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 8 138.22 0.01 2 3 6 3 143.98 0.55 3 3 7 4 143.52 0.11 4 4 7 3 146.33 0.93 5 4 8 4 144.10 0.35 6 4 118 114 23.74 0.25 7 5 8 3 147.58 1.34 8 5 9 4 144.56 0.14 9 5 116 111 24.74 0.56 10 5 117 112 23.82 0.28 11 5 118 113 23.82 0.29 12 6 9 3 144.88 0.09 13 6 10 4 144.56 0.14 14 7 10 3 148.78 0.46 15 7 11 4 144.11 0.35 16 8 11 3 146.44 0.72 17 8 12 4 144.08 0.36 18 8 13 5 142.59 0.24 19 8 54 46 73.52 3.65 20 8 108 100 34.04 0.24 21 8 117 109 34.88 0.17 22 8 118 110 34.04 0.24 23 8 119 111 34.01 0.23 24 8 120 112 34.00 0.24 25 9 12 3 151.91 2.02 26 9 13 4 141.21 0.91 27 9 33 24 119.20 0.96 28 9 51 42 79.70 0.70 29 10 33 23 119.12 0.92 30 10 34 24 119.24 0.98 31 10 35 25 119.24 0.98 32 11 35 24 119.24 0.98 33 11 41 30 119.28 0.99 34 11 44 33 116.03 0.01 35 11 46 35 115.93 0.04 36 12 41 29 119.37 1.00 37 12 44 32 116.21 0.06 38 12 45 33 115.98 0.04 39 12 46 34 115.92 0.04 40 12 47 35 115.92 0.04 41 12 120 108 34.93 0.17 42 13 33 20 119.40 0.93 43 13 47 34 115.95 0.04 44 13 49 36 115.90 0.05 45 13 50 37 115.64 0.01 46 13 51 38 111.17 1.32 47 13 54 41 102.87 2.60 48 14 17 3 172.50 2.77 49 14 25 11 119.35 0.90 50 14 29 15 119.39 0.92 51 14 33 19 119.44 0.94 52 14 46 32 118.40 0.64 53 14 47 33 116.39 0.02 54 14 48 34 115.97 0.04 55 15 48 33 115.98 0.04 56 15 49 34 115.97 0.04 57 15 50 35 115.90 0.06 58 17 20 3 171.56 2.97 59 17 25 8 119.56 0.88 60 17 48 31 119.20 0.96 61 18 48 30 119.22 0.96 62 18 80 62 119.22 0.96 63 19 80 61 119.23 0.97 64 19 101 82 119.31 0.98 65 20 101 81 119.55 0.89 66 21 25 4 124.46 3.31 67 21 48 27 119.90 1.06 68 21 82 61 119.66 0.95 69 21 99 78 125.02 1.66 70 21 101 80 119.59 0.91 71 22 25 3 134.28 0.68 72 22 99 77 145.37 2.10 73 23 99 76 150.60 0.27 74 25 46 21 188.50 4.35 75 25 48 23 164.07 0.82 76 25 82 57 168.85 1.72 77 25 99 74 181.81 0.46 78 26 30 4 337.50 0.67 79 26 82 56 244.44 0.51 80 26 97 71 216.70 0.60 81 26 98 72 213.56 0.12 82 26 99 73 203.27 1.48 83 27 96 69 228.93 1.49 84 27 97 70 224.13 0.07 85 29 46 17 230.76 0.84 86 30 35 5 332.76 0.15 87 30 36 6 287.58 13.64 88 30 41 11 231.50 0.61 89 30 44 14 231.37 0.64 90 30 46 16 231.25 0.65 91 30 97 67 230.99 0.52 92 31 36 5 320.13 6.22 93 33 46 13 231.24 0.65 94 35 41 6 231.55 0.61 95 35 44 9 231.53 0.62 96 35 46 11 231.46 0.66 97 36 40 4 336.79 0.41 98 36 95 59 336.85 0.38 99 36 97 61 336.80 0.40 100 40 86 46 231.46 0.63 101 42 85 43 231.44 0.64 102 42 86 44 231.44 0.64 103 43 84 41 231.38 0.63 104 43 85 42 231.40 0.63 105 44 83 39 231.38 0.64 106 44 84 40 231.31 0.62 107 45 81 36 231.42 0.63 108 45 82 37 231.38 0.64 109 45 83 38 231.30 0.63 110 45 120 75 36.45 0.33 111 46 81 35 231.38 0.64 112 46 82 36 231.35 0.63 113 46 84 38 231.30 0.63 114 47 54 7 338.05 0.18 115 47 79 32 231.43 0.64 116 47 80 33 231.38 0.63 117 47 81 34 231.31 0.62 118 47 106 59 284.37 8.59 119 47 120 73 37.01 0.06 120 48 80 32 231.33 0.64 121 48 81 33 231.29 0.63 122 48 82 34 231.28 0.63 123 49 79 30 231.34 0.64 124 49 80 31 231.33 0.65 125 53 79 26 231.12 0.60 126 54 79 25 224.22 0.70 127 54 117 63 59.52 0.97 128 55 116 61 59.69 1.04 129 55 117 62 59.56 0.98 130 57 73 16 231.19 0.63 131 57 74 17 231.12 0.61 132 57 75 18 219.40 0.30 133 57 79 22 206.91 0.24 134 58 73 15 231.11 0.60 135 58 115 57 60.50 1.08 136 58 116 58 60.29 1.03 137 58 117 59 60.23 1.03 138 60 73 13 231.29 0.64 139 60 74 14 231.19 0.61 140 60 75 15 230.61 0.83 141 60 76 16 225.59 0.01 142 61 73 12 231.33 0.65 143 61 74 13 231.23 0.63 144 61 76 15 230.99 0.60 145 62 70 8 235.83 2.23 146 62 72 10 231.35 0.64 147 62 73 11 231.34 0.65 148 63 72 9 231.39 0.66 149 63 73 10 231.37 0.65 150 63 74 11 231.37 0.64 151 63 107 44 231.44 0.59 152 64 72 8 252.54 1.32 153 65 109 44 231.17 0.64 154 65 121 56 59.80 0.98 155 66 121 55 59.84 0.98 156 66 122 56 59.90 1.01 157 71 109 38 231.21 0.62 158 71 110 39 231.15 0.62 159 71 111 40 231.11 0.61 160 71 115 44 156.87 1.20 161 72 107 35 231.28 0.64 162 72 108 36 231.21 0.62 163 72 109 37 231.05 0.61 164 72 121 49 59.59 0.96 165 73 107 34 231.22 0.62 166 73 108 35 231.12 0.60 167 73 110 37 230.81 0.50 168 73 115 42 128.44 2.05 169 74 105 31 231.31 0.65 170 74 106 32 231.22 0.62 171 74 107 33 230.99 0.57 172 74 124 50 40.02 0.62 173 75 79 4 213.11 0.03 174 75 105 30 231.16 0.61 175 75 106 31 231.12 0.60 176 76 105 29 231.15 0.60 177 77 105 28 230.78 0.52 178 78 103 25 231.12 0.60 179 78 104 26 219.13 0.42 180 78 105 27 213.18 0.07 181 79 103 24 225.93 1.50 182 79 104 25 216.94 0.58 183 79 106 27 203.09 0.07 184 80 102 22 230.64 0.75 185 80 103 23 214.27 0.48 186 81 101 20 229.66 0.26 187 81 102 21 216.56 0.67 188 81 104 23 208.11 0.84 189 81 106 25 170.79 3.01 190 81 123 42 36.55 0.33 191 82 99 17 231.12 0.59 192 82 100 18 224.25 0.66 193 82 101 19 213.13 0.06 194 83 98 15 231.15 0.59 195 83 99 16 225.84 2.16 196 83 100 17 214.20 0.42 197 84 97 13 231.08 0.60 198 84 98 14 217.55 0.87 199 85 97 12 231.12 0.58 200 85 98 13 230.77 0.68 201 86 90 4 294.58 0.87 202 86 96 10 231.36 0.63 203 86 97 11 231.15 0.59 204 87 90 3 332.62 0.04 205 87 96 9 231.38 0.64 206 87 97 10 231.36 0.63 207 87 98 11 231.34 0.64 208 90 95 5 231.54 0.62 209 90 96 6 231.50 0.61 210 104 123 19 37.02 0.12 211 104 124 20 36.78 0.16 212 105 123 18 37.03 0.11 213 105 124 19 36.97 0.10 214 106 120 14 58.45 0.58 215 106 122 16 46.58 3.04 216 106 123 17 39.02 0.90 217 107 120 13 58.67 0.58 218 107 121 14 57.45 0.65 219 107 122 15 46.59 3.04 220 107 124 17 40.84 0.17 221 108 117 9 59.99 1.02 222 108 119 11 59.66 1.02 223 108 120 12 58.93 0.71 224 108 121 13 58.38 0.55 225 109 117 8 60.37 0.96 226 109 118 9 59.95 1.02 227 109 119 10 59.72 1.02 228 110 115 5 65.75 0.91 229 110 116 6 60.41 0.96 230 110 117 7 60.24 1.03 231 110 118 8 60.23 1.03 232 111 115 4 129.21 2.44 233 111 116 5 65.76 0.90 234 111 118 7 60.40 0.97 235 112 115 3 150.38 1.84