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 8 137.33 0.18 2 3 6 3 152.02 0.40 3 3 7 4 145.96 0.56 4 4 7 3 152.02 0.40 5 4 8 4 149.09 1.01 6 4 118 114 23.21 0.59 7 5 8 3 155.75 0.68 8 5 9 4 152.19 2.56 9 5 116 111 24.41 0.82 10 5 117 112 24.34 0.79 11 5 118 113 23.94 0.92 12 6 9 3 153.88 1.72 13 6 10 4 147.82 1.60 14 7 10 3 152.80 2.25 15 7 11 4 147.83 1.60 16 8 11 3 153.74 1.79 17 8 12 4 146.57 0.97 18 8 13 5 144.05 0.29 19 8 54 46 66.00 0.87 20 8 108 100 33.95 0.04 21 8 117 109 38.05 1.08 22 8 118 110 34.96 0.47 23 8 119 111 33.84 0.10 24 8 120 112 33.37 0.34 25 9 12 3 149.34 0.41 26 9 13 4 136.13 0.79 27 9 33 24 110.64 0.97 28 9 51 42 89.95 0.09 29 10 33 23 110.64 0.96 30 10 34 24 110.65 0.96 31 10 35 25 110.64 0.96 32 11 35 24 110.61 0.97 33 11 44 33 109.66 1.22 34 11 46 35 110.33 0.88 35 12 44 32 110.38 0.90 36 12 45 33 110.38 0.90 37 12 46 34 110.33 0.88 38 12 47 35 109.45 1.32 39 12 120 108 36.36 0.35 40 13 33 20 112.09 1.60 41 13 47 34 110.34 0.88 42 13 49 36 109.81 1.16 43 13 50 37 109.78 1.15 44 13 51 38 109.16 1.18 45 13 54 41 103.28 1.76 46 14 17 3 170.82 1.41 47 14 25 11 112.23 1.50 48 14 29 15 112.27 1.53 49 14 33 19 112.27 1.54 50 14 46 32 110.55 0.97 51 14 47 33 110.53 0.97 52 14 48 34 110.37 0.89 53 15 48 33 110.39 0.89 54 15 49 34 110.38 0.89 55 15 50 35 110.33 0.87 56 17 48 31 111.98 1.59 57 18 48 30 112.20 1.51 58 18 80 62 112.20 1.51 59 19 48 29 112.27 1.53 60 19 80 61 112.22 1.51 61 19 101 82 112.30 1.51 62 20 48 28 112.31 1.52 63 20 82 62 112.28 1.53 64 20 99 79 112.33 1.51 65 20 101 81 112.31 1.51 66 21 25 4 128.98 0.70 67 22 25 3 144.93 0.53 68 22 99 77 144.31 0.23 69 23 99 76 144.31 0.24 70 25 46 21 184.50 2.71 71 25 48 23 163.83 0.94 72 25 82 57 164.34 0.71 73 25 99 74 186.88 1.65 74 26 82 56 238.17 1.20 75 26 97 71 212.88 0.14 76 26 98 72 212.86 0.14 77 26 99 73 197.22 1.53 78 27 96 69 223.78 0.88 79 27 97 70 215.20 0.58 80 29 46 17 226.66 0.11 81 30 41 11 227.54 0.32 82 30 44 14 227.47 0.34 83 30 46 16 227.33 0.29 84 30 97 67 227.12 0.30 85 31 36 5 324.86 0.84 86 33 46 13 227.42 0.31 87 35 41 6 264.70 18.76 88 35 44 9 227.53 0.32 89 35 46 11 227.50 0.33 90 36 95 59 333.43 1.46 91 36 97 61 331.55 0.52 92 40 86 46 227.63 0.25 93 42 85 43 227.50 0.31 94 42 86 44 227.53 0.30 95 43 84 41 227.45 0.32 96 43 85 42 227.46 0.32 97 44 83 39 227.46 0.31 98 44 84 40 227.36 0.29 99 45 81 36 227.48 0.32 100 45 82 37 227.44 0.31 101 45 83 38 227.35 0.29 102 45 120 75 39.55 0.35 103 46 81 35 227.43 0.32 104 46 82 36 227.38 0.30 105 46 84 38 227.35 0.29 106 47 79 32 227.48 0.32 107 47 80 33 227.44 0.30 108 47 81 34 227.38 0.30 109 47 106 59 271.86 17.12 110 47 120 73 40.01 0.13 111 48 80 32 227.40 0.30 112 48 81 33 227.38 0.30 113 48 82 34 227.36 0.29 114 49 79 30 227.40 0.30 115 49 80 31 227.39 0.30 116 53 79 26 227.08 0.35 117 54 79 25 223.90 0.72 118 54 117 63 53.08 2.27 119 55 117 62 53.09 2.27 120 57 73 16 227.15 0.33 121 57 74 17 227.13 0.33 122 57 75 18 217.22 0.35 123 57 79 22 212.56 0.24 124 58 73 15 227.09 0.35 125 58 115 57 62.25 1.50 126 58 116 58 58.45 3.19 127 58 117 59 58.41 3.18 128 60 74 14 227.22 0.34 129 60 75 15 225.82 0.23 130 60 76 16 220.71 0.19 131 61 73 12 227.34 0.29 132 61 74 13 227.22 0.34 133 61 76 15 227.05 0.35 134 62 70 8 252.62 2.96 135 62 72 10 227.40 0.30 136 62 73 11 227.36 0.29 137 63 70 7 332.57 2.81 138 63 72 9 227.46 0.31 139 63 73 10 227.41 0.29 140 63 74 11 227.41 0.30 141 63 107 44 227.49 0.31 142 64 72 8 255.39 0.85 143 65 109 44 226.97 0.35 144 65 121 56 56.15 2.83 145 66 121 55 56.82 3.08 146 66 122 56 56.79 3.10 147 71 109 38 227.13 0.36 148 71 110 39 227.06 0.36 149 71 115 44 164.85 0.51 150 72 107 35 227.37 0.30 151 72 108 36 227.15 0.36 152 72 109 37 226.89 0.35 153 72 121 49 55.86 2.85 154 73 107 34 227.24 0.35 155 73 108 35 227.13 0.33 156 73 110 37 225.91 0.09 157 73 115 42 144.03 0.76 158 74 105 31 227.38 0.30 159 74 106 32 227.23 0.35 160 74 107 33 226.97 0.30 161 74 124 50 40.80 0.25 162 75 79 4 212.75 0.18 163 75 105 30 227.22 0.35 164 75 106 31 227.15 0.32 165 76 105 29 227.22 0.35 166 77 105 28 226.38 0.32 167 78 103 25 227.15 0.32 168 78 104 26 217.32 1.07 169 78 105 27 212.77 0.17 170 79 103 24 221.64 1.85 171 79 104 25 214.16 0.51 172 79 106 27 208.35 1.87 173 80 101 21 227.19 0.34 174 80 102 22 224.76 0.30 175 80 103 23 212.81 0.14 176 81 101 20 216.33 0.63 177 81 102 21 214.16 0.51 178 81 104 23 208.97 0.04 179 81 106 25 170.85 2.04 180 81 123 42 39.95 0.10 181 82 99 17 227.19 0.34 182 82 100 18 214.77 0.81 183 82 101 19 212.75 0.18 184 83 98 15 227.33 0.29 185 83 99 16 216.04 0.44 186 83 100 17 212.76 0.18 187 84 97 13 227.14 0.32 188 84 98 14 215.16 0.98 189 85 97 12 227.22 0.35 190 85 98 13 226.78 0.22 191 86 90 4 315.09 9.64 192 86 96 10 227.40 0.32 193 86 97 11 227.34 0.29 194 87 90 3 321.91 6.24 195 87 96 9 227.42 0.31 196 87 97 10 227.40 0.31 197 87 98 11 227.38 0.30 198 89 96 7 227.68 0.24 199 90 95 5 227.69 0.24 200 90 96 6 227.68 0.24 201 104 123 19 40.13 0.06 202 104 124 20 39.94 0.03 203 105 123 18 40.14 0.05 204 105 124 19 40.07 0.04 205 106 120 14 52.98 2.23 206 106 122 16 40.92 0.21 207 106 123 17 40.42 0.09 208 107 120 13 53.12 2.31 209 107 121 14 49.57 1.37 210 107 122 15 44.13 0.12 211 107 124 17 41.10 0.10 212 108 117 9 58.20 3.08 213 108 119 11 56.54 3.18 214 108 120 12 53.06 2.27 215 108 121 13 52.93 2.24 216 109 117 8 58.45 3.19 217 109 118 9 58.12 3.12 218 109 119 10 56.78 3.12 219 110 115 5 129.59 5.06 220 110 116 6 61.83 1.67 221 110 117 7 58.44 3.19 222 110 118 8 58.40 3.18 223 111 115 4 142.52 1.40 224 111 116 5 92.36 13.45 225 111 118 7 58.48 3.17 226 112 115 3 145.84 0.15