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 4 8 4 216.55 3.94 2 4 9 5 209.49 0.41 3 5 9 4 285.44 3.63 4 5 40 35 127.26 2.34 5 6 10 4 295.28 0.24 6 6 40 34 135.34 5.10 7 7 10 3 316.95 0.35 8 7 11 4 309.31 4.17 9 8 11 3 310.92 3.38 10 8 12 4 310.93 3.37 11 9 12 3 310.94 3.38 12 9 13 4 310.93 3.37 13 9 30 21 162.26 0.96 14 9 40 31 161.90 0.87 15 10 13 3 316.03 0.82 16 10 14 4 310.93 3.37 17 10 40 30 161.88 0.86 18 10 44 34 161.87 0.87 19 11 14 3 306.72 1.27 20 11 15 4 309.55 1.99 21 11 70 59 51.88 1.26 22 12 15 3 311.87 0.83 23 12 16 4 309.34 2.09 24 12 29 17 162.53 0.94 25 13 16 3 312.93 0.30 26 13 17 4 308.98 2.28 27 13 26 13 162.41 0.94 28 13 37 24 162.29 0.98 29 13 40 27 162.24 1.01 30 13 41 28 162.12 0.96 31 13 44 31 162.19 0.99 32 13 50 37 161.85 0.89 33 14 17 3 315.63 1.04 34 14 18 4 305.64 3.95 35 14 49 35 161.84 0.89 36 14 63 49 79.64 5.26 37 14 66 52 69.30 0.31 38 14 67 53 61.80 0.24 39 15 18 3 310.49 1.52 40 15 67 52 64.92 1.67 41 16 21 5 194.14 0.41 42 16 26 10 162.53 0.95 43 17 20 3 290.25 0.94 44 17 50 33 162.16 1.01 45 17 57 40 162.12 0.99 46 17 58 41 161.87 0.88 47 17 59 42 161.57 0.78 48 18 59 41 161.85 0.89 49 19 59 40 162.19 1.02 50 20 56 36 162.55 1.06 51 20 57 37 162.34 1.03 52 20 58 38 162.18 1.02 53 21 25 4 304.74 1.31 54 21 56 35 162.72 0.98 55 21 57 36 162.59 0.98 56 22 25 3 314.23 0.01 57 22 26 4 309.70 2.27 58 22 56 34 162.77 1.01 59 22 57 35 162.80 0.97 60 23 26 3 314.23 0.01 61 23 27 4 309.85 2.19 62 23 32 9 181.72 2.50 63 23 34 11 163.28 0.90 64 23 41 18 162.96 1.01 65 23 57 34 162.85 0.96 66 24 27 3 315.01 0.37 67 25 28 3 321.05 1.91 68 26 29 3 311.74 1.78 69 26 30 4 311.43 1.93 70 26 32 6 201.62 2.31 71 26 41 15 163.07 0.95 72 26 57 31 162.91 0.97 73 27 30 3 311.56 1.86 74 27 32 5 193.94 3.61 75 32 37 5 234.78 15.03 76 33 36 3 307.29 2.27 77 33 37 4 234.78 15.03 78 34 37 3 293.66 4.00 79 34 38 4 275.36 5.24 80 36 39 3 319.13 1.19 81 37 40 3 309.68 3.53 82 37 41 4 305.46 0.40 83 38 41 3 314.82 0.94 84 38 42 4 303.54 0.56 85 39 42 3 313.06 1.83 86 39 43 4 303.54 0.56 87 40 43 3 307.03 1.19 88 40 44 4 307.03 1.19 89 41 44 3 313.06 1.83 90 41 45 4 302.19 3.60 91 41 50 9 198.35 1.04 92 41 57 16 172.68 1.28 93 42 45 3 306.94 1.23 94 42 46 4 300.53 2.79 95 43 46 3 304.71 0.70 96 43 47 4 300.29 2.91 97 44 47 3 304.70 0.70 98 44 48 4 294.38 0.54 99 44 49 5 257.16 5.87 100 44 50 6 243.81 0.81 101 45 48 3 299.71 3.20 102 45 50 5 228.91 8.26 103 45 57 12 173.68 0.95 104 48 60 12 173.44 0.97 105 48 62 14 172.49 1.28 106 49 59 10 173.69 0.91 107 49 60 11 173.56 0.92 108 49 62 13 172.00 1.53 109 49 63 14 171.05 2.00 110 49 66 17 170.88 2.08 111 50 57 7 173.88 0.91 112 50 58 8 173.83 0.88 113 50 59 9 173.68 0.91 114 50 60 10 173.65 0.90 115 51 56 5 223.62 0.85 116 51 57 6 173.90 0.90 117 51 58 7 173.83 0.88 118 51 59 8 173.81 0.87 119 51 60 9 173.74 0.90 120 51 61 10 173.80 0.87 121 52 55 3 303.69 1.50 122 52 56 4 246.97 10.83 123 53 56 3 283.63 1.20 124 53 58 5 206.45 8.29 125 59 64 5 287.00 0.14 126 60 63 3 304.30 2.64 127 60 64 4 306.12 1.71 128 61 64 3 320.73 2.52 129 61 65 4 298.86 0.09 130 62 65 3 312.01 1.84 131 62 66 4 303.04 0.11 132 63 66 3 306.52 1.48 133 63 67 4 306.13 1.66 134 64 67 3 306.16 1.66 135 64 68 4 306.13 1.66 136 65 68 3 319.02 0.42 137 65 69 4 303.04 0.11 138 66 69 3 307.24 1.10 139 66 70 4 299.97 1.42 140 67 70 3 310.56 0.60 141 67 71 4 300.07 1.24 142 68 71 3 313.27 0.75 143 68 72 4 304.68 3.54 144 69 72 3 313.27 0.74 145 69 73 4 300.69 1.55 146 70 73 3 321.92 3.58 147 70 74 4 300.69 1.55 148 71 74 3 310.02 0.83 149 71 75 4 298.38 0.42 150 72 75 3 294.57 2.32 151 72 76 4 294.16 2.12 152 73 76 3 307.10 0.68 153 73 77 4 289.23 4.58 154 74 77 3 304.58 0.70 155 74 78 4 289.12 4.63 156 75 79 4 292.82 2.77 157 76 79 3 302.16 1.89 158 76 80 4 300.65 1.14 159 77 80 3 308.98 0.25 160 77 81 4 300.32 0.94 161 78 81 3 307.40 0.54 162 78 82 4 299.52 0.56 163 79 82 3 305.69 1.74 164 79 83 4 299.55 0.57 165 80 83 3 301.72 0.52 166 80 84 4 299.56 0.58 167 81 84 3 304.81 0.39 168 81 85 4 303.49 1.20 169 82 85 3 308.41 1.26 170 82 86 4 303.50 1.20 171 83 86 3 312.13 3.12 172 83 87 4 303.51 1.20 173 84 87 3 312.30 3.04 174 84 88 4 306.49 2.62 175 85 88 3 315.06 1.65 176 85 89 4 303.69 1.26 177 86 89 3 313.07 0.67 178 86 90 4 303.70 1.25 179 87 90 3 313.62 0.89 180 87 91 4 298.23 0.93 181 88 91 3 313.56 0.91 182 88 92 4 292.53 2.10 183 88 93 5 243.41 5.93 184 89 92 3 305.94 4.72 185 92 95 3 302.95 1.40