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 9 104 95 124.19 2.52 2 10 13 3 430.27 2.49 3 10 57 47 123.64 2.64 4 10 104 94 124.19 2.52 5 11 59 48 124.36 2.47 6 11 60 49 124.36 2.47 7 11 61 50 124.33 2.46 8 11 64 53 124.27 2.51 9 11 104 93 124.19 2.52 10 11 105 94 124.19 2.52 11 12 32 20 124.25 2.50 12 12 58 46 124.37 2.46 13 12 59 47 124.37 2.47 14 12 71 59 124.24 2.51 15 12 95 83 124.24 2.51 16 12 105 93 124.20 2.52 17 12 107 95 124.19 2.52 18 13 104 91 124.27 2.50 19 13 105 92 124.23 2.50 20 13 106 93 124.20 2.52 21 13 107 94 124.20 2.52 22 14 30 16 137.53 0.26 23 14 49 35 144.85 0.80 24 14 53 39 145.81 0.69 25 14 54 40 144.85 0.80 26 14 55 41 144.49 0.70 27 14 58 44 142.94 1.09 28 14 73 59 131.88 1.31 29 14 107 93 124.20 2.52 30 15 52 37 150.56 1.38 31 15 53 38 145.90 0.65 32 15 54 39 145.49 0.58 33 15 106 91 124.27 2.50 34 15 107 92 124.24 2.50 35 15 108 93 124.20 2.52 36 15 109 94 124.20 2.52 37 16 24 8 150.87 1.52 38 16 25 9 150.59 1.39 39 16 28 12 147.63 0.06 40 16 30 14 145.47 0.58 41 16 49 33 147.47 0.14 42 16 53 37 147.75 0.03 43 16 73 57 143.83 0.38 44 16 109 93 124.20 2.52 45 16 111 95 124.19 2.52 46 17 23 6 309.79 3.16 47 17 24 7 150.87 1.52 48 17 25 8 150.92 1.49 49 17 109 92 124.25 2.50 50 17 110 93 124.20 2.52 51 17 111 94 124.20 2.52 52 18 21 3 404.19 3.04 53 18 22 4 344.85 1.62 54 18 23 5 318.63 7.57 55 18 25 7 151.18 1.37 56 18 78 60 151.35 1.42 57 18 79 61 151.87 1.20 58 18 111 93 124.20 2.52 59 19 110 91 124.27 2.50 60 19 111 92 124.25 2.50 61 19 112 93 124.22 2.52 62 20 79 59 169.43 0.89 63 20 112 92 124.25 2.50 64 20 113 93 124.25 2.50 65 21 82 61 193.48 1.48 66 24 51 27 286.75 2.38 67 24 52 28 285.81 2.04 68 24 53 29 285.55 2.12 69 25 28 3 420.91 2.54 70 25 49 24 287.36 2.30 71 25 53 28 285.60 2.14 72 25 78 53 210.08 0.18 73 25 111 86 124.22 2.51 74 26 49 23 287.36 2.29 75 26 50 24 287.32 2.28 76 26 51 25 286.88 2.42 77 26 78 52 210.26 0.21 78 27 48 21 287.72 2.39 79 27 49 22 287.58 2.32 80 28 48 20 287.78 2.36 81 28 49 21 287.72 2.39 82 28 73 45 211.34 0.26 83 28 74 46 211.21 0.30 84 28 78 50 210.31 0.21 85 29 47 18 288.01 2.33 86 29 48 19 287.74 2.38 87 29 73 44 211.56 0.36 88 29 74 45 211.22 0.30 89 30 46 16 294.10 1.71 90 30 47 17 288.17 2.37 91 30 49 19 288.05 2.31 92 30 55 25 286.89 2.35 93 30 58 28 286.82 2.35 94 30 71 41 212.69 0.64 95 30 72 42 212.51 0.69 96 30 73 43 212.34 0.76 97 31 43 12 302.11 1.85 98 31 45 14 299.94 2.06 99 31 46 15 294.10 1.71 100 31 71 40 212.69 0.64 101 31 72 41 212.62 0.64 102 32 43 11 302.12 1.84 103 32 44 12 302.09 1.84 104 32 45 13 301.69 1.67 105 32 58 26 286.83 2.35 106 32 69 37 241.33 1.03 107 32 70 38 235.72 1.70 108 32 71 39 223.04 4.54 109 33 41 8 317.01 0.25 110 33 42 9 307.69 3.15 111 33 43 10 302.12 1.84 112 33 44 11 302.11 1.84 113 33 69 36 245.49 3.07 114 33 70 37 237.26 0.96 115 34 41 7 317.60 0.04 116 34 42 8 317.01 0.24 117 34 44 10 307.69 3.14 118 34 65 31 283.09 2.58 119 34 68 34 245.89 3.02 120 34 69 35 245.61 3.02 121 35 39 4 364.19 2.72 122 35 40 5 336.69 3.88 123 35 41 6 335.50 3.29 124 35 68 33 248.65 1.61 125 36 39 3 394.58 0.61 126 36 40 4 344.48 1.87 127 36 41 5 336.69 3.87 128 36 42 6 335.78 3.42 129 41 68 27 255.44 1.74 130 41 69 28 249.36 1.29 131 41 70 29 249.02 1.38 132 41 94 53 210.31 0.18 133 43 46 3 482.90 0.04 134 44 59 15 286.83 2.35 135 44 63 19 283.06 2.59 136 44 69 25 248.90 1.50 137 45 58 13 286.83 2.35 138 45 59 14 286.80 2.36 139 47 55 8 286.88 2.35 140 49 53 4 343.74 2.85 141 49 54 5 327.95 0.70 142 50 53 3 383.78 0.01 143 50 54 4 352.53 1.55 144 50 56 6 342.91 2.46 145 55 58 3 403.62 4.25 146 59 63 4 392.25 2.52 147 59 64 5 382.43 3.10 148 60 63 3 402.28 2.48 149 60 64 4 392.25 2.52 150 61 64 3 396.35 0.48 151 64 69 5 390.92 2.29 152 64 95 31 210.16 0.18 153 64 97 33 206.43 0.56 154 64 105 41 124.27 2.50 155 65 69 4 441.10 0.38 156 66 97 31 208.97 0.48 157 66 98 32 204.94 0.38 158 67 96 29 210.05 0.15 159 67 97 30 209.89 0.10 160 68 94 26 210.25 0.14 161 68 95 27 210.16 0.16 162 68 96 28 210.04 0.16 163 69 94 25 210.22 0.15 164 69 95 26 210.12 0.18 165 69 97 28 209.80 0.13 166 70 92 22 210.28 0.16 167 70 93 23 210.19 0.17 168 70 94 24 210.11 0.18 169 71 92 21 210.23 0.15 170 71 93 22 210.16 0.16 171 71 95 24 210.16 0.16 172 71 107 36 124.31 2.49 173 72 90 18 210.30 0.17 174 72 91 19 210.24 0.14 175 72 92 20 210.12 0.18 176 73 90 17 210.23 0.14 177 73 91 18 210.21 0.14 178 73 93 20 210.16 0.16 179 73 107 34 124.37 2.48 180 73 109 36 124.29 2.49 181 74 77 3 408.55 0.23 182 74 78 4 392.93 0.51 183 74 90 16 210.22 0.14 184 75 78 3 397.63 4.71 185 75 79 4 392.49 0.83 186 75 90 15 210.23 0.14 187 75 91 16 210.22 0.14 188 75 109 34 124.36 2.48 189 75 111 36 124.27 2.49 190 76 79 3 402.31 2.42 191 76 80 4 393.09 1.13 192 76 86 10 314.91 0.21 193 76 88 12 258.64 24.00 194 76 89 13 210.27 0.15 195 77 80 3 397.48 0.00 196 77 81 4 391.22 2.06 197 78 81 3 403.12 1.95 198 78 82 4 391.18 2.09 199 78 111 33 124.31 2.48 200 79 82 3 391.18 2.09 201 79 83 4 391.18 2.09 202 79 84 5 373.00 0.70 203 79 86 7 345.00 2.65 204 79 111 32 124.32 2.48 205 79 112 33 124.31 2.48 206 79 113 34 124.20 2.50 207 80 83 3 394.42 0.47 208 80 84 4 376.69 0.30 209 80 86 6 366.51 2.54 210 84 113 29 124.31 2.48 211 85 114 29 124.30 2.49 212 86 113 27 124.23 2.48 213 86 114 28 124.22 2.49 214 87 113 26 124.24 2.48 215 87 114 27 124.02 2.52 216 88 114 26 124.04 2.50 217 88 115 27 123.58 2.33 218 88 116 28 123.04 2.20 219 91 109 18 124.35 2.48 220 91 116 25 52.84 0.43 221 93 107 14 124.35 2.48 222 93 118 25 44.12 0.49 223 95 105 10 168.44 24.44 224 95 107 12 124.34 2.48 225 97 105 8 320.00 6.04 226 98 105 7 333.86 3.03 227 99 103 4 340.31 0.18 228 99 104 5 345.29 2.31 229 99 105 6 345.30 2.67 230 103 123 20 16.59 0.13 231 104 122 18 18.27 0.25 232 104 123 19 16.49 0.11 233 105 121 16 23.32 0.21 234 105 122 17 18.77 0.50 235 106 120 14 25.78 0.32 236 106 121 15 23.86 0.38 237 107 119 12 35.05 0.01 238 107 120 13 29.86 0.48 239 108 118 10 44.01 0.45 240 108 119 11 39.08 1.23 241 109 116 7 137.09 43.80 242 109 117 8 49.77 0.24 243 109 118 9 43.63 0.63 244 110 116 6 137.10 43.80 245 110 117 7 50.09 0.30 246 111 115 4 368.85 3.92 247 111 116 5 180.59 65.55 248 112 115 3 382.56 2.81