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 6 3 329.58 0.06 2 3 7 4 330.25 0.28 3 3 13 10 73.50 22.25 4 3 17 14 20.59 0.79 5 4 7 3 330.31 0.31 6 4 8 4 326.45 0.96 7 5 8 3 324.99 0.23 8 5 9 4 323.89 0.32 9 6 9 3 329.94 0.37 10 6 10 4 323.63 0.45 11 6 11 5 282.41 6.42 12 6 14 8 221.83 9.22 13 6 17 11 89.70 27.89 14 6 67 61 79.04 24.96 15 6 68 62 78.58 24.73 16 6 69 63 77.63 24.26 17 7 10 3 323.57 0.41 18 7 13 6 210.93 3.79 19 13 17 4 322.30 6.80 20 13 18 5 311.63 6.04 21 14 17 3 328.42 3.76 22 14 18 4 330.12 2.91 23 14 66 52 203.74 1.47 24 14 67 53 203.63 1.51 25 15 18 3 333.96 0.99 26 15 19 4 330.11 2.91 27 15 66 51 203.74 1.47 28 15 111 96 73.38 1.48 29 15 114 99 73.38 1.48 30 15 115 100 73.27 1.48 31 15 118 103 73.27 1.48 32 16 19 3 336.97 0.40 33 16 20 4 330.12 2.91 34 16 21 5 284.47 5.74 35 16 22 6 293.16 1.39 36 16 25 9 281.28 5.96 37 16 63 47 203.72 1.48 38 16 66 50 203.75 1.47 39 16 67 51 203.74 1.47 40 16 68 52 203.70 1.48 41 16 69 53 203.74 1.47 42 17 20 3 331.37 2.26 43 17 21 4 293.98 0.97 44 18 111 93 74.19 1.16 45 18 114 96 74.17 1.16 46 19 24 5 313.12 6.74 47 19 25 6 308.73 8.96 48 19 66 47 204.15 1.28 49 19 102 83 82.17 5.15 50 19 107 88 74.20 1.16 51 19 111 92 74.19 1.16 52 19 115 96 74.17 1.16 53 20 24 4 313.12 6.74 54 21 24 3 332.48 1.88 55 21 25 4 331.11 2.55 56 22 25 3 332.48 1.88 57 22 26 4 331.11 2.55 58 22 59 37 204.53 1.09 59 23 26 3 332.47 1.87 60 23 27 4 332.80 1.71 61 24 27 3 332.80 1.71 62 24 28 4 328.49 0.45 63 25 28 3 330.79 0.70 64 25 29 4 327.08 0.23 65 25 59 34 204.64 1.15 66 25 62 37 204.55 1.22 67 25 63 38 204.44 1.27 68 25 66 41 204.31 1.34 69 26 29 3 334.91 2.76 70 26 30 4 327.04 0.20 71 26 59 33 204.66 1.16 72 27 30 3 335.34 2.97 73 27 31 4 329.30 1.32 74 27 105 78 110.15 9.21 75 28 31 3 330.14 0.91 76 28 32 4 326.49 0.06 77 28 62 34 209.38 0.20 78 28 98 70 111.70 8.46 79 28 101 73 110.91 8.86 80 28 102 74 110.92 8.85 81 28 105 77 110.30 9.15 82 29 32 3 329.28 1.33 83 29 33 4 326.50 0.05 84 29 55 26 323.91 1.18 85 29 58 29 319.73 3.25 86 29 59 30 251.47 4.87 87 29 62 33 209.44 0.22 88 30 33 3 336.89 0.44 89 30 34 4 475.46 4.54 90 30 55 25 326.06 0.15 91 31 101 70 111.84 8.45 92 31 104 73 111.82 8.44 93 32 94 62 112.70 8.54 94 32 97 65 112.53 8.60 95 32 98 66 112.52 8.60 96 32 101 69 111.84 8.45 97 35 97 62 112.62 8.59 98 35 100 65 112.62 8.59 99 35 101 66 112.58 8.59 100 35 104 69 112.59 8.60 101 36 97 61 112.64 8.57 102 39 97 58 117.89 6.05 103 41 89 48 120.43 5.11 104 41 93 52 120.09 5.26 105 42 90 48 120.14 5.24 106 42 93 51 120.08 5.26 107 42 94 52 120.05 5.25 108 42 97 55 119.89 5.21 109 45 86 41 120.58 5.09 110 45 90 45 120.23 5.25 111 57 61 4 448.66 2.43 112 57 72 15 204.42 1.38 113 57 73 16 204.38 1.39 114 57 74 17 204.03 1.35 115 58 61 3 324.30 0.41 116 58 62 4 283.92 2.12 117 59 63 4 308.70 2.56 118 60 63 3 328.95 0.87 119 60 64 4 324.22 0.40 120 60 71 11 204.43 1.38 121 60 72 12 204.42 1.38 122 60 73 13 204.43 1.38 123 61 64 3 325.92 0.42 124 61 65 4 324.24 0.41 125 61 72 11 204.40 1.38 126 61 77 16 158.86 8.77 127 61 122 61 98.55 11.13 128 62 65 3 329.44 2.17 129 62 66 4 324.66 0.20 130 62 98 36 112.34 8.72 131 62 115 53 101.95 12.71 132 62 119 57 100.39 12.04 133 63 66 3 340.45 4.21 134 63 67 4 324.66 0.20 135 63 68 5 256.42 8.75 136 64 67 3 324.66 0.19 137 64 68 4 289.86 2.23 138 65 118 53 100.42 12.05 139 65 119 54 100.41 12.05 140 66 115 49 100.74 12.20 141 66 118 52 100.41 12.05 142 75 80 5 287.12 15.38 143 76 79 3 333.01 1.94 144 76 80 4 320.83 1.43 145 77 80 3 330.29 3.30 146 77 81 4 320.83 1.42 147 77 122 45 95.16 9.50 148 77 125 48 83.83 6.63 149 77 126 49 83.81 6.63 150 78 81 3 337.65 0.38 151 78 82 4 317.79 0.08 152 78 125 47 83.83 6.62 153 81 84 3 341.51 0.01 154 81 86 5 180.44 12.50 155 81 125 44 88.84 6.42 156 81 126 45 83.47 6.42 157 85 90 5 319.86 0.14 158 85 128 43 83.23 6.31 159 86 90 4 319.86 0.14 160 86 126 40 88.83 6.42 161 86 127 41 83.33 6.25 162 86 128 42 83.22 6.32 163 87 90 3 320.80 0.61 164 87 91 4 319.99 0.21 165 87 127 40 84.59 5.64 166 88 91 3 331.66 0.75 167 88 92 4 325.70 3.06 168 88 123 35 100.38 9.72 169 88 127 39 83.29 6.29 170 89 92 3 335.07 0.96 171 89 93 4 332.50 0.33 172 90 93 3 335.16 0.99 173 90 94 4 335.15 0.99 174 91 94 3 335.09 1.03 175 91 95 4 331.00 3.07 176 91 119 28 106.93 9.53 177 91 120 29 106.12 9.15 178 91 123 32 94.61 6.88 179 91 126 35 85.89 5.29 180 91 127 36 83.04 6.39 181 92 95 3 331.03 3.06 182 92 96 4 331.01 3.06 183 93 96 3 331.02 3.06 184 93 97 4 332.81 2.16 185 94 97 3 332.92 0.07 186 94 98 4 324.66 1.93 187 95 98 3 332.38 0.34 188 95 99 4 325.24 1.64 189 95 116 21 108.93 9.53 190 96 99 3 326.00 1.25 191 96 100 4 323.55 0.79 192 97 100 3 327.55 2.79 193 97 101 4 323.54 0.79 194 98 101 3 328.87 1.92 195 98 102 4 321.38 0.29 196 98 115 17 109.13 9.54 197 98 116 18 109.01 9.48 198 98 119 21 106.17 9.17 199 99 102 3 333.62 0.46 200 99 103 4 320.31 0.30 201 99 112 13 109.28 9.52 202 99 116 17 109.12 9.54 203 100 103 3 324.21 2.23 204 100 104 4 320.31 0.30 205 101 104 3 330.52 1.08 206 101 105 4 324.88 2.58 207 102 105 3 330.50 4.08 208 102 106 4 329.20 0.42 209 102 107 5 281.79 11.23 210 102 112 10 109.28 9.52 211 102 115 13 109.14 9.54 212 103 106 3 333.50 2.58 213 103 112 9 140.74 4.18 214 107 111 4 320.34 1.60 215 107 112 5 317.00 1.17 216 108 111 3 337.69 6.70 217 108 112 4 318.24 0.56 218 109 112 3 330.67 4.66 219 109 113 4 323.66 3.26 220 110 113 3 332.33 2.19 221 110 114 4 326.92 4.90 222 111 114 3 326.90 4.91 223 111 115 4 318.22 0.57 224 112 115 3 326.89 4.92 225 112 116 4 318.37 0.66 226 113 116 3 328.98 3.85 227 113 117 4 320.47 0.39 228 114 117 3 328.56 3.65 229 114 118 4 327.79 3.19 230 115 118 3 324.72 1.65 231 115 119 4 324.63 1.69 232 116 119 3 324.11 1.42 233 116 120 4 315.98 1.86 234 117 121 4 338.96 3.20 235 118 121 3 361.31 5.77 236 119 122 3 333.13 0.18 237 120 123 3 340.50 3.21 238 121 124 3 351.29 0.77 239 122 125 3 330.25 1.63 240 122 126 4 322.44 2.36 241 123 126 3 320.38 1.33 242 123 127 4 312.01 1.74