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 3 7 4 145.40 0.61 2 4 7 3 151.31 0.56 3 4 8 4 148.31 2.06 4 4 118 114 23.27 0.00 5 5 8 3 151.52 0.66 6 5 9 4 151.33 0.56 7 5 116 111 23.82 0.26 8 5 117 112 23.82 0.26 9 5 118 113 23.35 0.02 10 6 9 3 157.03 2.10 11 6 10 4 156.83 2.20 12 7 10 3 157.03 2.10 13 7 11 4 153.90 3.67 14 8 11 3 157.00 2.12 15 8 12 4 145.88 0.61 16 8 54 46 53.94 5.81 17 8 108 100 33.87 0.94 18 8 117 109 34.34 0.70 19 8 118 110 33.83 0.96 20 8 119 111 32.77 0.39 21 8 120 112 32.70 0.42 22 9 12 3 156.84 2.19 23 9 13 4 140.07 2.29 24 9 33 24 114.06 0.01 25 9 51 42 63.02 9.02 26 10 33 23 113.09 0.44 27 11 35 24 115.78 0.48 28 11 41 30 116.11 0.35 29 11 44 33 113.11 0.21 30 11 46 35 112.78 0.30 31 12 44 32 113.47 0.38 32 12 45 33 112.80 0.30 33 12 46 34 112.75 0.30 34 12 47 35 112.75 0.30 35 12 120 108 34.52 0.63 36 13 33 20 116.86 0.31 37 13 49 36 112.77 0.30 38 13 50 37 112.73 0.30 39 13 51 38 111.34 0.88 40 13 54 41 101.77 0.16 41 14 17 3 178.53 1.10 42 14 25 11 115.89 0.42 43 14 29 15 116.26 0.60 44 14 33 19 116.86 0.31 45 14 46 32 114.98 0.35 46 14 47 33 113.12 0.23 47 14 48 34 112.78 0.30 48 15 49 34 112.79 0.29 49 15 50 35 112.75 0.32 50 17 48 31 115.88 0.43 51 18 48 30 116.00 0.48 52 18 80 62 116.02 0.48 53 19 48 29 116.25 0.42 54 19 80 61 116.22 0.47 55 19 101 82 116.29 0.47 56 20 25 5 116.98 0.33 57 20 48 28 116.67 0.32 58 20 82 62 116.69 0.32 59 20 99 79 116.99 0.27 60 20 101 81 116.41 0.42 61 21 25 4 127.78 2.08 62 22 25 3 154.44 1.93 63 22 99 77 151.52 0.26 64 23 99 76 151.52 0.26 65 24 27 3 336.25 0.06 66 24 28 4 333.70 0.14 67 25 29 4 331.19 1.40 68 25 46 21 181.38 0.04 69 25 48 23 163.81 1.68 70 25 82 57 166.27 0.70 71 25 99 74 183.06 1.17 72 26 29 3 335.79 0.18 73 26 30 4 331.16 1.39 74 26 82 56 235.86 1.52 75 26 97 71 215.09 0.85 76 26 99 73 201.56 0.75 77 27 96 69 226.56 0.12 78 27 97 70 219.31 0.03 79 29 46 17 227.46 0.46 80 30 35 5 333.63 1.26 81 30 36 6 330.47 0.32 82 30 41 11 228.06 0.60 83 30 44 14 227.96 0.60 84 30 46 16 227.77 0.55 85 30 97 67 227.69 0.58 86 31 36 5 330.25 0.35 87 33 46 13 227.92 0.60 88 35 41 6 270.41 21.78 89 35 44 9 228.06 0.61 90 35 46 11 228.00 0.59 91 36 40 4 331.02 0.51 92 36 95 59 328.88 0.12 93 36 97 61 317.56 5.77 94 40 86 46 228.00 0.62 95 42 85 43 227.95 0.60 96 42 86 44 227.96 0.59 97 43 84 41 227.90 0.59 98 43 85 42 227.90 0.59 99 44 83 39 227.90 0.59 100 44 84 40 227.85 0.58 101 45 81 36 227.94 0.59 102 45 82 37 227.89 0.59 103 45 83 38 227.83 0.58 104 45 120 75 35.52 0.84 105 46 81 35 227.89 0.59 106 46 82 36 227.87 0.58 107 46 84 38 227.82 0.58 108 47 54 7 336.08 0.01 109 47 79 32 227.93 0.58 110 47 80 33 227.90 0.59 111 47 81 34 227.84 0.59 112 47 106 59 289.86 19.62 113 47 120 73 35.66 0.79 114 48 80 32 227.86 0.58 115 48 81 33 227.83 0.58 116 48 82 34 227.83 0.58 117 49 79 30 227.87 0.58 118 49 80 31 227.85 0.58 119 53 79 26 227.63 0.57 120 54 79 25 223.24 1.39 121 54 117 63 65.27 2.02 122 55 117 62 65.51 1.90 123 57 73 16 227.71 0.54 124 57 74 17 227.66 0.56 125 57 75 18 218.12 0.65 126 57 79 22 210.50 0.33 127 58 73 15 227.66 0.56 128 58 115 57 94.28 15.41 129 58 116 58 68.15 3.05 130 58 117 59 67.82 2.96 131 60 73 13 227.81 0.58 132 60 74 14 227.75 0.59 133 60 75 15 226.91 0.44 134 60 76 16 218.12 0.65 135 61 73 12 227.81 0.58 136 61 74 13 227.79 0.58 137 61 76 15 226.98 0.27 138 62 70 8 248.06 3.14 139 62 72 10 227.90 0.59 140 62 73 11 227.83 0.58 141 63 72 9 227.91 0.59 142 63 73 10 227.90 0.59 143 63 74 11 227.87 0.58 144 63 107 44 227.95 0.60 145 64 70 6 336.20 0.55 146 64 72 8 250.76 1.42 147 65 109 44 227.65 0.57 148 65 121 56 65.60 1.94 149 66 121 55 65.99 2.11 150 71 109 38 227.75 0.56 151 71 110 39 227.68 0.57 152 71 115 44 172.01 0.86 153 72 107 35 227.83 0.58 154 72 108 36 227.73 0.57 155 72 109 37 227.53 0.54 156 72 121 49 65.47 2.00 157 73 107 34 227.75 0.57 158 73 108 35 227.71 0.58 159 73 110 37 226.91 0.45 160 73 115 42 133.09 0.62 161 74 105 31 227.85 0.59 162 74 106 32 227.76 0.57 163 74 107 33 226.87 0.22 164 75 79 4 218.70 4.03 165 75 105 30 227.74 0.57 166 75 106 31 227.70 0.57 167 76 105 29 227.73 0.57 168 77 105 28 225.63 0.19 169 78 103 25 227.70 0.57 170 78 104 26 218.09 0.65 171 78 105 27 211.93 0.66 172 79 103 24 220.25 0.13 173 79 104 25 215.11 0.84 174 79 106 27 205.32 0.44 175 80 101 21 227.74 0.57 176 80 102 22 226.08 0.04 177 80 103 23 213.30 0.03 178 81 101 20 219.22 0.07 179 81 102 21 215.11 0.84 180 81 104 23 202.51 0.48 181 81 106 25 165.53 0.45 182 81 123 42 35.56 0.85 183 82 99 17 227.72 0.57 184 82 100 18 218.07 0.62 185 82 101 19 212.98 0.18 186 83 98 15 227.75 0.58 187 83 99 16 218.11 0.65 188 83 100 17 213.09 0.14 189 84 97 13 227.71 0.57 190 84 98 14 218.06 0.63 191 85 97 12 227.72 0.57 192 85 98 13 227.36 0.41 193 86 90 4 285.69 13.68 194 86 96 10 227.85 0.58 195 86 97 11 227.76 0.58 196 87 90 3 334.06 0.01 197 87 96 9 227.91 0.59 198 87 97 10 227.87 0.58 199 87 98 11 227.81 0.58 200 90 94 4 331.96 0.14 201 90 95 5 228.03 0.64 202 90 96 6 228.03 0.63 203 104 123 19 36.30 1.10 204 104 124 20 35.61 0.81 205 105 123 18 36.61 1.24 206 105 124 19 35.62 0.84 207 106 120 14 59.22 0.14 208 106 122 16 47.47 3.44 209 106 123 17 36.31 1.09 210 107 120 13 59.42 0.24 211 107 121 14 58.85 0.12 212 107 122 15 52.23 1.06 213 107 124 17 46.88 3.68 214 108 117 9 67.37 2.77 215 108 119 11 64.98 2.14 216 108 120 12 59.43 0.24 217 108 121 13 59.20 0.13 218 109 117 8 67.83 2.95 219 109 118 9 67.39 2.76 220 109 119 10 66.87 2.58 221 110 115 5 131.54 1.28 222 110 116 6 90.33 14.14 223 110 117 7 67.81 2.96 224 110 118 8 67.81 2.96 225 111 115 4 131.53 1.29 226 111 116 5 129.62 2.23 227 111 118 7 72.06 5.08 228 112 115 3 142.53 2.07