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 5 8 3 323.81 2.45 2 5 9 4 274.58 10.27 3 5 39 34 32.76 0.99 4 5 40 35 37.08 1.17 5 6 9 3 308.22 3.43 6 10 14 4 300.83 1.05 7 10 36 26 69.73 1.19 8 10 37 27 69.58 1.11 9 10 38 28 69.58 1.11 10 11 14 3 327.63 0.33 11 11 15 4 308.72 2.85 12 12 15 3 313.61 2.17 13 12 16 4 308.75 2.84 14 13 16 3 315.74 1.10 15 13 17 4 318.25 0.14 16 14 17 3 325.07 0.57 17 14 18 4 316.25 0.86 18 14 37 23 70.03 1.29 19 15 18 3 323.95 1.12 20 15 19 4 316.33 0.94 21 15 37 22 70.05 1.30 22 16 19 3 322.42 2.10 23 16 20 4 316.35 4.00 24 17 20 3 316.34 4.00 25 17 21 4 316.33 4.00 26 18 21 3 306.78 2.10 27 18 22 4 306.57 2.20 28 18 32 14 73.73 0.69 29 18 33 15 73.22 0.95 30 18 36 18 73.17 0.96 31 18 37 19 72.00 0.39 32 19 22 3 307.42 1.78 33 19 23 4 299.94 0.89 34 19 49 30 67.52 1.96 35 20 23 3 316.75 1.06 36 20 24 4 298.82 0.33 37 21 24 3 308.26 2.96 38 21 25 4 298.74 0.38 39 21 32 11 91.21 3.38 40 21 36 15 85.07 0.32 41 22 25 3 304.08 1.22 42 22 26 4 291.88 1.73 43 22 27 5 280.14 2.98 44 22 32 10 204.93 10.39 45 22 33 11 85.09 0.30 46 22 49 27 67.68 2.00 47 23 26 3 308.12 0.83 48 23 49 26 67.69 2.00 49 25 29 4 310.29 1.41 50 25 32 7 273.04 13.63 51 27 30 3 337.87 1.46 52 27 49 22 67.75 1.98 53 29 32 3 326.03 0.23 54 29 33 4 323.93 1.96 55 30 33 3 326.72 0.57 56 30 34 4 317.84 2.18 57 30 42 12 70.01 1.31 58 30 45 15 70.00 1.31 59 30 46 16 69.97 1.30 60 30 49 19 69.28 1.65 61 30 50 20 69.28 1.64 62 31 34 3 329.69 0.92 63 31 35 4 312.77 0.15 64 32 35 3 313.06 0.20 65 32 36 4 312.75 0.16 66 33 36 3 317.81 2.38 67 33 37 4 297.31 1.99 68 33 42 9 69.99 1.30 69 34 37 3 318.79 10.41 70 34 38 4 297.73 0.95 71 34 42 8 69.98 1.29 72 35 38 3 339.44 0.09 73 43 46 3 351.99 4.41 74 45 48 3 330.85 0.41 75 46 49 3 317.97 2.19 76 46 50 4 265.58 1.12 77 46 51 5 272.78 2.48 78 47 51 4 272.76 2.48 79 48 51 3 310.81 4.69 80 48 52 4 264.38 1.72 81 55 59 4 314.18 4.70 82 56 59 3 317.29 3.14 83 56 60 4 308.42 1.81 84 56 61 5 289.98 11.01 85 56 62 6 243.19 6.79 86 56 63 7 208.63 3.71 87 57 61 4 304.86 3.58 88 57 62 5 243.19 6.79 89 57 63 6 221.49 5.00 90 57 64 7 216.43 7.53 91 57 67 10 213.06 5.88 92 58 61 3 308.44 1.79 93 60 91 31 148.79 1.68 94 61 91 30 148.80 1.69 95 62 66 4 312.87 0.36 96 62 70 8 272.87 0.99 97 62 91 29 148.76 1.70 98 62 95 33 148.37 1.69 99 62 96 34 147.88 1.87 100 62 99 37 147.09 1.48 101 63 66 3 312.98 0.41 102 63 67 4 313.05 0.38 103 64 67 3 315.63 1.68 104 64 68 4 313.11 0.41 105 65 68 3 314.31 1.00 106 65 69 4 313.11 0.41 107 66 69 3 322.00 2.85 108 66 70 4 313.05 0.38 109 66 88 22 149.63 1.72 110 67 70 3 326.76 1.55 111 67 71 4 304.64 0.20 112 67 99 32 148.12 1.80 113 67 104 37 125.50 0.42 114 68 71 3 313.23 3.04 115 68 72 4 303.86 0.58 116 69 72 3 304.40 0.03 117 69 73 4 303.92 3.34 118 69 87 18 150.43 1.72 119 69 88 19 150.24 1.63 120 70 73 3 305.39 2.61 121 70 74 4 307.43 1.59 122 70 84 14 149.95 1.56 123 70 96 26 148.85 1.66 124 70 99 29 148.77 1.70 125 70 100 30 148.37 1.68 126 71 75 4 317.41 1.69 127 71 100 29 148.42 1.85 128 71 104 33 128.22 1.66 129 72 75 3 331.01 0.21 130 72 76 4 317.38 1.68 131 73 76 3 312.46 0.79 132 73 77 4 303.62 0.30 133 73 84 11 150.90 1.96 134 73 87 14 150.84 1.92 135 74 78 4 275.62 3.73 136 74 79 5 271.24 5.92 137 74 81 7 227.79 1.67 138 74 84 10 157.07 1.11 139 74 100 26 149.06 1.77 140 77 80 3 337.64 0.29 141 77 84 7 224.71 0.67 142 80 83 3 313.62 0.78 143 80 84 4 301.73 1.46 144 81 84 3 305.11 0.23 145 81 85 4 308.80 1.61 146 81 93 12 150.88 1.78 147 81 96 15 150.87 1.77 148 81 97 16 150.78 1.74 149 81 100 19 150.80 1.78 150 82 86 4 313.69 0.83 151 82 93 11 150.91 1.78 152 83 86 3 313.88 0.92 153 83 87 4 313.88 0.92 154 84 87 3 326.69 3.00 155 84 88 4 319.48 1.86 156 84 96 12 151.41 1.94 157 85 88 3 316.44 2.12 158 85 91 6 164.70 4.61 159 85 92 7 151.53 1.97 160 85 93 8 151.51 1.97 161 85 96 11 151.42 1.94 162 91 95 4 304.99 2.22 163 91 96 5 304.98 2.22 164 92 95 3 311.77 0.11 165 92 96 4 309.49 1.03 166 93 96 3 317.31 0.82 167 93 97 4 309.12 2.94 168 94 97 3 318.35 0.54 169 94 98 4 311.06 2.01 170 95 98 3 319.18 0.12 171 95 99 4 310.16 2.47 172 96 99 3 310.69 2.20 173 96 100 4 311.45 1.86 174 97 100 3 319.77 0.53 175 97 101 4 314.28 3.27 176 98 101 3 312.20 1.79 177 98 102 4 311.43 1.85 178 99 102 3 311.44 1.86 179 99 103 4 311.43 1.85 180 99 104 5 297.48 1.00 181 100 104 4 288.88 5.29 182 100 105 5 274.78 1.75 183 101 105 4 288.88 5.30 184 102 105 3 340.58 2.45 185 103 106 3 356.97 3.04 186 105 108 3 338.11 2.23 187 106 109 3 359.88 2.81