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 8 12 4 371.64 5.09 2 8 59 51 108.20 16.55 3 8 62 54 108.23 16.50 4 8 63 55 107.88 16.39 5 9 12 3 382.86 0.52 6 9 13 4 371.54 5.15 7 9 59 50 108.21 16.55 8 9 82 73 103.00 15.89 9 9 85 76 98.15 13.71 10 9 86 77 98.12 13.71 11 10 14 4 391.55 3.83 12 10 91 81 84.07 12.67 13 10 92 82 82.61 13.38 14 11 14 3 399.13 0.04 15 11 15 4 393.35 2.85 16 12 15 3 399.13 0.03 17 12 16 4 395.10 1.99 18 12 55 43 114.10 15.82 19 12 58 46 112.25 15.56 20 12 59 47 109.66 16.15 21 12 62 50 109.38 15.96 22 12 82 70 105.69 15.14 23 13 16 3 398.12 0.47 24 13 17 4 395.02 2.02 25 13 35 22 268.81 2.98 26 13 55 42 114.10 15.82 27 13 86 73 104.14 15.04 28 13 92 79 86.22 11.61 29 14 17 3 395.46 0.10 30 14 18 4 390.14 1.55 31 14 27 13 269.38 3.26 32 14 112 98 54.16 0.84 33 15 18 3 392.28 2.62 34 15 19 4 386.73 3.26 35 16 19 3 398.24 0.35 36 16 20 4 385.66 2.73 37 16 21 5 379.01 3.61 38 16 22 6 365.45 2.87 39 16 25 9 270.67 3.88 40 16 55 39 115.95 15.37 41 17 20 3 390.73 3.40 42 17 25 8 270.64 3.89 43 17 26 9 269.38 3.25 44 17 27 10 269.39 3.25 45 17 35 18 269.38 3.25 46 18 27 9 269.41 3.25 47 18 32 14 269.31 3.29 48 22 25 3 404.41 1.14 49 22 54 32 136.23 5.43 50 22 55 33 136.20 5.44 51 22 58 36 136.25 5.42 52 23 38 15 270.16 2.94 53 24 36 12 271.17 2.46 54 24 38 14 269.50 3.26 55 25 35 10 272.81 2.28 56 25 36 11 271.17 2.46 57 25 37 12 270.27 2.91 58 25 38 13 270.27 2.91 59 25 55 30 136.41 5.33 60 26 35 9 272.82 2.28 61 26 36 10 272.79 2.29 62 27 32 5 283.91 3.22 63 27 33 6 283.92 3.23 64 27 34 7 279.61 5.38 65 27 35 8 272.86 2.26 66 27 112 85 102.38 11.40 67 28 34 6 280.52 4.93 68 28 35 7 273.09 2.21 69 28 36 8 273.12 2.21 70 28 109 81 103.06 11.45 71 29 32 3 404.22 2.48 72 29 33 4 382.68 0.91 73 29 34 5 292.63 1.12 74 33 112 79 102.28 11.42 75 34 95 61 116.12 5.01 76 34 109 75 103.22 11.53 77 34 110 76 102.83 11.62 78 34 111 77 102.33 11.44 79 35 92 57 125.53 0.34 80 35 109 74 102.95 11.67 81 35 110 75 102.91 11.65 82 35 112 77 102.85 11.64 83 36 107 71 103.47 11.57 84 36 108 72 103.30 11.55 85 36 109 73 102.94 11.67 86 37 107 70 103.52 11.60 87 37 108 71 103.32 11.58 88 38 106 68 103.78 11.62 89 38 107 69 103.53 11.61 90 39 83 44 131.81 2.46 91 39 86 47 131.84 2.44 92 39 101 62 103.83 11.62 93 39 106 67 103.80 11.63 94 39 107 68 103.73 11.63 95 39 108 69 103.73 11.63 96 40 106 66 103.81 11.63 97 42 47 5 336.39 4.55 98 44 47 3 398.56 1.28 99 45 49 4 402.00 1.15 100 47 52 5 387.22 0.56 101 48 52 4 386.47 0.94 102 49 52 3 386.47 0.94 103 49 53 4 380.22 4.05 104 50 53 3 393.30 2.48 105 50 54 4 374.12 4.84 106 50 57 7 365.11 3.70 107 51 54 3 376.39 5.98 108 52 56 4 391.97 1.20 109 53 56 3 388.37 2.67 110 53 57 4 377.56 5.42 111 53 78 25 166.37 14.83 112 55 58 3 396.06 0.23 113 55 59 4 393.14 1.68 114 55 82 27 166.09 14.96 115 56 59 3 398.68 1.09 116 56 60 4 395.73 0.39 117 56 78 22 166.06 14.99 118 56 79 23 166.06 14.98 119 56 82 26 166.05 14.98 120 57 60 3 404.26 1.70 121 57 61 4 386.56 0.26 122 57 66 9 294.23 2.12 123 57 78 21 166.24 14.89 124 58 61 3 397.47 1.70 125 58 62 4 384.94 0.54 126 59 62 3 397.53 0.42 127 59 63 4 387.12 1.63 128 59 81 22 166.04 15.00 129 59 82 23 165.72 15.15 130 59 85 26 165.61 15.21 131 60 63 3 390.72 0.44 132 60 64 4 381.78 1.03 133 60 78 18 166.06 15.00 134 61 64 3 390.25 0.21 135 61 66 5 306.64 4.08 136 66 71 5 348.88 4.24 137 66 73 7 263.31 15.62 138 66 78 12 202.85 3.40 139 67 70 3 397.32 0.94 140 67 71 4 301.70 1.01 141 73 78 5 391.56 2.09 142 74 77 3 394.30 1.50 143 74 78 4 391.56 2.09 144 75 78 3 399.23 1.69 145 75 79 4 391.56 2.09 146 76 79 3 405.18 1.28 147 76 80 4 391.55 2.09 148 77 80 3 398.45 0.88 149 77 81 4 385.54 0.91 150 78 81 3 396.45 0.48 151 78 82 4 384.34 0.31 152 79 82 3 399.87 2.17 153 79 83 4 390.23 2.63 154 80 83 3 393.03 1.25 155 80 84 4 388.30 1.67 156 81 84 3 399.75 1.41 157 81 85 4 396.53 3.02 158 82 85 3 399.75 1.41 159 82 86 4 396.53 3.02 160 83 86 3 400.50 1.04 161 83 87 4 396.53 3.02 162 84 87 3 400.50 1.04 163 84 88 4 389.92 0.28 164 85 88 3 389.93 0.27 165 85 89 4 386.22 1.57 166 86 89 3 396.32 0.39 167 86 92 6 312.76 3.43 168 86 110 24 104.56 12.62 169 89 92 3 390.09 0.04 170 91 112 21 104.58 12.86 171 91 113 22 103.95 13.02 172 92 111 19 105.28 13.17 173 92 112 20 104.58 12.86 174 92 113 21 104.45 12.79 175 93 110 17 105.69 13.12 176 93 111 18 105.31 13.16 177 93 113 20 104.66 12.86 178 94 110 16 105.78 13.12 179 95 98 3 400.64 0.52 180 95 99 4 363.23 0.89 181 95 109 14 153.97 9.68 182 95 110 15 148.78 8.38 183 95 111 16 148.76 8.38 184 96 99 3 370.31 2.66 185 98 109 11 200.03 0.48 186 99 107 8 220.69 3.05 187 99 108 9 205.84 1.89 188 99 109 10 176.91 9.68 189 100 103 3 406.43 0.78 190 100 106 6 224.62 1.21 191 100 107 7 222.47 2.27 192 101 106 5 224.62 1.22 193 101 107 6 224.62 1.22 194 101 108 7 224.61 1.22 195 103 106 3 400.13 2.90 196 103 107 4 407.83 1.57 197 114 117 3 376.56 0.34