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 4 54 50 78.08 0.72 2 4 57 53 78.14 0.72 3 6 22 16 152.06 3.62 4 6 49 43 145.90 3.61 5 6 50 44 80.34 0.35 6 6 51 45 80.34 0.35 7 6 54 48 80.34 0.35 8 7 22 15 155.96 5.12 9 7 48 41 152.78 3.97 10 8 22 14 155.99 5.11 11 8 48 40 152.78 3.97 12 9 12 3 326.84 1.82 13 9 22 13 155.99 5.11 14 9 48 39 155.77 5.22 15 9 49 40 154.87 5.02 16 10 21 11 156.00 5.11 17 10 22 12 155.99 5.11 18 10 49 39 155.88 5.16 19 11 19 8 157.56 4.53 20 11 20 9 156.24 5.18 21 11 21 10 156.00 5.11 22 11 49 38 156.02 5.09 23 12 19 7 157.76 4.62 24 12 20 8 156.25 5.19 25 12 47 35 156.81 5.10 26 12 49 37 156.05 5.09 27 13 18 5 191.94 1.43 28 13 47 34 157.86 4.69 29 14 17 3 306.54 7.40 30 14 18 4 208.92 9.90 31 14 19 5 183.47 2.81 32 14 20 6 182.98 2.58 33 14 43 29 157.88 4.69 34 14 47 33 158.49 4.42 35 15 47 32 160.30 4.46 36 16 43 27 161.60 5.12 37 19 24 5 287.06 1.33 38 20 24 4 287.06 1.33 39 20 40 20 163.88 4.33 40 20 43 23 163.72 4.40 41 20 44 24 163.71 4.40 42 20 49 29 163.69 4.40 43 21 24 3 305.76 1.58 44 21 25 4 305.64 1.53 45 21 49 28 163.93 4.33 46 22 25 3 315.53 0.23 47 22 49 27 163.94 4.33 48 25 41 16 165.22 4.06 49 25 44 19 165.25 4.07 50 25 49 24 165.26 4.08 51 25 50 25 165.27 4.08 52 25 58 33 168.62 4.74 53 25 59 34 168.81 4.83 54 26 30 4 301.30 3.71 55 26 33 7 192.43 0.56 56 26 37 11 165.22 4.00 57 26 40 14 165.97 3.71 58 26 41 15 165.28 4.06 59 26 59 33 168.83 4.83 60 27 30 3 306.75 0.97 61 27 59 32 168.84 4.83 62 28 58 30 168.81 4.83 63 28 59 31 168.81 4.83 64 30 33 3 339.77 2.01 65 30 37 7 287.58 4.04 66 31 59 28 172.62 3.12 67 31 60 29 172.70 3.08 68 31 61 30 172.59 3.12 69 32 37 5 302.49 0.01 70 33 37 4 300.94 0.77 71 33 38 5 296.36 3.03 72 33 41 8 293.05 1.36 73 33 59 26 173.12 2.94 74 33 69 36 172.19 3.17 75 34 37 3 306.93 0.60 76 34 38 4 300.96 0.77 77 35 38 3 304.75 1.12 78 35 39 4 300.95 0.77 79 36 39 3 304.74 1.12 80 36 40 4 303.32 0.42 81 37 40 3 304.71 1.25 82 37 41 4 304.02 1.47 83 38 41 3 304.51 1.23 84 38 42 4 304.02 1.47 85 38 65 27 173.05 2.91 86 38 69 31 172.59 2.98 87 39 42 3 304.41 1.28 88 39 43 4 300.74 3.10 89 39 73 34 170.33 2.23 90 40 43 3 304.51 1.23 91 40 44 4 303.08 0.52 92 41 44 3 306.16 0.36 93 41 45 4 303.12 0.49 94 41 55 14 173.22 2.91 95 41 59 18 173.41 2.85 96 41 66 25 173.04 2.92 97 41 69 28 173.01 2.92 98 42 45 3 314.42 4.97 99 42 46 4 303.06 0.46 100 42 66 24 173.09 2.87 101 42 69 27 173.00 2.91 102 42 70 28 172.85 2.88 103 42 73 31 171.69 2.79 104 43 46 3 303.04 0.45 105 43 47 4 303.03 0.45 106 43 73 30 172.16 2.77 107 44 47 3 306.82 0.82 108 44 48 4 299.29 2.31 109 44 49 5 266.20 3.50 110 44 50 6 214.70 7.71 111 45 48 3 296.97 1.34 112 45 50 5 232.00 0.95 113 45 51 6 197.37 0.42 114 45 52 7 197.36 0.42 115 45 55 10 197.36 0.42 116 45 66 21 173.45 2.85 117 46 74 28 171.97 2.68 118 46 91 45 24.96 0.57 119 50 54 4 307.54 2.88 120 50 55 5 301.62 0.07 121 51 54 3 315.38 1.04 122 51 55 4 309.12 2.09 123 52 55 3 310.46 1.43 124 52 56 4 307.55 2.88 125 52 63 11 204.73 2.41 126 52 66 14 189.14 2.04 127 52 70 18 186.63 3.14 128 53 56 3 310.45 1.43 129 53 57 4 307.52 2.88 130 53 63 10 204.75 2.42 131 54 57 3 310.44 1.42 132 54 58 4 307.29 3.00 133 55 58 3 311.79 3.38 134 55 59 4 295.53 4.36 135 55 66 11 203.25 3.10 136 56 60 4 284.38 0.46 137 56 61 5 241.93 6.91 138 56 62 6 222.77 3.69 139 56 63 7 221.76 3.17 140 56 66 10 204.70 2.44 141 57 60 3 307.62 1.30 142 61 65 4 296.10 1.75 143 61 69 8 288.62 1.31 144 62 65 3 301.32 0.19 145 62 66 4 296.94 1.92 146 63 66 3 305.42 1.85 147 63 67 4 297.00 1.95 148 64 67 3 312.38 1.26 149 64 68 4 301.63 1.62 150 65 68 3 305.53 2.17 151 65 69 4 304.19 2.91 152 66 69 3 305.39 2.31 153 66 70 4 299.00 2.94 154 67 70 3 309.97 3.07 155 67 71 4 298.93 2.95 156 68 71 3 302.79 1.02 157 68 72 4 298.85 2.99 158 69 72 3 304.45 0.18 159 69 73 4 298.30 3.27 160 70 73 3 308.22 2.07 161 70 74 4 275.95 3.22 162 70 75 5 278.86 1.20 163 70 92 22 26.32 0.91 164 70 93 23 26.32 0.91 165 70 94 24 26.18 0.89 166 71 75 4 272.23 4.50 167 71 76 5 240.80 0.71 168 71 95 24 25.16 0.83 169 72 76 4 255.27 6.52 170 73 76 3 300.01 3.41 171 74 88 14 28.41 0.39 172 74 92 18 28.44 0.41 173 75 78 3 319.74 0.24 174 75 89 14 28.46 0.42 175 75 92 17 28.46 0.41 176 75 95 20 25.92 0.88 177 77 85 8 48.52 0.12 178 78 89 11 114.57 33.13 179 78 95 17 28.73 0.12 180 81 85 4 283.86 1.67 181 81 89 8 273.99 3.27 182 82 85 3 306.75 1.06 183 82 86 4 306.72 1.07 184 83 86 3 317.20 0.40 185 84 87 3 312.63 1.89 186 84 88 4 306.25 1.30 187 85 88 3 308.56 1.26 188 85 89 4 304.84 0.60 189 86 89 3 307.98 0.97 190 86 90 4 302.22 0.70 191 87 90 3 302.63 0.91 192 87 91 4 302.19 0.69 193 88 91 3 310.81 0.10 194 88 92 4 295.93 0.58 195 89 92 3 296.32 0.33 196 89 95 6 244.44 9.97 197 92 95 3 352.10 1.08