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 1 672 675 3 846.51 3.02 2 672 676 4 838.70 0.88 3 673 676 3 852.89 0.16 4 673 677 4 834.94 2.76 5 673 723 50 29.52 1.42 6 673 806 133 27.40 0.72 7 673 834 161 27.35 0.74 8 673 837 164 27.21 0.68 9 674 677 3 842.89 1.62 10 674 678 4 829.49 5.49 11 674 802 128 27.89 0.59 12 674 841 167 27.39 0.72 13 675 678 3 846.20 0.04 14 675 679 4 829.49 5.50 15 676 679 3 840.07 0.21 16 676 680 4 829.49 5.50 17 676 723 47 35.66 1.10 18 677 680 3 848.05 4.21 19 677 681 4 823.70 2.60 20 677 722 45 36.05 1.04 21 677 723 46 35.88 0.99 22 677 805 128 34.68 0.62 23 677 806 129 34.72 0.64 24 677 809 132 35.57 1.06 25 678 681 3 839.94 5.11 26 678 805 127 35.70 0.99 27 680 718 38 36.26 1.07 28 680 721 41 36.27 1.06 29 680 722 42 36.26 1.07 30 681 718 37 36.29 1.07 31 681 804 123 36.15 1.02 32 681 805 124 36.13 1.01 33 681 808 127 36.13 1.01 34 682 714 32 40.91 0.06 35 682 718 36 36.77 1.24 36 684 766 82 86.77 0.17 37 685 707 22 87.21 0.33 38 685 710 25 87.06 0.39 39 685 711 26 79.00 0.34 40 685 714 29 79.06 0.31 41 685 765 80 86.26 0.21 42 685 766 81 87.24 0.32 43 686 707 21 87.22 0.33 44 686 710 24 87.23 0.34 45 686 765 79 87.16 0.33 46 686 766 80 87.24 0.32 47 686 767 81 87.46 0.42 48 687 703 16 87.59 0.46 49 687 706 19 87.44 0.43 50 687 707 20 87.23 0.33 51 687 710 23 87.30 0.35 52 687 765 78 87.45 0.42 53 687 767 80 87.78 0.37 54 687 768 81 87.56 0.47 55 688 710 22 87.81 0.35 56 688 767 79 87.98 0.35 57 689 699 10 88.02 0.38 58 689 700 11 87.97 0.35 59 689 703 14 87.93 0.34 60 689 767 78 87.99 0.35 61 689 768 79 87.98 0.35 62 689 774 85 88.11 0.37 63 690 693 3 857.00 3.16 64 691 767 76 88.25 0.36 65 691 774 83 271.24 90.23 66 695 700 5 818.87 1.67 67 695 773 78 312.73 93.36 68 695 774 79 312.20 93.22 69 695 777 82 313.06 93.43 70 696 699 3 833.72 2.06 71 696 700 4 833.80 8.06 72 696 777 81 313.20 93.40 73 697 700 3 851.21 0.63 74 697 701 4 833.84 8.04 75 697 777 80 313.24 93.41 76 697 778 81 313.17 93.39 77 697 779 82 313.23 93.41 78 697 880 183 171.77 14.96 79 697 887 190 171.76 14.20 80 697 889 192 171.84 14.13 81 698 701 3 851.20 0.62 82 698 702 4 821.63 1.74 83 698 887 189 171.76 14.20 84 698 888 190 171.75 14.19 85 698 889 191 171.73 14.18 86 699 702 3 851.19 0.63 87 699 703 4 821.63 1.75 88 700 703 3 849.19 1.62 89 700 704 4 821.63 1.75 90 700 768 68 324.12 90.25 91 700 770 70 324.12 90.26 92 700 774 74 324.30 90.34 93 700 777 77 326.76 91.58 94 701 704 3 838.47 0.39 95 701 705 4 821.64 1.76 96 701 778 77 326.61 91.50 97 701 876 175 182.00 19.20 98 701 880 179 174.08 13.80 99 701 889 188 174.39 12.87 100 702 705 3 838.08 0.58 101 702 706 4 829.63 2.23 102 702 889 187 174.39 12.88 103 702 890 188 174.38 12.87 104 703 706 3 832.63 3.31 105 703 707 4 829.64 2.22 106 703 768 65 331.00 91.01 107 704 707 3 836.06 2.26 108 704 708 4 830.06 2.02 109 704 764 60 330.71 90.87 110 704 768 64 331.89 90.61 111 704 770 66 332.60 91.08 112 705 708 3 832.98 3.83 113 705 709 4 830.17 1.96 114 705 889 184 183.57 8.46 115 705 890 185 183.43 8.40 116 705 891 186 181.67 9.22 117 705 892 187 183.37 8.37 118 705 895 190 174.44 6.48 119 706 709 3 834.47 3.08 120 706 710 4 830.16 1.95 121 706 892 186 183.88 8.12 122 707 710 3 837.93 2.65 123 707 711 4 839.43 6.59 124 707 764 57 339.61 88.21 125 707 765 58 341.38 87.39 126 707 768 61 340.44 88.14 127 708 711 3 842.84 4.88 128 708 712 4 837.03 1.98 129 708 745 37 338.11 87.45 130 708 895 187 183.88 6.79 131 709 712 3 854.26 0.83 132 709 713 4 842.85 4.88 133 709 892 183 185.49 7.36 134 709 893 184 186.89 6.65 135 709 894 185 185.43 7.33 136 709 895 186 183.94 6.81 137 710 713 3 863.57 3.31 138 710 714 4 842.85 4.88 139 711 714 3 861.40 4.40 140 711 715 4 837.06 1.99 141 711 745 34 344.05 86.62 142 711 752 41 347.57 88.30 143 712 715 3 841.77 2.37 144 712 716 4 833.74 3.67 145 712 737 25 345.51 85.95 146 712 741 29 344.14 86.59 147 712 745 33 344.51 86.77 148 712 894 182 187.84 6.17 149 712 898 186 186.43 5.52 150 713 716 3 849.09 1.28 151 713 717 4 839.47 0.81 152 714 717 3 842.19 2.17 153 714 718 4 839.46 0.81 154 715 718 3 839.47 0.81 155 715 719 4 839.43 0.82 156 715 737 22 350.89 86.25 157 715 744 29 349.85 86.77 158 715 745 30 350.25 86.96 159 716 719 3 844.78 2.90 160 716 720 4 839.28 0.74 161 716 734 18 357.49 82.98 162 716 737 21 351.50 85.95 163 717 720 3 846.27 2.58 164 717 721 4 839.46 0.83 165 718 721 3 846.73 0.25 166 718 722 4 839.44 0.83 167 718 744 26 357.92 83.15 168 718 808 90 357.86 83.17 169 718 809 91 357.75 83.06 170 718 812 94 357.57 82.97 171 719 722 3 839.45 0.83 172 719 725 6 670.96 30.37 173 719 737 18 357.98 83.12 174 719 812 93 357.56 82.97 175 720 725 5 662.06 34.81 176 720 726 6 556.62 15.63 177 720 733 13 358.69 82.82 178 720 734 14 358.63 82.80 179 722 725 3 832.24 7.49 180 722 809 87 358.56 82.83 181 722 812 90 358.63 82.79 182 722 813 91 358.63 82.79 183 722 834 112 253.52 30.30 184 723 830 107 258.27 32.61 185 723 834 111 253.59 30.28 186 724 727 3 850.93 0.20 187 724 830 106 254.24 30.59 188 725 728 3 857.64 2.42 189 725 733 8 586.40 1.62 190 725 736 11 576.81 6.42 191 725 737 12 576.82 6.42 192 725 812 87 359.41 82.40 193 725 813 88 359.32 82.36 194 725 830 105 254.61 30.41 195 726 733 7 725.12 1.07 196 727 826 99 285.48 43.12 197 728 732 4 822.74 4.31 198 728 733 5 822.73 4.32 199 728 736 8 745.88 3.95 200 728 813 85 370.75 76.77 201 728 826 98 285.48 43.12 202 728 827 99 285.47 43.12 203 728 830 102 292.79 37.81 204 729 732 3 843.14 2.52 205 729 733 4 822.75 4.30 206 729 822 93 297.74 38.20 207 729 823 94 297.02 38.53 208 730 733 3 839.28 0.34 209 730 734 4 841.15 0.59 210 731 734 3 872.00 4.71 211 731 735 4 840.55 4.40 212 731 822 91 303.12 35.50 213 732 735 3 845.46 5.74 214 732 736 4 844.21 6.36 215 732 821 89 303.12 35.51 216 732 822 90 303.12 35.50 217 732 823 91 307.20 33.44 218 733 736 3 867.38 5.30 219 733 737 4 850.00 3.46 220 734 737 3 850.00 3.46 221 734 738 4 850.00 3.46 222 735 738 3 845.23 1.06 223 735 739 4 837.87 0.32 224 735 821 86 317.03 28.56 225 736 739 3 853.47 6.67 226 736 740 4 837.87 0.32 227 736 812 76 385.42 69.49 228 736 821 85 319.06 27.55 229 736 827 91 305.49 28.91 230 737 740 3 833.77 3.08 231 737 741 4 832.03 2.59 232 737 812 75 387.37 68.52 233 738 741 3 860.18 3.31 234 738 898 160 233.43 21.32 235 738 902 164 220.74 24.96 236 739 815 76 394.77 64.53 237 739 817 78 394.59 64.34 238 739 902 163 220.78 25.20 239 739 905 166 214.85 25.69 240 739 906 167 213.89 26.00 241 739 911 172 209.41 28.19 242 740 743 3 846.50 0.51 243 740 744 4 831.48 5.58 244 740 811 71 395.20 64.67 245 740 812 72 395.19 64.66 246 740 815 75 394.67 64.40 247 741 744 3 836.19 3.23 248 741 745 4 831.49 5.58 249 741 895 154 244.56 22.20 250 741 898 157 237.97 23.64 251 741 899 158 237.86 23.69 252 741 903 162 225.23 28.66 253 742 745 3 846.86 3.90 254 742 746 4 838.25 2.19 255 742 870 128 252.66 14.87 256 742 873 131 252.72 14.91 257 742 874 132 252.72 14.91 258 742 877 135 255.83 16.55 259 743 746 3 854.65 0.01 260 743 747 4 831.59 5.50 261 743 811 68 403.61 60.62 262 743 866 123 259.08 11.58 263 743 870 127 252.72 14.91 264 744 747 3 847.72 6.88 265 744 748 4 832.50 3.75 266 744 808 64 403.70 60.61 267 744 811 67 403.68 60.61 268 744 812 68 403.67 60.61 269 745 748 3 840.62 3.56 270 745 749 4 831.71 2.47 271 746 749 3 831.71 2.47 272 746 750 4 831.78 2.52 273 746 787 41 435.37 73.14 274 746 790 44 435.37 73.14 275 746 869 123 256.29 16.39 276 746 873 127 255.96 16.57 277 747 750 3 837.46 4.71 278 747 751 4 831.80 2.51 279 747 790 43 435.38 73.14 280 747 794 47 435.19 73.03 281 747 804 57 407.19 59.04 282 747 807 60 407.12 59.02 283 747 808 61 407.09 59.00 284 747 811 64 407.06 58.98 285 747 862 115 266.69 11.20 286 747 866 119 256.31 16.38 287 748 751 3 835.23 0.80 288 748 752 4 831.79 2.52 289 748 804 56 407.19 59.01 290 748 808 60 407.09 58.97 291 749 752 3 849.14 4.75 292 749 753 4 835.23 0.80 293 749 762 13 438.82 72.38 294 749 763 14 438.76 72.41 295 749 764 15 438.60 72.50 296 749 787 38 436.72 72.58 297 750 753 3 842.82 1.46 298 750 754 4 835.23 0.80 299 750 791 41 436.32 72.66 300 750 794 44 436.44 72.42 301 751 754 3 842.96 4.15 302 751 755 4 816.77 1.89 303 751 794 43 436.42 72.42 304 751 799 48 408.74 58.58 305 751 800 49 408.88 58.51 306 751 801 50 408.78 58.46 307 751 804 53 408.38 58.41 308 752 755 3 845.95 1.14 309 752 756 4 814.61 0.87 310 752 763 11 438.85 72.39 311 752 764 12 438.94 72.44 312 753 757 4 748.69 23.88 313 753 758 5 687.20 22.16 314 753 759 6 439.92 72.37 315 753 761 8 439.71 72.46 316 753 762 9 438.89 72.36 317 753 763 10 438.82 72.40 318 753 791 38 436.90 72.48 319 754 758 4 555.96 14.44 320 754 759 5 554.40 15.13 321 754 791 37 436.90 72.48 322 754 794 40 436.61 72.34 323 754 795 41 436.57 72.34 324 756 763 7 439.63 72.38 325 757 760 3 847.21 2.16 326 757 761 4 764.10 12.04 327 757 763 6 439.84 72.38 328 759 788 29 437.04 72.45 329 759 791 32 437.00 72.44 330 759 792 33 437.00 72.44 331 760 788 28 437.21 72.38 332 761 769 8 438.76 72.55 333 761 770 9 438.69 72.55 334 761 771 10 438.68 72.55 335 762 769 7 438.72 72.57 336 762 770 8 438.70 72.57 337 762 775 13 438.66 72.56 338 762 784 22 437.23 72.42 339 762 787 25 437.15 72.39 340 762 788 26 437.11 72.39 341 763 766 3 898.69 0.84 342 763 769 6 438.73 72.56 343 764 768 4 813.43 0.95 344 764 770 6 662.82 38.76 345 764 787 23 437.13 72.39 346 765 768 3 843.80 1.75 347 765 769 4 818.75 1.72 348 766 769 3 875.00 0.45 349 769 774 5 820.18 7.58 350 770 774 4 813.34 11.00 351 770 775 5 813.43 10.95 352 770 778 8 791.76 0.64 353 770 784 14 438.94 71.61 354 771 774 3 841.53 0.66 355 771 775 4 830.90 2.21 356 772 775 3 835.92 4.72 357 772 776 4 830.90 2.21 358 772 781 9 594.21 4.98 359 773 776 3 838.21 3.58 360 773 777 4 830.88 2.21 361 774 777 3 833.32 1.14 362 774 778 4 818.74 3.54 363 775 778 3 848.93 0.43 364 775 779 4 836.05 2.68 365 775 781 6 579.43 2.39 366 775 784 9 440.59 70.95 367 775 788 13 451.88 65.14 368 776 779 3 845.56 1.25 369 776 781 5 655.01 27.21 370 778 876 98 313.94 46.76 371 779 876 97 313.94 46.76 372 779 887 108 305.04 52.36 373 780 783 3 835.15 3.65 374 780 784 4 831.24 5.60 375 780 787 7 811.30 4.30 376 780 873 93 315.19 46.20 377 780 876 96 313.94 46.76 378 781 784 3 834.76 3.84 379 781 785 4 824.00 1.98 380 782 785 3 838.82 5.43 381 782 786 4 827.58 0.19 382 783 786 3 839.08 5.30 383 783 787 4 827.58 0.19 384 783 872 89 315.65 46.43 385 783 873 90 315.74 46.47 386 783 876 93 315.63 47.09 387 784 787 3 835.84 0.93 388 784 788 4 825.39 0.91 389 785 788 3 844.62 3.47 390 785 789 4 823.51 0.04 391 786 789 3 842.69 0.07 392 786 790 4 839.51 6.04 393 786 868 82 317.14 46.85 394 786 869 83 316.90 46.97 395 786 872 86 317.00 47.05 396 787 790 3 847.22 2.19 397 787 791 4 837.58 7.00 398 787 869 82 316.99 47.01 399 787 873 86 317.12 47.15 400 788 791 3 831.00 3.73 401 788 792 4 822.12 0.71 402 789 792 3 842.86 3.12 403 789 793 4 829.41 2.95 404 789 796 7 780.41 6.23 405 790 793 3 841.23 0.82 406 790 794 4 831.24 3.56 407 790 862 72 327.56 41.85 408 790 866 76 317.44 46.95 409 790 869 79 317.47 47.06 410 791 794 3 859.56 4.96 411 792 795 3 845.82 1.91 412 792 796 4 827.55 3.88 413 793 796 3 836.36 0.53 414 793 797 4 822.42 6.44 415 793 862 69 327.74 41.90 416 794 798 4 781.82 6.95 417 794 799 5 638.25 7.53 418 794 804 10 530.71 2.46 419 794 862 68 328.00 41.91 420 795 798 3 815.12 11.15 421 797 855 58 328.88 41.84 422 797 858 61 328.23 41.80 423 797 862 65 328.12 41.86 424 798 855 57 329.03 41.91 425 799 803 4 807.35 2.02 426 799 804 5 805.74 1.31 427 799 807 8 773.14 0.77 428 799 855 56 335.24 44.93 429 799 859 60 328.76 42.05 430 799 862 63 328.74 42.05 431 800 803 3 834.66 4.08 432 800 804 4 829.86 3.45 433 801 804 3 839.71 1.47 434 801 805 4 829.87 3.46 435 802 805 3 838.90 1.06 436 802 806 4 829.87 3.45 437 802 841 39 385.78 38.96 438 803 806 3 835.51 0.62 439 803 807 4 826.65 4.19 440 803 841 38 389.11 40.64 441 803 855 52 354.77 54.40 442 803 859 56 354.12 54.72 443 804 807 3 837.98 1.40 444 804 808 4 825.95 3.84 445 805 808 3 860.53 0.68 446 805 809 4 828.84 3.10 447 806 809 3 838.21 2.22 448 806 810 4 830.22 3.79 449 806 834 28 401.48 43.70 450 806 837 31 399.04 44.92 451 806 838 32 398.46 45.17 452 806 841 35 398.37 45.23 453 807 810 3 846.98 2.51 454 807 811 4 833.14 2.45 455 807 838 31 398.51 45.20 456 807 859 52 366.72 61.02 457 807 862 55 366.76 61.04 458 807 863 56 366.66 61.04 459 808 811 3 847.31 2.35 460 808 812 4 843.93 0.65 461 809 812 3 862.15 0.87 462 809 813 4 843.94 0.66 463 809 834 25 402.77 44.34 464 810 813 3 852.60 0.23 465 810 814 4 843.93 0.66 466 810 834 24 402.77 44.34 467 810 835 25 402.76 44.34 468 810 838 28 399.79 45.84 469 810 863 53 368.02 61.72 470 811 814 3 843.92 0.67 471 811 863 52 367.94 61.75 472 811 866 55 367.73 61.93 473 811 867 56 367.79 61.98 474 813 827 14 423.19 34.56 475 813 830 17 403.36 44.47 476 813 831 18 403.18 44.51 477 813 834 21 403.14 44.52 478 813 914 101 320.64 85.78 479 814 831 17 403.25 44.52 480 814 867 53 368.08 62.10 481 814 913 99 320.69 85.80 482 814 914 100 320.57 85.81 483 815 906 91 327.51 82.42 484 815 911 96 323.12 84.61 485 815 912 97 322.54 84.88 486 815 913 98 320.63 85.83 487 816 821 5 640.84 57.41 488 816 824 8 434.80 30.37 489 816 827 11 433.12 29.74 490 816 911 95 323.12 84.61 491 816 912 96 323.08 84.61 492 816 914 98 321.25 85.52 493 817 820 3 824.07 9.26 494 817 821 4 774.27 9.30 495 817 910 93 323.64 84.39 496 817 911 94 323.10 84.62 497 818 909 91 327.23 82.66 498 818 910 92 323.75 84.40 499 818 912 94 323.50 84.48 500 820 824 4 816.06 3.39 501 821 824 3 822.43 0.20 502 821 827 6 796.26 11.19 503 823 826 3 856.17 0.27 504 823 827 4 830.80 3.79 505 824 827 3 832.91 2.73 506 824 828 4 832.90 2.73 507 825 828 3 835.18 1.59 508 825 829 4 832.53 2.54 509 826 829 3 834.87 3.71 510 826 830 4 834.87 3.71 511 827 830 3 837.21 2.54 512 827 831 4 832.95 4.67 513 827 914 87 323.33 84.70 514 828 831 3 844.50 1.09 515 828 832 4 832.95 4.67 516 829 832 3 844.50 1.09 517 829 833 4 837.21 2.54 518 830 833 3 839.86 1.23 519 830 834 4 836.63 0.34 520 831 834 3 839.30 0.99 521 831 835 4 836.69 0.31 522 831 914 83 323.28 84.75 523 831 916 85 321.95 85.40 524 832 835 3 847.00 2.86 525 832 836 4 836.71 0.30 526 833 836 3 838.30 0.28 527 833 837 4 836.71 0.30 528 834 837 3 837.70 0.25 529 834 838 4 833.90 1.12 530 835 838 3 849.49 6.15 531 835 839 4 833.90 1.12 532 835 856 21 369.62 61.82 533 835 916 81 321.19 85.78 534 836 839 3 838.91 1.38 535 836 840 4 839.34 3.83 536 837 840 3 842.10 2.45 537 837 841 4 839.34 3.83 538 838 841 3 840.56 3.21 539 838 842 4 839.26 3.87 540 838 856 18 369.91 61.95 541 838 859 21 369.78 61.90 542 839 842 3 847.07 3.55 543 839 843 4 839.34 3.83 544 839 856 17 369.88 61.86 545 840 843 3 842.20 2.38 546 840 844 4 835.02 5.96 547 841 844 3 849.29 1.02 548 842 846 4 818.34 4.16 549 842 852 10 371.10 62.46 550 842 855 13 370.24 62.04 551 842 856 14 370.24 62.04 552 842 859 17 370.19 62.05 553 843 846 3 818.35 4.16 554 843 852 9 376.41 65.09 555 846 851 5 780.05 1.43 556 846 852 6 474.18 45.66 557 846 855 9 449.55 71.39 558 848 851 3 855.30 0.63 559 848 852 4 837.59 0.72 560 849 852 3 850.75 2.90 561 849 853 4 837.60 0.71 562 850 853 3 847.80 4.38 563 850 854 4 847.78 4.38 564 851 854 3 847.78 4.38 565 851 855 4 834.00 1.08 566 852 855 3 846.48 2.04 567 852 856 4 833.98 1.03 568 853 856 3 841.62 4.46 569 853 857 4 822.45 4.74 570 854 857 3 849.92 3.75 571 854 858 4 822.46 4.73 572 855 858 3 831.60 0.15 573 855 859 4 834.07 1.08 574 856 859 3 851.63 2.27 575 856 860 4 829.24 0.20 576 856 916 60 321.69 86.46 577 857 860 3 851.63 2.27 578 857 861 4 832.57 1.82 579 857 917 60 321.52 86.50 580 858 861 3 856.51 0.17 581 858 862 4 832.59 1.81 582 859 862 3 832.59 1.81 583 859 863 4 832.83 1.94 584 860 863 3 834.16 2.60 585 860 864 4 832.85 1.93 586 860 916 56 321.52 86.55 587 860 917 57 321.52 86.55 588 861 864 3 840.96 0.29 589 861 865 4 832.87 1.94 590 861 917 56 321.66 86.64 591 862 865 3 843.86 1.75 592 862 866 4 843.94 1.71 593 863 866 3 851.12 1.89 594 863 916 53 321.74 86.66 595 864 867 3 860.47 2.79 596 864 868 4 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