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 92 89 17.69 0.42 2 4 55 51 91.23 0.70 3 4 56 52 78.41 0.75 4 4 57 53 76.19 0.18 5 4 92 88 17.70 0.42 6 5 9 4 321.04 0.12 7 5 10 5 317.45 1.67 8 5 55 50 94.26 0.03 9 5 56 51 85.59 0.48 10 5 70 65 95.16 0.24 11 5 92 87 17.70 0.42 12 6 9 3 329.65 0.15 13 6 10 4 320.12 0.36 14 6 54 48 96.31 0.65 15 6 55 49 94.48 0.08 16 6 70 64 95.19 0.24 17 6 92 86 18.18 0.66 18 7 10 3 321.00 0.07 19 7 11 4 318.36 1.24 20 7 12 5 318.51 1.29 21 7 54 47 96.56 0.58 22 7 70 63 95.19 0.24 23 7 79 72 95.18 0.24 24 8 12 4 327.80 1.01 25 9 12 3 332.96 1.49 26 9 13 4 319.62 0.77 27 9 90 81 39.01 1.05 28 10 13 3 325.31 2.25 29 10 14 4 316.26 0.17 30 10 68 58 96.86 0.42 31 10 70 60 102.28 1.16 32 10 79 69 100.30 0.74 33 10 81 71 95.97 0.46 34 11 14 3 325.06 2.12 35 11 79 68 101.85 0.33 36 13 81 68 101.89 0.33 37 13 82 69 101.88 0.33 38 13 84 71 69.92 1.10 39 13 86 73 67.31 0.21 40 13 87 74 67.30 0.21 41 13 90 77 60.91 0.01 42 14 79 65 103.10 0.86 43 14 80 66 102.98 0.82 44 14 81 67 101.89 0.33 45 14 82 68 101.92 0.34 46 15 31 16 157.12 1.43 47 15 32 17 157.10 1.43 48 15 65 50 103.10 0.86 49 15 80 65 106.13 0.64 50 15 81 66 103.10 0.86 51 15 82 67 103.06 0.85 52 16 30 14 157.24 1.41 53 16 31 15 157.12 1.44 54 16 32 16 157.11 1.43 55 16 33 17 157.10 1.44 56 16 79 63 112.33 0.62 57 16 80 64 108.00 0.29 58 17 29 12 157.50 1.34 59 17 30 13 157.27 1.42 60 17 33 16 157.16 1.43 61 17 77 60 112.67 0.69 62 17 78 61 112.46 0.59 63 17 79 62 112.37 0.61 64 18 26 8 167.74 1.74 65 18 28 10 158.06 1.11 66 18 29 11 157.55 1.33 67 18 33 15 157.24 1.41 68 18 38 20 156.77 1.28 69 18 41 23 155.91 1.00 70 18 77 59 113.65 0.21 71 18 78 60 112.48 0.59 72 18 80 62 112.47 0.59 73 19 26 7 167.81 1.74 74 19 27 8 167.71 1.76 75 19 28 9 158.07 1.11 76 19 76 57 130.35 0.96 77 19 77 58 114.01 0.32 78 20 24 4 239.51 24.16 79 20 25 5 170.87 0.24 80 20 26 6 167.78 1.73 81 20 27 7 167.72 1.76 82 20 38 18 157.27 1.40 83 20 41 21 156.80 1.31 84 20 42 22 156.60 1.41 85 20 45 25 155.77 1.06 86 20 75 55 136.00 3.23 87 20 76 56 132.59 1.92 88 21 24 3 296.91 2.15 89 21 25 4 187.11 2.03 90 21 27 6 169.68 0.82 91 21 75 54 136.06 3.25 92 21 76 55 135.94 3.25 93 22 75 53 136.10 3.27 94 22 76 54 136.09 3.27 95 24 42 18 155.84 1.02 96 24 45 21 155.84 1.02 97 24 46 22 155.84 1.02 98 24 76 52 136.12 3.26 99 26 29 3 388.42 2.29 100 26 38 12 157.27 1.40 101 27 75 48 136.12 3.26 102 29 33 4 312.31 2.35 103 29 34 5 292.12 1.85 104 29 38 9 182.08 2.17 105 30 33 3 337.59 0.16 106 30 34 4 310.50 1.44 107 31 34 3 341.50 1.30 108 32 35 3 329.81 0.35 109 32 36 4 315.86 0.57 110 32 65 33 112.36 0.61 111 33 36 3 316.84 2.17 112 33 38 5 305.20 3.16 113 33 80 47 112.37 0.61 114 36 60 24 128.97 1.36 115 36 65 29 112.68 0.65 116 36 80 44 114.03 0.34 117 37 41 4 329.87 0.17 118 37 60 23 129.22 1.49 119 38 41 3 325.37 0.29 120 40 43 3 334.53 4.15 121 40 44 4 325.25 0.33 122 40 60 20 135.44 3.37 123 41 44 3 334.37 4.22 124 41 45 4 321.35 2.28 125 41 59 18 135.46 3.37 126 41 60 19 135.34 3.42 127 41 78 37 135.53 3.34 128 41 80 39 135.53 3.34 129 42 45 3 334.11 1.57 130 42 46 4 321.36 2.27 131 43 46 3 334.12 1.56 132 43 47 4 320.83 2.53 133 44 47 3 323.86 1.02 134 44 48 4 319.17 1.71 135 44 59 15 148.25 9.54 136 45 48 3 321.78 2.04 137 45 49 4 319.19 1.72 138 45 71 26 214.34 1.27 139 45 76 31 207.47 1.96 140 45 78 33 173.19 2.85 141 46 49 3 319.73 1.45 142 46 50 4 319.21 1.73 143 47 50 3 329.99 2.16 144 47 51 4 319.21 1.73 145 48 51 3 317.94 2.39 146 48 52 4 313.00 0.01 147 48 57 9 190.20 0.76 148 48 59 11 190.21 0.77 149 48 69 21 190.58 0.57 150 48 71 23 227.99 1.12 151 49 52 3 331.97 0.61 152 49 71 22 227.97 1.12 153 49 76 27 223.57 3.33 154 51 57 6 250.82 7.58 155 52 55 3 326.68 1.24 156 52 56 4 315.30 3.72 157 52 57 5 270.66 2.16 158 52 69 17 247.39 0.51 159 52 70 18 252.56 0.56 160 52 71 19 263.38 0.52 161 53 71 18 264.52 0.00 162 54 70 16 264.56 0.01 163 55 69 14 264.67 0.01 164 55 70 15 264.65 0.01 165 55 92 37 18.17 0.66 166 56 68 12 264.61 0.01 167 56 69 13 264.67 0.01 168 56 70 14 264.67 0.01 169 57 68 11 264.69 0.01 170 57 69 12 264.71 0.01 171 58 66 8 265.25 0.26 172 58 67 9 265.24 0.25 173 58 68 10 264.71 0.02 174 59 67 8 265.31 0.24 175 59 68 9 265.31 0.23 176 59 69 10 265.25 0.18 177 59 78 19 265.17 0.13 178 60 66 6 265.38 0.24 179 60 67 7 265.31 0.24 180 60 80 20 265.11 0.10 181 61 65 4 296.90 5.76 182 61 66 5 265.38 0.24 183 61 83 22 264.66 0.03 184 62 65 3 324.23 3.29 185 62 83 21 264.75 0.04 186 63 83 20 264.76 0.04 187 64 83 19 264.77 0.03 188 65 81 16 265.14 0.07 189 65 82 17 264.68 0.01 190 65 83 18 264.68 0.02 191 66 80 14 265.30 0.06 192 66 81 15 265.14 0.07 193 66 83 17 264.56 0.06 194 67 78 11 265.56 0.01 195 67 79 12 265.50 0.01 196 67 80 13 265.23 0.03 197 68 78 10 265.57 0.01 198 68 79 11 265.55 0.01 199 68 81 13 265.47 0.02 200 69 77 8 265.64 0.02 201 69 78 9 265.59 0.01 202 70 76 6 266.25 0.07 203 70 77 7 265.87 0.04 204 70 79 9 265.63 0.03 205 71 75 4 302.68 2.56 206 71 76 5 266.25 0.07 207 72 75 3 313.93 6.08 208 72 77 5 271.32 2.56 209 72 79 7 271.33 2.57 210 81 84 3 323.43 1.85 211 85 88 3 348.69 0.61