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 7 91 84 38.11 0.66 2 7 92 85 37.86 0.78 3 7 93 86 36.13 0.09 4 8 11 3 172.87 0.45 5 8 93 85 39.97 1.06 6 9 12 3 172.87 0.45 7 9 13 4 172.88 0.45 8 9 76 67 59.66 1.15 9 10 13 3 188.53 0.35 10 11 16 5 173.02 0.37 11 11 93 82 75.95 0.19 12 11 94 83 75.98 0.19 13 11 95 84 75.98 0.18 14 12 16 4 186.87 1.61 15 12 42 30 74.92 0.46 16 12 44 32 75.38 0.41 17 12 51 39 75.24 0.35 18 12 76 64 75.98 0.26 19 12 90 78 75.81 0.27 20 12 93 81 76.00 0.19 21 12 98 86 75.98 0.19 22 13 42 29 75.20 0.42 23 13 43 30 75.30 0.41 24 13 44 31 75.38 0.41 25 13 48 35 75.98 0.28 26 14 41 27 75.48 0.35 27 14 42 28 75.50 0.36 28 15 40 25 75.53 0.36 29 15 41 26 75.50 0.36 30 15 119 104 149.84 3.14 31 16 39 23 75.86 0.25 32 16 40 24 75.87 0.23 33 16 41 25 76.00 0.27 34 16 42 26 76.03 0.27 35 16 93 77 150.06 3.28 36 16 94 78 150.07 3.28 37 16 96 80 150.56 3.02 38 16 97 81 149.94 3.22 39 16 98 82 149.87 3.21 40 16 117 101 149.85 3.18 41 16 118 102 149.93 3.19 42 16 119 103 149.84 3.14 43 17 39 22 75.93 0.24 44 17 40 23 76.00 0.27 45 17 117 100 151.85 2.23 46 17 118 101 151.44 2.44 47 17 120 103 151.81 2.21 48 17 149 132 75.58 0.36 49 18 21 3 254.38 5.72 50 18 37 19 76.03 0.27 51 18 38 20 76.00 0.27 52 18 39 21 76.03 0.27 53 18 115 97 150.38 2.92 54 18 116 98 151.88 2.25 55 18 117 99 151.85 2.23 56 18 148 130 75.98 0.28 57 18 149 131 75.60 0.36 58 19 116 97 152.31 2.18 59 19 118 99 152.31 2.16 60 19 120 101 152.40 2.10 61 19 121 102 152.30 2.07 62 19 122 103 152.19 2.08 63 19 123 104 152.17 2.08 64 19 147 128 76.07 0.26 65 19 148 129 76.03 0.26 66 19 149 130 75.56 0.37 67 20 115 95 152.37 2.18 68 20 116 96 152.34 2.17 69 20 123 103 152.33 2.08 70 20 128 108 152.05 2.02 71 20 131 111 148.92 0.95 72 20 145 125 78.12 0.81 73 20 146 126 77.03 0.44 74 20 147 127 76.07 0.26 75 21 29 8 76.75 0.58 76 21 113 92 152.66 2.06 77 21 114 93 152.66 2.06 78 21 115 94 152.48 2.12 79 21 131 110 151.41 1.69 80 21 145 124 78.14 0.81 81 21 146 125 77.89 0.69 82 21 148 127 76.28 0.36 83 22 29 7 140.55 1.07 84 22 113 91 152.66 2.06 85 22 114 92 152.68 2.06 86 22 131 109 151.49 1.66 87 22 135 113 132.42 1.16 88 22 140 118 126.86 0.27 89 22 144 122 78.98 1.22 90 22 145 123 78.14 0.81 91 23 29 6 145.56 0.73 92 23 111 88 152.68 2.06 93 23 112 89 152.77 2.10 94 23 113 90 152.66 2.06 95 23 140 117 126.87 0.27 96 23 141 118 126.86 0.27 97 23 144 121 109.64 1.44 98 24 111 87 152.97 2.03 99 24 112 88 152.95 2.04 100 24 141 117 126.94 0.23 101 24 144 120 125.10 0.59 102 25 28 3 168.46 2.19 103 25 109 84 153.00 2.02 104 25 110 85 153.01 2.02 105 25 111 86 153.00 2.02 106 26 29 3 169.43 1.71 107 26 30 4 159.44 1.17 108 26 144 118 126.76 0.31 109 26 146 120 125.61 0.57 110 27 30 3 165.84 0.09 111 27 33 6 153.31 1.90 112 27 109 82 153.33 1.90 113 28 33 5 153.31 1.90 114 28 34 6 153.31 1.89 115 28 35 7 153.25 1.90 116 28 36 8 153.28 1.90 117 28 106 78 153.30 1.89 118 28 109 81 153.37 1.92 119 28 111 83 153.21 1.97 120 29 35 6 153.25 1.90 121 29 36 7 153.11 1.83 122 29 113 84 153.23 1.98 123 29 144 115 127.12 0.27 124 29 146 117 126.82 0.28 125 30 33 3 158.19 0.54 126 30 36 6 153.32 1.86 127 30 146 116 126.82 0.28 128 31 36 5 153.49 1.80 129 31 38 7 153.35 1.86 130 31 58 27 105.42 0.84 131 31 151 120 113.23 0.33 132 33 36 3 161.96 0.05 133 34 37 3 215.63 1.64 134 34 57 23 123.62 0.01 135 34 82 48 154.36 1.98 136 34 83 49 154.37 1.98 137 35 82 47 154.37 1.98 138 35 104 69 154.66 2.09 139 35 111 76 154.75 2.10 140 35 113 78 154.16 2.39 141 36 57 21 125.01 0.48 142 36 146 110 127.26 0.16 143 36 148 112 126.95 0.20 144 36 151 115 125.59 0.53 145 37 55 18 125.66 0.55 146 37 56 19 125.59 0.54 147 37 57 20 125.02 0.48 148 37 82 45 154.63 1.91 149 37 148 111 127.19 0.14 150 38 55 17 125.70 0.54 151 38 56 18 125.66 0.56 152 38 58 20 125.64 0.56 153 38 148 110 127.26 0.16 154 38 151 113 126.55 0.12 155 38 152 114 123.50 0.49 156 39 42 3 302.88 2.92 157 39 53 14 127.70 0.37 158 39 54 15 127.23 0.17 159 39 55 16 126.36 0.48 160 39 88 49 155.21 2.19 161 39 115 76 117.64 21.00 162 39 117 78 117.33 20.93 163 40 54 14 127.67 0.36 164 40 55 15 127.22 0.14 165 40 56 16 127.21 0.14 166 40 152 112 127.14 0.13 167 40 154 114 123.01 0.09 168 40 155 115 96.92 4.29 169 40 156 116 15.02 0.29 170 41 53 12 127.73 0.36 171 41 54 13 127.68 0.37 172 42 51 9 134.99 0.92 173 42 52 10 128.83 0.45 174 42 98 56 163.69 2.29 175 43 51 8 142.02 2.58 176 43 52 9 128.86 0.43 177 44 50 6 164.15 1.12 178 44 51 7 146.74 0.23 179 45 50 5 174.90 3.29 180 45 52 7 151.52 1.54 181 48 51 3 166.93 0.27 182 48 72 24 232.98 0.17 183 48 78 30 232.99 0.17 184 49 71 22 232.97 0.17 185 49 72 23 232.98 0.17 186 50 69 19 232.84 0.17 187 50 70 20 232.96 0.16 188 50 71 21 232.97 0.17 189 50 78 28 233.00 0.17 190 51 69 18 232.95 0.17 191 51 70 19 232.98 0.17 192 51 78 27 233.03 0.17 193 51 88 37 233.06 0.18 194 52 67 15 232.76 0.16 195 52 68 16 232.96 0.17 196 52 69 17 232.97 0.17 197 53 67 14 232.95 0.17 198 53 68 15 232.97 0.17 199 53 80 27 233.96 0.24 200 53 88 35 234.52 0.03 201 54 65 11 232.94 0.17 202 54 66 12 232.96 0.17 203 54 67 13 232.96 0.17 204 55 65 10 232.96 0.17 205 55 66 11 232.96 0.17 206 55 68 13 233.03 0.18 207 55 82 27 321.89 0.50 208 56 63 7 222.83 0.92 209 56 64 8 232.95 0.17 210 56 65 9 232.96 0.17 211 56 154 98 168.09 0.26 212 56 155 99 165.13 0.21 213 57 62 5 232.97 0.17 214 57 63 6 232.94 0.17 215 57 64 7 232.97 0.17 216 57 66 9 233.02 0.17 217 57 82 25 322.28 0.36 218 57 83 26 322.36 0.33 219 58 62 4 232.97 0.17 220 58 63 5 232.96 0.17 221 58 151 93 233.01 0.17 222 58 153 95 232.98 0.17 223 58 154 96 232.96 0.17 224 59 62 3 232.99 0.17 225 59 64 5 233.00 0.17 226 121 149 28 248.53 37.70