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 8 134.71 0.22 2 3 6 3 141.26 0.23 3 3 7 4 141.26 0.23 4 4 7 3 141.27 0.23 5 4 8 4 141.27 0.23 6 4 130 112 24.09 0.23 7 5 8 3 144.74 0.95 8 5 9 4 141.58 0.39 9 5 128 109 27.05 0.93 10 5 129 110 25.02 0.62 11 5 130 111 24.15 0.22 12 6 9 3 145.62 1.10 13 6 10 4 141.25 0.25 14 7 10 3 147.69 0.07 15 7 11 4 140.65 0.56 16 8 11 3 144.94 1.30 17 8 12 4 140.37 0.67 18 8 13 5 140.28 0.62 19 8 54 46 75.86 1.40 20 8 108 100 35.59 0.26 21 8 129 107 36.56 0.27 22 8 130 108 36.05 0.49 23 8 131 109 35.59 0.26 24 8 134 110 34.19 0.42 25 9 12 3 143.83 1.03 26 9 13 4 137.51 1.51 27 9 33 24 111.69 0.74 28 9 51 42 82.00 1.62 29 10 33 23 111.69 0.74 30 10 34 24 111.77 0.71 31 10 35 25 111.78 0.70 32 11 35 24 111.79 0.67 33 11 41 30 111.72 0.69 34 11 44 33 109.94 1.05 35 11 46 35 109.84 1.07 36 12 41 29 111.92 0.69 37 12 44 32 111.50 0.77 38 12 45 33 109.87 1.08 39 12 46 34 109.83 1.07 40 12 47 35 109.81 1.06 41 12 134 106 37.37 0.14 42 13 33 20 112.45 0.54 43 13 47 34 109.87 1.08 44 13 49 36 109.81 1.06 45 13 50 37 109.74 1.04 46 13 51 38 103.74 0.03 47 13 54 41 90.08 1.34 48 14 17 3 161.54 0.43 49 14 25 11 112.64 0.53 50 14 29 15 112.48 0.53 51 14 33 19 112.47 0.54 52 14 46 32 111.52 0.76 53 14 47 33 110.05 1.02 54 14 48 34 109.84 1.06 55 15 49 34 109.83 1.07 56 15 50 35 109.81 1.06 57 15 51 36 109.79 1.05 58 17 48 31 112.27 0.45 59 18 48 30 112.31 0.47 60 18 80 62 112.31 0.47 61 19 48 29 112.34 0.46 62 19 80 61 112.34 0.46 63 19 101 82 112.68 0.54 64 20 25 5 112.75 0.53 65 20 48 28 112.70 0.53 66 20 82 62 112.71 0.53 67 20 99 79 112.77 0.54 68 20 101 81 112.70 0.53 69 22 25 3 146.99 0.24 70 22 99 77 145.38 0.07 71 23 99 76 142.45 1.40 72 24 27 3 332.10 0.43 73 24 28 4 332.10 0.44 74 25 29 4 331.98 0.48 75 25 46 21 171.03 1.00 76 25 48 23 160.85 0.08 77 25 82 57 162.01 0.49 78 25 99 74 176.91 0.43 79 26 30 4 330.26 0.36 80 26 82 56 237.24 0.35 81 26 97 71 210.02 1.07 82 26 98 72 210.00 1.07 83 26 99 73 198.19 0.71 84 27 96 69 222.35 0.32 85 27 97 70 219.88 0.40 86 29 46 17 222.88 0.15 87 30 35 5 331.53 0.45 88 30 36 6 327.22 0.88 89 30 41 11 224.05 0.51 90 30 44 14 223.87 0.53 91 30 46 16 223.65 0.47 92 30 97 67 223.57 0.55 93 31 36 5 322.92 4.25 94 33 46 13 223.82 0.48 95 35 41 6 224.09 0.51 96 35 44 9 224.05 0.49 97 35 46 11 224.03 0.49 98 36 40 4 330.72 0.34 99 36 95 59 331.06 0.36 100 36 97 61 315.07 8.09 101 40 86 46 223.97 0.52 102 42 85 43 223.95 0.53 103 42 86 44 223.97 0.52 104 43 84 41 223.91 0.53 105 43 85 42 223.92 0.52 106 44 83 39 223.91 0.53 107 44 84 40 223.84 0.54 108 45 81 36 223.95 0.52 109 45 82 37 223.91 0.53 110 45 83 38 223.82 0.54 111 45 134 73 38.43 0.56 112 46 81 35 223.91 0.52 113 46 82 36 223.88 0.53 114 46 84 38 223.82 0.54 115 47 54 7 330.48 0.62 116 47 79 32 223.96 0.52 117 47 80 33 223.91 0.52 118 47 81 34 223.83 0.54 119 47 106 59 166.05 0.29 120 47 134 71 38.34 0.52 121 48 80 32 223.84 0.52 122 48 81 33 223.80 0.53 123 48 82 34 223.78 0.53 124 49 79 30 223.89 0.52 125 49 80 31 223.84 0.52 126 53 79 26 223.47 0.58 127 54 79 25 221.33 0.32 128 54 129 61 52.93 1.51 129 55 128 59 53.70 1.84 130 55 129 60 52.96 1.49 131 57 73 16 223.58 0.56 132 57 74 17 223.50 0.58 133 57 75 18 217.12 2.39 134 57 79 22 205.53 0.62 135 58 73 15 223.38 0.57 136 58 127 55 132.75 2.79 137 58 128 56 55.61 1.14 138 58 129 57 55.59 1.15 139 60 73 13 223.72 0.51 140 60 74 14 223.59 0.55 141 60 75 15 221.56 0.39 142 60 76 16 218.68 1.60 143 61 73 12 223.73 0.51 144 61 74 13 223.69 0.49 145 61 76 15 222.70 0.51 146 62 70 8 232.66 0.74 147 62 72 10 223.90 0.51 148 62 73 11 223.83 0.53 149 63 72 9 223.91 0.51 150 63 73 10 223.90 0.51 151 63 74 11 223.90 0.51 152 63 107 44 223.90 0.55 153 64 72 8 238.97 2.75 154 65 109 44 223.69 0.51 155 65 135 54 54.29 0.85 156 66 135 53 55.18 1.27 157 71 109 38 223.50 0.60 158 71 110 39 223.47 0.59 159 71 127 42 217.34 0.17 160 72 107 35 223.78 0.53 161 72 108 36 223.59 0.55 162 72 109 37 223.40 0.57 163 72 135 47 53.01 1.43 164 73 107 34 223.63 0.52 165 73 108 35 223.56 0.55 166 73 110 37 221.63 0.47 167 73 127 40 168.96 0.07 168 74 105 31 223.78 0.52 169 74 106 32 223.64 0.52 170 74 107 33 222.59 0.38 171 74 138 48 44.28 0.15 172 75 79 4 223.87 0.54 173 75 105 30 223.59 0.54 174 75 106 31 223.56 0.55 175 76 105 29 223.59 0.55 176 77 105 28 221.75 0.10 177 78 103 25 223.56 0.55 178 78 104 26 218.66 1.60 179 78 105 27 209.84 1.02 180 79 103 24 218.71 1.60 181 79 104 25 210.04 1.07 182 79 106 27 203.86 1.19 183 80 101 21 223.59 0.55 184 80 102 22 221.59 0.43 185 80 103 23 209.90 1.03 186 81 101 20 216.38 0.42 187 81 102 21 210.00 1.07 188 81 104 23 200.56 0.00 189 81 106 25 166.01 0.54 190 81 137 40 37.91 0.35 191 82 99 17 223.58 0.55 192 82 100 18 215.01 1.11 193 82 101 19 209.74 0.95 194 83 98 15 223.64 0.53 195 83 99 16 214.78 1.23 196 83 100 17 209.99 1.07 197 83 104 21 181.87 1.53 198 84 97 13 223.57 0.55 199 84 98 14 211.74 1.94 200 85 97 12 223.60 0.55 201 85 98 13 223.30 0.58 202 86 90 4 250.58 5.82 203 86 96 10 223.85 0.53 204 86 97 11 223.68 0.52 205 87 90 3 310.04 3.58 206 87 96 9 223.90 0.52 207 87 97 10 223.89 0.53 208 87 98 11 223.83 0.54 209 90 95 5 224.08 0.51 210 90 96 6 224.06 0.51 211 104 137 17 38.91 0.70 212 104 138 18 38.29 0.51 213 105 137 16 39.91 1.17 214 105 138 17 38.34 0.48 215 106 134 12 52.38 1.36 216 106 136 14 45.48 0.20 217 106 137 15 39.87 1.20 218 107 134 11 52.44 1.39 219 107 135 12 50.02 0.32 220 107 136 13 47.83 0.71 221 107 138 15 44.37 0.22 222 108 129 7 56.16 0.83 223 108 131 9 53.41 1.28 224 108 134 10 52.72 1.53 225 108 135 11 50.14 0.27 226 109 129 6 56.25 0.84 227 109 130 7 55.50 1.16 228 109 131 8 54.63 1.06 229 110 127 3 160.62 2.93 230 110 128 4 58.54 0.76 231 110 129 5 55.61 1.15 232 110 130 6 55.59 1.14 233 111 128 3 147.85 0.81 234 111 130 5 55.97 0.97 235 134 137 3 332.28 0.19