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 63 85 22 81.31 1.65 2 63 115 52 82.28 1.13 3 64 85 21 81.90 1.35 4 64 87 23 82.34 1.16 5 64 115 51 82.28 1.13 6 64 117 53 82.28 1.14 7 65 117 52 82.38 1.14 8 67 75 8 218.91 0.01 9 67 80 13 216.34 1.04 10 67 117 50 82.44 1.16 11 68 93 25 82.34 1.15 12 68 109 41 219.00 0.00 13 68 117 49 82.45 1.17 14 68 120 52 82.33 1.14 15 70 73 3 218.99 0.01 16 70 93 23 82.46 1.15 17 70 120 50 82.39 1.14 18 70 121 51 82.38 1.13 19 70 122 52 82.08 1.17 20 70 123 53 80.19 1.18 21 72 95 23 82.36 1.13 22 72 96 24 82.23 1.18 23 72 99 27 82.08 1.18 24 72 124 52 82.09 1.18 25 73 93 20 82.67 1.13 26 73 94 21 82.42 1.13 27 73 95 22 82.36 1.12 28 73 124 51 82.30 1.09 29 74 93 19 82.70 1.13 30 74 94 20 82.59 1.10 31 75 91 16 87.18 0.99 32 75 92 17 87.06 1.01 33 75 93 18 82.70 1.13 34 75 94 19 82.68 1.14 35 76 92 16 87.11 1.02 36 76 93 17 86.98 0.99 37 76 94 18 82.66 1.14 38 79 91 12 180.19 2.89 39 79 92 13 180.19 2.88 40 80 85 5 218.99 0.01 41 85 111 26 105.09 10.10 42 86 111 25 82.58 1.16 43 87 111 24 82.53 1.18 44 87 112 25 82.55 1.19 45 87 113 26 83.61 0.68 46 87 114 27 207.78 4.97 47 87 115 28 216.22 1.06 48 88 111 23 82.34 1.15 49 89 109 20 82.61 1.17 50 89 110 21 82.34 1.15 51 89 111 22 82.33 1.15 52 89 117 28 218.38 0.29 53 90 108 18 82.53 1.18 54 90 109 19 82.38 1.14 55 90 110 20 82.33 1.15 56 91 107 16 82.64 1.15 57 91 108 17 82.38 1.14 58 91 109 18 82.33 1.15 59 91 117 26 218.33 0.28 60 92 107 15 82.40 1.12 61 93 101 8 219.00 0.00 62 93 109 16 82.26 1.17 63 95 99 4 217.74 0.56 64 95 100 5 174.90 3.62 65 95 101 6 105.42 9.90 66 96 99 3 218.99 0.00 67 97 172 75 40.16 1.25 68 97 173 76 42.83 2.26 69 98 126 28 82.62 1.15 70 98 127 29 79.09 0.19 71 98 172 74 51.19 1.80 72 99 124 25 192.36 6.74 73 99 125 26 82.66 1.15 74 99 126 27 82.49 1.11 75 99 127 28 82.35 1.13 76 100 124 24 82.67 1.14 77 100 125 25 82.61 1.15 78 100 126 26 82.58 1.15 79 100 127 27 82.39 1.15 80 101 123 22 82.64 1.14 81 101 124 23 82.59 1.16 82 102 105 3 218.97 0.01 83 102 122 20 82.97 0.99 84 102 123 21 82.62 1.14 85 102 124 22 82.59 1.16 86 105 123 18 82.41 1.12 87 106 123 17 82.37 1.14 88 107 123 16 81.88 1.32 89 108 118 10 82.61 1.16 90 109 117 8 82.53 1.18 91 109 118 9 82.37 1.15 92 109 119 10 82.36 1.15 93 109 120 11 82.35 1.15 94 110 117 7 82.37 1.15 95 110 118 8 82.34 1.15 96 111 115 4 82.45 1.17 97 111 117 6 82.34 1.15 98 112 116 4 82.44 1.14 99 112 117 5 82.31 1.17 100 112 118 6 82.31 1.17 101 120 123 3 169.90 2.32 102 126 148 22 124.42 0.90 103 127 177 50 123.50 0.97 104 128 147 19 124.33 0.85 105 128 148 20 124.53 0.90 106 128 177 49 124.31 0.95 107 129 146 17 124.50 0.88 108 129 147 18 124.50 0.88 109 129 148 19 124.55 0.90 110 129 172 43 124.77 0.84 111 129 177 48 124.39 0.96 112 129 179 50 124.52 0.89 113 130 177 47 124.70 0.84 114 131 146 15 124.69 0.85 115 132 140 8 218.79 0.10 116 132 142 10 217.84 0.24 117 132 146 14 124.74 0.85 118 132 152 20 124.67 0.84 119 132 179 47 124.70 0.84 120 133 140 7 218.84 0.08 121 134 140 6 218.81 0.10 122 134 183 49 124.55 0.90 123 135 139 4 218.92 0.04 124 135 140 5 218.84 0.08 125 135 154 19 124.70 0.85 126 135 162 27 131.07 2.27 127 135 183 48 124.55 0.90 128 135 184 49 124.55 0.90 129 135 186 51 124.03 0.99 130 136 183 47 124.70 0.84 131 136 184 48 124.69 0.84 132 136 185 49 124.52 0.88 133 136 186 50 122.98 0.73 134 136 187 51 124.25 0.93 135 137 156 19 124.67 0.84 136 137 157 20 124.66 0.85 137 137 160 23 124.60 0.83 138 137 186 49 124.50 0.89 139 138 155 17 124.69 0.85 140 138 156 18 124.55 0.90 141 138 157 19 124.64 0.85 142 139 154 15 124.70 0.84 143 139 155 16 124.66 0.84 144 140 152 12 124.77 0.86 145 140 153 13 124.73 0.85 146 140 154 14 124.65 0.85 147 141 152 11 124.77 0.86 148 141 153 12 124.75 0.88 149 141 155 14 124.65 0.84 150 142 146 4 218.98 0.01 151 142 152 10 124.76 0.87 152 143 151 8 218.68 0.14 153 146 150 4 219.00 0.00 154 146 151 5 219.00 0.00 155 146 152 6 219.00 0.01 156 147 150 3 219.00 0.00 157 147 170 23 124.73 0.85 158 148 170 22 124.72 0.85 159 148 172 24 124.72 0.85 160 149 170 21 124.67 0.84 161 150 169 19 124.70 0.84 162 150 170 20 124.53 0.90 163 151 168 17 124.69 0.84 164 151 169 18 124.55 0.90 165 151 170 19 124.54 0.89 166 152 167 15 124.70 0.85 167 152 168 16 124.58 0.88 168 153 166 13 124.70 0.85 169 153 167 14 124.55 0.90 170 154 162 8 124.76 0.85 171 154 165 11 124.71 0.84 172 154 166 12 124.55 0.90 173 154 167 13 124.55 0.90 174 154 168 14 124.55 0.90 175 155 162 7 124.75 0.85 176 156 160 4 124.76 0.85 177 156 162 6 124.72 0.84 178 157 160 3 124.77 0.84 179 159 188 29 124.67 0.83 180 160 186 26 124.72 0.84 181 160 187 27 124.70 0.84 182 160 188 28 122.98 1.08 183 161 186 25 124.70 0.84 184 161 187 26 124.56 0.89 185 161 189 28 123.23 0.62 186 162 165 3 124.71 0.82 187 162 166 4 124.49 0.92 188 162 184 22 124.73 0.84 189 162 185 23 124.70 0.84 190 162 186 24 124.55 0.89 191 163 185 22 124.66 0.84 192 163 187 24 124.52 0.89 193 164 184 20 124.64 0.84 194 164 185 21 124.55 0.89 195 165 181 16 124.73 0.84 196 165 184 19 124.55 0.89 197 168 179 11 124.71 0.84 198 168 181 13 124.54 0.89 199 169 179 10 124.67 0.84 200 169 180 11 124.54 0.89 201 170 178 8 124.68 0.84 202 170 179 9 124.53 0.89 203 171 178 7 124.70 0.84 204 171 179 8 124.58 0.89 205 172 176 4 124.70 0.84 206 172 177 5 124.70 0.84 207 172 178 6 124.70 0.84 208 175 178 3 141.12 5.38