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 36 35 31.01 0.05 2 1 84 83 27.02 0.20 3 2 5 3 306.08 1.92 4 2 6 4 287.07 1.95 5 2 28 26 30.18 0.49 6 2 29 27 33.88 0.63 7 2 30 28 41.15 1.35 8 2 36 34 38.28 0.19 9 2 83 81 29.53 0.52 10 2 84 82 30.12 0.52 11 3 84 81 32.51 0.70 12 5 28 23 55.81 0.32 13 5 29 24 55.21 0.04 14 6 27 21 56.44 0.44 15 6 28 22 55.81 0.32 16 6 43 37 54.11 0.48 17 6 83 77 54.01 0.48 18 6 88 82 54.00 0.48 19 7 26 19 62.48 0.11 20 7 27 20 58.91 1.67 21 7 29 22 58.91 1.67 22 7 88 81 54.04 0.49 23 8 25 17 70.75 0.39 24 8 26 18 62.49 0.11 25 8 81 73 58.64 1.81 26 8 91 83 54.04 0.49 27 9 24 15 83.04 0.47 28 9 25 16 82.64 0.43 29 10 13 3 366.05 3.96 30 10 23 13 85.62 0.64 31 10 24 14 82.97 0.43 32 10 25 15 82.89 0.40 33 11 14 3 350.42 1.60 34 11 23 12 85.71 0.63 35 11 24 13 85.70 0.63 36 12 22 10 85.68 0.61 37 12 23 11 85.69 0.62 38 12 24 12 85.69 0.62 39 13 22 9 85.83 0.58 40 13 24 11 85.82 0.58 41 13 47 34 85.77 0.59 42 13 69 56 85.83 0.58 43 13 77 64 85.79 0.59 44 13 79 66 85.65 0.59 45 13 95 82 54.12 0.52 46 14 95 81 54.26 0.47 47 15 77 62 86.62 0.20 48 15 95 80 54.26 0.47 49 15 96 81 54.12 0.52 50 15 97 82 54.04 0.48 51 16 96 80 54.25 0.46 52 16 97 81 54.04 0.48 53 16 98 82 54.04 0.48 54 17 20 3 315.69 2.79 55 17 77 60 126.93 0.76 56 17 97 80 54.12 0.45 57 18 71 53 139.84 1.33 58 18 72 54 142.10 0.59 59 18 73 55 142.14 0.57 60 18 74 56 140.98 0.34 61 18 75 57 134.33 0.74 62 18 77 59 129.99 0.42 63 18 97 79 54.15 0.43 64 18 100 82 35.88 1.45 65 19 72 53 142.69 0.44 66 19 73 54 142.82 0.50 67 19 100 81 34.34 1.86 68 20 70 50 143.17 0.48 69 21 70 49 143.60 0.41 70 22 68 46 144.22 0.12 71 22 69 47 143.61 0.41 72 23 67 44 150.50 2.88 73 23 68 45 144.32 0.07 74 24 47 23 154.04 1.39 75 24 66 42 154.57 1.34 76 24 67 43 154.03 1.37 77 24 69 45 154.02 1.38 78 24 79 55 144.19 0.15 79 25 65 40 156.87 2.15 80 25 66 41 156.42 2.25 81 26 43 17 160.60 0.97 82 26 45 19 159.47 1.14 83 26 64 38 159.99 1.33 84 26 65 39 157.94 1.62 85 26 66 40 156.88 2.15 86 26 67 41 156.88 2.15 87 26 81 55 143.80 0.29 88 27 35 8 226.87 4.70 89 27 43 16 160.87 0.93 90 27 63 36 167.25 2.16 91 27 64 37 160.25 1.21 92 28 35 7 226.77 4.71 93 28 43 15 167.71 2.50 94 28 63 35 167.92 2.50 95 28 83 55 143.69 0.32 96 29 34 5 250.79 1.56 97 29 35 6 226.84 4.69 98 30 33 3 325.42 1.25 99 30 34 4 284.49 2.21 100 30 35 5 256.77 5.50 101 30 36 6 229.30 5.91 102 35 38 3 320.72 2.78 103 35 41 6 285.05 3.41 104 35 63 28 202.03 0.22 105 35 64 29 206.31 1.04 106 36 40 4 315.60 0.21 107 36 41 5 285.06 3.41 108 36 42 6 285.05 3.41 109 36 83 47 144.15 0.13 110 36 84 48 144.13 0.12 111 37 40 3 320.51 2.67 112 37 41 4 309.82 0.10 113 38 41 3 320.31 2.12 114 38 61 23 209.44 0.50 115 38 62 24 212.68 2.11 116 38 63 25 212.06 1.83 117 41 63 22 213.16 2.33 118 41 65 24 213.44 2.35 119 41 83 42 144.15 0.13 120 42 82 40 144.22 0.14 121 42 83 41 143.74 0.34 122 42 84 42 143.71 0.34 123 43 65 22 213.47 2.35 124 43 81 38 144.24 0.16 125 43 82 39 144.16 0.15 126 43 83 40 143.73 0.35 127 44 81 37 144.23 0.16 128 44 82 38 144.13 0.17 129 45 57 12 213.83 2.32 130 45 67 22 213.79 2.34 131 45 80 35 144.22 0.15 132 45 81 36 143.88 0.28 133 45 91 46 55.29 0.35 134 46 57 11 216.51 0.98 135 46 79 33 144.28 0.18 136 46 80 34 144.17 0.17 137 47 54 7 216.62 0.94 138 47 55 8 216.56 0.94 139 47 67 20 213.86 2.33 140 47 69 22 213.81 2.33 141 47 78 31 144.33 0.18 142 47 79 32 144.25 0.18 143 48 54 6 216.61 0.95 144 48 77 29 152.72 4.31 145 48 78 30 152.64 4.33 146 48 80 32 152.63 4.34 147 49 54 5 253.11 7.53 148 49 76 27 174.06 4.66 149 50 73 23 213.62 2.35 150 50 74 24 213.27 2.21 151 50 75 25 199.06 0.74 152 50 76 26 200.47 1.45 153 51 54 3 317.94 1.82 154 51 71 20 213.85 2.35 155 52 72 20 213.97 2.38 156 53 56 3 343.67 0.90 157 53 69 16 214.09 2.38 158 54 69 15 214.09 2.38 159 56 67 11 219.61 0.14 160 56 68 12 214.58 2.27 161 56 69 13 214.49 2.30 162 57 66 9 220.78 0.69 163 57 67 10 219.61 0.14 164 58 65 7 230.58 5.39 165 58 66 8 220.80 0.69 166 58 68 10 230.30 5.45 167 59 65 6 242.16 0.41 168 60 64 4 305.95 0.44 169 60 65 5 270.79 1.47 170 61 65 4 307.48 0.33 171 62 65 3 363.41 1.02 172 69 77 8 223.24 4.10 173 71 77 6 277.01 0.95 174 73 97 24 54.40 0.42 175 73 98 25 54.21 0.47 176 73 99 26 53.38 0.42 177 73 100 27 45.29 0.81 178 74 97 23 54.41 0.42 179 74 98 24 54.16 0.45 180 74 99 25 53.86 0.52 181 75 96 21 54.43 0.41 182 75 97 22 54.39 0.42 183 76 94 18 55.05 0.34 184 76 95 19 54.52 0.41 185 76 96 20 54.33 0.46 186 76 97 21 54.32 0.46 187 77 94 17 54.81 0.28 188 77 95 18 54.44 0.41 189 77 97 20 54.33 0.46 190 78 93 15 55.09 0.34 191 78 94 16 54.44 0.40 192 79 90 11 55.58 0.22 193 79 91 12 55.26 0.33 194 79 92 13 55.25 0.33 195 79 93 14 55.15 0.30 196 80 91 11 55.26 0.33 197 81 87 6 227.03 2.62 198 81 88 7 227.03 2.62 199 81 91 10 55.25 0.34 200 82 86 4 266.72 0.25 201 82 87 5 228.47 1.90 202 83 86 3 324.83 1.43 203 87 91 4 302.46 2.56 204 87 92 5 286.94 0.81 205 88 91 3 320.45 1.48 206 88 92 4 311.52 0.59