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 79 125 46 23.62 0.68 2 79 126 47 18.98 0.54 3 80 125 45 25.04 0.04 4 80 126 46 23.46 0.60 5 80 128 48 23.41 0.84 6 81 84 3 314.22 2.77 7 81 114 33 31.82 0.05 8 81 125 44 25.04 0.04 9 81 128 47 24.82 0.17 10 82 85 3 294.55 0.87 11 83 89 6 279.20 0.20 12 84 89 5 279.20 0.20 13 84 90 6 278.54 0.06 14 84 114 30 38.39 0.00 15 84 125 41 36.47 0.96 16 85 90 5 293.70 0.26 17 85 125 40 43.86 0.90 18 86 89 3 298.09 0.94 19 86 90 4 297.10 1.44 20 87 90 3 301.00 0.52 21 87 91 4 297.12 1.42 22 87 109 22 47.60 0.01 23 87 110 23 47.60 0.01 24 88 91 3 301.48 0.63 25 88 92 4 297.12 1.42 26 89 92 3 299.18 0.52 27 89 93 4 296.20 0.96 28 90 93 3 300.79 1.32 29 90 94 4 297.36 0.39 30 90 109 19 62.27 0.87 31 90 112 22 62.27 0.87 32 90 113 23 61.63 1.19 33 90 114 24 61.63 1.19 34 90 125 35 62.27 0.87 35 90 153 63 62.32 0.89 36 91 94 3 300.85 0.53 37 91 105 14 84.70 4.55 38 91 106 15 84.75 4.58 39 91 109 18 66.10 0.97 40 92 95 3 310.03 1.68 41 93 114 21 86.93 3.46 42 93 115 22 87.01 3.46 43 94 97 3 284.82 2.23 44 94 105 11 87.08 3.48 45 94 108 14 87.08 3.48 46 94 109 15 87.08 3.48 47 94 113 19 87.08 3.48 48 94 114 20 87.06 3.46 49 94 115 21 87.08 3.48 50 94 122 28 87.08 3.48 51 96 115 19 139.73 8.92 52 97 100 3 308.44 2.54 53 97 103 6 257.94 11.93 54 97 105 8 139.82 8.94 55 97 108 11 139.83 8.94 56 97 115 18 139.74 8.92 57 97 120 23 139.88 8.97 58 97 122 25 139.85 8.97 59 97 134 37 148.60 4.68 60 98 115 17 148.56 4.70 61 98 119 21 148.62 4.69 62 98 120 22 148.58 4.69 63 99 102 3 289.82 1.34 64 99 103 4 280.06 0.86 65 99 120 21 148.96 4.53 66 99 134 35 148.63 4.70 67 100 104 4 255.34 13.21 68 100 105 5 262.37 9.70 69 102 136 34 152.56 2.81 70 102 137 35 152.56 2.81 71 103 108 5 283.69 3.86 72 103 134 31 152.60 2.82 73 103 135 32 152.61 2.81 74 103 138 35 152.58 2.81 75 103 140 37 152.59 2.81 76 104 107 3 298.01 1.09 77 104 108 4 291.54 0.12 78 105 108 3 291.55 0.12 79 105 109 4 288.63 1.57 80 106 109 3 298.29 0.82 81 106 110 4 288.64 1.57 82 107 110 3 297.53 0.42 83 107 111 4 292.44 2.12 84 107 140 33 162.81 0.16 85 108 111 3 295.06 0.82 86 108 112 4 292.45 2.12 87 108 113 5 256.44 2.67 88 108 122 14 194.25 2.00 89 108 134 26 163.71 0.15 90 108 140 32 162.72 0.22 91 109 112 3 296.28 0.20 92 109 113 4 264.34 5.92 93 110 141 31 163.35 0.10 94 111 140 29 163.53 0.14 95 111 141 30 163.08 0.09 96 111 144 33 163.04 0.10 97 111 153 42 147.00 6.12 98 112 124 12 205.24 3.44 99 112 125 13 205.18 3.48 100 112 153 41 147.00 6.13 101 113 122 9 205.34 3.38 102 113 123 10 205.33 3.40 103 113 124 11 205.25 3.44 104 113 131 18 205.09 3.50 105 113 140 27 163.80 0.21 106 113 144 31 163.77 0.20 107 114 122 8 205.59 3.27 108 114 123 9 205.37 3.38 109 114 125 11 205.47 3.48 110 115 118 3 356.86 2.48 111 115 119 4 314.37 1.92 112 115 120 5 257.07 3.85 113 115 121 6 211.71 6.07 114 115 122 7 205.65 3.25 115 116 121 5 219.97 7.28 116 116 122 6 205.92 3.23 117 116 123 7 205.96 3.25 118 118 121 3 304.44 2.04 119 120 132 12 205.29 3.60 120 120 133 13 205.29 3.60 121 120 134 14 205.28 3.59 122 121 131 10 205.35 3.62 123 121 132 11 205.28 3.60 124 122 130 8 205.37 3.62 125 122 131 9 205.36 3.62 126 122 134 12 205.32 3.62 127 123 128 5 206.06 3.35 128 123 129 6 205.43 3.65 129 123 130 7 205.36 3.62 130 124 127 3 299.91 0.16 131 124 128 4 209.06 1.86 132 124 129 5 206.06 3.37 133 124 144 20 163.83 0.18 134 124 151 27 148.47 6.75 135 125 153 28 147.47 6.32 136 126 151 25 149.84 6.08 137 126 152 26 148.47 6.75 138 126 153 27 147.46 6.31 139 127 144 17 163.88 0.20 140 127 148 21 163.75 0.15 141 127 151 24 148.45 6.77 142 129 148 19 163.79 0.16 143 130 148 18 163.86 0.19 144 131 134 3 360.66 1.43 145 131 143 12 163.94 0.20 146 131 147 16 163.86 0.18 147 131 148 17 163.88 0.20 148 134 138 4 286.42 2.77 149 134 140 6 260.66 1.97 150 134 143 9 198.42 6.83 151 135 138 3 298.57 0.51 152 138 143 5 279.26 1.03 153 139 142 3 292.14 0.24 154 139 143 4 287.60 2.35 155 140 143 3 300.53 2.27 156 140 144 4 287.62 2.38 157 141 144 3 300.53 2.27 158 141 145 4 300.52 2.27 159 141 153 12 169.92 17.57 160 141 154 13 169.66 17.50 161 141 157 16 158.46 21.61 162 141 158 17 103.08 0.02 163 141 162 21 96.56 3.17 164 142 145 3 300.53 2.27 165 142 146 4 287.63 2.37 166 142 162 20 96.56 3.17 167 142 166 24 73.75 0.63 168 143 146 3 288.62 1.89 169 143 147 4 287.63 2.37 170 144 147 3 307.53 5.45 171 144 148 4 281.06 0.23 172 144 151 7 239.25 5.49 173 144 154 10 169.68 17.48 174 145 149 4 250.06 5.29 175 145 154 9 175.11 20.20 176 145 162 17 96.58 3.16 177 145 163 18 95.81 3.10 178 145 166 21 73.75 0.62 179 145 167 22 73.75 0.62 180 146 149 3 310.00 0.23 181 146 166 20 73.76 0.63 182 146 167 21 73.74 0.64 183 148 151 3 295.25 0.63 184 148 154 6 271.19 1.42 185 149 154 5 271.31 1.36 186 149 163 14 96.53 3.15 187 149 167 18 84.31 4.66 188 151 154 3 300.44 4.92 189 151 155 4 282.57 1.19 190 152 155 3 287.45 1.25 191 152 156 4 279.58 2.70 192 153 156 3 299.62 0.51 193 153 157 4 283.20 0.89 194 154 157 3 297.05 0.78 195 154 158 4 283.18 0.88 196 154 162 8 254.46 4.75 197 154 163 9 243.21 0.87 198 155 158 3 296.06 4.04 199 155 159 4 277.14 3.71 200 155 160 5 258.90 5.63 201 155 163 8 243.21 0.88 202 158 162 4 285.45 0.56 203 159 162 3 300.72 2.54 204 159 163 4 287.33 0.26 205 160 163 3 300.72 2.54 206 160 164 4 287.32 0.26 207 161 164 3 303.66 0.23 208 161 165 4 295.36 4.38 209 162 165 3 301.36 1.38 210 162 166 4 295.12 1.74 211 163 166 3 301.37 1.38 212 163 167 4 295.12 1.74 213 164 167 3 297.18 0.71