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 10 113 103 26.84 0.02 2 11 109 98 27.68 0.06 3 11 113 102 26.84 0.02 4 12 109 97 28.03 0.06 5 12 110 98 27.14 0.13 6 12 113 101 27.14 0.13 7 12 114 102 27.14 0.13 8 13 17 4 372.85 0.18 9 13 18 5 365.10 1.39 10 13 103 90 40.28 0.08 11 13 106 93 29.28 0.55 12 13 107 94 29.02 0.14 13 13 110 97 28.00 0.04 14 14 17 3 390.81 0.59 15 14 18 4 374.69 2.89 16 15 18 3 385.06 2.29 17 15 19 4 374.19 3.13 18 15 50 35 235.54 0.52 19 15 53 38 234.56 0.27 20 15 56 41 234.33 0.27 21 16 19 3 398.51 4.44 22 16 20 4 374.20 3.12 23 16 56 40 234.40 0.30 24 16 59 43 234.31 0.27 25 16 60 44 234.28 0.24 26 16 63 47 234.04 0.36 27 17 20 3 378.06 1.70 28 17 21 4 377.55 1.45 29 17 99 82 64.28 1.10 30 17 103 86 55.75 0.47 31 18 21 3 384.41 1.27 32 18 22 4 383.54 0.59 33 18 45 27 236.12 0.62 34 18 50 32 235.80 0.46 35 19 22 3 383.55 0.59 36 19 23 4 374.74 3.36 37 19 41 22 235.44 0.48 38 19 50 31 235.94 0.53 39 19 52 33 234.80 0.34 40 19 56 37 234.68 0.35 41 19 57 38 234.57 0.37 42 19 60 41 234.38 0.28 43 20 23 3 383.55 0.59 44 20 24 4 376.64 1.86 45 20 60 40 234.38 0.29 46 20 63 43 234.32 0.31 47 20 64 44 233.97 0.48 48 20 99 79 64.33 1.12 49 21 24 3 381.13 1.80 50 21 25 4 378.83 2.95 51 21 99 78 64.40 1.08 52 21 100 79 64.25 1.09 53 21 103 82 61.95 1.82 54 21 107 86 61.84 1.78 55 22 25 3 375.70 0.91 56 22 26 4 372.94 0.01 57 22 44 22 236.54 0.50 58 22 45 23 236.53 0.50 59 23 26 3 373.80 0.43 60 23 27 4 373.81 0.44 61 23 32 9 238.25 0.09 62 23 37 14 237.57 0.03 63 23 41 18 237.08 0.23 64 23 57 34 234.74 0.36 65 23 60 37 234.66 0.35 66 23 61 38 234.41 0.29 67 23 64 41 234.28 0.36 68 24 27 3 379.88 0.47 69 24 28 4 373.82 0.44 70 24 64 40 234.20 0.42 71 24 90 66 159.09 0.13 72 24 96 72 66.39 0.24 73 24 99 75 64.67 0.97 74 24 100 76 64.33 1.12 75 25 28 3 373.83 0.43 76 25 29 4 373.83 0.43 77 25 100 75 64.62 0.98 78 26 29 3 375.83 0.57 79 26 30 4 373.83 0.43 80 26 31 5 334.07 10.46 81 26 32 6 238.30 0.10 82 26 37 11 237.81 0.11 83 26 40 14 237.58 0.17 84 26 41 15 237.44 0.18 85 27 30 3 375.82 0.56 86 27 32 5 269.57 12.53 87 27 70 43 188.38 2.15 88 27 88 61 159.86 0.07 89 27 89 62 159.38 0.05 90 27 90 63 159.31 0.06 91 28 90 62 159.33 0.06 92 28 93 65 143.78 0.89 93 28 100 72 74.15 1.78 94 32 37 5 339.36 9.22 95 32 70 38 211.28 9.29 96 32 87 55 160.15 0.02 97 32 88 56 159.97 0.04 98 33 37 4 370.23 1.27 99 33 85 52 160.34 0.04 100 33 86 53 160.28 0.04 101 33 87 54 160.13 0.01 102 33 88 55 160.12 0.01 103 34 37 3 377.01 0.68 104 34 86 52 160.28 0.05 105 34 88 54 160.13 0.01 106 35 39 4 385.54 1.27 107 36 39 3 379.64 0.49 108 36 40 4 375.48 1.34 109 37 40 3 377.23 0.48 110 37 41 4 376.35 0.91 111 37 57 20 236.06 0.67 112 37 61 24 235.68 0.49 113 38 41 3 377.25 0.47 114 38 42 4 375.43 1.35 115 38 52 14 237.53 0.65 116 38 54 16 236.81 0.72 117 38 57 19 236.06 0.67 118 39 42 3 378.98 1.52 119 39 43 4 375.39 1.33 120 40 43 3 379.18 1.42 121 40 44 4 374.75 0.79 122 41 44 3 377.19 0.42 123 41 45 4 374.77 0.79 124 41 52 11 237.63 0.69 125 41 57 16 237.21 0.52 126 42 45 3 383.60 2.79 127 42 46 4 372.46 0.36 128 42 51 9 237.64 0.68 129 42 52 10 237.63 0.69 130 42 54 12 237.63 0.69 131 43 46 3 386.49 0.29 132 45 48 3 380.89 3.31 133 45 49 4 371.43 7.82 134 45 50 5 237.83 0.76 135 45 52 7 237.79 0.74 136 46 49 3 365.65 2.98 137 52 57 5 363.90 3.14 138 53 56 3 378.62 3.79 139 53 57 4 367.42 1.83 140 54 57 3 382.47 1.86 141 54 58 4 373.79 1.32 142 55 58 3 374.06 1.19 143 55 59 4 373.78 1.32 144 56 59 3 377.15 2.74 145 56 60 4 376.66 0.80 146 57 60 3 383.75 2.15 147 57 61 4 376.67 0.80 148 58 61 3 392.63 1.23 149 58 62 4 376.66 0.80 150 59 62 3 386.66 4.21 151 59 63 4 370.26 0.18 152 60 63 3 383.25 5.91 153 60 64 4 370.31 0.15 154 61 64 3 374.97 0.65 155 61 65 4 370.73 0.36 156 61 70 9 256.37 1.47 157 61 88 27 159.88 0.04 158 62 65 3 370.23 0.12 159 62 66 4 370.23 0.12 160 63 66 3 385.62 0.97 161 63 67 4 370.20 0.12 162 64 67 3 372.40 1.28 163 64 68 4 365.86 1.99 164 64 69 5 311.18 2.72 165 64 70 6 257.82 0.73 166 65 68 3 377.51 0.29 167 65 70 5 256.37 1.47 168 65 71 6 250.53 4.38 169 65 72 7 250.53 4.37 170 65 88 23 160.02 0.01 171 68 91 23 156.38 1.02 172 68 92 24 152.98 0.65 173 69 90 21 159.31 0.05 174 69 91 22 156.83 0.80 175 69 92 23 152.72 0.79 176 69 95 26 123.22 0.17 177 69 96 27 104.03 9.43 178 69 99 30 97.73 4.65 179 70 88 18 159.91 0.04 180 70 89 19 159.69 0.09 181 70 90 20 158.41 0.11 182 70 91 21 157.32 0.56 183 71 88 17 160.03 0.03 184 71 89 18 159.86 0.07 185 71 90 19 159.73 0.11 186 71 91 20 158.66 0.01 187 72 86 14 160.34 0.03 188 72 87 15 160.28 0.04 189 72 88 16 160.09 0.00 190 73 86 13 160.40 0.01 191 73 87 14 160.29 0.04 192 73 89 16 160.27 0.04 193 74 84 10 160.65 0.06 194 74 85 11 160.62 0.05 195 74 86 12 160.41 0.00 196 75 84 9 160.66 0.05 197 75 85 10 160.64 0.06 198 76 84 8 160.66 0.05 199 77 80 3 371.18 3.27 200 77 84 7 160.69 0.04 201 77 85 8 160.69 0.04 202 90 93 3 374.49 0.29 203 90 96 6 348.99 2.06 204 92 95 3 385.96 2.90 205 92 96 4 371.14 1.30 206 93 96 3 377.05 4.25 207 93 97 4 371.15 1.30 208 94 97 3 376.41 1.33 209 94 98 4 371.14 1.29 210 95 98 3 376.73 1.50 211 95 99 4 370.97 1.39 212 96 99 3 376.43 0.56 213 96 100 4 368.93 0.56 214 97 100 3 375.16 2.27 215 97 101 4 379.79 0.15 216 98 101 3 380.07 0.01 217 98 102 4 379.89 0.10 218 99 102 3 381.17 0.54 219 99 103 4 379.94 0.15 220 100 103 3 379.94 0.15 221 100 104 4 379.94 0.14 222 101 104 3 385.72 2.74 223 101 105 4 379.98 0.14 224 102 105 3 385.73 2.73 225 102 106 4 379.98 0.14 226 103 106 3 379.98 0.14 227 103 107 4 379.94 0.13 228 104 107 3 380.87 0.59 229 104 108 4 379.94 0.13 230 105 108 3 383.35 1.59 231 105 109 4 364.67 6.96 232 106 109 3 382.57 1.98 233 106 110 4 366.05 6.28 234 107 110 3 385.29 5.59 235 107 111 4 370.97 3.81 236 108 111 3 388.59 3.94 237 108 112 4 370.97 3.81 238 109 112 3 376.31 1.16 239 109 113 4 370.96 3.81 240 110 113 3 380.25 0.23 241 110 114 4 370.94 3.80 242 111 114 3 382.23 1.18 243 111 115 4 370.74 3.75 244 112 115 3 378.79 1.67 245 112 116 4 370.21 4.01 246 113 116 3 389.53 1.51 247 113 117 4 381.37 1.56 248 114 117 3 381.22 1.64 249 114 118 4 381.22 1.64 250 115 118 3 381.06 1.71 251 115 119 4 381.06 1.71 252 116 119 3 382.44 1.02 253 116 120 4 371.95 2.83 254 117 120 3 372.66 2.00 255 117 121 4 364.12 0.09 256 118 121 3 380.31 0.49 257 118 122 4 341.23 4.07