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 8 140.06 1.13 2 3 6 3 147.60 2.62 3 3 7 4 147.02 2.91 4 4 7 3 151.76 3.50 5 4 8 4 150.00 4.39 6 4 118 114 23.84 0.64 7 5 8 3 151.97 3.41 8 5 9 4 151.41 3.69 9 5 116 111 24.16 0.61 10 5 117 112 24.10 0.60 11 5 118 113 23.95 0.68 12 6 9 3 151.98 3.40 13 6 10 4 151.71 3.54 14 7 10 3 151.34 1.55 15 7 11 4 149.55 2.46 16 8 11 3 152.18 1.16 17 8 12 4 148.69 2.02 18 8 13 5 143.75 0.44 19 8 54 46 69.92 0.21 20 8 108 100 34.44 0.36 21 8 117 109 34.52 0.34 22 8 118 110 34.44 0.36 23 8 119 111 34.44 0.36 24 8 120 112 34.36 0.39 25 9 12 3 151.32 0.72 26 9 13 4 143.36 0.63 27 9 33 24 121.20 0.28 28 9 51 42 85.16 0.77 29 10 33 23 121.12 0.24 30 10 34 24 121.21 0.28 31 10 35 25 121.20 0.28 32 11 35 24 121.20 0.28 33 11 41 30 121.13 0.28 34 11 44 33 116.31 0.76 35 11 45 34 116.31 0.76 36 11 46 35 116.25 0.76 37 12 44 32 120.03 0.45 38 12 45 33 116.29 0.76 39 12 46 34 116.25 0.76 40 12 47 35 116.25 0.76 41 12 120 108 34.51 0.38 42 13 33 20 121.98 0.12 43 13 47 34 116.27 0.77 44 13 49 36 116.22 0.77 45 13 50 37 115.97 0.84 46 13 51 38 106.92 0.76 47 13 54 41 100.17 2.17 48 14 17 3 171.90 1.95 49 14 25 11 122.00 0.16 50 14 29 15 121.99 0.14 51 14 33 19 122.01 0.13 52 14 46 32 120.50 0.22 53 14 47 33 117.31 0.30 54 14 48 34 116.27 0.77 55 15 48 33 116.34 0.79 56 15 49 34 116.28 0.77 57 15 50 35 116.16 0.74 58 17 48 31 120.83 0.34 59 18 48 30 121.42 0.07 60 18 80 62 121.42 0.08 61 19 48 29 121.56 0.12 62 19 80 61 121.47 0.09 63 19 101 82 121.98 0.19 64 20 25 5 122.25 0.14 65 20 48 28 121.84 0.21 66 20 82 62 121.97 0.18 67 20 99 79 122.23 0.14 68 20 101 81 121.98 0.19 69 22 25 3 142.24 0.24 70 22 99 77 147.41 2.82 71 23 99 76 151.63 0.71 72 24 28 4 337.69 0.49 73 25 29 4 337.80 0.55 74 25 46 21 185.34 2.79 75 25 48 23 167.56 0.27 76 25 82 57 175.32 0.39 77 25 99 74 189.21 1.66 78 26 30 4 337.79 0.55 79 26 82 56 237.62 2.11 80 26 97 71 213.92 0.16 81 26 98 72 213.88 0.15 82 26 99 73 207.55 0.61 83 27 96 69 226.12 0.91 84 27 97 70 219.47 2.35 85 29 33 4 337.98 0.51 86 29 46 17 227.80 1.30 87 30 35 5 336.31 0.28 88 30 36 6 312.22 6.92 89 30 41 11 228.18 1.23 90 30 44 14 228.09 1.23 91 30 46 16 227.86 1.31 92 30 97 67 227.53 1.35 93 31 36 5 333.28 1.79 94 33 46 13 228.06 1.26 95 35 41 6 228.25 1.24 96 35 44 9 228.17 1.23 97 35 46 11 228.15 1.24 98 36 40 4 333.64 1.42 99 36 95 59 336.36 0.49 100 36 97 61 333.66 1.42 101 40 86 46 228.19 1.24 102 42 85 43 228.13 1.26 103 42 86 44 228.21 1.23 104 43 84 41 228.04 1.26 105 43 85 42 228.04 1.26 106 44 83 39 228.05 1.26 107 44 84 40 227.94 1.27 108 45 81 36 228.14 1.24 109 45 82 37 228.04 1.26 110 45 83 38 227.94 1.27 111 46 81 35 228.03 1.27 112 46 82 36 227.98 1.27 113 46 84 38 227.88 1.30 114 47 54 7 336.76 0.43 115 47 79 32 228.15 1.24 116 47 80 33 228.04 1.27 117 47 81 34 227.94 1.28 118 47 106 59 239.05 30.19 119 48 80 32 227.97 1.28 120 48 81 33 227.94 1.28 121 48 82 34 227.94 1.28 122 49 79 30 227.99 1.28 123 49 80 31 227.96 1.28 124 53 79 26 227.50 1.39 125 54 79 25 225.75 0.97 126 54 117 63 57.42 1.09 127 55 116 61 58.02 0.80 128 55 117 62 57.36 1.13 129 57 73 16 227.44 1.44 130 57 74 17 227.42 1.43 131 57 75 18 215.69 0.08 132 57 79 22 213.44 0.07 133 58 73 15 227.40 1.44 134 58 115 57 63.64 0.73 135 58 116 58 62.98 0.84 136 58 117 59 62.97 0.83 137 60 73 13 227.80 1.34 138 60 74 14 227.68 1.35 139 60 75 15 227.10 1.19 140 60 76 16 217.47 0.96 141 61 73 12 227.84 1.35 142 61 74 13 227.69 1.35 143 61 76 15 226.76 1.02 144 62 70 8 236.02 4.58 145 62 72 10 227.99 1.29 146 62 73 11 227.88 1.33 147 63 72 9 228.02 1.28 148 63 73 10 227.99 1.29 149 63 74 11 227.98 1.29 150 63 107 44 228.12 1.28 151 64 72 8 254.35 2.04 152 65 109 44 227.59 1.43 153 65 121 56 57.66 1.24 154 66 121 55 58.77 1.74 155 71 109 38 227.47 1.35 156 71 110 39 227.44 1.35 157 71 115 44 162.69 0.07 158 72 107 35 227.80 1.34 159 72 108 36 227.57 1.40 160 72 109 37 227.05 1.29 161 72 121 49 57.33 1.13 162 73 107 34 227.77 1.33 163 73 108 35 227.56 1.41 164 73 110 37 226.02 0.84 165 73 115 42 146.47 0.49 166 74 105 31 227.91 1.29 167 74 106 32 227.76 1.33 168 74 107 33 226.48 1.07 169 74 124 50 37.05 0.03 170 75 79 4 219.44 2.98 171 75 105 30 227.75 1.33 172 75 106 31 227.61 1.39 173 76 105 29 227.75 1.31 174 77 105 28 225.76 0.52 175 78 103 25 227.57 1.40 176 78 104 26 214.61 0.47 177 78 105 27 213.86 0.14 178 79 103 24 216.87 0.07 179 79 104 25 214.41 0.41 180 79 106 27 209.57 1.25 181 80 101 21 227.77 1.32 182 80 102 22 226.37 1.55 183 80 103 23 213.82 0.16 184 81 101 20 215.50 0.02 185 81 102 21 214.41 0.41 186 81 104 23 212.88 0.41 187 81 106 25 171.83 1.65 188 82 99 17 227.75 1.31 189 82 100 18 215.80 0.28 190 82 101 19 213.83 0.15 191 83 98 15 227.78 1.32 192 83 99 16 220.43 0.23 193 83 100 17 214.40 0.42 194 83 104 21 195.47 1.34 195 84 97 13 227.59 1.39 196 84 98 14 215.62 0.18 197 85 97 12 227.75 1.32 198 85 98 13 227.44 1.35 199 86 90 4 260.94 7.04 200 86 96 10 227.98 1.28 201 86 97 11 227.79 1.33 202 87 90 3 332.22 1.82 203 87 96 9 228.04 1.26 204 87 97 10 227.99 1.28 205 87 98 11 227.93 1.30 206 89 96 7 228.25 1.20 207 90 94 4 330.62 3.23 208 90 95 5 228.27 1.19 209 90 96 6 228.24 1.18 210 91 94 3 337.52 0.21 211 92 95 3 337.89 0.29 212 104 123 19 35.63 0.57 213 104 124 20 35.26 0.58 214 105 123 18 35.97 0.41 215 105 124 19 35.40 0.55 216 106 122 16 39.66 1.27 217 106 123 17 35.58 0.59 218 107 120 13 52.83 0.77 219 107 121 14 43.86 0.04 220 107 122 15 39.67 1.27 221 107 123 16 37.05 0.03 222 107 124 17 37.08 0.01 223 108 117 9 62.96 0.83 224 108 119 11 57.36 1.12 225 108 120 12 54.33 0.01 226 108 121 13 52.47 0.92 227 109 117 8 62.98 0.83 228 109 118 9 62.97 0.83 229 109 119 10 61.07 0.55 230 110 115 5 110.03 18.71 231 110 116 6 63.22 0.92 232 110 117 7 62.98 0.83 233 110 118 8 62.97 0.83 234 111 115 4 146.47 0.50 235 111 116 5 69.44 1.58 236 111 118 7 62.98 0.83 237 112 115 3 150.06 0.52