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 7 4 269.27 1.41 2 3 8 5 267.37 1.03 3 3 62 59 53.12 2.31 4 3 65 62 45.29 0.18 5 3 69 66 41.57 1.66 6 4 7 3 277.88 0.82 7 4 8 4 269.97 2.29 8 4 57 53 63.77 0.68 9 4 58 54 66.49 0.62 10 4 62 58 61.10 0.54 11 5 8 3 273.39 2.27 12 5 9 4 271.52 3.06 13 6 9 3 289.33 1.84 14 6 10 4 271.39 2.98 15 6 57 51 66.94 0.41 16 7 10 3 271.91 3.00 17 7 11 4 273.01 2.17 18 7 56 49 66.92 0.41 19 7 57 50 69.52 0.46 20 7 62 55 71.16 0.95 21 7 66 59 63.68 0.70 22 8 11 3 285.93 2.16 23 8 12 4 275.43 0.04 24 9 12 3 273.87 0.82 25 9 13 4 273.87 0.82 26 10 13 3 280.54 5.43 27 10 14 4 281.66 4.87 28 10 52 42 71.28 0.90 29 10 55 45 75.25 0.42 30 10 56 46 74.61 0.75 31 11 14 3 282.87 4.26 32 11 15 4 282.54 4.42 33 11 66 55 71.69 0.97 34 11 69 58 71.36 0.85 35 11 70 59 68.98 0.24 36 12 15 3 279.13 0.72 37 12 16 4 274.02 1.05 38 13 16 3 279.14 0.72 39 13 17 4 272.84 1.65 40 13 52 39 80.78 0.49 41 14 17 3 272.85 1.65 42 14 18 4 272.83 1.65 43 14 48 34 77.11 0.51 44 14 52 38 80.78 0.48 45 15 18 3 269.22 1.32 46 15 19 4 266.72 0.07 47 15 70 55 80.78 0.48 48 15 73 58 77.75 0.03 49 15 74 59 74.60 0.12 50 15 77 62 74.51 0.07 51 16 19 3 270.38 0.33 52 16 20 4 264.86 0.12 53 17 20 3 286.05 1.89 54 17 21 4 264.86 0.12 55 17 48 31 81.34 0.29 56 17 52 35 81.53 0.33 57 18 21 3 273.79 1.28 58 18 22 4 263.76 0.67 59 18 41 23 81.28 0.30 60 18 44 26 81.30 0.32 61 18 45 27 81.28 0.30 62 18 48 30 81.37 0.29 63 18 74 56 81.20 0.33 64 18 77 59 81.16 0.32 65 18 78 60 81.16 0.30 66 19 22 3 272.36 2.00 67 19 23 4 262.38 1.35 68 19 77 58 81.17 0.32 69 20 23 3 275.12 0.62 70 20 24 4 258.97 0.74 71 21 24 3 281.19 1.76 72 21 25 4 275.12 0.62 73 21 44 23 81.35 0.30 74 21 48 27 81.48 0.29 75 22 25 3 278.92 2.52 76 22 77 55 81.23 0.32 77 22 78 56 81.22 0.32 78 22 81 59 80.98 0.36 79 25 44 19 81.67 0.30 80 25 81 56 81.21 0.32 81 26 29 3 289.65 4.15 82 27 30 3 278.38 0.62 83 27 81 54 81.36 0.30 84 27 84 57 81.14 0.34 85 27 85 58 78.69 0.11 86 27 88 61 52.75 1.09 87 28 88 60 59.54 0.97 88 30 37 7 224.02 17.00 89 30 85 55 81.39 0.21 90 32 36 4 264.69 2.02 91 32 37 5 263.39 2.66 92 32 85 53 81.69 0.29 93 33 36 3 266.68 1.03 94 33 37 4 264.62 2.06 95 34 37 3 275.41 0.59 96 34 38 4 271.14 0.82 97 34 85 51 81.72 0.29 98 34 86 52 81.66 0.29 99 35 38 3 289.67 2.49 100 35 39 4 275.08 2.77 101 36 39 3 279.30 4.88 102 36 40 4 275.09 2.76 103 37 40 3 275.11 2.77 104 37 41 4 275.09 2.76 105 37 81 44 82.00 0.29 106 37 82 45 81.91 0.35 107 37 85 48 81.81 0.27 108 38 41 3 275.09 2.75 109 38 42 4 275.06 2.75 110 38 82 44 81.94 0.33 111 39 42 3 275.09 2.76 112 39 43 4 271.59 1.07 113 40 43 3 271.59 1.08 114 40 44 4 271.04 0.81 115 41 44 3 275.58 0.91 116 41 45 4 268.77 0.29 117 41 78 37 82.34 0.33 118 41 81 40 82.31 0.32 119 41 82 41 82.25 0.35 120 42 45 3 281.52 2.06 121 42 46 4 267.61 0.27 122 42 71 29 84.70 0.51 123 43 46 3 274.12 0.64 124 43 47 4 265.58 3.64 125 44 47 3 271.07 0.90 126 44 48 4 271.06 0.90 127 45 48 3 271.07 0.90 128 45 49 4 271.06 0.91 129 45 74 29 83.55 0.54 130 45 75 30 83.75 0.43 131 45 78 33 83.17 0.70 132 46 49 3 280.08 2.33 133 46 50 4 272.23 0.33 134 46 71 25 84.75 0.49 135 47 50 3 279.36 1.98 136 47 51 4 272.24 0.34 137 48 51 3 275.41 0.74 138 48 52 4 271.82 0.54 139 48 74 26 84.58 0.45 140 49 52 3 280.82 2.77 141 49 53 4 275.29 2.27 142 49 70 21 86.25 1.24 143 49 71 22 84.77 0.49 144 49 74 25 84.75 0.49 145 50 53 3 277.75 1.05 146 50 54 4 280.90 0.52 147 51 54 3 284.57 0.15 148 51 55 4 277.57 1.14 149 52 55 3 272.08 2.40 150 52 56 4 272.06 2.41 151 52 67 15 96.87 3.21 152 52 70 18 96.80 3.20 153 53 56 3 282.19 1.17 154 53 67 14 96.88 3.21 155 56 63 7 120.81 3.88 156 56 66 10 103.30 0.08 157 56 67 11 107.95 2.41 158 57 62 5 226.41 3.79 159 59 62 3 274.92 5.73 160 59 63 4 233.06 5.53 161 60 63 3 259.77 1.25 162 60 64 4 245.05 0.47 163 61 65 4 269.87 0.07 164 62 65 3 274.74 2.50 165 62 66 4 270.05 0.01 166 63 66 3 278.74 0.50 167 63 67 4 274.91 2.42 168 64 67 3 279.66 0.04 169 64 68 4 274.90 2.42 170 65 68 3 277.41 1.15 171 65 69 4 270.33 0.13 172 66 69 3 281.14 1.67 173 66 70 4 270.19 0.21 174 67 70 3 272.43 0.92 175 67 71 4 266.20 2.16 176 68 72 4 268.72 1.12 177 69 72 3 276.41 2.71 178 69 73 4 270.73 0.12 179 70 73 3 273.68 0.72 180 70 74 4 271.35 0.43 181 71 74 3 274.38 0.52 182 71 75 4 272.94 1.24 183 72 75 3 278.80 0.30 184 72 76 4 275.32 0.05 185 73 76 3 275.32 0.05 186 73 77 4 276.50 0.64 187 74 77 3 282.22 3.06 188 74 78 4 271.37 0.51 189 75 78 3 277.45 1.11 190 75 79 4 274.07 1.86 191 76 79 3 284.99 1.67 192 76 80 4 276.61 1.54 193 77 80 3 292.30 0.12 194 77 81 4 275.11 0.78 195 78 81 3 275.67 1.07 196 78 82 4 272.97 0.21 197 79 82 3 275.03 0.82 198 79 83 4 272.51 0.44 199 80 83 3 274.70 0.57 200 80 84 4 271.81 2.00 201 81 84 3 274.71 0.57 202 81 85 4 259.98 7.93 203 82 85 3 271.80 2.02 204 82 86 4 267.12 2.75 205 83 86 3 268.74 3.56 206 83 87 4 270.51 2.67 207 84 87 3 272.26 0.19 208 84 88 4 272.25 0.18 209 85 88 3 274.68 1.27 210 86 89 3 285.59 1.17 211 87 91 4 257.74 7.17 212 88 91 3 271.25 3.46