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 8 137.61 0.54 2 3 6 3 142.78 0.07 3 3 7 4 142.83 0.09 4 4 7 3 148.19 1.72 5 4 8 4 144.49 0.90 6 4 118 114 24.14 0.06 7 5 8 3 153.76 0.59 8 5 9 4 144.54 0.90 9 5 116 111 25.09 0.39 10 5 117 112 24.23 0.09 11 5 118 113 24.22 0.08 12 6 9 3 153.78 0.60 13 6 10 4 144.53 0.90 14 7 10 3 153.78 0.60 15 7 11 4 144.52 0.91 16 8 11 3 150.68 2.16 17 8 12 4 144.34 0.98 18 8 13 5 143.00 0.31 19 8 54 46 73.14 2.66 20 8 108 100 34.68 0.56 21 8 117 109 35.63 0.19 22 8 118 110 34.66 0.56 23 8 119 111 34.65 0.55 24 8 120 112 34.61 0.54 25 9 12 3 150.75 2.12 26 9 13 4 141.12 0.56 27 9 33 24 121.76 0.01 28 9 51 42 84.59 1.97 29 10 33 23 121.73 0.01 30 10 34 24 121.95 0.09 31 10 35 25 122.16 0.18 32 11 35 24 122.16 0.18 33 11 41 30 122.14 0.20 34 11 44 33 120.20 0.06 35 11 46 35 117.45 0.72 36 12 41 29 122.20 0.19 37 12 44 32 120.30 0.09 38 12 45 33 117.48 0.71 39 12 46 34 117.45 0.72 40 12 47 35 117.40 0.70 41 12 120 108 36.18 0.09 42 13 33 20 122.50 0.12 43 13 47 34 117.47 0.72 44 13 49 36 117.40 0.70 45 13 50 37 117.31 0.65 46 13 51 38 111.64 1.21 47 13 54 41 87.76 3.29 48 14 17 3 166.00 0.48 49 14 25 11 122.48 0.11 50 14 29 15 122.50 0.10 51 14 33 19 122.53 0.11 52 14 46 32 121.70 0.01 53 14 47 33 118.26 0.92 54 14 48 34 117.49 0.72 55 15 48 33 117.50 0.72 56 15 49 34 117.50 0.72 57 15 50 35 117.39 0.69 58 17 25 8 122.61 0.12 59 17 48 31 122.18 0.14 60 18 48 30 122.22 0.16 61 18 80 62 122.23 0.17 62 19 48 29 122.33 0.18 63 19 80 61 122.28 0.18 64 19 101 82 122.43 0.12 65 20 25 5 122.70 0.15 66 20 48 28 122.51 0.11 67 20 82 62 122.52 0.10 68 20 99 79 122.56 0.12 69 20 101 81 122.50 0.10 70 21 25 4 131.38 3.20 71 22 25 3 140.94 0.49 72 22 99 77 151.43 0.66 73 23 99 76 151.47 0.67 74 24 27 3 336.11 0.04 75 24 28 4 335.50 0.28 76 25 29 4 335.50 0.28 77 25 46 21 197.62 2.31 78 25 48 23 166.13 0.52 79 25 82 57 170.54 0.62 80 25 99 74 185.80 2.23 81 26 29 3 336.06 0.14 82 26 30 4 335.44 0.27 83 26 82 56 243.46 1.00 84 26 97 71 214.53 0.53 85 26 98 72 214.48 0.55 86 26 99 73 199.14 3.54 87 27 96 69 230.50 1.31 88 27 97 70 224.09 0.74 89 29 46 17 231.06 1.02 90 30 35 5 325.53 3.83 91 30 36 6 310.17 1.26 92 30 41 11 231.52 1.10 93 30 44 14 231.40 1.06 94 30 46 16 231.25 1.06 95 30 97 67 231.08 1.03 96 31 36 5 325.54 3.83 97 33 46 13 231.25 1.06 98 35 41 6 231.62 1.08 99 35 44 9 231.57 1.09 100 35 46 11 231.44 1.03 101 36 95 59 333.49 1.48 102 36 97 61 332.97 1.22 103 40 86 46 231.49 1.07 104 42 85 43 231.44 1.07 105 42 86 44 231.46 1.07 106 43 84 41 231.40 1.06 107 43 85 42 231.40 1.06 108 44 83 39 231.40 1.06 109 44 84 40 231.28 1.09 110 45 81 36 231.43 1.06 111 45 82 37 231.39 1.06 112 45 83 38 231.22 1.08 113 45 120 75 36.79 0.20 114 46 81 35 231.38 1.06 115 46 82 36 231.31 1.08 116 46 84 38 231.22 1.08 117 47 54 7 336.47 0.26 118 47 79 32 231.43 1.06 119 47 80 33 231.40 1.06 120 47 81 34 231.25 1.10 121 47 106 59 201.39 16.32 122 47 120 73 37.66 0.22 123 48 80 32 231.31 1.08 124 48 81 33 231.22 1.08 125 48 82 34 231.22 1.08 126 49 79 30 231.34 1.08 127 49 80 31 231.30 1.08 128 53 79 26 230.86 1.06 129 54 79 25 224.62 0.50 130 54 117 63 60.41 0.66 131 55 116 61 60.48 0.69 132 55 117 62 60.41 0.66 133 57 73 16 230.92 1.06 134 57 74 17 230.91 1.06 135 57 75 18 218.06 0.66 136 57 79 22 208.81 1.19 137 58 73 15 230.91 1.07 138 58 115 57 62.89 1.12 139 58 116 58 62.66 1.01 140 58 117 59 62.34 0.88 141 60 73 13 231.21 1.07 142 60 74 14 231.12 1.06 143 60 75 15 230.98 1.08 144 60 76 16 220.22 1.74 145 61 73 12 231.28 1.09 146 61 74 13 231.14 1.07 147 61 76 15 230.53 1.28 148 62 70 8 239.40 4.11 149 62 72 10 231.36 1.06 150 62 73 11 231.28 1.09 151 63 72 9 231.38 1.07 152 63 73 10 231.36 1.06 153 63 74 11 231.35 1.06 154 63 107 44 231.46 1.08 155 64 72 8 247.91 1.33 156 65 109 44 230.97 1.08 157 65 121 56 60.59 0.59 158 66 121 55 60.70 0.63 159 66 122 56 60.70 0.63 160 71 109 38 231.00 1.03 161 71 110 39 230.93 1.06 162 71 111 40 230.93 1.06 163 71 115 44 158.02 0.92 164 72 107 35 231.27 1.09 165 72 108 36 231.04 1.05 166 72 109 37 230.86 1.07 167 72 121 49 60.42 0.66 168 73 107 34 231.13 1.05 169 73 108 35 231.00 1.08 170 73 110 37 230.21 1.13 171 73 115 42 130.00 1.53 172 74 105 31 231.27 1.06 173 74 106 32 231.13 1.05 174 74 107 33 230.65 1.07 175 74 124 50 47.19 3.41 176 75 79 4 214.32 0.52 177 75 105 30 231.08 1.08 178 75 106 31 231.03 1.10 179 76 105 29 231.08 1.08 180 77 105 28 229.65 1.14 181 78 103 25 231.00 1.08 182 78 104 26 218.63 0.94 183 78 105 27 214.34 0.52 184 79 103 24 223.08 0.31 185 79 104 25 214.54 0.53 186 79 106 27 204.71 0.26 187 80 101 21 231.08 1.07 188 80 102 22 229.58 0.80 189 80 103 23 214.45 0.53 190 81 101 20 220.37 0.51 191 81 102 21 214.53 0.53 192 81 104 23 206.53 1.52 193 81 106 25 168.10 3.25 194 81 123 42 36.80 0.21 195 82 99 17 231.03 1.09 196 82 100 18 217.47 0.93 197 82 101 19 214.25 0.45 198 83 98 15 231.12 1.08 199 83 99 16 220.31 0.24 200 83 100 17 214.47 0.53 201 84 97 13 231.00 1.08 202 84 98 14 217.47 0.93 203 85 97 12 231.08 1.07 204 85 98 13 230.70 1.21 205 86 90 4 280.44 12.55 206 86 96 10 231.29 1.08 207 86 97 11 231.16 1.09 208 87 90 3 333.66 0.20 209 87 96 9 231.38 1.05 210 87 97 10 231.31 1.07 211 87 98 11 231.27 1.09 212 90 95 5 232.81 0.43 213 90 96 6 231.56 1.04 214 104 123 19 38.58 0.29 215 104 124 20 37.44 0.32 216 105 123 18 38.71 0.22 217 105 124 19 37.96 0.58 218 106 120 14 59.46 0.22 219 106 122 16 47.85 3.17 220 106 123 17 38.76 0.20 221 107 120 13 60.25 0.60 222 107 121 14 57.32 0.85 223 107 122 15 55.95 0.88 224 107 124 17 47.32 3.41 225 108 117 9 62.26 0.81 226 108 119 11 60.42 0.66 227 108 120 12 59.98 0.46 228 108 121 13 59.19 0.20 229 109 117 8 62.34 0.84 230 109 118 9 62.23 0.83 231 109 119 10 60.59 0.62 232 110 115 5 67.52 0.85 233 110 116 6 62.84 1.05 234 110 117 7 62.65 1.01 235 110 118 8 62.36 0.86 236 111 115 4 116.77 13.32 237 111 116 5 68.15 0.38 238 111 118 7 62.66 1.01 239 112 115 3 153.61 0.57