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 35.37 1.17 2 77 126 49 42.21 0.36 3 77 152 75 35.48 1.23 4 77 156 79 37.44 1.26 5 79 82 3 304.61 3.66 6 79 125 46 44.26 0.71 7 79 126 47 42.22 0.36 8 80 125 45 46.16 0.24 9 80 126 46 44.33 0.67 10 80 128 48 44.27 0.70 11 81 84 3 329.95 0.33 12 81 85 4 317.49 3.26 13 81 114 33 57.77 0.04 14 81 125 44 47.50 0.70 15 82 85 3 321.06 1.48 16 83 89 6 305.70 0.37 17 84 89 5 305.01 0.71 18 84 90 6 277.06 4.57 19 84 93 9 274.43 4.99 20 84 114 30 70.44 0.69 21 84 125 41 58.19 0.14 22 85 90 5 310.73 2.81 23 85 125 40 70.15 0.44 24 86 89 3 320.49 0.65 25 86 90 4 320.25 0.53 26 87 90 3 321.58 1.19 27 87 91 4 320.25 0.53 28 87 109 22 74.14 0.82 29 87 110 23 73.85 0.96 30 88 91 3 325.57 1.06 31 88 92 4 325.47 1.89 32 89 92 3 328.44 1.15 33 89 93 4 327.88 0.87 34 90 93 3 330.19 2.02 35 90 94 4 330.14 1.99 36 90 109 19 92.20 0.61 37 90 112 22 92.21 0.62 38 90 113 23 92.20 0.61 39 90 114 24 89.92 1.75 40 90 125 35 92.31 0.57 41 90 153 63 94.16 0.35 42 91 94 3 334.16 3.80 43 91 105 14 95.78 1.14 44 91 106 15 95.79 1.15 45 91 109 18 94.17 0.35 46 92 95 3 331.98 1.07 47 93 96 3 372.00 1.02 48 93 114 21 96.64 0.96 49 93 115 22 96.67 0.98 50 94 97 3 316.34 1.14 51 94 105 11 96.70 0.97 52 94 108 14 96.70 0.97 53 94 109 15 96.77 1.01 54 94 113 19 96.70 0.97 55 94 114 20 96.70 0.97 56 94 115 21 96.70 0.97 57 94 122 28 113.70 5.98 58 96 115 19 139.47 2.15 59 96 118 22 147.16 1.63 60 97 101 4 301.99 2.44 61 97 103 6 277.02 1.93 62 97 105 8 139.45 2.16 63 97 108 11 139.52 2.18 64 97 115 18 139.47 2.15 65 97 120 23 147.18 1.64 66 97 122 25 144.84 0.48 67 97 134 37 159.33 4.38 68 98 101 3 314.87 0.48 69 98 118 20 166.12 1.06 70 98 119 21 153.22 4.34 71 98 120 22 147.35 1.56 72 101 120 19 177.96 0.04 73 102 134 32 178.86 0.42 74 102 135 33 178.87 0.42 75 102 136 34 178.87 0.42 76 103 108 5 309.15 1.19 77 103 134 31 178.91 0.40 78 103 135 32 179.93 0.10 79 103 138 35 178.87 0.42 80 103 140 37 178.86 0.42 81 104 107 3 331.24 1.30 82 104 108 4 320.19 0.44 83 105 108 3 320.19 0.44 84 105 109 4 314.68 2.31 85 106 109 3 325.28 2.98 86 106 110 4 310.82 0.39 87 107 110 3 327.55 1.81 88 107 111 4 320.62 5.28 89 107 140 33 188.63 0.96 90 108 111 3 324.20 3.49 91 108 112 4 324.20 3.49 92 108 113 5 296.50 3.48 93 108 122 14 215.87 14.35 94 108 134 26 188.99 0.80 95 108 140 32 188.65 0.96 96 109 112 3 324.17 3.50 97 109 113 4 297.68 4.06 98 110 141 31 188.75 0.92 99 110 153 43 183.75 1.59 100 111 140 29 188.75 0.92 101 111 141 30 188.75 0.91 102 111 144 33 188.75 0.91 103 111 153 42 183.57 1.69 104 112 124 12 215.97 14.50 105 112 125 13 215.67 14.35 106 112 153 41 183.53 1.71 107 113 122 9 216.38 14.41 108 113 123 10 216.18 14.44 109 113 124 11 216.06 14.45 110 113 131 18 215.84 14.13 111 113 140 27 189.03 0.83 112 113 144 31 188.97 0.84 113 114 122 8 216.44 14.43 114 114 123 9 216.36 14.41 115 114 124 10 216.35 14.41 116 114 125 11 216.30 14.43 117 114 128 14 216.05 14.25 118 115 118 3 461.60 4.46 119 115 119 4 343.92 0.21 120 115 121 6 216.60 14.40 121 115 122 7 216.45 14.42 122 116 121 5 216.61 14.40 123 116 123 7 216.58 14.42 124 120 132 12 237.56 3.27 125 120 133 13 237.50 3.29 126 120 134 14 237.46 3.31 127 121 131 10 237.63 3.26 128 121 132 11 237.55 3.27 129 122 130 8 237.66 3.25 130 122 131 9 237.63 3.24 131 122 134 12 237.62 3.23 132 123 128 5 237.87 3.33 133 123 129 6 237.84 3.31 134 123 130 7 237.66 3.25 135 124 127 3 319.63 1.55 136 124 128 4 237.87 3.33 137 124 129 5 237.87 3.32 138 124 144 20 210.81 10.06 139 124 151 27 205.93 12.47 140 125 153 28 205.86 12.51 141 126 151 25 205.90 12.51 142 126 152 26 205.89 12.51 143 126 153 27 205.81 12.48 144 127 144 17 210.90 10.10 145 127 148 21 210.74 10.12 146 127 151 24 205.87 12.48 147 129 148 19 210.75 10.06 148 130 148 18 210.76 10.06 149 131 134 3 403.31 4.28 150 131 143 12 210.82 10.03 151 131 147 16 210.77 10.05 152 131 148 17 210.76 10.06 153 134 138 4 306.33 0.01 154 134 140 6 264.00 7.02 155 134 143 9 232.96 20.27 156 135 138 3 320.81 1.60 157 138 143 5 305.21 2.77 158 139 142 3 318.07 0.43 159 139 143 4 313.99 1.61 160 140 143 3 318.12 0.45 161 140 144 4 313.99 1.61 162 141 144 3 314.00 1.61 163 141 145 4 313.99 1.61 164 141 153 12 217.15 12.88 165 141 154 13 217.05 12.86 166 141 157 16 190.25 19.34 167 141 158 17 158.51 22.09 168 141 162 21 116.62 1.71 169 142 145 3 325.30 2.32 170 142 146 4 313.95 1.62 171 142 162 20 116.62 1.71 172 142 166 24 110.06 0.23 173 143 146 3 323.88 0.37 174 143 147 4 306.82 3.55 175 144 147 3 333.31 3.16 176 144 148 4 304.81 4.55 177 144 151 7 265.62 0.55 178 144 153 9 262.45 1.03 179 144 154 10 238.03 8.92 180 145 149 4 275.94 4.61 181 145 154 9 254.17 0.85 182 145 162 17 116.78 1.67 183 145 163 18 116.52 1.69 184 145 166 21 110.07 0.24 185 145 167 22 110.06 0.24 186 146 166 20 110.09 0.24 187 146 167 21 110.06 0.23 188 148 151 3 328.14 1.10 189 148 154 6 311.80 1.58 190 149 154 5 311.83 1.59 191 149 155 6 311.79 1.59 192 149 163 14 116.63 1.72 193 149 167 18 110.59 0.28 194 150 155 5 312.75 1.11 195 151 154 3 328.21 1.73 196 151 155 4 313.62 0.70 197 152 155 3 318.54 3.11 198 152 156 4 313.62 0.70 199 153 156 3 322.26 1.00 200 153 157 4 312.80 1.11 201 154 157 3 316.69 0.50 202 154 158 4 308.26 0.11 203 154 162 8 275.18 0.10 204 154 163 9 158.63 18.46 205 155 159 4 258.25 5.82 206 155 160 5 258.24 5.83 207 155 163 8 158.66 18.48 208 158 162 4 312.32 0.35 209 159 162 3 327.81 2.87 210 159 163 4 322.82 0.38 211 160 163 3 334.20 0.33 212 160 164 4 319.51 2.00 213 161 164 3 322.80 0.37 214 161 165 4 319.51 2.00 215 162 165 3 324.03 0.58 216 162 166 4 323.93 0.20 217 163 166 3 324.75 0.21 218 163 167 4 322.25 1.04 219 164 167 3 324.75 0.21 220 164 168 4 317.07 0.86 221 165 169 4 314.13 3.02 222 166 169 3 328.70 1.53