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 36 33 94.66 8.41 2 3 37 34 85.05 3.61 3 3 40 37 93.20 7.78 4 4 9 5 218.85 2.58 5 4 10 6 214.71 0.52 6 4 14 10 192.53 0.29 7 4 40 36 111.36 2.45 8 5 9 4 284.47 1.20 9 5 44 39 112.89 2.79 10 6 9 3 285.76 0.55 11 6 10 4 284.47 1.20 12 6 44 38 112.92 2.80 13 7 10 3 292.53 2.83 14 7 15 8 224.89 1.42 15 7 44 37 113.08 2.77 16 7 45 38 113.04 2.77 17 7 72 65 73.97 0.47 18 7 76 69 64.38 0.18 19 7 83 76 24.79 0.14 20 7 84 77 24.68 0.12 21 8 82 74 26.93 0.07 22 8 83 75 24.93 0.22 23 8 84 76 24.69 0.12 24 8 85 77 24.55 0.15 25 9 85 76 24.55 0.07 26 10 14 4 275.10 0.60 27 10 15 5 272.78 0.56 28 10 18 8 253.72 3.43 29 10 40 30 130.55 2.77 30 10 44 34 129.38 2.23 31 10 84 74 24.66 0.13 32 10 85 75 24.50 0.10 33 11 14 3 283.63 2.01 34 11 15 4 278.89 1.30 35 11 85 74 24.53 0.12 36 12 15 3 281.91 0.60 37 12 16 4 280.14 2.12 38 12 69 57 77.11 0.91 39 12 73 61 76.92 0.98 40 12 84 72 24.71 0.14 41 13 16 3 282.30 1.69 42 13 17 4 280.35 2.04 43 14 17 3 284.49 0.04 44 14 18 4 285.00 2.76 45 15 18 3 287.88 1.32 46 15 19 4 281.95 1.24 47 15 41 26 131.75 3.35 48 15 44 29 131.85 3.31 49 15 45 30 131.82 3.31 50 15 69 54 85.34 4.99 51 15 72 57 85.28 5.02 52 15 84 69 24.71 0.14 53 16 19 3 284.81 0.21 54 16 20 4 277.22 1.14 55 16 65 49 85.78 4.80 56 16 66 50 85.76 4.80 57 16 69 53 85.50 4.92 58 17 20 3 284.14 0.55 59 17 21 4 284.13 0.55 60 18 21 3 284.13 0.55 61 18 22 4 279.62 1.71 62 18 37 19 132.19 3.39 63 18 41 23 131.89 3.33 64 19 22 3 282.93 3.98 65 19 23 4 276.93 1.06 66 19 41 22 131.91 3.33 67 19 54 35 129.79 2.77 68 19 65 46 85.91 4.83 69 19 68 49 85.88 4.83 70 19 69 50 85.86 4.82 71 20 23 3 279.56 0.25 72 20 24 4 276.93 1.06 73 20 65 45 85.96 4.79 74 21 24 3 284.55 2.44 75 21 25 4 282.05 1.49 76 21 37 16 132.31 3.36 77 22 25 3 286.50 1.46 78 22 26 4 284.30 0.36 79 22 34 12 132.49 3.30 80 22 37 15 132.31 3.36 81 22 38 16 132.30 3.36 82 22 41 19 132.31 3.35 83 22 54 32 131.31 3.16 84 23 26 3 285.02 0.01 85 23 65 42 86.05 4.76 86 24 27 3 292.79 1.76 87 24 28 4 284.30 0.36 88 25 28 3 277.79 0.40 89 25 33 8 132.68 3.27 90 25 34 9 132.64 3.25 91 25 37 12 132.59 3.31 92 26 34 8 132.66 3.27 93 26 55 29 132.15 3.35 94 31 34 3 277.37 2.69 95 31 35 4 274.29 0.92 96 32 36 4 278.13 2.31 97 33 36 3 279.37 1.70 98 33 37 4 274.83 0.66 99 34 37 3 283.54 2.13 100 34 38 4 274.83 0.65 101 35 38 3 281.75 0.74 102 35 39 4 274.15 0.46 103 36 39 3 281.75 0.73 104 36 40 4 281.19 3.96 105 37 40 3 289.95 0.42 106 37 41 4 289.94 0.42 107 38 41 3 289.95 0.42 108 38 42 4 289.94 0.42 109 38 51 13 157.76 5.12 110 38 54 16 157.69 5.17 111 38 55 17 157.69 5.16 112 39 42 3 290.38 0.20 113 39 43 4 289.93 0.42 114 40 43 3 289.94 0.42 115 40 44 4 287.81 0.64 116 41 44 3 291.55 0.35 117 41 45 4 284.62 2.23 118 41 50 9 165.84 1.13 119 41 51 10 157.88 5.11 120 41 53 12 157.85 5.08 121 41 54 13 157.85 5.08 122 41 68 27 86.08 4.94 123 42 45 3 293.42 0.58 124 42 46 4 272.44 1.33 125 42 50 8 157.90 5.10 126 42 51 9 157.90 5.11 127 43 46 3 296.31 0.86 128 45 72 27 85.06 5.16 129 45 76 31 80.14 7.61 130 46 76 30 80.17 7.62 131 47 50 3 282.95 1.26 132 47 53 6 246.19 7.41 133 47 71 24 85.48 5.19 134 47 75 28 83.81 5.79 135 48 75 27 85.06 5.30 136 49 52 3 286.33 0.05 137 49 53 4 272.54 1.22 138 50 53 3 303.13 4.25 139 51 54 3 288.92 1.24 140 51 55 4 272.68 1.28 141 52 55 3 283.68 2.29 142 52 56 4 263.82 1.40 143 52 57 5 263.82 1.40 144 53 61 8 178.34 4.62 145 53 68 15 86.25 5.00 146 53 71 18 86.20 5.01 147 53 72 19 86.21 5.01 148 54 57 3 296.97 2.11 149 54 68 14 86.25 5.00 150 57 61 4 268.57 4.65 151 57 63 6 150.59 4.40 152 58 61 3 292.70 2.21 153 61 67 6 183.65 1.75 154 61 68 7 193.34 3.10 155 61 71 10 163.05 1.59 156 62 67 5 183.65 1.75 157 64 67 3 289.88 6.21 158 64 68 4 274.64 1.57 159 65 68 3 284.45 2.44 160 65 69 4 275.48 1.99 161 66 69 3 276.66 1.40 162 66 70 4 274.55 2.46 163 67 70 3 281.78 1.16 164 67 71 4 280.57 0.57 165 68 71 3 281.94 0.12 166 68 72 4 280.58 0.57 167 69 72 3 281.95 0.12 168 69 73 4 280.56 0.58 169 69 84 15 27.93 0.36 170 70 73 3 287.51 4.04 171 70 74 4 280.56 0.58 172 71 74 3 291.56 2.02 173 71 75 4 280.66 0.50 174 72 75 3 288.25 0.26 175 72 76 4 280.30 0.85 176 72 84 12 95.58 31.64 177 73 76 3 285.71 0.90 178 73 77 4 280.99 0.51 179 73 84 11 29.62 0.14 180 74 77 3 283.67 1.03 181 74 78 4 281.00 0.50 182 75 78 3 288.37 3.29 183 75 79 4 281.32 0.65 184 76 79 3 288.37 3.29 185 76 80 4 281.32 0.65 186 76 81 5 242.44 0.31 187 76 82 6 229.61 6.73 188 76 83 7 161.09 0.38 189 77 80 3 278.13 0.25