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 3 111 108 54.55 0.50 2 4 7 3 176.07 1.64 3 4 8 4 169.89 1.45 4 5 8 3 173.02 0.12 5 5 9 4 174.90 2.23 6 5 108 103 64.27 0.18 7 5 113 108 55.66 0.12 8 6 9 3 176.07 1.64 9 6 10 4 174.90 2.23 10 6 50 44 81.46 4.57 11 6 54 48 67.02 0.21 12 6 111 105 65.52 0.42 13 6 112 106 64.02 0.06 14 6 113 107 56.80 0.41 15 7 10 3 178.18 0.58 16 7 11 4 174.89 2.23 17 8 11 3 171.56 0.58 18 8 12 4 169.33 0.54 19 9 12 3 169.85 0.42 20 9 13 4 167.99 1.20 21 9 46 37 116.41 1.02 22 9 53 44 81.52 4.51 23 9 105 96 67.31 0.23 24 9 112 103 67.46 0.27 25 9 113 104 67.13 0.18 26 9 114 105 66.92 0.25 27 9 115 106 66.89 0.24 28 10 13 3 173.81 3.03 29 10 14 4 133.09 9.68 30 10 33 23 138.31 0.10 31 10 50 40 87.30 7.11 32 11 33 22 138.08 0.21 33 12 35 23 138.66 0.09 34 12 40 28 138.66 0.09 35 12 43 31 138.01 0.21 36 12 45 33 137.41 0.07 37 13 43 30 138.47 0.02 38 13 44 31 138.00 0.21 39 13 45 32 137.40 0.08 40 13 46 33 137.40 0.08 41 13 115 102 69.10 1.13 42 13 117 104 68.81 1.07 43 14 33 19 139.59 0.34 44 14 46 32 137.99 0.21 45 14 48 34 137.41 0.07 46 14 50 36 125.66 0.70 47 14 53 39 101.73 0.44 48 15 18 3 185.69 0.46 49 15 25 10 144.95 0.58 50 15 29 14 139.77 0.34 51 15 33 18 139.66 0.31 52 15 45 30 138.56 0.02 53 15 46 31 138.06 0.23 54 15 47 32 138.03 0.24 55 16 47 31 138.03 0.23 56 16 48 32 138.02 0.23 57 18 21 3 199.87 0.70 58 18 25 7 147.40 1.71 59 18 47 29 138.59 0.01 60 20 25 5 157.24 1.80 61 21 25 4 161.44 1.60 62 21 47 26 147.22 1.77 63 21 77 56 147.27 1.74 64 21 78 57 147.27 1.74 65 21 79 58 147.28 1.74 66 21 96 75 160.90 1.88 67 21 98 77 147.26 1.74 68 21 99 78 147.33 1.71 69 22 25 3 174.33 3.08 70 22 26 4 172.53 0.38 71 22 96 74 161.13 1.77 72 23 26 3 178.97 0.76 73 23 27 4 260.08 1.08 74 23 94 71 180.90 0.62 75 23 95 72 170.25 0.77 76 23 96 73 164.59 0.48 77 24 27 3 283.81 3.04 78 24 28 4 269.63 0.45 79 25 28 3 298.06 4.08 80 25 29 4 270.11 4.60 81 25 47 22 182.06 0.32 82 25 79 54 262.85 0.21 83 26 29 3 306.56 2.73 84 26 30 4 269.63 0.46 85 26 79 53 303.08 2.91 86 26 94 68 242.53 1.10 87 26 96 70 227.11 0.25 88 27 30 3 336.95 4.40 89 27 31 4 289.56 0.86 90 27 92 65 242.86 1.14 91 27 93 66 242.80 1.15 92 27 94 67 242.59 1.15 93 27 95 68 242.59 1.15 94 28 31 3 332.25 5.17 95 28 32 4 289.69 6.76 96 29 32 3 294.42 4.40 97 29 33 4 281.95 2.89 98 29 45 16 243.01 1.12 99 30 33 3 351.38 8.34 100 30 34 4 284.99 3.16 101 30 35 5 244.10 0.79 102 30 36 6 243.50 1.09 103 30 40 10 243.48 1.09 104 30 43 13 243.31 1.05 105 30 45 15 243.12 1.07 106 30 94 64 242.77 1.18 107 31 34 3 310.32 0.14 108 31 36 5 244.11 0.79 109 33 45 12 243.15 1.15 110 35 39 4 267.36 0.62 111 35 40 5 245.50 2.10 112 35 43 8 243.33 1.06 113 35 45 10 243.34 1.05 114 36 39 3 267.35 0.62 115 36 92 56 274.56 2.98 116 39 83 44 243.46 1.10 117 39 88 49 262.07 0.54 118 40 83 43 243.41 1.09 119 41 82 41 243.33 1.06 120 41 83 42 243.34 1.06 121 42 80 38 243.31 1.07 122 42 81 39 243.22 1.09 123 42 82 40 243.24 1.09 124 42 117 75 69.07 1.20 125 42 120 78 69.03 1.19 126 42 121 79 68.45 1.20 127 43 80 37 243.23 1.10 128 43 81 38 243.19 1.09 129 43 117 74 69.03 1.18 130 44 78 34 243.30 1.08 131 44 79 35 243.21 1.09 132 44 80 36 243.05 1.09 133 44 115 71 69.28 1.16 134 44 117 73 68.66 1.16 135 44 120 76 68.56 1.16 136 45 78 33 243.21 1.09 137 45 79 34 243.16 1.07 138 45 81 36 243.03 1.11 139 46 53 7 275.66 1.20 140 46 76 30 243.30 1.08 141 46 77 31 243.24 1.10 142 46 78 32 243.13 1.07 143 46 103 57 193.13 0.90 144 46 115 69 69.36 1.11 145 47 77 30 243.13 1.07 146 47 78 31 243.03 1.11 147 47 79 32 243.03 1.11 148 52 76 24 242.80 1.14 149 53 76 23 242.61 1.15 150 53 112 59 88.31 0.01 151 54 111 57 88.61 0.10 152 54 112 58 88.31 0.01 153 55 61 6 285.33 0.69 154 56 61 5 245.16 0.35 155 56 62 6 243.19 1.28 156 56 70 14 242.90 1.12 157 56 71 15 242.88 1.12 158 56 72 16 242.57 1.10 159 56 76 20 234.59 0.61 160 57 70 13 242.88 1.12 161 57 110 53 117.40 14.33 162 57 111 54 88.94 0.10 163 57 112 55 88.94 0.10 164 58 61 3 268.53 1.86 165 58 62 4 243.61 1.07 166 58 70 12 242.98 1.10 167 59 62 3 256.08 0.77 168 59 70 11 243.16 1.07 169 59 73 14 242.62 1.13 170 60 73 13 242.64 1.13 171 61 72 11 242.68 1.14 172 61 73 12 242.62 1.14 173 61 74 13 242.58 1.11 174 61 76 15 242.58 1.11 175 62 70 8 243.25 1.06 176 62 71 9 243.12 1.07 177 62 72 10 242.85 1.03 178 62 73 11 242.61 1.12 179 63 70 7 243.28 1.07 180 63 71 8 243.18 1.08 181 63 73 10 243.08 1.05 182 64 69 5 243.31 1.07 183 64 70 6 243.30 1.08 184 65 69 4 243.33 1.07 185 65 70 5 243.30 1.08 186 65 71 6 243.28 1.07 187 65 104 39 243.03 1.07 188 66 69 3 258.45 0.82 189 69 104 35 243.04 1.08 190 69 105 36 242.85 1.12 191 69 106 37 242.81 1.12 192 69 116 47 86.16 0.90 193 70 104 34 242.93 1.12 194 70 105 35 242.85 1.12 195 70 107 37 242.72 1.09 196 71 102 31 243.08 1.10 197 71 103 32 242.92 1.13 198 71 104 33 242.81 1.14 199 72 76 4 268.37 1.94 200 72 102 30 242.89 1.12 201 72 103 31 242.87 1.12 202 74 102 28 242.72 1.17 203 75 100 25 242.85 1.14 204 75 101 26 242.55 1.10 205 75 102 27 240.00 1.07 206 76 100 24 242.61 1.12 207 76 101 25 242.55 1.10 208 76 103 27 230.16 0.96 209 77 99 22 242.70 1.16 210 77 100 23 239.22 0.66 211 78 98 20 242.65 1.14 212 78 99 21 242.06 0.86 213 78 103 25 189.47 0.93 214 78 120 42 68.83 1.27 215 79 96 17 242.88 1.12 216 79 97 18 242.61 1.12 217 79 98 19 238.68 0.77 218 80 95 15 242.89 1.12 219 80 96 16 242.57 1.11 220 80 97 17 241.63 1.06 221 80 120 40 68.62 1.17 222 81 94 13 242.84 1.14 223 81 95 14 242.53 1.10 224 82 94 12 242.89 1.12 225 82 95 13 242.75 1.18 226 83 87 4 275.34 2.23 227 83 88 5 243.53 1.14 228 83 92 9 243.24 1.11 229 83 93 10 243.19 1.11 230 83 94 11 242.91 1.13 231 84 93 9 243.22 1.12 232 84 95 11 243.00 1.14 233 101 119 18 74.33 1.09 234 101 120 19 74.23 1.09 235 102 119 17 74.42 1.05 236 103 115 12 80.56 1.13 237 103 119 16 74.42 1.05 238 103 120 17 74.40 1.06 239 104 115 11 84.97 1.07 240 104 116 12 75.43 0.84 241 104 119 15 74.86 0.87 242 105 112 7 88.73 0.09 243 105 114 9 86.23 1.03 244 105 115 10 85.16 0.97 245 106 112 6 88.96 0.10 246 106 113 7 88.75 0.07 247 106 114 8 86.87 0.72 248 107 111 4 117.86 14.09 249 107 112 5 88.95 0.10 250 107 113 6 88.94 0.10 251 108 111 3 170.45 0.81 252 108 113 5 88.98 0.10