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 22.16 0.21 2 79 126 47 21.23 0.57 3 80 125 45 24.80 0.12 4 80 126 46 22.09 0.22 5 80 127 47 22.07 0.21 6 80 128 48 22.09 0.17 7 81 84 3 314.22 2.77 8 81 114 33 34.02 0.82 9 81 125 44 24.82 0.11 10 81 128 47 24.80 0.12 11 82 85 3 293.14 1.57 12 83 89 6 281.38 2.47 13 84 89 5 281.38 2.47 14 84 90 6 263.94 1.60 15 84 114 30 41.08 1.20 16 84 125 41 35.20 0.33 17 85 90 5 290.14 2.06 18 85 125 40 42.55 1.55 19 86 89 3 298.09 0.94 20 86 90 4 292.37 0.96 21 87 90 3 301.00 0.52 22 87 91 4 292.37 0.96 23 87 109 22 48.41 0.42 24 87 110 23 47.15 0.21 25 88 91 3 301.48 0.63 26 88 92 4 297.11 1.42 27 89 92 3 299.18 0.52 28 89 93 4 296.19 0.96 29 90 93 3 300.79 1.32 30 90 94 4 297.36 0.39 31 90 109 19 76.97 6.46 32 90 112 22 63.22 0.40 33 90 113 23 63.22 0.40 34 90 114 24 63.21 0.40 35 90 125 35 63.26 0.38 36 90 153 63 63.33 0.40 37 91 94 3 302.22 0.61 38 91 105 14 84.76 3.82 39 91 106 15 83.51 3.20 40 91 109 18 83.46 3.20 41 92 95 3 310.03 1.68 42 93 114 21 86.23 4.21 43 93 115 22 86.22 4.22 44 94 97 3 288.00 0.34 45 94 105 11 86.26 4.21 46 94 108 14 86.26 4.21 47 94 109 15 86.26 4.21 48 94 113 19 86.28 4.21 49 94 114 20 86.28 4.21 50 94 115 21 86.28 4.21 51 94 122 28 86.28 4.21 52 96 115 19 143.27 6.76 53 97 100 3 310.36 3.50 54 97 103 6 275.83 2.98 55 97 105 8 177.35 10.27 56 97 108 11 177.63 10.22 57 97 115 18 143.40 6.70 58 97 120 23 144.21 6.52 59 97 122 25 143.94 6.65 60 97 134 37 144.51 6.54 61 98 115 17 144.49 6.54 62 98 119 21 144.50 6.54 63 98 120 22 144.33 6.46 64 99 102 3 290.90 1.29 65 99 103 4 279.58 3.70 66 99 120 21 144.64 6.47 67 99 134 35 145.39 6.09 68 100 103 3 295.00 0.06 69 100 104 4 270.77 5.49 70 100 105 5 251.27 4.26 71 102 136 34 150.90 3.83 72 102 137 35 150.95 3.83 73 103 108 5 280.38 5.46 74 103 134 31 150.96 3.77 75 103 135 32 151.01 3.81 76 103 138 35 151.00 3.81 77 103 140 37 150.97 3.83 78 104 107 3 298.37 1.27 79 104 108 4 292.32 0.49 80 105 108 3 292.33 0.49 81 105 109 4 292.31 0.50 82 106 109 3 298.29 0.82 83 106 110 4 289.41 1.95 84 107 110 3 297.53 0.42 85 107 111 4 289.10 3.79 86 107 140 33 155.33 5.25 87 108 111 3 294.25 1.23 88 108 112 4 289.11 3.79 89 108 113 5 264.43 5.39 90 108 122 14 192.05 0.69 91 108 134 26 155.65 5.39 92 108 140 32 155.40 5.30 93 109 112 3 298.88 1.09 94 109 113 4 273.40 4.15 95 110 141 31 155.60 5.38 96 111 140 29 155.60 5.38 97 111 141 30 155.58 5.37 98 111 144 33 155.56 5.38 99 111 153 42 138.77 0.96 100 112 124 12 207.23 5.57 101 112 125 13 207.25 5.56 102 112 153 41 138.78 0.96 103 113 122 9 207.38 5.53 104 113 123 10 207.27 5.58 105 113 124 11 207.25 5.57 106 113 131 18 207.22 5.56 107 113 140 27 155.64 5.38 108 113 144 31 155.58 5.39 109 114 122 8 207.62 5.62 110 114 123 9 207.38 5.53 111 114 125 11 207.44 5.57 112 115 118 3 350.83 0.54 113 115 119 4 314.37 1.92 114 115 121 6 207.70 5.61 115 115 122 7 207.64 5.62 116 116 121 5 221.37 1.23 117 116 122 6 207.69 5.60 118 116 123 7 207.69 5.60 119 118 121 3 304.87 1.83 120 120 132 12 207.36 5.58 121 120 133 13 207.35 5.58 122 120 134 14 207.27 5.56 123 121 131 10 207.38 5.58 124 121 132 11 207.36 5.58 125 122 130 8 207.39 5.58 126 122 131 9 207.38 5.58 127 122 134 12 207.33 5.59 128 123 128 5 209.52 4.59 129 123 129 6 209.49 4.59 130 123 130 7 207.38 5.59 131 124 127 3 299.91 0.16 132 124 128 4 209.53 4.59 133 124 129 5 209.52 4.59 134 124 144 20 155.59 5.39 135 124 151 27 139.50 0.93 136 125 153 28 139.44 0.94 137 126 151 25 140.37 0.48 138 126 152 26 140.37 0.48 139 126 153 27 139.44 0.94 140 127 144 17 155.68 5.38 141 127 148 21 155.08 5.28 142 127 151 24 140.35 0.49 143 129 148 19 155.13 5.29 144 130 148 18 155.20 5.31 145 131 134 3 362.78 0.36 146 131 143 12 155.66 5.38 147 131 147 16 155.42 5.33 148 131 148 17 155.24 5.33 149 134 138 4 286.41 2.77 150 134 140 6 233.79 1.99 151 134 143 9 215.72 1.70 152 135 138 3 297.49 1.05 153 138 143 5 287.75 2.28 154 139 142 3 291.99 0.17 155 139 143 4 289.20 1.56 156 140 143 3 300.52 2.27 157 140 144 4 289.23 1.57 158 141 144 3 300.52 2.27 159 141 145 4 294.19 0.90 160 141 153 12 176.90 19.78 161 141 154 13 138.22 0.71 162 141 157 16 123.36 0.01 163 141 158 17 105.78 8.78 164 141 162 21 81.49 0.28 165 142 145 3 302.41 1.32 166 142 146 4 289.23 1.57 167 142 162 20 81.48 0.28 168 142 166 24 73.66 0.58 169 143 146 3 289.21 1.59 170 143 147 4 288.01 2.19 171 144 147 3 307.53 5.45 172 144 148 4 276.42 3.48 173 144 151 7 251.43 5.67 174 144 154 10 138.76 0.96 175 145 149 4 262.63 0.06 176 145 154 9 176.28 19.48 177 145 162 17 81.49 0.28 178 145 163 18 79.45 0.45 179 145 166 21 73.73 0.55 180 145 167 22 73.72 0.55 181 146 149 3 310.00 0.23 182 146 166 20 73.72 0.55 183 146 167 21 73.64 0.58 184 148 151 3 295.25 0.62 185 148 154 6 272.68 3.75 186 149 154 5 282.70 1.22 187 149 163 14 81.42 0.28 188 149 167 18 73.81 0.58 189 151 154 3 291.39 0.83 190 151 155 4 283.31 0.92 191 152 155 3 287.55 1.20 192 152 156 4 283.31 0.92 193 153 156 3 299.62 0.51 194 153 157 4 283.30 0.92 195 154 157 3 293.20 2.70 196 154 158 4 283.22 0.90 197 154 163 9 226.37 3.46 198 155 158 3 293.20 2.70 199 155 159 4 273.31 5.81 200 155 160 5 273.31 5.81 201 155 163 8 251.03 5.30 202 158 162 4 285.57 0.49 203 159 162 3 300.72 2.54 204 159 163 4 291.73 1.95 205 160 163 3 300.72 2.54 206 160 164 4 285.92 0.34 207 161 164 3 304.95 0.42 208 161 165 4 295.35 4.38 209 162 165 3 301.51 1.30 210 162 166 4 295.12 1.74 211 163 166 3 303.28 0.42 212 163 167 4 287.68 1.99 213 164 167 3 295.12 1.74