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 8 136.02 2.42 2 3 6 3 144.03 0.98 3 3 7 4 146.64 2.29 4 4 7 3 146.65 2.29 5 4 8 4 149.25 0.99 6 4 118 114 24.29 0.33 7 5 8 3 154.69 3.66 8 5 9 4 149.26 0.99 9 5 116 111 24.34 0.32 10 5 117 112 24.33 0.32 11 6 9 3 151.34 2.02 12 6 10 4 149.25 0.99 13 7 10 3 148.25 1.50 14 7 11 4 143.98 1.13 15 8 11 3 145.27 1.18 16 8 12 4 141.74 1.19 17 8 13 5 141.72 1.19 18 8 54 46 66.56 0.74 19 8 108 100 31.55 0.77 20 8 117 109 31.64 0.72 21 8 118 110 31.55 0.77 22 8 119 111 31.52 0.76 23 8 120 112 31.41 0.81 24 9 13 4 141.60 1.24 25 9 33 24 114.56 0.39 26 9 51 42 86.11 1.23 27 10 33 23 113.19 0.29 28 10 34 24 115.05 0.64 29 10 35 25 115.11 0.67 30 11 35 24 115.06 0.69 31 11 44 33 114.55 0.81 32 11 46 35 112.34 0.20 33 12 44 32 114.86 0.69 34 12 45 33 112.59 0.17 35 12 46 34 112.33 0.21 36 12 47 35 112.33 0.21 37 12 120 108 31.86 0.70 38 13 33 20 116.50 0.30 39 13 47 34 112.34 0.21 40 13 49 36 112.31 0.21 41 13 50 37 112.30 0.20 42 13 51 38 111.66 0.14 43 13 54 41 102.88 0.72 44 14 17 3 167.00 1.69 45 14 25 11 116.15 0.10 46 14 29 15 116.43 0.24 47 14 33 19 116.53 0.29 48 14 46 32 114.98 0.66 49 14 47 33 114.78 0.64 50 14 48 34 112.34 0.20 51 15 49 34 112.34 0.20 52 15 50 35 112.32 0.21 53 17 48 31 115.83 0.33 54 18 48 30 116.02 0.29 55 18 80 62 116.05 0.28 56 19 48 29 116.16 0.27 57 19 80 61 116.17 0.25 58 19 101 82 116.47 0.24 59 20 25 5 116.70 0.30 60 20 48 28 116.49 0.29 61 20 82 62 116.56 0.27 62 20 99 79 116.56 0.27 63 20 101 81 116.50 0.24 64 21 25 4 131.63 1.88 65 22 25 3 156.60 2.37 66 22 99 77 149.81 1.11 67 23 99 76 148.84 1.60 68 24 28 4 337.27 0.02 69 25 46 21 175.87 0.65 70 25 48 23 163.30 0.29 71 25 82 57 164.47 0.58 72 25 99 74 183.09 1.85 73 26 30 4 336.41 0.78 74 26 82 56 235.16 0.70 75 26 97 71 218.03 1.20 76 26 98 72 218.02 1.21 77 26 99 73 198.37 0.45 78 27 96 69 229.66 1.58 79 27 97 70 227.41 0.46 80 29 46 17 229.81 1.55 81 30 35 5 335.47 0.23 82 30 36 6 320.07 1.55 83 30 41 11 230.37 1.59 84 30 44 14 230.23 1.58 85 30 46 16 230.03 1.58 86 30 97 67 229.98 1.66 87 31 36 5 326.30 4.67 88 33 46 13 230.11 1.59 89 35 41 6 230.38 1.59 90 35 44 9 230.35 1.60 91 35 46 11 230.32 1.58 92 36 95 59 336.00 0.32 93 36 97 61 335.24 0.41 94 40 86 46 230.35 1.60 95 42 85 43 230.34 1.60 96 42 86 44 230.35 1.59 97 43 84 41 230.28 1.59 98 43 85 42 230.30 1.58 99 44 83 39 230.28 1.59 100 44 84 40 230.18 1.58 101 45 81 36 230.31 1.58 102 45 82 37 230.25 1.58 103 45 120 75 32.91 0.48 104 46 81 35 230.28 1.59 105 46 82 36 230.21 1.59 106 46 84 38 230.12 1.61 107 47 54 7 337.04 0.24 108 47 79 32 230.31 1.58 109 47 80 33 230.30 1.58 110 47 81 34 230.14 1.60 111 47 106 59 222.58 28.61 112 47 120 73 35.01 1.53 113 48 80 32 230.23 1.59 114 48 81 33 230.13 1.60 115 48 82 34 230.13 1.60 116 49 79 30 230.26 1.60 117 49 80 31 230.20 1.59 118 53 79 26 229.86 1.61 119 54 117 63 61.70 1.08 120 55 116 61 62.65 0.69 121 55 117 62 61.74 1.07 122 57 73 16 229.99 1.65 123 57 74 17 229.88 1.61 124 57 75 18 222.83 0.66 125 57 79 22 209.96 1.15 126 58 73 15 229.88 1.61 127 58 115 57 91.59 14.38 128 58 116 58 64.00 0.93 129 58 117 59 64.02 0.95 130 60 73 13 230.12 1.61 131 60 74 14 230.09 1.61 132 60 75 15 227.73 1.13 133 60 76 16 222.19 0.97 134 61 73 12 230.15 1.61 135 61 74 13 230.11 1.61 136 61 76 15 229.90 1.63 137 62 70 8 244.11 0.32 138 62 72 10 230.25 1.58 139 62 73 11 230.16 1.61 140 63 72 9 230.27 1.59 141 63 73 10 230.24 1.60 142 63 74 11 230.24 1.60 143 63 107 44 230.44 1.68 144 64 72 8 256.62 1.38 145 65 109 44 229.87 1.62 146 65 121 56 62.22 1.02 147 66 121 55 62.26 1.02 148 66 122 56 62.26 1.02 149 71 109 38 230.08 1.61 150 71 110 39 229.92 1.62 151 71 111 40 229.88 1.62 152 71 115 44 156.41 1.75 153 72 107 35 230.15 1.61 154 72 108 36 230.00 1.65 155 72 109 37 229.87 1.62 156 72 121 49 61.87 1.11 157 73 107 34 230.08 1.61 158 73 108 35 229.93 1.62 159 73 110 37 229.86 1.62 160 73 115 42 135.62 0.39 161 74 105 31 230.15 1.61 162 74 106 32 230.09 1.61 163 74 107 33 229.84 1.64 164 74 124 50 37.87 0.97 165 75 79 4 230.28 1.59 166 75 105 30 230.08 1.61 167 75 106 31 229.97 1.64 168 76 105 29 230.00 1.65 169 77 105 28 229.62 1.54 170 78 103 25 229.91 1.62 171 78 104 26 218.61 0.92 172 78 105 27 215.00 0.26 173 79 103 24 224.23 0.99 174 79 104 25 218.59 0.92 175 79 106 27 206.76 0.26 176 80 101 21 230.00 1.66 177 80 102 22 229.70 1.57 178 80 103 23 214.91 0.15 179 81 101 20 224.06 0.29 180 81 102 21 218.59 0.91 181 81 104 23 198.96 0.18 182 81 106 25 168.60 1.41 183 82 99 17 229.99 1.66 184 82 100 18 221.06 1.21 185 82 101 19 215.08 0.26 186 83 98 15 230.00 1.66 187 83 99 16 221.25 0.18 188 83 100 17 217.90 1.22 189 84 97 13 229.97 1.66 190 84 98 14 219.75 0.35 191 85 97 12 229.99 1.66 192 85 98 13 229.78 1.60 193 86 90 4 309.29 8.54 194 86 96 10 230.22 1.57 195 86 97 11 230.08 1.61 196 87 90 3 335.76 0.23 197 87 96 9 230.28 1.60 198 87 97 10 230.22 1.59 199 87 98 11 230.12 1.61 200 90 94 4 329.85 2.90 201 90 95 5 230.49 1.64 202 90 96 6 230.42 1.61 203 104 123 19 35.16 1.56 204 104 124 20 34.68 1.44 205 105 123 18 35.63 1.34 206 105 124 19 34.70 1.45 207 106 120 14 61.21 1.15 208 106 122 16 42.14 2.06 209 106 123 17 35.87 1.41 210 107 120 13 61.30 1.11 211 107 121 14 59.90 1.63 212 107 122 15 49.87 0.45 213 107 124 17 37.87 0.97 214 108 117 9 64.00 0.94 215 108 119 11 61.88 1.10 216 108 120 12 61.30 1.10 217 108 121 13 61.20 1.14 218 109 117 8 64.03 0.95 219 109 118 9 63.99 0.94 220 109 119 10 63.07 0.94 221 110 115 5 120.01 0.12 222 110 116 6 64.10 0.94 223 110 117 7 64.03 0.95 224 110 118 8 64.00 0.94 225 111 115 4 138.08 1.62 226 111 116 5 120.00 0.12 227 111 118 7 64.05 0.93 228 112 115 3 151.41 0.06