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 21.66 0.34 2 79 126 47 20.07 0.03 3 80 125 45 24.84 0.14 4 80 126 46 23.50 0.58 5 80 128 48 23.68 0.67 6 81 84 3 314.22 2.77 7 81 114 33 33.87 1.10 8 81 125 44 25.04 0.04 9 81 128 47 24.85 0.15 10 82 85 3 294.55 0.87 11 83 89 6 279.53 0.04 12 84 89 5 283.81 2.10 13 84 90 6 263.10 1.93 14 84 114 30 38.19 0.03 15 84 125 41 35.26 0.35 16 85 90 5 291.90 1.19 17 85 125 40 43.05 0.23 18 86 89 3 297.71 1.12 19 86 90 4 291.92 1.19 20 87 90 3 297.12 1.42 21 87 91 4 293.67 0.31 22 87 109 22 47.37 0.30 23 87 110 23 47.36 0.29 24 88 91 3 301.48 0.63 25 88 92 4 293.68 0.29 26 89 92 3 299.18 0.52 27 89 93 4 296.19 0.96 28 90 93 3 301.62 0.92 29 90 94 4 297.36 0.39 30 90 109 19 69.61 5.17 31 90 112 22 69.61 5.17 32 90 113 23 69.60 5.17 33 90 114 24 69.34 5.04 34 90 125 35 69.35 5.04 35 90 153 63 69.61 5.17 36 91 94 3 301.62 0.92 37 91 105 14 87.52 2.45 38 91 106 15 86.58 2.92 39 91 109 18 69.69 5.17 40 92 95 3 310.03 1.68 41 93 114 21 89.09 2.04 42 93 115 22 89.17 2.04 43 94 97 3 283.13 1.62 44 94 105 11 89.18 2.02 45 94 108 14 89.20 2.02 46 94 109 15 89.20 2.01 47 94 113 19 89.20 2.02 48 94 114 20 89.20 2.02 49 94 115 21 89.21 2.02 50 94 122 28 89.23 2.02 51 97 100 3 307.57 2.98 52 97 103 6 259.19 2.16 53 97 105 8 128.55 3.35 54 97 108 11 128.56 3.34 55 97 115 18 124.92 1.57 56 97 120 23 128.57 3.37 57 97 122 25 126.24 2.21 58 97 134 37 128.65 3.37 59 98 115 17 128.62 3.37 60 98 119 21 131.57 1.94 61 98 120 22 128.62 3.37 62 99 102 3 290.41 1.04 63 99 103 4 270.55 5.62 64 99 120 21 132.02 2.12 65 99 134 35 138.19 3.27 66 100 104 4 249.49 7.00 67 100 105 5 249.47 7.00 68 102 136 34 143.41 5.42 69 102 137 35 143.43 5.42 70 103 108 5 282.87 2.13 71 103 134 31 143.43 5.42 72 103 135 32 151.38 1.46 73 103 138 35 147.11 3.58 74 103 140 37 147.12 3.58 75 104 107 3 298.37 1.27 76 104 108 4 289.42 1.95 77 105 108 3 292.31 0.51 78 105 109 4 285.97 3.67 79 106 109 3 300.12 0.10 80 106 110 4 289.95 1.68 81 107 110 3 297.50 0.42 82 107 111 4 291.63 2.52 83 107 140 33 163.91 0.82 84 108 111 3 297.98 0.66 85 108 112 4 294.78 0.95 86 108 113 5 270.81 6.20 87 108 122 14 187.14 2.06 88 108 134 26 164.18 0.79 89 108 140 32 163.91 0.82 90 109 112 3 298.87 1.10 91 109 113 4 263.61 0.11 92 110 141 31 164.24 0.71 93 111 140 29 164.24 0.71 94 111 141 30 164.23 0.71 95 111 144 33 164.21 0.70 96 111 153 42 141.89 4.82 97 112 124 12 200.86 4.75 98 112 125 13 200.85 4.75 99 112 153 41 141.89 4.82 100 113 122 9 201.09 4.66 101 113 123 10 200.87 4.75 102 113 124 11 200.86 4.75 103 113 131 18 200.65 4.76 104 113 140 27 164.34 0.68 105 113 144 31 164.31 0.66 106 114 122 8 201.16 4.68 107 114 123 9 201.09 4.70 108 114 125 11 200.88 4.76 109 115 119 4 313.38 2.42 110 115 120 5 237.94 1.74 111 115 121 6 207.88 7.98 112 115 122 7 201.16 4.68 113 116 121 5 232.61 4.38 114 116 122 6 201.27 4.67 115 116 123 7 201.25 4.67 116 118 121 3 304.50 2.02 117 120 132 12 200.68 4.78 118 120 133 13 200.67 4.77 119 120 134 14 200.65 4.77 120 121 131 10 200.69 4.77 121 121 132 11 200.65 4.78 122 122 130 8 200.70 4.76 123 122 131 9 200.68 4.78 124 122 134 12 200.63 4.77 125 123 128 5 200.96 4.79 126 123 129 6 200.86 4.74 127 123 130 7 200.66 4.75 128 124 127 3 299.91 0.16 129 124 128 4 207.94 1.30 130 124 129 5 200.96 4.79 131 124 144 20 164.34 0.67 132 124 151 27 155.89 1.95 133 125 153 28 155.74 2.02 134 126 151 25 159.65 0.07 135 126 152 26 159.63 0.07 136 126 153 27 142.05 4.83 137 127 144 17 164.44 0.64 138 127 148 21 163.91 0.69 139 127 151 24 156.50 1.65 140 129 148 19 164.15 0.64 141 130 148 18 164.28 0.67 142 131 134 3 370.95 3.73 143 131 143 12 164.44 0.65 144 131 147 16 164.32 0.66 145 131 148 17 164.29 0.67 146 134 138 4 286.42 2.77 147 134 140 6 251.12 3.65 148 134 143 9 212.38 0.07 149 135 138 3 297.76 0.92 150 138 143 5 287.56 2.38 151 139 142 3 291.34 0.49 152 139 143 4 287.56 2.38 153 140 143 3 300.52 2.27 154 140 144 4 287.69 2.34 155 141 144 3 300.56 2.25 156 141 145 4 294.19 0.90 157 141 153 12 211.06 3.21 158 141 154 13 173.75 15.36 159 141 157 16 162.53 19.57 160 141 158 17 104.95 4.91 161 141 162 21 85.75 5.03 162 142 145 3 301.31 1.88 163 142 146 4 289.24 1.57 164 142 162 20 85.78 5.01 165 142 166 24 69.42 1.53 166 143 146 3 289.24 1.58 167 143 147 4 289.24 1.58 168 144 147 3 309.01 4.71 169 144 148 4 286.82 2.71 170 144 151 7 231.24 2.35 171 144 154 10 211.47 3.01 172 145 149 4 263.20 0.97 173 145 154 9 220.33 2.98 174 145 162 17 86.82 4.50 175 145 163 18 85.49 5.08 176 145 166 21 69.59 1.52 177 145 167 22 69.53 1.49 178 146 149 3 310.00 0.23 179 146 166 20 69.53 1.48 180 146 167 21 69.41 1.54 181 148 151 3 302.70 3.41 182 148 154 6 273.37 3.41 183 149 154 5 281.16 0.44 184 149 163 14 85.61 5.08 185 149 167 18 69.66 1.54 186 151 154 3 301.68 4.31 187 151 155 4 282.76 1.22 188 152 155 3 296.85 1.90 189 152 156 4 282.79 1.23 190 153 156 3 299.63 0.51 191 153 157 4 282.78 1.24 192 154 157 3 299.62 0.51 193 154 158 4 280.53 2.36 194 154 163 9 231.81 3.96 195 155 158 3 293.20 2.71 196 155 159 4 268.63 0.89 197 155 160 5 261.34 0.01 198 155 163 8 241.40 1.77 199 158 162 4 283.12 0.73 200 159 162 3 301.25 2.27 201 159 163 4 295.29 0.18 202 160 163 3 300.72 2.54 203 160 164 4 286.25 0.79 204 161 164 3 304.95 0.42 205 161 165 4 295.98 4.07 206 162 165 3 301.51 1.30 207 162 166 4 295.12 1.74 208 163 166 3 303.28 0.42 209 163 167 4 287.06 2.29 210 164 167 3 295.10 1.72