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 8 141.34 0.31 2 3 6 3 154.07 1.51 3 3 7 4 151.96 2.56 4 4 7 3 153.39 1.85 5 4 8 4 152.06 2.52 6 4 111 107 26.62 0.52 7 4 118 114 24.69 0.44 8 5 8 3 154.31 1.40 9 5 9 4 154.30 1.40 10 5 116 111 30.19 0.79 11 5 117 112 26.68 0.48 12 5 118 113 24.70 0.43 13 6 9 3 156.78 0.17 14 6 10 4 147.56 0.33 15 7 10 3 157.93 0.74 16 7 11 4 152.00 2.55 17 8 11 3 157.00 2.29 18 8 12 4 145.81 0.29 19 8 13 5 144.28 1.04 20 8 54 46 74.39 1.54 21 8 108 100 32.85 0.37 22 8 117 109 32.90 0.39 23 8 118 110 32.84 0.38 24 8 119 111 32.83 0.37 25 8 120 112 32.82 0.36 26 9 12 3 158.27 0.93 27 9 13 4 139.87 0.76 28 9 33 24 114.75 0.19 29 9 51 42 80.75 0.48 30 10 33 23 114.47 0.33 31 10 34 24 114.78 0.20 32 10 35 25 114.77 0.20 33 11 29 18 114.47 0.33 34 11 35 24 114.77 0.20 35 11 41 30 114.76 0.21 36 11 44 33 113.87 0.35 37 12 44 32 114.03 0.40 38 12 45 33 113.84 0.35 39 12 46 34 113.73 0.32 40 12 47 35 113.68 0.29 41 12 120 108 33.04 0.29 42 13 33 20 115.84 0.29 43 13 47 34 113.75 0.32 44 13 49 36 113.76 0.32 45 13 50 37 113.57 0.35 46 13 51 38 106.42 1.87 47 13 54 41 89.69 4.82 48 14 17 3 168.63 0.64 49 14 25 11 115.94 0.27 50 14 33 19 115.85 0.29 51 14 46 32 114.00 0.41 52 14 47 33 113.86 0.34 53 14 48 34 113.82 0.33 54 15 48 33 113.84 0.34 55 15 49 34 113.81 0.34 56 15 50 35 113.73 0.31 57 17 20 3 158.66 0.73 58 17 25 8 116.16 0.31 59 17 48 31 114.12 0.43 60 19 22 3 146.81 0.35 61 19 25 6 116.21 0.29 62 20 25 5 116.45 0.17 63 20 48 28 115.84 0.36 64 20 82 62 115.97 0.31 65 20 99 79 116.22 0.29 66 20 101 81 115.98 0.32 67 21 99 78 124.78 4.58 68 21 101 80 116.00 0.32 69 22 25 3 139.17 3.40 70 22 99 77 142.61 2.60 71 23 99 76 146.21 0.80 72 25 46 21 179.80 2.29 73 25 48 23 160.84 0.01 74 25 82 57 163.41 1.02 75 25 99 74 185.33 0.73 76 26 82 56 235.69 1.63 77 26 97 71 214.68 0.40 78 26 98 72 214.66 0.39 79 26 99 73 208.98 1.40 80 27 96 69 227.62 1.94 81 27 97 70 219.17 1.37 82 29 44 15 228.74 1.72 83 29 46 17 220.69 3.16 84 30 41 11 228.82 1.71 85 30 44 14 228.74 1.72 86 30 97 67 228.40 1.78 87 35 40 5 327.04 2.81 88 35 41 6 270.06 3.33 89 35 44 9 228.78 1.73 90 36 40 4 327.05 2.81 91 36 95 59 335.14 1.24 92 36 97 61 335.13 1.24 93 40 86 46 228.79 1.74 94 42 85 43 228.77 1.74 95 42 86 44 228.77 1.74 96 43 83 40 228.76 1.74 97 43 84 41 228.67 1.75 98 43 85 42 228.74 1.75 99 44 83 39 228.68 1.75 100 44 84 40 228.64 1.73 101 45 81 36 228.76 1.74 102 45 82 37 228.66 1.74 103 45 83 38 228.59 1.74 104 45 120 75 33.44 0.14 105 46 81 35 228.65 1.74 106 46 82 36 228.63 1.73 107 47 79 32 228.75 1.73 108 47 80 33 228.66 1.74 109 47 81 34 228.58 1.75 110 47 106 59 235.11 33.22 111 47 120 73 33.62 0.07 112 48 80 32 228.61 1.74 113 48 81 33 228.53 1.75 114 48 82 34 228.52 1.76 115 49 79 30 228.63 1.74 116 49 80 31 228.61 1.74 117 53 79 26 228.25 1.76 118 54 79 25 221.26 0.27 119 54 117 63 58.58 1.44 120 55 117 62 58.58 1.44 121 57 73 16 228.33 1.79 122 57 74 17 228.30 1.77 123 57 75 18 216.30 0.14 124 57 79 22 214.38 0.49 125 58 73 15 228.30 1.77 126 58 115 57 62.47 2.58 127 58 116 58 61.70 2.21 128 58 117 59 61.65 2.21 129 60 73 13 228.52 1.74 130 60 74 14 228.40 1.79 131 60 75 15 227.53 1.49 132 60 76 16 221.95 2.43 133 61 73 12 228.53 1.73 134 61 74 13 228.43 1.78 135 61 76 15 228.33 1.79 136 62 70 8 231.57 0.42 137 62 72 10 228.65 1.75 138 62 73 11 228.59 1.74 139 63 72 9 228.69 1.74 140 63 73 10 228.66 1.75 141 63 74 11 228.65 1.75 142 63 107 44 228.74 1.70 143 64 72 8 245.68 0.99 144 65 109 44 228.28 1.78 145 65 121 56 58.80 1.58 146 66 121 55 60.63 2.27 147 66 122 56 59.03 1.48 148 71 109 38 228.33 1.79 149 71 110 39 228.32 1.79 150 71 115 44 166.84 1.04 151 72 107 35 228.50 1.75 152 72 108 36 228.36 1.79 153 72 109 37 228.25 1.79 154 72 121 49 58.62 1.50 155 73 107 34 228.47 1.75 156 73 108 35 228.34 1.78 157 73 110 37 228.01 1.73 158 73 115 42 131.45 0.80 159 74 105 31 228.54 1.75 160 74 106 32 228.42 1.78 161 74 107 33 227.85 1.55 162 75 79 4 223.81 4.20 163 75 105 30 228.43 1.78 164 75 106 31 228.38 1.79 165 76 105 29 228.40 1.78 166 77 105 28 227.84 1.65 167 78 103 25 228.39 1.78 168 78 104 26 214.66 0.41 169 78 105 27 214.62 0.40 170 79 102 23 228.43 1.78 171 79 103 24 214.70 0.40 172 79 104 25 214.66 0.41 173 79 106 27 211.59 0.21 174 80 101 21 228.43 1.78 175 80 102 22 219.12 1.04 176 80 103 23 214.62 0.40 177 81 101 20 216.18 0.86 178 81 102 21 214.65 0.40 179 81 104 23 214.41 0.49 180 81 106 25 165.35 1.21 181 81 123 42 33.57 0.07 182 82 99 17 228.41 1.78 183 82 100 18 215.91 0.99 184 82 101 19 214.61 0.40 185 83 98 15 228.43 1.78 186 83 99 16 215.80 0.15 187 83 100 17 214.65 0.40 188 84 97 13 228.40 1.78 189 84 98 14 214.75 0.39 190 85 97 12 228.40 1.78 191 85 98 13 228.17 1.79 192 86 90 4 279.64 13.12 193 86 96 10 228.56 1.73 194 86 97 11 228.44 1.78 195 87 90 3 335.60 0.93 196 87 96 9 228.68 1.75 197 87 97 10 228.61 1.75 198 87 98 11 228.52 1.74 199 90 94 4 326.60 6.21 200 90 95 5 228.91 1.76 201 90 96 6 228.87 1.76 202 104 123 19 33.99 0.13 203 104 124 20 33.56 0.02 204 105 123 18 34.00 0.14 205 105 124 19 33.57 0.01 206 106 120 14 56.25 1.83 207 106 122 16 38.47 0.27 208 106 123 17 33.99 0.14 209 107 120 13 56.66 2.04 210 107 121 14 55.43 2.02 211 107 122 15 38.87 0.47 212 107 124 17 35.34 0.18 213 108 117 9 61.55 2.21 214 108 119 11 58.69 1.51 215 108 120 12 56.80 2.06 216 108 121 13 56.22 1.85 217 109 117 8 61.65 2.23 218 109 118 9 61.58 2.20 219 109 119 10 58.98 1.43 220 110 115 5 95.32 18.62 221 110 116 6 62.55 2.44 222 110 117 7 61.62 2.20 223 110 118 8 61.62 2.19 224 111 115 4 128.17 4.44 225 111 116 5 62.98 2.46 226 111 118 7 61.94 2.35 227 112 115 3 151.04 0.61