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 6 9 3 323.03 0.06 2 6 10 4 317.87 2.52 3 6 63 57 30.38 0.21 4 6 64 58 30.36 0.20 5 6 67 61 30.61 0.30 6 6 69 63 30.38 0.21 7 7 10 3 322.65 0.12 8 7 11 4 317.87 2.52 9 7 69 62 30.62 0.29 10 8 11 3 322.49 0.21 11 8 12 4 317.85 2.53 12 9 12 3 323.17 0.14 13 9 13 4 317.83 2.52 14 9 45 36 38.13 1.25 15 9 50 41 38.16 1.23 16 9 60 51 35.96 1.28 17 9 64 55 32.10 0.49 18 10 13 3 319.24 2.17 19 10 14 4 316.88 1.57 20 10 64 54 35.66 1.41 21 10 69 59 31.54 0.61 22 10 70 60 31.54 0.61 23 10 99 89 19.59 0.15 24 11 14 3 318.67 2.45 25 11 15 4 316.88 1.56 26 12 15 3 325.33 0.80 27 12 19 7 176.21 6.28 28 12 44 32 38.68 1.19 29 13 19 6 176.16 6.30 30 13 20 7 176.15 6.30 31 13 41 28 37.80 1.57 32 13 44 31 38.67 1.19 33 13 45 32 38.67 1.19 34 13 64 51 37.12 1.85 35 13 99 86 23.73 1.68 36 14 99 85 23.46 1.86 37 15 18 3 335.31 4.78 38 15 19 4 212.81 3.12 39 15 22 7 186.44 1.21 40 16 22 6 176.25 6.30 41 18 44 26 45.02 1.22 42 19 44 25 45.02 1.22 43 20 36 16 43.88 0.64 44 20 44 24 45.02 1.22 45 20 99 79 40.55 0.79 46 22 34 12 43.88 0.65 47 23 34 11 44.90 0.15 48 23 35 12 45.80 0.40 49 24 31 7 186.48 3.60 50 24 32 8 185.41 3.08 51 24 34 10 51.28 0.52 52 25 31 6 194.38 0.34 53 25 32 7 185.41 3.08 54 25 35 10 53.93 0.72 55 26 30 4 274.68 7.71 56 26 31 5 194.38 0.34 57 27 30 3 335.04 1.95 58 27 32 5 255.50 0.76 59 32 35 3 325.30 2.66 60 33 98 65 77.15 1.14 61 33 99 66 74.70 0.06 62 34 98 64 80.61 1.55 63 34 99 65 74.98 0.05 64 35 96 61 91.86 0.45 65 35 98 63 80.78 1.48 66 36 40 4 315.35 1.51 67 36 41 5 310.95 1.18 68 36 70 34 91.83 0.43 69 36 96 60 91.91 0.46 70 36 97 61 91.76 0.41 71 36 98 62 91.74 0.41 72 36 99 63 91.75 0.41 73 37 40 3 321.17 3.89 74 37 93 56 106.05 1.54 75 37 95 58 104.62 0.83 76 38 41 3 333.72 1.85 77 38 42 4 318.51 1.18 78 38 89 51 107.06 1.27 79 38 90 52 107.04 1.27 80 38 91 53 108.55 0.51 81 38 92 54 108.53 0.50 82 38 95 57 106.14 1.50 83 38 97 59 93.84 0.27 84 39 42 3 323.98 1.55 85 39 43 4 316.60 2.13 86 39 91 52 108.73 0.58 87 40 43 3 326.30 2.71 88 40 44 4 311.66 1.53 89 41 44 3 317.90 0.24 90 41 45 4 311.64 1.53 91 41 61 20 179.52 1.86 92 41 89 48 109.67 0.89 93 42 45 3 323.04 3.66 94 42 46 4 306.64 1.75 95 42 54 12 200.59 1.77 96 42 57 15 181.72 0.83 97 42 58 16 180.35 1.51 98 42 61 19 179.56 1.83 99 42 89 47 109.70 0.88 100 42 91 49 109.15 0.71 101 43 46 3 321.80 4.27 102 43 47 4 304.39 2.87 103 44 47 3 319.68 5.33 104 44 48 4 303.25 0.28 105 45 48 3 316.68 3.12 106 45 50 5 256.63 2.96 107 45 51 6 230.24 1.55 108 45 57 12 196.03 4.04 109 45 60 15 197.59 3.08 110 46 51 5 227.12 2.48 111 46 52 6 226.22 2.93 112 46 53 7 213.30 4.44 113 46 54 8 212.24 4.03 114 46 57 11 200.66 1.74 115 48 51 3 342.12 0.51 116 51 56 5 287.73 2.86 117 51 57 6 221.96 1.77 118 51 60 9 220.38 0.98 119 52 56 4 310.55 0.29 120 53 56 3 317.12 3.58 121 53 57 4 319.50 1.51 122 54 57 3 322.50 1.49 123 54 58 4 319.50 1.50 124 55 58 3 320.39 1.95 125 55 59 4 319.50 1.50 126 56 59 3 324.06 0.70 127 56 60 4 319.49 1.50 128 57 60 3 317.37 0.98 129 57 61 4 312.89 1.07 130 58 61 3 317.79 0.54 131 58 62 4 313.06 1.15 132 58 91 33 157.56 2.02 133 59 62 3 316.94 0.80 134 59 63 4 316.98 0.78 135 60 63 3 321.73 0.04 136 60 64 4 319.01 1.79 137 61 64 3 320.11 1.25 138 61 65 4 319.94 1.33 139 61 89 28 159.15 2.54 140 62 65 3 321.80 1.16 141 62 66 4 318.99 1.80 142 62 89 27 158.33 2.15 143 63 66 3 321.00 0.80 144 63 67 4 318.99 1.80 145 64 67 3 322.46 0.07 146 64 68 4 320.97 0.79 147 64 69 5 276.46 0.27 148 64 70 6 259.28 8.30 149 65 68 3 317.24 1.08 150 65 70 5 239.40 5.28 151 65 71 6 239.40 5.29 152 65 72 7 239.25 5.36 153 65 88 23 159.36 2.54 154 65 89 24 159.36 2.54 155 65 97 32 159.27 2.54 156 70 97 27 159.46 2.64 157 70 98 28 159.09 2.50 158 70 99 29 156.96 1.72 159 71 97 26 159.50 2.64 160 71 98 27 159.31 2.60 161 72 77 5 254.28 8.26 162 72 96 24 159.69 2.60 163 72 97 25 159.60 2.59 164 72 98 26 159.61 2.59 165 73 77 4 304.68 0.48 166 73 96 23 159.69 2.60 167 73 98 25 159.63 2.60 168 74 78 4 305.76 0.39 169 74 96 22 160.03 2.69 170 75 78 3 318.30 6.66 171 75 79 4 306.70 0.83 172 76 79 3 320.66 5.48 173 76 80 4 309.05 0.32 174 76 90 14 161.88 2.93 175 76 94 18 161.57 3.02 176 76 95 19 161.19 2.82 177 77 80 3 318.32 1.15 178 77 81 4 315.16 2.73 179 77 90 13 161.88 2.93 180 77 95 18 161.19 2.82 181 77 97 20 161.13 2.81 182 78 81 3 322.43 0.55 183 78 82 4 312.62 2.09 184 79 82 3 319.61 0.52 185 79 83 4 316.03 2.31 186 80 84 4 307.91 0.26 187 80 85 5 281.49 5.48 188 80 90 10 166.81 2.99 189 81 85 4 238.12 1.02 190 81 88 7 197.27 0.63 191 85 88 3 319.27 1.05 192 87 90 3 351.19 0.56 193 88 97 9 192.38 1.42 194 89 97 8 185.94 4.65 195 90 95 5 242.84 2.69 196 90 97 7 199.34 0.41 197 92 95 3 325.58 0.95 198 93 96 3 349.19 2.40