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 76 152 76 33.89 1.86 2 77 126 49 41.93 0.23 3 77 152 75 35.24 1.35 4 77 156 79 39.71 0.45 5 79 82 3 298.97 1.09 6 79 125 46 43.45 0.32 7 79 126 47 41.45 0.01 8 80 125 45 43.60 0.28 9 80 126 46 42.89 0.03 10 80 128 48 42.98 0.01 11 81 84 3 329.70 0.20 12 81 114 33 58.76 0.13 13 81 125 44 47.25 0.83 14 82 85 3 314.64 4.43 15 83 89 6 307.56 1.54 16 84 89 5 307.59 1.53 17 84 90 6 282.30 0.30 18 84 93 9 272.64 5.15 19 84 114 30 68.70 0.07 20 84 125 41 58.84 0.14 21 85 90 5 315.13 0.23 22 85 125 40 70.11 0.46 23 86 89 3 317.26 0.84 24 86 90 4 317.43 0.90 25 87 90 3 328.91 2.67 26 87 91 4 321.44 1.09 27 87 109 22 74.34 0.38 28 87 110 23 74.34 0.39 29 88 91 3 325.85 1.09 30 88 92 4 327.63 1.00 31 89 92 3 328.19 1.28 32 89 93 4 329.12 1.74 33 90 93 3 329.94 2.15 34 90 94 4 329.95 2.15 35 90 109 19 92.91 1.17 36 90 112 22 92.83 1.21 37 90 113 23 92.02 0.80 38 90 114 24 92.01 0.80 39 90 125 35 94.47 2.02 40 90 153 63 94.58 1.97 41 91 94 3 335.55 3.10 42 91 105 14 98.09 2.34 43 91 106 15 98.09 2.35 44 91 109 18 97.66 2.25 45 92 95 3 333.31 0.41 46 93 96 3 371.75 1.15 47 93 114 21 102.10 1.23 48 93 115 22 102.14 1.24 49 94 97 3 317.24 1.58 50 94 105 11 102.12 1.23 51 94 108 14 102.14 1.23 52 94 109 15 102.15 1.24 53 94 113 19 102.20 1.25 54 94 114 20 102.20 1.25 55 94 115 21 102.21 1.25 56 94 122 28 113.56 4.41 57 96 115 19 134.03 0.45 58 96 118 22 135.00 0.90 59 97 101 4 302.48 5.73 60 97 103 6 260.62 6.02 61 97 105 8 134.09 0.52 62 97 108 11 134.13 0.49 63 97 115 18 134.16 0.51 64 97 120 23 150.05 2.04 65 97 122 25 134.21 0.51 66 97 134 37 150.13 2.08 67 98 101 3 316.92 0.53 68 98 118 20 152.86 0.70 69 98 119 21 150.12 2.07 70 102 134 32 176.90 0.56 71 102 135 33 176.87 0.54 72 102 136 34 176.93 0.51 73 103 108 5 314.02 1.32 74 103 134 31 176.95 0.54 75 103 135 32 177.00 0.51 76 103 138 35 176.97 0.53 77 103 140 37 176.95 0.52 78 104 107 3 330.99 1.43 79 104 108 4 317.28 1.65 80 105 108 3 318.32 1.13 81 105 109 4 314.17 1.25 82 106 109 3 329.94 0.41 83 106 110 4 315.71 0.47 84 107 110 3 330.96 0.11 85 107 111 4 319.24 1.25 86 107 140 33 181.80 0.53 87 108 111 3 330.96 0.11 88 108 112 4 319.24 1.25 89 108 113 5 284.49 2.54 90 108 122 14 193.06 6.12 91 108 134 26 181.96 0.57 92 108 140 32 181.82 0.52 93 109 112 3 325.58 1.96 94 109 113 4 308.20 1.63 95 110 141 31 181.88 0.52 96 110 153 43 179.61 0.01 97 111 140 29 181.90 0.51 98 111 141 30 181.84 0.51 99 111 144 33 181.84 0.52 100 111 153 42 179.61 0.01 101 112 124 12 193.04 6.13 102 112 125 13 192.88 6.15 103 112 153 41 179.71 0.03 104 113 122 9 193.44 6.08 105 113 123 10 193.28 6.04 106 113 124 11 193.02 6.09 107 113 131 18 192.82 5.77 108 113 140 27 181.97 0.53 109 113 144 31 182.00 0.56 110 114 122 8 193.46 6.08 111 114 123 9 193.44 6.07 112 114 125 11 193.39 6.07 113 114 128 14 193.24 5.96 114 115 119 4 334.56 1.36 115 115 121 6 193.61 6.13 116 115 122 7 193.47 6.07 117 116 121 5 193.62 6.13 118 116 123 7 193.54 6.09 119 120 132 12 221.71 8.68 120 120 133 13 221.63 8.71 121 120 134 14 221.63 8.71 122 121 131 10 221.85 8.74 123 121 132 11 221.68 8.73 124 122 130 8 221.88 8.75 125 122 131 9 221.86 8.75 126 122 134 12 221.75 8.78 127 123 128 5 222.08 8.71 128 123 129 6 221.94 8.77 129 123 130 7 221.88 8.75 130 124 127 3 325.92 2.65 131 124 128 4 221.97 8.77 132 124 129 5 221.97 8.77 133 124 144 20 211.12 14.01 134 124 151 27 209.66 14.64 135 125 153 28 209.63 14.66 136 126 151 25 209.72 14.67 137 126 152 26 209.71 14.67 138 126 153 27 209.64 14.64 139 127 144 17 211.19 14.04 140 127 148 21 211.03 14.11 141 127 151 24 209.66 14.63 142 129 148 19 211.09 14.07 143 130 148 18 211.22 14.01 144 131 134 3 407.28 2.29 145 131 143 12 211.28 13.98 146 131 147 16 211.22 14.02 147 131 148 17 211.24 14.00 148 134 138 4 300.82 3.27 149 134 140 6 264.19 4.41 150 134 143 9 247.83 3.95 151 135 138 3 320.56 1.73 152 139 142 3 317.82 0.56 153 139 143 4 304.54 1.86 154 140 143 3 319.29 0.40 155 140 144 4 312.71 2.23 156 141 144 3 317.86 0.32 157 141 145 4 316.70 0.26 158 141 153 12 243.11 4.71 159 141 154 13 230.42 4.57 160 141 157 16 219.34 2.71 161 141 158 17 166.33 18.73 162 141 162 21 122.18 3.17 163 142 145 3 328.23 0.61 164 142 146 4 312.74 2.24 165 142 162 20 121.81 3.34 166 142 166 24 102.13 4.20 167 143 146 3 320.40 0.13 168 143 147 4 312.74 2.23 169 144 147 3 335.55 1.79 170 144 148 4 312.57 2.19 171 144 151 7 279.38 6.89 172 144 153 9 261.31 2.14 173 144 154 10 247.46 3.96 174 145 149 4 267.17 0.79 175 145 154 9 253.94 0.71 176 145 162 17 122.27 3.12 177 145 163 18 120.64 2.91 178 145 166 21 102.14 4.20 179 145 167 22 102.11 4.21 180 146 166 20 104.86 2.83 181 146 167 21 102.09 4.21 182 148 151 3 327.89 0.97 183 148 154 6 311.03 4.49 184 149 154 5 317.49 1.26 185 149 155 6 309.20 0.61 186 149 163 14 121.80 3.35 187 149 167 18 116.91 3.19 188 150 155 5 317.53 1.28 189 151 154 3 327.95 1.61 190 151 155 4 317.58 1.27 191 152 155 3 320.87 0.23 192 152 156 4 317.56 1.28 193 153 156 3 324.52 2.04 194 153 157 4 317.54 1.27 195 154 157 3 320.88 0.22 196 154 158 4 314.07 3.01 197 154 162 8 292.80 2.46 198 154 163 9 278.30 9.71 199 155 158 3 329.75 0.82 200 155 159 4 292.80 2.46 201 155 160 5 284.88 6.43 202 155 163 8 258.91 0.02 203 158 162 4 314.73 1.44 204 159 162 3 327.57 2.75 205 159 163 4 322.55 0.24 206 160 163 3 333.96 0.45 207 160 164 4 320.32 1.35 208 161 164 3 320.55 1.25 209 161 165 4 320.32 1.35 210 162 165 3 322.99 0.07 211 162 166 4 322.00 1.16 212 163 166 3 324.50 0.09 213 163 167 4 323.72 0.30 214 164 167 3 324.50 0.09 215 164 168 4 322.81 0.15 216 165 169 4 327.80 1.74 217 166 169 3 330.19 0.57