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 5 8 3 304.99 0.01 2 5 9 4 305.00 0.00 3 5 116 111 27.15 0.06 4 5 117 112 27.10 0.07 5 5 118 113 27.05 0.06 6 8 54 46 70.91 0.70 7 8 108 100 27.14 0.04 8 8 117 109 27.50 0.21 9 8 118 110 27.11 0.07 10 8 119 111 27.09 0.07 11 8 120 112 27.03 0.07 12 9 13 4 163.97 7.99 13 9 33 24 97.64 0.09 14 9 51 42 70.93 0.69 15 10 33 23 97.37 0.04 16 10 34 24 97.61 0.10 17 10 35 25 97.52 0.14 18 11 35 24 97.52 0.14 19 11 41 30 97.56 0.17 20 11 44 33 93.28 0.76 21 11 46 35 89.86 0.29 22 12 44 32 96.37 0.41 23 12 45 33 89.97 0.27 24 12 46 34 89.84 0.29 25 12 47 35 89.83 0.29 26 12 120 108 27.07 0.07 27 13 33 20 98.52 0.01 28 13 47 34 89.95 0.28 29 13 49 36 89.81 0.30 30 13 50 37 89.77 0.33 31 13 51 38 88.70 0.79 32 13 54 41 81.17 4.01 33 14 17 3 143.33 0.13 34 14 25 11 98.17 0.18 35 14 29 15 98.17 0.17 36 14 33 19 98.58 0.01 37 14 46 32 97.14 0.10 38 14 47 33 93.80 0.89 39 14 48 34 89.95 0.27 40 15 49 34 89.96 0.27 41 15 50 35 89.92 0.26 42 15 51 36 89.77 0.33 43 17 48 31 97.67 0.09 44 18 48 30 97.69 0.09 45 18 80 62 98.08 0.11 46 19 48 29 98.14 0.12 47 19 80 61 98.12 0.12 48 19 101 82 98.27 0.14 49 20 25 5 99.51 0.05 50 20 48 28 98.48 0.03 51 20 82 62 98.48 0.04 52 20 99 79 101.96 0.43 53 20 101 81 98.34 0.12 54 22 25 3 127.26 1.98 55 22 99 77 130.54 0.11 56 23 99 76 130.54 0.11 57 24 27 3 305.00 0.00 58 24 28 4 305.00 0.00 59 25 29 4 305.00 0.00 60 25 46 21 194.78 0.48 61 25 48 23 194.55 0.46 62 25 99 74 186.75 0.79 63 26 97 71 194.50 0.43 64 26 98 72 194.43 0.47 65 26 99 73 191.03 0.67 66 27 96 69 194.63 0.46 67 27 97 70 194.49 0.48 68 28 31 3 304.99 0.01 69 28 32 4 304.87 0.03 70 29 32 3 304.96 0.01 71 29 33 4 304.79 0.06 72 29 46 17 194.79 0.48 73 30 34 4 304.78 0.07 74 30 35 5 303.28 0.61 75 30 36 6 303.27 0.61 76 30 41 11 195.11 0.48 77 30 44 14 195.00 0.48 78 30 46 16 194.84 0.47 79 30 97 67 194.59 0.50 80 31 34 3 304.78 0.07 81 31 36 5 302.11 0.05 82 33 46 13 194.81 0.47 83 34 37 3 304.97 0.01 84 35 39 4 304.99 0.01 85 35 41 6 270.58 3.64 86 35 44 9 195.18 0.48 87 35 46 11 195.19 0.50 88 36 40 4 302.80 0.72 89 36 95 59 304.01 0.15 90 36 97 61 304.29 0.29 91 40 86 46 195.16 0.47 92 40 90 50 304.99 0.01 93 41 44 3 305.00 0.00 94 42 85 43 195.09 0.48 95 42 86 44 195.12 0.46 96 43 83 40 195.10 0.46 97 43 84 41 195.06 0.47 98 43 85 42 195.06 0.48 99 44 83 39 195.05 0.47 100 44 84 40 195.00 0.48 101 45 81 36 195.02 0.48 102 45 82 37 194.93 0.50 103 45 83 38 194.95 0.51 104 45 120 75 27.68 0.24 105 46 81 35 194.92 0.51 106 46 82 36 194.79 0.48 107 46 84 38 194.94 0.50 108 47 54 7 304.66 0.01 109 47 79 32 195.02 0.48 110 47 80 33 194.91 0.51 111 47 81 34 194.78 0.48 112 47 106 59 257.44 22.21 113 47 120 73 27.66 0.24 114 48 80 32 194.79 0.48 115 48 81 33 194.75 0.48 116 48 82 34 194.75 0.48 117 49 79 30 194.85 0.51 118 49 80 31 194.78 0.48 119 50 53 3 304.99 0.01 120 50 54 4 305.00 0.00 121 51 54 3 305.00 0.00 122 52 56 4 305.00 0.00 123 53 56 3 305.00 0.00 124 53 57 4 305.00 0.00 125 53 79 26 194.52 0.46 126 54 57 3 304.98 0.00 127 54 79 25 194.34 0.40 128 54 117 63 45.30 0.04 129 55 58 3 304.99 0.01 130 55 116 61 49.34 0.39 131 55 117 62 45.31 0.03 132 57 60 3 305.00 0.00 133 57 73 16 194.66 0.48 134 57 74 17 194.56 0.45 135 57 75 18 191.26 0.56 136 57 79 22 174.23 0.69 137 58 73 15 194.56 0.45 138 58 115 57 107.88 0.62 139 58 116 58 79.31 13.22 140 58 117 59 79.09 13.33 141 60 73 13 194.67 0.49 142 60 74 14 194.64 0.49 143 60 75 15 194.38 0.39 144 60 76 16 191.74 0.80 145 61 73 12 194.71 0.51 146 61 74 13 194.65 0.48 147 61 76 15 194.53 0.46 148 62 70 8 211.06 0.36 149 62 71 9 195.00 0.48 150 62 72 10 194.89 0.53 151 62 73 11 194.87 0.53 152 63 72 9 194.97 0.48 153 63 73 10 194.88 0.52 154 63 74 11 194.88 0.52 155 63 107 44 195.12 0.52 156 64 70 6 304.43 0.26 157 64 72 8 216.50 1.56 158 65 121 56 47.10 0.90 159 66 121 55 47.95 0.58 160 71 109 38 194.66 0.49 161 71 110 39 194.56 0.45 162 71 111 40 194.53 0.46 163 71 115 44 131.28 1.84 164 72 107 35 194.74 0.49 165 72 108 36 194.63 0.48 166 72 109 37 194.53 0.46 167 72 121 49 45.26 0.03 168 73 107 34 194.63 0.48 169 73 108 35 194.58 0.46 170 73 110 37 194.46 0.46 171 73 115 42 113.29 2.33 172 74 105 31 194.75 0.48 173 74 106 32 194.64 0.48 174 74 107 33 194.47 0.48 175 74 124 50 31.91 0.47 176 75 79 4 191.24 1.33 177 75 105 30 194.62 0.48 178 75 106 31 194.56 0.46 179 76 105 29 194.62 0.48 180 77 105 28 194.50 0.48 181 78 103 25 194.54 0.47 182 78 104 26 191.53 0.43 183 78 105 27 183.94 1.13 184 79 103 24 194.30 0.41 185 79 104 25 191.02 0.67 186 79 106 27 165.21 0.52 187 80 101 21 194.58 0.46 188 80 102 22 194.43 0.47 189 80 103 23 185.93 0.56 190 81 101 20 194.05 0.56 191 81 102 21 190.38 0.96 192 81 104 23 164.29 0.47 193 81 106 25 136.28 0.53 194 81 123 42 27.58 0.26 195 82 99 17 194.53 0.47 196 82 100 18 194.33 0.42 197 82 101 19 178.98 0.98 198 83 98 15 194.86 0.51 199 83 99 16 194.61 0.48 200 83 100 17 194.52 0.47 201 84 97 13 194.78 0.49 202 84 98 14 194.55 0.47 203 85 97 12 194.92 0.51 204 85 98 13 194.71 0.48 205 86 90 4 297.31 1.15 206 86 96 10 195.01 0.48 207 86 97 11 194.94 0.50 208 87 90 3 304.08 0.35 209 87 96 9 195.06 0.48 210 87 97 10 195.00 0.48 211 87 98 11 194.99 0.48 212 90 94 4 305.00 0.00 213 90 95 5 258.14 4.37 214 90 96 6 204.97 2.72 215 91 94 3 305.00 0.00 216 104 123 19 28.12 0.48 217 104 124 20 27.57 0.26 218 105 123 18 28.29 0.57 219 105 124 19 27.77 0.35 220 106 120 14 42.55 0.36 221 106 122 16 32.30 0.32 222 106 123 17 28.25 0.58 223 107 121 14 38.55 0.54 224 107 122 15 34.15 1.12 225 107 123 16 32.37 0.28 226 107 124 17 32.29 0.32 227 108 117 9 51.34 0.48 228 108 119 11 45.30 0.04 229 108 120 12 44.98 0.08 230 108 121 13 43.25 0.51 231 109 117 8 51.43 0.49 232 109 118 9 51.40 0.51 233 109 119 10 48.61 0.09 234 110 115 5 108.95 0.20 235 110 116 6 79.41 13.18 236 110 117 7 51.43 0.49 237 110 118 8 51.40 0.50 238 111 115 4 110.41 0.53 239 111 116 5 108.02 0.66 240 111 118 7 79.11 13.33 241 112 115 3 122.17 2.10 242 120 123 3 304.99 0.01