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 2 7 5 315.19 2.48 2 3 6 3 380.47 1.61 3 3 7 4 330.89 4.51 4 4 7 3 367.21 0.10 5 6 9 3 381.63 1.16 6 8 11 3 385.85 1.35 7 8 12 4 347.39 0.99 8 9 16 7 333.66 2.93 9 10 16 6 344.86 0.60 10 11 16 5 342.87 1.60 11 12 16 4 347.61 0.76 12 13 16 3 369.24 2.52 13 13 17 4 361.86 1.03 14 14 17 3 373.66 0.33 15 14 18 4 361.86 1.03 16 15 18 3 377.98 1.56 17 16 19 3 389.95 0.27 18 17 20 3 378.72 0.12 19 17 21 4 342.67 1.42 20 17 22 5 324.88 1.12 21 18 22 4 282.53 3.95 22 18 23 5 282.53 3.95 23 24 27 3 373.03 0.24 24 25 30 5 324.52 9.68 25 30 105 75 64.93 3.79 26 32 35 3 379.24 0.69 27 32 78 46 108.81 0.92 28 32 79 47 105.67 2.43 29 33 78 45 108.81 0.92 30 33 79 46 105.89 2.38 31 33 80 47 108.78 0.93 32 33 81 48 108.78 0.93 33 34 37 3 387.31 0.75 34 34 67 33 123.28 1.97 35 34 78 44 108.86 0.92 36 35 38 3 350.04 0.64 37 35 78 43 121.69 1.18 38 36 42 6 343.86 2.48 39 37 42 5 339.49 0.30 40 37 43 6 310.03 6.05 41 37 46 9 308.42 6.86 42 37 67 30 124.48 1.51 43 37 78 41 124.46 1.50 44 38 43 5 357.48 1.02 45 38 78 40 124.54 1.45 46 39 42 3 368.73 1.93 47 39 43 4 364.54 2.63 48 40 43 3 367.47 1.29 49 40 44 4 367.48 1.30 50 40 62 22 124.62 1.50 51 40 63 23 136.25 7.32 52 40 112 72 85.75 1.36 53 41 44 3 368.66 0.71 54 41 45 4 368.66 0.71 55 42 45 3 389.30 0.42 56 42 46 4 377.46 0.12 57 43 46 3 377.46 0.12 58 43 47 4 377.46 0.12 59 43 62 19 140.06 9.21 60 43 65 22 140.09 9.21 61 43 78 35 141.09 8.81 62 43 106 63 132.19 5.24 63 44 47 3 377.46 0.12 64 44 59 15 141.91 9.06 65 45 48 3 370.93 3.39 66 46 67 21 141.80 8.85 67 46 68 22 142.06 8.93 68 47 50 3 350.00 0.20 69 47 58 11 165.37 1.16 70 47 59 12 165.44 1.19 71 47 61 14 165.36 1.16 72 47 62 15 165.37 1.17 73 47 66 19 164.27 0.83 74 47 68 21 143.38 9.59 75 50 54 4 368.57 0.68 76 50 56 6 331.25 4.79 77 50 57 7 283.10 9.16 78 50 58 8 181.44 2.89 79 50 61 11 184.44 4.38 80 50 68 18 172.12 1.63 81 50 75 25 172.15 1.61 82 51 54 3 368.57 0.68 83 54 73 19 180.30 2.52 84 55 87 32 183.53 2.49 85 55 88 33 183.62 2.50 86 55 89 34 183.63 2.49 87 56 91 35 183.92 2.45 88 56 92 36 183.62 2.49 89 56 93 37 183.61 2.49 90 57 60 3 368.98 1.88 91 57 61 4 365.49 0.12 92 58 61 3 372.12 0.31 93 58 62 4 365.50 0.12 94 59 62 3 371.85 0.45 95 59 63 4 365.24 0.01 96 60 63 3 365.50 0.12 97 60 64 4 362.41 1.43 98 60 92 32 189.41 3.24 99 61 64 3 358.48 0.54 100 61 65 4 358.48 0.54 101 61 66 5 336.54 2.67 102 61 75 14 207.62 12.06 103 61 93 32 189.40 3.23 104 62 65 3 357.78 0.51 105 62 66 4 341.25 0.80 106 63 106 43 170.32 2.58 107 63 110 47 131.25 10.14 108 64 94 30 189.50 3.28 109 64 106 42 170.29 2.56 110 65 77 12 208.19 12.34 111 65 78 13 208.22 12.35 112 65 106 41 170.28 2.56 113 66 75 9 208.23 12.32 114 66 76 10 208.25 12.31 115 66 77 11 208.19 12.35 116 66 93 27 189.72 3.23 117 66 94 28 189.71 3.23 118 67 76 9 208.26 12.33 119 67 77 10 208.27 12.33 120 67 78 11 208.59 12.48 121 68 71 3 415.04 1.19 122 68 72 4 383.72 0.07 123 68 74 6 271.10 3.50 124 69 74 5 326.76 2.83 125 69 76 7 255.80 0.03 126 71 74 3 360.73 2.62 127 71 83 12 224.94 4.61 128 73 87 14 223.81 4.84 129 74 83 9 225.03 4.59 130 74 84 10 224.95 4.58 131 74 85 11 224.71 4.49 132 74 87 13 224.71 4.49 133 75 83 8 225.03 4.59 134 75 84 9 224.98 4.57 135 75 87 12 224.94 4.58 136 76 82 6 225.12 4.58 137 76 83 7 225.01 4.60 138 77 80 3 384.32 1.79 139 77 81 4 275.23 7.47 140 77 82 5 232.44 0.95 141 77 97 20 204.59 4.13 142 77 104 27 199.71 5.63 143 79 104 25 200.75 5.26 144 79 105 26 200.74 5.26 145 80 97 17 204.78 4.09 146 80 104 24 199.74 5.63 147 81 101 20 204.65 4.10 148 82 101 19 204.62 4.11 149 83 101 18 204.64 4.10 150 84 87 3 416.78 4.28 151 84 96 12 204.71 4.08 152 84 97 13 204.68 4.10 153 84 100 16 204.65 4.10 154 87 92 5 345.60 3.10 155 87 93 6 310.33 1.90 156 87 96 9 268.44 3.98 157 88 91 3 371.69 0.14 158 91 96 5 343.92 3.97 159 91 99 8 336.06 0.29 160 92 95 3 353.37 1.31 161 92 96 4 357.00 3.12 162 93 96 3 389.06 2.58 163 93 97 4 363.39 0.82 164 94 97 3 358.10 2.58 165 94 98 4 365.57 1.16 166 94 107 13 202.84 2.94 167 94 110 16 177.19 15.35 168 95 98 3 375.32 0.04 169 95 99 4 368.33 0.22 170 96 99 3 368.92 0.09 171 96 100 4 360.81 3.96 172 97 100 3 368.92 0.09 173 97 101 4 349.13 1.31 174 97 104 7 316.11 6.36 175 97 107 10 229.74 10.48 176 98 101 3 358.74 4.82 177 98 102 4 331.26 1.67 178 98 107 9 229.74 10.48 179 99 102 3 370.57 6.23 180 101 104 3 389.85 1.69 181 104 107 3 360.38 4.32 182 104 108 4 353.20 5.88 183 106 110 4 297.25 0.04 184 106 111 5 278.51 4.61 185 107 110 3 342.56 2.10 186 110 114 4 381.73 0.74 187 111 114 3 427.61 1.62