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 5 116 111 24.98 0.98 2 5 117 112 24.94 0.96 3 5 118 113 24.43 1.20 4 8 13 5 305.00 0.00 5 8 54 46 69.53 2.00 6 8 108 100 24.95 0.96 7 8 117 109 25.00 0.98 8 8 118 110 24.98 0.98 9 8 119 111 24.94 0.96 10 8 120 112 24.45 1.21 11 9 12 3 305.00 0.00 12 9 13 4 148.55 0.01 13 9 33 24 93.53 1.95 14 9 51 42 71.94 1.50 15 10 33 23 92.47 2.41 16 10 34 24 93.06 2.11 17 10 35 25 93.00 2.12 18 11 35 24 93.00 2.12 19 11 41 30 92.86 2.13 20 11 44 33 90.59 2.02 21 11 46 35 87.64 0.82 22 12 44 32 91.81 2.44 23 12 45 33 87.70 0.83 24 12 46 34 87.64 0.82 25 12 47 35 87.62 0.81 26 12 120 108 24.89 1.00 27 13 33 20 94.58 1.96 28 13 47 34 87.63 0.81 29 13 49 36 87.56 0.78 30 13 50 37 87.36 0.71 31 13 51 38 81.67 0.55 32 13 54 41 75.98 1.44 33 14 17 3 136.68 1.48 34 14 25 11 94.61 1.95 35 14 29 15 94.59 1.96 36 14 33 19 94.59 1.97 37 14 46 32 92.38 2.35 38 14 47 33 90.69 2.00 39 14 48 34 87.59 0.80 40 15 49 34 87.81 0.66 41 15 50 35 87.53 0.79 42 17 48 31 93.87 1.77 43 18 48 30 94.08 1.80 44 18 80 62 94.40 1.95 45 19 48 29 94.47 1.96 46 19 80 61 94.44 1.96 47 19 101 82 94.51 1.99 48 20 25 5 104.28 0.27 49 20 48 28 94.58 1.99 50 20 82 62 94.58 1.99 51 20 99 79 101.24 0.07 52 20 101 81 94.52 1.99 53 21 25 4 116.62 1.11 54 22 25 3 124.79 0.65 55 22 99 77 130.43 0.80 56 23 99 76 130.27 0.87 57 24 27 3 304.92 0.04 58 24 28 4 304.89 0.06 59 25 28 3 304.92 0.04 60 25 29 4 304.89 0.06 61 25 46 21 198.04 1.22 62 25 48 23 197.70 1.21 63 25 99 74 184.18 1.23 64 26 29 3 305.00 0.00 65 26 30 4 304.93 0.04 66 26 97 71 197.66 1.23 67 26 98 72 197.56 1.24 68 26 99 73 192.45 0.04 69 27 31 4 305.00 0.00 70 27 95 68 198.16 1.24 71 27 96 69 197.71 1.25 72 27 97 70 197.52 1.26 73 29 33 4 304.99 0.01 74 29 46 17 198.09 1.22 75 30 34 4 304.99 0.01 76 30 35 5 303.90 0.17 77 30 36 6 302.31 0.96 78 30 41 11 198.41 1.25 79 30 44 14 198.31 1.24 80 30 46 16 198.12 1.21 81 30 97 67 197.58 1.25 82 31 34 3 304.99 0.01 83 31 36 5 301.74 1.23 84 33 46 13 198.28 1.23 85 34 37 3 304.86 0.06 86 35 39 4 304.99 0.01 87 35 41 6 239.44 19.19 88 35 44 9 198.38 1.25 89 35 46 11 198.36 1.25 90 36 39 3 304.99 0.01 91 36 40 4 302.00 0.14 92 36 92 56 305.00 0.00 93 36 95 59 303.03 0.65 94 36 97 61 299.88 0.07 95 40 86 46 198.54 1.26 96 40 90 50 304.98 0.01 97 40 92 52 305.00 0.00 98 41 44 3 304.97 0.01 99 42 85 43 198.37 1.26 100 42 86 44 198.40 1.26 101 43 84 41 198.31 1.24 102 43 85 42 198.31 1.24 103 44 83 39 198.28 1.23 104 44 84 40 198.20 1.26 105 45 81 36 198.25 1.24 106 45 82 37 198.16 1.24 107 45 83 38 198.16 1.24 108 45 120 75 25.37 0.83 109 46 81 35 198.14 1.24 110 46 82 36 198.09 1.23 111 46 84 38 198.16 1.24 112 47 54 7 303.86 0.39 113 47 79 32 198.25 1.24 114 47 80 33 198.15 1.24 115 47 81 34 197.91 1.27 116 47 106 59 258.58 5.82 117 47 120 73 26.70 0.18 118 48 80 32 198.07 1.22 119 48 81 33 197.87 1.26 120 48 82 34 197.86 1.25 121 49 79 30 198.10 1.24 122 49 80 31 198.06 1.23 123 51 55 4 305.00 0.00 124 52 56 4 305.00 0.00 125 53 56 3 305.00 0.00 126 53 57 4 305.00 0.01 127 53 79 26 197.68 1.20 128 54 57 3 304.99 0.01 129 54 79 25 197.23 1.10 130 54 106 52 304.99 0.01 131 54 117 63 51.83 0.48 132 55 58 3 304.95 0.02 133 55 116 61 74.63 11.79 134 55 117 62 74.53 11.80 135 57 60 3 304.99 0.01 136 57 73 16 197.72 1.22 137 57 74 17 197.69 1.21 138 57 75 18 192.75 0.10 139 57 79 22 172.69 0.96 140 57 106 49 305.00 0.00 141 58 73 15 197.69 1.21 142 58 115 57 105.55 0.58 143 58 116 58 76.64 11.87 144 58 117 59 76.38 11.75 145 60 73 13 197.76 1.21 146 60 74 14 197.70 1.22 147 60 75 15 197.38 1.16 148 60 76 16 193.73 0.59 149 61 73 12 197.90 1.24 150 61 74 13 197.72 1.21 151 61 76 15 197.35 1.15 152 62 70 8 210.30 0.60 153 62 71 9 198.26 1.27 154 62 72 10 198.15 1.23 155 62 73 11 197.99 1.19 156 63 72 9 198.16 1.22 157 63 73 10 198.15 1.22 158 63 74 11 198.07 1.23 159 63 107 44 198.30 1.27 160 64 70 6 303.12 0.81 161 64 72 8 212.29 0.25 162 65 68 3 305.00 0.01 163 65 109 44 197.71 1.20 164 65 121 56 51.13 0.98 165 66 121 55 52.02 0.54 166 66 122 56 52.02 0.55 167 71 109 38 197.72 1.20 168 71 110 39 197.71 1.21 169 71 111 40 197.69 1.21 170 71 115 44 140.12 0.07 171 72 107 35 197.87 1.26 172 72 108 36 197.74 1.21 173 72 109 37 197.65 1.23 174 72 121 49 51.12 0.98 175 73 107 34 197.72 1.22 176 73 108 35 197.70 1.21 177 73 110 37 197.57 1.21 178 73 115 42 117.13 0.41 179 74 105 31 198.06 1.23 180 74 106 32 197.73 1.22 181 74 107 33 197.50 1.23 182 74 124 50 30.23 0.29 183 75 79 4 191.09 4.62 184 75 105 30 197.72 1.22 185 75 106 31 197.71 1.22 186 76 105 29 197.72 1.22 187 77 105 28 197.58 1.22 188 78 103 25 197.69 1.22 189 78 104 26 191.31 0.82 190 78 105 27 184.13 1.23 191 79 103 24 197.19 1.09 192 79 104 25 190.55 0.90 193 79 106 27 168.27 0.73 194 80 101 21 197.72 1.22 195 80 102 22 197.50 1.25 196 80 103 23 181.40 0.05 197 81 101 20 195.99 0.51 198 81 102 21 190.53 0.90 199 81 104 23 167.02 0.30 200 81 106 25 138.58 1.67 201 81 123 42 24.98 0.97 202 82 99 17 197.68 1.22 203 82 100 18 196.84 0.94 204 82 101 19 178.29 0.64 205 83 98 15 198.15 1.24 206 83 99 16 197.70 1.21 207 83 100 17 197.20 1.09 208 84 97 13 198.07 1.21 209 84 98 14 197.63 1.26 210 85 97 12 198.16 1.24 211 85 98 13 198.00 1.20 212 86 90 4 300.67 1.36 213 86 96 10 198.29 1.26 214 86 97 11 198.16 1.23 215 87 90 3 304.56 0.21 216 87 96 9 198.34 1.26 217 87 97 10 198.28 1.27 218 87 98 11 198.24 1.26 219 90 94 4 304.97 0.01 220 90 95 5 254.77 0.16 221 90 96 6 204.98 2.71 222 91 94 3 304.98 0.01 223 104 123 19 26.16 0.45 224 104 124 20 25.03 1.00 225 105 123 18 27.48 0.21 226 105 124 19 25.20 0.92 227 106 120 14 44.68 0.23 228 106 122 16 31.48 0.69 229 106 123 17 28.12 0.55 230 107 121 14 40.34 1.94 231 107 122 15 32.38 0.28 232 107 124 17 31.30 0.79 233 108 117 9 75.59 11.53 234 108 119 11 51.98 0.56 235 108 120 12 46.98 0.79 236 108 121 13 44.22 0.00 237 109 117 8 75.92 11.65 238 109 118 9 75.61 11.54 239 109 119 10 52.40 0.36 240 110 115 5 108.26 0.55 241 110 116 6 80.17 13.47 242 110 117 7 75.92 11.65 243 110 118 8 75.87 11.67 244 111 114 3 304.94 0.01 245 111 115 4 111.19 0.14 246 111 116 5 108.24 0.54 247 111 118 7 76.37 11.73 248 112 115 3 124.49 1.55