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 1 9 8 261.91 2.09 2 1 53 52 87.31 1.35 3 1 79 78 15.40 0.57 4 2 5 3 277.11 0.33 5 2 6 4 274.83 0.04 6 3 6 3 277.24 0.26 7 3 7 4 274.84 0.04 8 3 72 69 35.41 0.27 9 3 76 73 34.41 0.75 10 4 7 3 275.70 0.38 11 4 8 4 276.48 0.83 12 5 8 3 277.29 0.42 13 5 9 4 276.48 0.83 14 6 9 3 276.48 0.83 15 6 10 4 276.48 0.83 16 6 53 47 97.26 0.69 17 6 72 66 54.51 1.15 18 6 75 69 48.96 0.54 19 6 76 70 46.85 0.04 20 6 79 73 37.76 0.26 21 7 10 3 276.49 0.83 22 7 11 4 276.49 0.84 23 7 25 18 131.56 1.98 24 7 27 20 122.92 2.25 25 7 68 61 55.88 0.48 26 7 72 65 54.52 1.14 27 8 11 3 276.49 0.84 28 8 12 4 276.06 1.06 29 9 12 3 285.04 2.87 30 9 13 4 272.68 2.75 31 9 52 43 97.59 0.63 32 9 53 44 97.57 0.64 33 10 13 3 284.51 3.14 34 10 14 4 269.49 4.36 35 10 49 39 97.57 0.63 36 10 53 43 97.61 0.62 37 10 68 58 57.73 1.10 38 10 71 61 57.72 1.10 39 10 72 62 57.72 1.10 40 10 75 65 57.71 1.10 41 11 14 3 278.25 0.01 42 11 15 4 269.39 4.30 43 11 22 11 143.68 7.33 44 11 23 12 145.12 6.64 45 11 25 14 126.71 0.45 46 12 15 3 281.46 1.61 47 12 16 4 269.50 4.36 48 13 16 3 281.44 1.61 49 13 17 4 263.68 1.52 50 13 45 32 97.83 0.68 51 13 48 35 97.68 0.62 52 13 49 36 97.67 0.62 53 13 52 39 97.67 0.63 54 14 17 3 277.92 0.70 55 14 18 4 261.21 2.37 56 14 20 6 221.68 0.00 57 14 25 11 134.71 1.15 58 14 31 17 122.87 2.23 59 14 35 21 122.89 2.25 60 14 45 31 97.73 0.63 61 14 68 54 92.26 0.08 62 15 19 4 233.94 6.13 63 15 20 5 198.60 3.41 64 15 22 7 158.44 0.12 65 15 25 10 136.77 2.18 66 16 19 3 261.20 2.38 67 17 41 24 98.57 0.59 68 17 44 27 98.30 0.69 69 17 45 28 98.17 0.70 70 17 48 31 98.16 0.69 71 18 35 17 122.92 2.25 72 18 37 19 112.81 2.67 73 18 41 23 98.58 0.59 74 18 45 27 98.38 0.59 75 20 25 5 247.75 3.45 76 21 24 3 285.76 0.99 77 21 25 4 274.25 1.02 78 22 25 3 281.85 0.96 79 24 34 10 144.78 1.74 80 24 35 11 135.40 1.03 81 25 35 10 135.41 1.03 82 25 68 43 95.09 0.29 83 26 29 3 275.96 1.88 84 26 68 42 95.54 0.48 85 27 68 41 95.54 0.48 86 27 69 42 95.09 0.28 87 28 67 39 95.83 0.47 88 28 69 41 95.54 0.48 89 29 34 5 170.06 0.40 90 29 35 6 170.05 0.40 91 29 67 38 95.84 0.46 92 29 68 39 95.83 0.46 93 30 33 3 276.49 0.26 94 30 34 4 210.52 5.98 95 30 35 5 183.91 7.32 96 30 66 36 96.01 0.47 97 30 67 37 95.88 0.47 98 31 35 4 183.91 7.32 99 31 36 5 183.90 7.32 100 31 37 6 169.97 0.36 101 31 45 14 132.93 1.34 102 31 65 34 96.05 0.48 103 31 66 35 95.95 0.44 104 31 67 36 95.91 0.45 105 31 68 37 95.89 0.46 106 31 71 40 95.34 0.49 107 32 36 4 183.90 7.32 108 32 37 5 170.01 0.38 109 33 66 33 96.03 0.46 110 35 68 33 95.88 0.46 111 37 41 4 250.20 3.41 112 38 41 3 275.61 2.23 113 38 42 4 272.42 0.59 114 39 42 3 281.01 0.46 115 39 43 4 278.00 1.04 116 40 43 3 280.23 0.91 117 40 44 4 278.00 1.04 118 41 44 3 277.15 0.61 119 41 45 4 274.76 0.58 120 42 45 3 278.68 1.39 121 42 46 4 274.74 0.58 122 43 46 3 278.67 1.40 123 43 47 4 274.68 0.60 124 44 47 3 278.62 1.42 125 44 48 4 268.20 1.65 126 45 48 3 276.47 2.48 127 45 49 4 268.20 1.65 128 46 49 3 274.57 0.45 129 46 50 4 267.82 1.45 130 46 57 11 160.85 5.83 131 46 62 16 96.01 0.48 132 47 50 3 268.04 1.33 133 47 51 4 267.80 1.44 134 48 51 3 272.58 0.96 135 48 52 4 269.69 0.48 136 49 52 3 275.07 2.21 137 49 53 4 268.67 0.04 138 49 55 6 235.78 0.19 139 49 57 8 211.85 1.59 140 49 71 22 60.40 0.06 141 49 75 26 57.80 1.11 142 50 53 3 279.63 0.07 143 50 54 4 259.04 0.26 144 50 55 5 234.43 0.48 145 50 56 6 228.33 2.47 146 50 57 7 201.91 6.57 147 51 54 3 269.92 0.15 148 53 75 22 57.81 1.11 149 53 79 26 53.18 2.76 150 55 74 19 64.93 2.17 151 55 75 20 58.09 1.22 152 55 78 23 57.48 1.20 153 57 61 4 270.84 0.21 154 57 62 5 266.26 2.10 155 57 65 8 239.29 7.02 156 57 74 17 75.49 3.08 157 58 61 3 278.22 3.47 158 58 62 4 270.56 0.17 159 59 62 3 275.14 0.28 160 59 63 4 272.80 0.93 161 60 63 3 283.79 0.69 162 60 64 4 279.93 2.62 163 61 64 3 283.78 0.70 164 61 65 4 272.81 0.94 165 61 74 13 136.81 2.60 166 62 65 3 280.45 2.35 167 65 70 5 209.42 3.94 168 65 71 6 221.59 2.15 169 65 74 9 183.13 3.94 170 66 70 4 268.70 0.52 171 67 70 3 271.81 0.51 172 67 71 4 270.26 1.28 173 68 71 3 271.81 0.51 174 68 72 4 268.74 0.51 175 69 72 3 270.28 0.26 176 69 73 4 270.78 1.53 177 70 73 3 279.12 0.26 178 70 74 4 272.23 0.80 179 71 74 3 278.36 0.64 180 71 75 4 272.31 0.83 181 72 75 3 276.08 0.50 182 72 76 4 275.45 0.81 183 73 76 3 276.08 0.50 184 73 77 4 269.52 0.58 185 74 77 3 279.39 3.77 186 74 78 4 269.54 0.57 187 75 78 3 276.24 1.97 188 75 79 4 268.49 0.43 189 76 80 4 260.33 1.63 190 77 80 3 273.49 1.91