1.92 108 37 41 4 308.72 0.24 109 38 41 3 313.72 1.21 110 38 42 4 308.81 0.29 111 38 51 13 178.27 0.72 112 38 54 16 178.29 0.73 113 38 55 17 178.28 0.72 114 39 42 3 312.88 0.59 115 39 43 4 311.74 1.18 116 40 43 3 316.68 1.29 117 40 44 4 311.75 1.18 118 41 44 3 319.47 2.38 119 41 45 4 311.75 1.18 120 41 50 9 181.45 0.94 121 41 51 10 179.80 0.12 122 41 53 12 179.80 0.12 123 41 54 13 179.75 0.10 124 41 68 27 137.69 19.12 125 41 72 31 136.71 19.59 126 42 45 3 321.37 1.43 127 42 46 4 310.55 1.78 128 42 50 8 179.78 0.12 129 42 51 9 179.80 0.12 130 43 46 3 322.79 0.71 131 44 76 32 135.90 19.93 132 45 72 27 136.68 19.61 133 45 76 31 135.90 19.93 134 46 75 29 136.69 19.60 135 46 76 30 136.59 19.61 136 46 81 35 104.60 15.88 137 47 50 3 322.63 3.03 138 47 53 6 241.22 12.02 139 47 75 28 136.69 19.60 140 48 75 27 136.73 19.58 141 49 52 3 324.53 2.09 142 50 53 3 328.45 0.12 143 51 54 3 319.05 1.23 144 51 55 4 301.31 1.78 145 52 55 3 311.77 1.11 146 52 56 4 271.13 2.37 147 52 57 5 277.32 0.72 148 53 57 4 271.13 2.37 149 53 61 8 211.75 0.06 150 53 68 15 137.74 19.14 151 53 71 18 137.74 19.14 152 53 72 19 137.72 19.14 153 54 57 3 321.78 0.41 154 54 68 14 137.74 19.14 155 57 61 4 308.82 5.70 156 57 63 6 144.47 16.68 157 58 61 3 322.69 0.64 158 61 67 6 236.44 14.29 159 61 68 7 238.34 13.33 160 61 71 10 178.88 1.35 161 62 67 5 236.44 14.29 162 64 67 3 310.33 0.02 163 64 68 4 309.63 0.35 164 65 68 3 314.85 1.43 165 65 69 4 309.69 0.33 166 66 69 3 316.68 1.95 167 66 70 4 309.69 0.33 168 67 70 3 316.71 1.49 169 67 71 4 308.89 0.70 170 68 71 3 319.29 0.52 171 68 72 4 314.25 2.00 172 69 72 3 319.64 2.96 173 69 73 4 298.82 5.63 174 69 84 15 58.00 0.39 175 70 73 3 319.92 2.37 176 70 74 4 304.12 5.53 177 71 74 3 322.61 1.02 178 71 75 4 304.12 5.53 179 72 75 3 313.80 0.69 180 72 76 4 310.43 0.18 181 72 84 12 59.20 0.19 182 73 76 3 315.62 0.22 183 73 77 4 310.23 0.28 184 73 84 11 58.07 0.42 185 74 77 3 314.73 0.22 186 74 78 4 310.20 0.29 187 75 78 3 312.63 1.37 188 75 79 4 307.70 1.54 189 75 81 6 288.79 6.57 190 76 79 3 310.04 2.54 191 76 80 4 296.23 4.08 192 76 81 5 275.93 3.12 193 76 82 6 265.27 1.98 194 77 80 3 315.22 3.07