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 2 10 8 133.97 0.67 2 3 6 3 147.91 1.46 3 3 7 4 145.24 0.87 4 4 7 3 145.99 0.49 5 4 8 4 145.25 0.86 6 4 118 114 24.27 0.12 7 5 8 3 160.72 0.47 8 5 9 4 145.58 0.70 9 5 116 111 25.62 0.49 10 5 117 112 24.35 0.12 11 5 118 113 24.34 0.12 12 6 9 3 151.30 2.16 13 6 10 4 144.56 0.43 14 7 10 3 149.49 0.38 15 7 11 4 143.85 0.78 16 8 11 3 154.38 0.06 17 8 12 4 141.77 0.20 18 8 13 5 141.77 0.20 19 8 54 46 74.64 1.14 20 8 108 100 34.84 1.10 21 8 117 109 35.59 0.99 22 8 118 110 33.88 0.61 23 8 119 111 33.86 0.61 24 8 120 112 33.78 0.60 25 9 12 3 143.09 0.10 26 9 13 4 140.87 0.14 27 9 33 24 116.90 0.23 28 9 51 42 87.95 0.65 29 10 33 23 116.28 0.08 30 10 34 24 117.31 0.42 31 11 35 24 117.31 0.43 32 11 41 30 117.39 0.48 33 11 44 33 115.56 0.01 34 11 46 35 115.25 0.09 35 12 44 32 116.67 0.36 36 12 45 33 115.55 0.01 37 12 46 34 115.25 0.09 38 12 47 35 115.24 0.09 39 12 120 108 35.63 0.71 40 13 33 20 118.86 0.55 41 13 47 34 115.27 0.10 42 13 49 36 115.25 0.10 43 13 50 37 115.19 0.07 44 13 51 38 110.62 0.89 45 13 54 41 101.74 2.91 46 14 17 3 160.95 0.89 47 14 25 11 119.05 0.48 48 14 29 15 118.91 0.55 49 14 47 33 115.57 0.01 50 14 48 34 115.31 0.11 51 15 48 33 115.53 0.01 52 15 49 34 115.27 0.10 53 15 50 35 115.25 0.10 54 17 25 8 119.30 0.52 55 17 48 31 118.89 0.55 56 18 48 30 118.95 0.54 57 18 80 62 118.99 0.51 58 19 48 29 118.99 0.52 59 19 80 61 119.00 0.51 60 19 101 82 119.13 0.45 61 20 25 5 127.36 3.35 62 20 48 28 119.09 0.51 63 20 82 62 119.12 0.49 64 20 99 79 119.20 0.45 65 20 101 81 119.14 0.45 66 21 25 4 127.40 3.37 67 22 25 3 147.06 0.27 68 22 99 77 145.85 0.82 69 23 99 76 143.53 1.98 70 25 46 21 204.53 5.64 71 25 48 23 171.74 0.89 72 25 82 57 174.78 2.04 73 25 99 74 191.03 3.83 74 26 82 56 238.62 0.62 75 26 97 71 222.27 0.89 76 26 98 72 222.22 0.87 77 26 99 73 199.16 1.25 78 27 95 68 234.28 0.22 79 27 96 69 234.18 0.18 80 27 97 70 231.09 0.45 81 29 46 17 234.25 0.15 82 30 35 5 334.19 1.28 83 30 36 6 332.17 2.27 84 30 41 11 234.66 0.16 85 30 44 14 234.56 0.15 86 30 46 16 234.49 0.15 87 30 97 67 234.35 0.17 88 31 36 5 330.58 1.49 89 33 46 13 234.46 0.10 90 35 41 6 260.18 12.91 91 35 44 9 234.62 0.15 92 35 46 11 234.60 0.14 93 36 40 4 324.88 3.29 94 36 95 59 335.83 0.32 95 36 97 61 311.26 12.60 96 40 86 46 234.68 0.17 97 41 86 45 234.67 0.17 98 42 85 43 234.60 0.17 99 42 86 44 234.63 0.17 100 43 84 41 234.56 0.15 101 43 85 42 234.56 0.15 102 44 84 40 234.47 0.16 103 45 81 36 234.59 0.17 104 45 82 37 234.55 0.15 105 45 83 38 234.46 0.17 106 45 120 75 36.55 0.57 107 46 81 35 234.56 0.15 108 46 82 36 234.50 0.16 109 46 84 38 234.46 0.17 110 47 79 32 234.59 0.17 111 47 80 33 234.57 0.15 112 47 81 34 234.47 0.17 113 47 106 59 166.09 2.07 114 47 120 73 37.09 0.57 115 48 80 32 234.53 0.16 116 48 81 33 234.47 0.17 117 48 82 34 234.46 0.17 118 49 79 30 234.53 0.16 119 53 79 26 234.30 0.17 120 54 79 25 226.92 0.60 121 54 117 63 60.97 0.01 122 55 116 61 61.53 0.27 123 55 117 62 61.00 0.03 124 57 73 16 234.34 0.20 125 57 74 17 234.30 0.18 126 57 75 18 222.25 0.88 127 58 73 15 234.28 0.18 128 58 115 57 64.97 1.06 129 58 116 58 64.47 0.83 130 58 117 59 64.40 0.84 131 60 73 13 234.44 0.17 132 60 74 14 234.38 0.15 133 60 75 15 230.59 0.45 134 60 76 16 222.26 0.89 135 60 77 17 222.27 0.89 136 61 73 12 234.50 0.17 137 61 74 13 234.45 0.18 138 61 75 14 234.38 0.14 139 61 76 15 233.74 0.12 140 62 70 8 240.66 2.19 141 62 72 10 234.53 0.17 142 62 73 11 234.50 0.16 143 63 72 9 234.54 0.16 144 63 73 10 234.53 0.17 145 63 74 11 234.52 0.17 146 63 107 44 234.59 0.15 147 64 72 8 250.38 1.08 148 65 109 44 234.40 0.14 149 65 121 56 61.06 0.22 150 66 121 55 63.38 1.14 151 66 122 56 61.30 0.10 152 71 109 38 234.38 0.18 153 71 110 39 234.32 0.19 154 71 111 40 234.28 0.18 155 71 115 44 158.46 3.64 156 72 107 35 234.46 0.15 157 72 108 36 234.39 0.17 158 72 109 37 234.10 0.25 159 72 121 49 61.24 0.12 160 73 107 34 234.41 0.17 161 73 108 35 234.38 0.15 162 73 110 37 233.73 0.40 163 73 115 42 138.94 0.08 164 74 105 31 234.49 0.16 165 74 106 32 234.41 0.17 166 74 107 33 233.28 0.62 167 74 124 50 40.47 1.81 168 75 105 30 234.41 0.16 169 75 106 31 234.38 0.17 170 76 105 29 234.41 0.16 171 77 105 28 233.91 0.29 172 78 103 25 234.37 0.18 173 78 104 26 225.11 0.56 174 78 105 27 222.18 0.89 175 79 103 24 224.88 0.42 176 79 104 25 222.22 0.87 177 79 106 27 204.02 1.54 178 80 101 21 234.42 0.16 179 80 102 22 228.28 0.07 180 80 103 23 221.78 0.96 181 81 101 20 222.28 0.89 182 81 102 21 222.23 0.87 183 81 104 23 206.03 0.18 184 81 106 25 162.12 1.90 185 81 123 42 36.89 0.47 186 82 99 17 234.36 0.18 187 82 100 18 225.02 0.48 188 82 101 19 222.08 0.94 189 83 98 15 234.42 0.16 190 83 99 16 226.84 0.58 191 83 100 17 222.18 0.90 192 84 97 13 234.27 0.17 193 84 98 14 222.26 0.89 194 85 97 12 234.42 0.15 195 85 98 13 234.20 0.20 196 85 100 15 222.22 0.89 197 86 90 4 331.69 2.40 198 86 96 10 234.53 0.18 199 86 97 11 234.43 0.15 200 87 96 9 234.56 0.17 201 90 94 4 330.82 0.72 202 90 95 5 234.75 0.18 203 90 96 6 234.72 0.18 204 104 123 19 37.46 0.40 205 104 124 20 37.15 0.39 206 105 123 18 37.47 0.38 207 105 124 19 37.15 0.39 208 106 120 14 60.59 0.15 209 106 122 16 41.34 1.46 210 106 123 17 37.38 0.45 211 107 121 14 59.09 0.18 212 107 122 15 42.10 1.50 213 107 123 16 40.51 1.81 214 107 124 17 40.49 1.81 215 108 117 9 64.16 0.75 216 108 119 11 61.12 0.03 217 108 120 12 60.72 0.14 218 108 121 13 60.30 0.31 219 109 117 8 64.44 0.82 220 109 118 9 64.19 0.75 221 109 119 10 63.19 0.93 222 110 115 5 65.50 1.31 223 110 116 6 64.64 0.89 224 110 117 7 64.42 0.85 225 111 115 4 70.27 0.93 226 111 116 5 65.64 1.39 227 111 118 7 64.45 0.84 228 112 115 3 157.55 4.09