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 35.60 1.05 2 77 126 49 41.10 0.18 3 77 152 75 35.77 1.08 4 77 156 79 36.74 0.88 5 79 82 3 305.19 2.44 6 79 125 46 44.47 0.72 7 79 126 47 38.36 1.17 8 80 125 45 44.50 0.72 9 80 126 46 44.38 0.77 10 80 128 48 44.48 0.72 11 81 84 3 331.45 1.07 12 81 85 4 316.67 5.17 13 81 114 33 58.83 0.42 14 81 125 44 44.73 0.78 15 82 85 3 317.12 4.94 16 83 89 6 298.76 3.88 17 84 89 5 300.05 3.25 18 84 90 6 280.00 3.08 19 84 93 9 276.75 4.65 20 84 114 30 67.19 2.31 21 84 125 41 58.89 0.44 22 85 90 5 311.43 0.60 23 85 125 40 69.59 0.72 24 86 89 3 321.98 1.39 25 86 90 4 318.75 0.23 26 87 90 3 318.75 0.23 27 87 91 4 318.78 0.24 28 87 109 22 74.26 0.04 29 87 110 23 74.25 0.04 30 88 91 3 326.19 0.75 31 88 92 4 324.20 2.46 32 89 92 3 329.94 0.40 33 89 93 4 324.49 2.33 34 90 93 3 331.69 1.27 35 90 94 4 331.63 1.25 36 90 109 19 104.70 6.86 37 90 112 22 103.96 7.23 38 90 113 23 103.97 7.23 39 90 114 24 103.96 7.23 40 90 125 35 103.98 7.22 41 90 153 63 104.81 6.81 42 91 94 3 331.70 1.27 43 91 105 14 111.38 6.84 44 91 106 15 109.92 7.96 45 91 109 18 106.69 7.33 46 92 95 3 332.31 0.90 47 93 96 3 371.62 1.22 48 93 114 21 114.37 6.45 49 93 115 22 114.38 6.45 50 94 97 3 317.75 0.09 51 94 105 11 114.48 6.42 52 94 108 14 114.50 6.42 53 94 109 15 114.50 6.42 54 94 113 19 114.50 6.42 55 94 114 20 114.50 6.42 56 94 115 21 114.50 6.42 57 94 122 28 121.75 2.80 58 96 115 19 147.50 0.64 59 96 118 22 154.54 1.55 60 97 101 4 304.03 0.58 61 97 103 6 272.97 3.96 62 97 105 8 147.52 0.64 63 97 108 11 147.59 0.62 64 97 115 18 147.54 0.65 65 97 120 23 152.23 2.87 66 97 122 25 152.06 2.79 67 97 134 37 154.84 1.69 68 98 101 3 316.37 1.24 69 98 118 20 168.44 1.41 70 98 119 21 154.94 1.74 71 98 120 22 154.83 1.70 72 101 120 19 177.20 0.34 73 102 134 32 177.44 0.29 74 102 135 33 177.43 0.29 75 102 136 34 177.40 0.28 76 103 108 5 309.95 0.71 77 103 134 31 177.59 0.21 78 103 135 32 177.61 0.21 79 103 138 35 177.43 0.29 80 103 140 37 177.39 0.31 81 104 107 3 323.01 1.38 82 104 108 4 314.54 0.77 83 105 108 3 321.98 1.59 84 105 109 4 312.21 0.41 85 106 109 3 315.93 1.44 86 106 110 4 312.23 0.42 87 107 110 3 325.70 2.74 88 107 111 4 322.12 4.53 89 107 140 33 197.47 2.77 90 108 111 3 322.12 4.53 91 108 112 4 322.12 4.53 92 108 113 5 284.44 0.75 93 108 122 14 213.63 2.41 94 108 134 26 197.68 2.74 95 108 140 32 197.49 2.77 96 109 112 3 324.45 3.36 97 109 113 4 294.20 2.12 98 110 141 31 197.75 2.81 99 110 153 43 181.15 0.66 100 111 140 29 197.75 2.81 101 111 141 30 197.74 2.81 102 111 144 33 197.70 2.82 103 111 153 42 181.09 0.63 104 112 124 12 214.28 3.06 105 112 125 13 214.30 3.07 106 112 153 41 181.15 0.66 107 113 122 9 215.25 2.94 108 113 123 10 215.16 2.96 109 113 124 11 214.33 3.04 110 113 131 18 214.07 3.19 111 113 134 21 213.94 3.17 112 113 140 27 197.93 2.85 113 113 144 31 197.87 2.87 114 114 122 8 215.25 2.95 115 114 123 9 215.23 2.96 116 114 124 10 215.19 2.98 117 114 125 11 215.06 3.01 118 114 128 14 214.46 3.14 119 115 118 3 463.10 3.71 120 115 119 4 343.08 0.21 121 115 121 6 215.39 3.00 122 115 122 7 215.27 2.94 123 116 121 5 235.19 10.18 124 116 123 7 215.37 3.00 125 120 132 12 214.09 3.19 126 120 133 13 214.08 3.19 127 120 134 14 214.06 3.20 128 121 131 10 214.17 3.18 129 121 132 11 214.07 3.19 130 122 130 8 214.17 3.18 131 122 131 9 214.13 3.18 132 122 134 12 214.08 3.19 133 123 128 5 214.31 3.21 134 123 129 6 214.26 3.20 135 123 130 7 214.18 3.20 136 124 127 3 321.35 1.39 137 124 128 4 214.30 3.21 138 124 129 5 214.29 3.21 139 124 144 20 197.93 2.84 140 124 151 27 182.22 0.56 141 125 153 28 182.20 0.56 142 126 151 25 182.22 0.56 143 126 152 26 182.22 0.56 144 126 153 27 182.19 0.56 145 127 144 17 197.98 2.84 146 127 148 21 197.58 2.83 147 127 151 24 182.22 0.56 148 129 148 19 197.63 2.85 149 130 148 18 197.77 2.92 150 131 134 3 403.43 4.22 151 131 143 12 198.02 2.83 152 131 147 16 197.84 2.89 153 131 148 17 197.81 2.90 154 134 138 4 294.16 9.78 155 134 140 6 270.11 3.23 156 134 143 9 259.57 8.47 157 135 138 3 316.35 1.32 158 138 143 5 304.12 2.26 159 139 142 3 316.31 1.31 160 139 143 4 314.39 1.42 161 140 143 3 318.72 0.75 162 140 144 4 314.39 1.41 163 141 144 3 318.46 0.61 164 141 145 4 318.44 0.62 165 141 153 12 238.62 0.79 166 141 154 13 226.38 0.77 167 141 157 16 170.58 21.41 168 141 158 17 113.41 5.24 169 141 162 21 113.26 5.23 170 142 145 3 323.35 1.83 171 142 146 4 314.37 1.40 172 142 162 20 113.23 5.21 173 142 166 24 104.74 4.95 174 143 146 3 323.17 0.01 175 143 147 4 305.95 2.47 176 144 147 3 337.30 2.67 177 144 148 4 297.33 0.51 178 144 151 7 270.61 3.06 179 144 153 9 255.86 2.06 180 144 154 10 242.87 3.50 181 145 149 4 259.91 0.56 182 145 154 9 239.04 5.40 183 145 162 17 113.23 5.21 184 145 163 18 112.66 4.98 185 145 166 21 106.64 4.00 186 145 167 22 104.67 4.98 187 146 166 20 106.70 3.97 188 146 167 21 104.67 4.98 189 148 151 3 329.64 1.85 190 148 154 6 308.58 3.20 191 149 154 5 312.00 1.49 192 149 155 6 311.99 1.49 193 149 163 14 112.95 5.08 194 149 167 18 106.70 3.97 195 150 155 5 312.06 1.47 196 151 154 3 319.13 2.79 197 151 155 4 315.12 0.04 198 152 155 3 315.12 0.04 199 152 156 4 314.29 0.37 200 153 156 3 321.90 3.35 201 153 157 4 314.28 0.38 202 154 157 3 321.38 3.17 203 154 158 4 304.62 2.26 204 154 162 8 285.21 7.99 205 154 163 9 242.70 8.07 206 155 159 4 238.51 5.01 207 155 160 5 238.51 5.01 208 155 163 8 215.80 5.77 209 158 162 4 316.00 0.78 210 159 162 3 329.31 3.62 211 159 163 4 322.28 2.12 212 160 163 3 335.70 0.42 213 160 164 4 316.29 0.62 214 161 164 3 322.29 2.12 215 161 165 4 316.00 0.77 216 162 165 3 321.84 0.67 217 162 166 4 318.72 2.08 218 163 166 3 323.98 0.17 219 163 167 4 318.65 1.57 220 164 167 3 323.06 0.63 221 164 168 4 311.33 1.43 222 165 169 4 312.01 1.86 223 166 169 3 330.20 2.28