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 12 64 52 28.98 2.15 2 12 65 53 33.68 1.06 3 13 63 50 32.18 0.54 4 13 64 51 32.27 0.50 5 14 64 50 41.09 0.18 6 15 19 4 274.62 4.35 7 15 24 9 116.86 39.26 8 15 27 12 116.82 39.24 9 15 59 44 41.12 0.17 10 15 64 49 41.26 0.10 11 16 64 48 41.40 0.03 12 16 65 49 41.41 0.03 13 16 66 50 45.31 1.66 14 17 21 4 326.36 2.65 15 17 66 49 52.31 1.84 16 17 67 50 52.90 1.55 17 17 76 59 44.23 1.06 18 18 21 3 359.37 1.09 19 19 24 5 292.25 2.08 20 19 76 57 66.42 0.04 21 20 23 3 296.66 4.03 22 20 24 4 298.62 0.21 23 21 24 3 305.04 2.99 24 21 25 4 298.64 0.21 25 21 76 55 66.59 0.04 26 21 80 59 66.48 0.01 27 21 83 62 66.50 0.00 28 21 85 64 66.52 0.01 29 22 25 3 310.91 1.69 30 22 26 4 301.86 2.29 31 22 85 63 66.50 0.01 32 23 26 3 305.63 0.41 33 23 27 4 300.90 1.34 34 24 27 3 313.20 0.91 35 24 28 4 307.48 1.95 36 24 60 36 70.92 0.36 37 24 76 52 70.56 0.19 38 24 80 56 70.44 0.24 39 25 28 3 313.33 0.97 40 25 29 4 307.48 1.95 41 25 80 55 70.49 0.22 42 25 85 60 70.41 0.26 43 26 29 3 307.49 1.95 44 26 30 4 307.47 1.95 45 27 30 3 305.00 0.70 46 27 33 6 221.82 6.01 47 27 59 32 71.19 0.39 48 27 63 36 71.30 0.40 49 28 33 5 227.50 8.85 50 28 35 7 130.69 3.84 51 28 36 8 125.80 1.43 52 28 37 9 125.80 1.43 53 28 56 28 70.92 0.37 54 28 59 31 71.14 0.39 55 28 60 32 71.17 0.41 56 28 80 52 70.91 0.29 57 29 37 8 125.77 1.43 58 29 103 74 41.65 0.41 59 30 33 3 302.55 0.03 60 31 36 5 206.15 2.54 61 33 36 3 323.36 0.95 62 33 59 26 100.67 0.91 63 33 63 30 100.68 0.90 64 34 59 25 100.67 0.91 65 34 63 29 100.69 0.90 66 35 40 5 291.89 0.24 67 35 51 16 105.75 3.46 68 35 55 20 100.67 0.92 69 35 56 21 100.67 0.92 70 35 59 24 100.69 0.91 71 36 51 15 117.24 2.29 72 37 51 14 117.25 2.29 73 37 103 66 88.18 0.22 74 38 48 10 132.41 1.47 75 38 49 11 120.64 0.62 76 39 47 8 170.05 14.30 77 39 48 9 132.71 1.31 78 39 49 10 132.40 1.47 79 40 46 6 226.14 3.98 80 40 47 7 222.06 5.99 81 40 50 10 132.63 1.35 82 40 51 11 132.64 1.34 83 40 55 15 120.50 0.66 84 41 44 3 322.34 1.09 85 41 45 4 246.96 0.43 86 41 46 5 226.15 3.98 87 41 47 6 226.15 3.98 88 42 45 3 312.16 0.72 89 42 47 5 243.77 2.02 90 42 100 58 101.33 0.80 91 43 100 57 101.37 0.79 92 47 50 3 326.53 0.22 93 49 102 53 106.03 1.55 94 50 100 50 107.49 1.77 95 50 101 51 107.45 1.76 96 50 102 52 106.79 1.93 97 51 55 4 282.74 1.81 98 51 56 5 287.31 0.48 99 51 101 50 107.50 1.77 100 51 102 51 107.48 1.77 101 52 55 3 308.44 0.26 102 52 56 4 297.55 0.32 103 52 97 45 111.75 2.17 104 52 98 46 111.75 2.16 105 52 99 47 111.70 2.15 106 52 100 48 110.92 2.16 107 52 101 49 107.50 1.77 108 53 56 3 298.91 0.36 109 53 57 4 299.16 0.48 110 53 95 42 111.74 2.16 111 53 97 44 111.75 2.16 112 54 57 3 306.56 0.68 113 54 58 4 300.46 0.16 114 54 97 43 111.73 2.17 115 55 58 3 309.12 0.85 116 55 59 4 300.45 0.15 117 56 59 3 309.13 0.86 118 56 60 4 300.80 0.32 119 56 80 24 112.16 2.33 120 56 86 30 111.43 2.06 121 57 60 3 310.49 0.18 122 57 61 4 300.79 0.32 123 57 73 16 112.35 2.34 124 57 74 17 112.29 2.31 125 57 77 20 112.17 2.31 126 57 97 40 112.22 2.29 127 58 62 4 289.41 0.15 128 59 62 3 289.41 0.15 129 59 63 4 289.40 0.14 130 60 64 4 276.30 6.67 131 60 65 5 251.34 5.75 132 60 67 7 236.96 1.44 133 60 76 16 112.37 2.33 134 60 77 17 112.34 2.33 135 61 64 3 310.35 3.27 136 67 72 5 231.17 4.76 137 67 73 6 226.96 6.85 138 67 76 9 206.12 1.03 139 68 72 4 290.94 1.45 140 69 72 3 307.62 2.19 141 69 73 4 294.86 1.19 142 70 73 3 306.74 0.61 143 70 74 4 296.37 1.05 144 71 74 3 302.93 1.29 145 71 75 4 298.79 0.78 146 72 75 3 301.80 2.27 147 72 76 4 299.62 0.36 148 73 76 3 308.88 2.80 149 73 77 4 301.97 0.91 150 74 77 3 301.97 0.91 151 74 78 4 301.54 0.69 152 74 97 23 187.84 1.06 153 75 78 3 302.79 0.07 154 75 79 4 299.11 0.49 155 76 79 3 304.69 0.82 156 76 80 4 298.36 0.24 157 77 80 3 301.54 1.82 158 77 81 4 301.91 0.77 159 77 95 18 190.07 0.35 160 77 97 20 188.25 0.97 161 78 81 3 304.25 0.47 162 78 82 4 301.92 0.77 163 78 95 17 189.03 0.88 164 79 82 3 307.07 0.95 165 79 83 4 301.04 0.96 166 80 83 3 307.78 0.59 167 80 84 4 304.02 0.53 168 80 85 5 292.53 0.46 169 80 86 6 288.14 1.73 170 81 84 3 309.50 1.66 171 81 85 4 295.00 0.69 172 81 86 5 272.39 2.48 173 81 88 7 268.35 4.50 174 81 93 12 193.50 0.86 175 81 94 13 193.03 0.62 176 81 95 14 192.36 0.70 177 82 93 11 193.74 0.74 178 82 94 12 192.81 0.72 179 82 95 13 192.63 0.80 180 85 103 18 186.59 1.16 181 85 104 19 183.04 0.53 182 86 93 7 202.44 1.18 183 86 95 9 194.00 0.59 184 86 101 15 187.92 1.08 185 86 102 16 187.16 1.01 186 86 103 17 186.59 1.16 187 86 104 18 186.53 1.18 188 87 93 6 202.46 1.18 189 87 101 14 187.93 1.08 190 87 102 15 187.44 0.97 191 87 103 16 186.87 1.03 192 87 104 17 186.51 1.19 193 87 105 18 186.59 1.16 194 88 93 5 205.83 2.87 195 88 94 6 213.59 6.73 196 88 95 7 202.42 1.17 197 88 96 8 202.36 1.16 198 88 101 13 187.93 1.08 199 89 99 10 192.49 0.85 200 89 101 12 188.53 1.10 201 90 93 3 315.98 0.18 202 90 94 4 307.28 2.46 203 90 101 11 191.81 0.99 204 96 101 5 271.81 3.04