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 8 135.24 0.54 2 3 6 3 148.08 0.76 3 3 7 4 145.31 0.62 4 4 7 3 154.62 1.73 5 4 8 4 148.06 0.76 6 4 118 114 22.73 0.02 7 5 8 3 150.41 0.38 8 5 9 4 145.68 0.43 9 5 116 111 24.52 0.87 10 5 117 112 24.46 0.85 11 5 118 113 22.87 0.06 12 6 9 3 151.43 0.93 13 6 10 4 147.58 0.78 14 7 10 3 151.47 1.17 15 7 11 4 147.57 0.78 16 8 11 3 150.66 0.77 17 8 12 4 146.81 1.15 18 8 13 5 143.85 0.03 19 8 54 46 61.88 4.69 20 8 108 100 36.11 0.26 21 8 117 109 36.15 0.27 22 8 118 110 36.11 0.26 23 8 119 111 36.10 0.25 24 8 120 112 36.09 0.24 25 9 12 3 151.58 0.30 26 9 13 4 142.87 0.44 27 9 33 24 119.70 0.14 28 9 51 42 90.70 0.60 29 10 33 23 119.70 0.14 30 10 34 24 119.95 0.27 31 10 35 25 119.97 0.26 32 11 35 24 120.03 0.29 33 11 41 30 120.27 0.43 34 11 44 33 119.50 0.26 35 11 46 35 119.42 0.25 36 12 41 29 120.39 0.46 37 12 44 32 119.52 0.26 38 12 45 33 119.46 0.24 39 12 46 34 119.42 0.25 40 12 47 35 119.42 0.24 41 12 120 108 36.59 0.47 42 13 33 20 120.83 0.31 43 13 47 34 119.43 0.25 44 13 49 36 119.42 0.24 45 13 50 37 119.31 0.24 46 13 51 38 117.53 0.74 47 13 54 41 105.75 0.29 48 14 17 3 176.85 2.78 49 14 25 11 120.14 0.04 50 14 29 15 120.83 0.30 51 14 33 19 120.84 0.32 52 14 46 32 119.83 0.32 53 14 47 33 119.56 0.23 54 14 48 34 119.42 0.25 55 15 49 34 119.42 0.24 56 15 50 35 119.38 0.25 57 15 51 36 119.34 0.27 58 17 21 4 144.09 0.39 59 17 48 31 120.08 0.29 60 18 48 30 120.34 0.37 61 18 80 62 120.25 0.23 62 19 48 29 120.55 0.39 63 19 80 61 120.39 0.20 64 19 101 82 120.47 0.12 65 20 25 5 121.00 0.29 66 20 48 28 120.89 0.30 67 20 82 62 120.85 0.29 68 20 99 79 120.85 0.29 69 20 101 81 120.78 0.26 70 21 25 4 134.06 2.24 71 22 25 3 141.69 0.81 72 22 99 77 142.15 0.58 73 23 99 76 141.58 0.86 74 24 27 3 233.62 0.45 75 24 28 4 233.62 0.45 76 25 28 3 233.62 0.45 77 25 29 4 233.57 0.43 78 25 46 21 230.33 1.30 79 25 48 23 176.91 0.23 80 25 82 57 318.97 1.24 81 25 99 74 187.22 2.10 82 26 29 3 233.62 0.45 83 26 30 4 233.41 0.36 84 26 97 71 219.91 0.48 85 26 98 72 219.34 0.21 86 26 99 73 211.35 4.04 87 27 30 3 233.60 0.46 88 27 31 4 304.27 2.02 89 27 96 69 232.30 0.01 90 27 97 70 219.91 0.49 91 30 97 67 253.70 10.20 92 40 86 46 323.02 1.24 93 41 86 45 323.03 1.24 94 42 85 43 318.46 1.62 95 42 86 44 318.49 1.63 96 43 83 40 321.04 0.35 97 43 84 41 259.09 4.44 98 43 85 42 300.05 5.12 99 44 83 39 258.88 4.54 100 44 84 40 233.61 0.45 101 45 82 37 321.37 0.83 102 45 83 38 233.68 0.45 103 45 120 75 37.16 0.32 104 46 82 36 239.01 2.56 105 46 84 38 233.65 0.47 106 47 54 7 206.67 3.70 107 47 81 34 233.65 0.45 108 47 106 59 157.16 1.36 109 47 120 73 37.36 0.23 110 48 80 32 233.74 0.46 111 48 81 33 233.64 0.45 112 48 82 34 233.64 0.46 113 48 101 53 323.05 0.04 114 49 53 4 223.56 0.79 115 49 54 5 219.31 0.21 116 49 79 30 251.09 6.75 117 49 80 31 233.71 0.44 118 50 53 3 229.44 0.31 119 50 54 4 224.03 1.02 120 51 54 3 230.09 0.33 121 51 55 4 221.42 0.27 122 52 55 3 227.66 1.26 123 52 56 4 221.42 0.27 124 53 56 3 228.31 0.93 125 53 57 4 229.46 0.36 126 53 79 26 233.34 0.42 127 54 57 3 232.63 0.23 128 54 79 25 224.68 0.22 129 54 117 63 65.55 0.40 130 55 58 3 232.33 0.07 131 55 116 61 65.84 0.27 132 55 117 62 65.56 0.41 133 57 73 16 233.41 0.45 134 57 74 17 233.38 0.43 135 57 75 18 219.95 0.47 136 57 79 22 215.53 0.54 137 58 73 15 233.34 0.42 138 58 115 57 103.72 18.36 139 58 116 58 66.49 0.23 140 58 117 59 66.48 0.23 141 60 73 13 233.53 0.42 142 60 74 14 233.49 0.43 143 60 75 15 232.56 0.35 144 60 76 16 220.56 0.17 145 61 73 12 233.63 0.46 146 61 74 13 233.50 0.43 147 61 76 15 232.60 0.33 148 62 72 10 255.63 3.10 149 62 73 11 233.69 0.45 150 63 72 9 322.39 0.19 151 63 73 10 250.94 0.14 152 63 74 11 245.28 2.69 153 65 109 44 233.34 0.42 154 65 121 56 64.75 0.46 155 66 121 55 64.77 0.45 156 71 109 38 233.42 0.41 157 71 110 39 233.35 0.42 158 71 115 44 157.61 1.98 159 72 107 35 233.59 0.45 160 72 108 36 233.44 0.42 161 72 109 37 233.28 0.41 162 72 121 49 64.75 0.46 163 73 107 34 233.48 0.43 164 73 108 35 233.38 0.40 165 73 110 37 231.12 0.29 166 73 115 42 144.35 1.80 167 74 105 31 233.63 0.42 168 74 106 32 233.53 0.42 169 74 107 33 232.99 0.41 170 74 124 50 39.63 0.58 171 75 105 30 233.52 0.41 172 75 106 31 233.47 0.42 173 76 105 29 233.51 0.41 174 77 105 28 231.21 0.23 175 78 103 25 233.46 0.42 176 78 104 26 219.95 0.48 177 78 105 27 219.30 0.21 178 79 103 24 222.96 0.37 179 79 104 25 219.36 0.21 180 79 106 27 212.49 0.00 181 80 101 21 233.53 0.42 182 80 102 22 232.30 0.32 183 80 103 23 219.31 0.20 184 81 101 20 226.33 2.71 185 81 102 21 219.34 0.21 186 81 104 23 210.21 0.57 187 81 106 25 172.03 1.24 188 82 99 17 233.52 0.42 189 82 100 18 220.59 0.16 190 82 101 19 219.31 0.21 191 83 98 15 233.53 0.42 192 83 99 16 224.49 1.05 193 83 100 17 219.33 0.21 194 84 97 13 233.47 0.44 195 84 98 14 223.78 1.44 196 85 97 12 233.56 0.42 197 85 98 13 233.37 0.40 198 86 96 10 233.88 0.34 199 86 97 11 233.59 0.43 200 87 96 9 234.00 0.34 201 87 97 10 233.89 0.35 202 87 98 11 233.62 0.45 203 90 96 6 307.95 0.93 204 104 123 19 37.81 0.10 205 104 124 20 37.19 0.32 206 105 123 18 37.81 0.10 207 105 124 19 37.20 0.31 208 106 120 14 64.59 0.39 209 106 122 16 49.64 0.39 210 106 123 17 37.79 0.11 211 107 120 13 64.64 0.41 212 107 121 14 64.06 0.55 213 107 122 15 52.11 0.47 214 107 124 17 39.80 0.67 215 108 117 9 66.39 0.27 216 108 119 11 64.75 0.45 217 108 120 12 64.65 0.41 218 108 121 13 64.28 0.55 219 109 117 8 66.48 0.23 220 109 118 9 66.37 0.26 221 109 119 10 65.67 0.36 222 110 115 5 106.98 16.74 223 110 116 6 66.78 0.13 224 110 117 7 66.49 0.22 225 110 118 8 66.47 0.21 226 111 115 4 135.65 2.42 227 111 116 5 107.34 16.56 228 111 118 7 66.53 0.21 229 112 115 3 149.35 0.39