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 10 8 137.31 0.24 2 3 6 3 146.38 1.64 3 3 7 4 146.19 1.70 4 4 7 3 149.87 0.41 5 4 8 4 146.20 1.70 6 4 118 114 22.04 0.73 7 5 8 3 150.30 0.19 8 5 9 4 145.04 2.28 9 5 116 111 25.01 0.17 10 5 117 112 22.34 0.67 11 5 118 113 22.33 0.66 12 6 9 3 146.19 1.70 13 6 10 4 146.80 1.40 14 7 10 3 152.41 0.48 15 7 11 4 144.25 0.12 16 8 11 3 151.33 1.02 17 8 12 4 141.49 1.07 18 8 13 5 141.48 1.07 19 8 54 46 68.42 0.72 20 8 108 100 33.59 0.48 21 8 117 109 35.66 0.04 22 8 118 110 33.81 0.59 23 8 119 111 33.37 0.60 24 8 120 112 33.33 0.59 25 9 12 3 153.58 0.10 26 9 13 4 141.47 1.07 27 9 33 24 115.34 0.09 28 9 51 42 88.18 1.33 29 10 33 23 114.79 0.31 30 10 34 24 115.44 0.07 31 10 35 25 115.42 0.07 32 11 35 24 115.43 0.06 33 11 41 30 115.44 0.04 34 11 44 33 114.23 0.20 35 11 46 35 112.98 0.42 36 12 44 32 115.22 0.06 37 12 45 33 114.26 0.23 38 12 46 34 112.96 0.42 39 12 47 35 112.94 0.43 40 12 120 108 38.24 0.97 41 13 33 20 116.06 0.24 42 13 47 34 113.00 0.41 43 13 49 36 112.98 0.41 44 13 50 37 112.84 0.43 45 13 51 38 106.82 0.24 46 13 54 41 92.09 0.87 47 14 17 3 171.10 0.10 48 14 25 11 115.94 0.30 49 14 29 15 115.95 0.30 50 14 33 19 116.09 0.24 51 14 46 32 115.25 0.04 52 14 47 33 114.35 0.18 53 14 48 34 113.00 0.41 54 15 49 34 113.00 0.41 55 15 50 35 112.97 0.40 56 17 48 31 115.53 0.10 57 18 48 30 115.55 0.10 58 18 80 62 115.59 0.12 59 19 48 29 115.62 0.12 60 19 80 61 115.60 0.12 61 19 101 82 115.78 0.18 62 20 25 5 116.17 0.26 63 20 48 28 115.76 0.11 64 20 82 62 116.00 0.24 65 20 99 79 116.14 0.24 66 20 101 81 115.97 0.26 67 22 25 3 149.74 1.04 68 23 99 76 143.74 0.47 69 24 27 3 337.38 0.06 70 24 28 4 337.37 0.07 71 25 28 3 337.48 0.01 72 25 29 4 337.37 0.07 73 25 46 21 179.58 1.12 74 25 48 23 163.59 1.06 75 25 82 57 166.19 1.28 76 25 99 74 181.31 1.00 77 26 29 3 337.48 0.01 78 26 30 4 335.14 0.29 79 26 82 56 241.35 1.57 80 26 97 71 215.80 0.27 81 26 98 72 215.75 0.26 82 26 99 73 199.78 0.28 83 27 96 69 228.37 1.03 84 27 97 70 223.09 0.27 85 29 46 17 228.48 0.96 86 30 35 5 334.06 1.16 87 30 36 6 326.78 2.48 88 30 41 11 228.87 1.01 89 30 44 14 228.84 0.99 90 30 46 16 228.68 0.96 91 30 97 67 228.56 0.94 92 31 36 5 328.55 0.55 93 33 46 13 228.69 1.05 94 35 40 5 331.44 2.94 95 35 41 6 245.86 7.38 96 35 44 9 228.92 0.99 97 35 46 11 228.86 0.99 98 36 40 4 331.44 2.94 99 36 95 59 337.43 0.36 100 36 97 61 325.85 0.13 101 40 86 46 228.94 1.01 102 42 85 43 228.91 1.00 103 42 86 44 228.91 1.00 104 43 84 41 228.84 0.99 105 43 85 42 228.86 0.99 106 44 84 40 228.81 0.99 107 45 81 36 228.88 0.99 108 45 82 37 228.84 0.99 109 45 83 38 228.81 0.99 110 45 120 75 39.18 0.68 111 46 81 35 228.84 0.99 112 46 82 36 228.83 0.98 113 46 84 38 228.78 0.99 114 47 54 7 337.19 0.49 115 47 79 32 228.89 0.99 116 47 80 33 228.84 0.99 117 47 81 34 228.81 0.98 118 47 106 59 230.60 32.29 119 47 120 73 39.18 0.68 120 48 80 32 228.82 0.99 121 48 81 33 228.81 0.98 122 48 82 34 228.78 0.99 123 49 79 30 228.83 0.99 124 49 80 31 228.82 0.98 125 53 79 26 228.57 0.96 126 54 79 25 225.65 0.14 127 54 117 63 57.80 3.94 128 55 116 61 59.61 3.35 129 55 117 62 57.82 3.93 130 57 73 16 228.59 0.95 131 57 74 17 228.59 0.95 132 57 75 18 219.62 0.07 133 57 79 22 212.63 0.44 134 58 73 15 228.52 0.93 135 58 115 57 62.72 2.44 136 58 116 58 62.57 2.46 137 58 117 59 62.56 2.46 138 60 73 13 228.71 0.98 139 60 74 14 228.68 0.97 140 60 75 15 227.26 0.45 141 60 76 16 222.67 1.27 142 61 73 12 228.72 0.98 143 61 74 13 228.69 0.97 144 61 76 15 228.56 1.01 145 62 70 8 246.80 0.12 146 62 71 9 228.93 1.00 147 62 72 10 228.85 0.99 148 62 73 11 228.75 0.97 149 63 70 7 322.01 2.39 150 63 72 9 228.88 0.99 151 63 73 10 228.87 0.99 152 63 74 11 228.84 0.98 153 63 107 44 228.94 0.99 154 64 70 6 337.30 0.07 155 64 72 8 248.30 0.62 156 65 109 44 228.56 0.95 157 65 121 56 58.30 3.71 158 66 121 55 60.06 2.83 159 66 122 56 58.30 3.71 160 71 109 38 228.68 0.98 161 71 110 39 228.64 0.98 162 71 111 40 228.51 0.93 163 71 115 44 163.59 3.60 164 72 107 35 228.73 0.97 165 72 108 36 228.68 0.98 166 72 109 37 228.47 0.92 167 72 121 49 58.30 3.71 168 73 107 34 228.69 0.98 169 73 108 35 228.65 0.98 170 73 110 37 227.38 0.40 171 73 115 42 136.69 1.85 172 74 105 31 228.77 0.98 173 74 106 32 228.69 0.98 174 74 107 33 228.38 0.88 175 74 124 50 42.09 0.49 176 75 79 4 223.36 3.75 177 75 105 30 228.68 0.98 178 75 106 31 228.66 0.98 179 76 105 29 228.67 0.99 180 77 105 28 227.92 0.79 181 78 103 25 228.65 0.98 182 78 104 26 218.19 0.63 183 78 105 27 215.59 0.18 184 79 103 24 223.76 0.80 185 79 104 25 215.89 0.32 186 79 106 27 211.00 0.79 187 80 101 21 228.69 0.98 188 80 102 22 227.92 0.78 189 80 103 23 215.59 0.18 190 81 101 20 222.97 0.59 191 81 102 21 215.90 0.32 192 81 104 23 200.56 1.03 193 81 106 25 162.88 0.61 194 82 99 17 228.66 0.99 195 82 100 18 222.92 0.61 196 82 101 19 215.66 0.21 197 83 98 15 228.68 0.98 198 83 99 16 217.76 0.38 199 83 100 17 215.66 0.21 200 84 97 13 228.65 0.98 201 84 98 14 216.69 0.15 202 85 97 12 228.66 0.98 203 85 98 13 228.46 0.96 204 86 90 4 295.51 2.70 205 86 96 10 228.81 0.99 206 86 97 11 228.68 0.98 207 87 90 3 335.69 0.57 208 87 96 9 228.84 1.01 209 87 97 10 228.81 0.99 210 87 98 11 228.79 1.00 211 90 94 4 336.97 0.12 212 90 95 5 229.11 1.02 213 90 96 6 229.06 1.02 214 104 123 19 40.31 0.33 215 104 124 20 39.03 0.60 216 105 123 18 41.11 0.05 217 105 124 19 39.10 0.64 218 106 120 14 57.76 3.85 219 106 122 16 43.23 0.97 220 106 123 17 41.12 0.01 221 107 121 14 54.59 3.16 222 107 122 15 43.79 0.70 223 107 124 17 42.49 0.70 224 108 117 9 62.45 2.51 225 108 119 11 58.43 3.77 226 108 120 12 57.77 3.85 227 108 121 13 57.53 3.88 228 109 117 8 62.57 2.46 229 109 118 9 62.51 2.45 230 109 119 10 61.55 2.31 231 110 115 5 135.63 1.33 232 110 116 6 63.29 2.15 233 110 117 7 62.57 2.46 234 110 118 8 62.56 2.46 235 111 115 4 136.26 1.65 236 111 116 5 65.32 1.16 237 111 118 7 62.57 2.46 238 112 115 3 153.33 1.54