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 1 671 674 3 854.82 1.42 2 671 675 4 838.39 2.94 3 671 840 169 118.44 45.24 4 672 675 3 846.86 1.25 5 672 676 4 843.68 4.21 6 673 676 3 854.57 2.48 7 673 677 4 848.06 2.02 8 673 723 50 119.04 45.35 9 673 806 133 118.95 45.34 10 673 834 161 118.95 45.35 11 673 837 164 118.94 45.36 12 673 840 167 119.33 45.53 13 674 677 3 846.85 1.29 14 674 678 4 838.38 2.94 15 674 802 128 119.03 45.30 16 674 841 167 119.03 45.30 17 675 678 3 863.25 6.00 18 675 679 4 835.67 1.81 19 676 679 3 836.78 2.02 20 676 680 4 831.53 0.18 21 676 721 45 126.22 45.00 22 676 723 47 124.57 45.83 23 677 680 3 838.84 2.66 24 677 681 4 819.44 6.22 25 677 722 45 126.12 45.05 26 677 723 46 126.30 45.21 27 677 805 128 123.28 44.68 28 677 806 129 123.28 44.68 29 677 809 132 123.29 44.68 30 678 681 3 836.80 2.46 31 678 805 127 123.89 44.98 32 680 718 38 126.91 45.13 33 680 721 41 127.00 45.19 34 680 722 42 126.91 45.14 35 681 718 37 127.39 44.98 36 681 804 123 126.66 45.23 37 681 805 124 126.65 45.23 38 681 808 127 126.66 45.23 39 682 714 32 127.81 44.80 40 682 718 36 127.41 44.98 41 684 766 82 243.44 77.55 42 685 707 22 243.42 77.54 43 685 710 25 243.21 77.51 44 685 711 26 235.70 80.53 45 685 714 29 239.05 78.85 46 685 765 80 242.96 77.77 47 685 766 81 243.56 77.55 48 686 707 21 243.45 77.55 49 686 710 24 243.44 77.55 50 686 765 79 243.27 77.63 51 686 766 80 243.58 77.54 52 686 767 81 243.62 77.56 53 687 703 16 243.56 77.56 54 687 706 19 243.53 77.56 55 687 707 20 243.46 77.55 56 687 710 23 243.53 77.56 57 687 765 78 243.58 77.54 58 687 767 80 243.69 77.56 59 687 768 81 243.64 77.56 60 688 710 22 243.63 77.55 61 688 767 79 243.84 77.56 62 689 700 11 243.77 77.53 63 689 703 14 243.72 77.55 64 689 767 78 243.86 77.56 65 689 768 79 243.83 77.56 66 689 774 85 244.71 77.98 67 690 693 3 863.35 4.24 68 691 767 76 244.09 77.61 69 691 774 83 274.45 92.51 70 695 700 5 788.53 8.38 71 695 773 78 306.12 90.02 72 695 774 79 305.27 89.91 73 695 777 82 306.12 90.02 74 696 699 3 831.26 0.56 75 696 700 4 824.89 3.75 76 697 700 3 844.15 2.10 77 697 701 4 830.47 3.54 78 697 777 80 310.91 90.11 79 697 778 81 309.79 89.56 80 697 779 82 307.52 90.70 81 697 880 183 168.84 11.12 82 697 887 190 133.38 6.94 83 697 889 192 127.28 9.95 84 698 701 3 857.59 4.62 85 698 702 4 830.49 3.56 86 698 887 189 133.25 7.00 87 698 888 190 127.33 9.96 88 698 889 191 126.83 10.16 89 699 702 3 861.38 2.72 90 699 703 4 840.63 1.53 91 700 703 3 866.13 0.35 92 700 704 4 840.64 1.54 93 700 770 70 327.43 90.12 94 700 774 74 327.81 90.31 95 700 777 77 327.88 90.28 96 700 778 78 327.79 90.28 97 701 704 3 840.61 1.56 98 701 705 4 829.58 7.07 99 701 778 77 327.88 90.28 100 701 876 175 173.30 13.00 101 701 880 179 162.93 7.79 102 701 889 188 128.31 11.50 103 702 705 3 854.58 5.42 104 702 706 4 827.71 8.01 105 702 889 187 128.31 11.50 106 702 890 188 128.27 11.52 107 703 706 3 836.38 3.67 108 703 707 4 836.42 3.65 109 703 768 65 334.45 90.45 110 704 707 3 837.88 2.86 111 704 708 4 825.85 1.65 112 704 764 60 333.53 90.62 113 704 768 64 334.66 90.34 114 704 770 66 335.01 90.52 115 704 780 76 334.54 90.42 116 705 708 3 836.38 3.61 117 705 709 4 836.36 3.61 118 705 889 184 133.98 14.34 119 705 890 185 133.85 14.36 120 705 891 186 132.88 14.79 121 705 892 187 131.82 15.41 122 705 895 190 131.72 15.38 123 706 709 3 843.27 0.16 124 706 710 4 836.36 3.61 125 706 892 186 131.84 15.42 126 707 710 3 847.20 3.72 127 707 711 4 829.11 0.05 128 707 764 57 339.60 88.54 129 707 765 58 339.88 88.65 130 707 768 61 339.88 88.66 131 708 711 3 836.28 3.64 132 708 712 4 836.28 3.64 133 708 745 37 338.94 88.19 134 708 895 187 133.00 16.08 135 709 712 3 836.40 3.70 136 709 713 4 842.79 0.39 137 709 892 183 136.31 17.65 138 709 893 184 137.33 18.16 139 709 894 185 136.24 17.69 140 709 895 186 134.21 16.80 141 710 713 3 854.00 5.40 142 710 714 4 853.39 5.69 143 711 714 3 858.50 3.14 144 711 715 4 842.78 0.39 145 711 745 34 342.94 87.14 146 712 715 3 853.39 5.69 147 712 716 4 836.31 2.85 148 712 741 29 343.56 86.89 149 712 745 33 343.26 87.11 150 712 894 182 137.37 18.26 151 712 895 183 137.18 18.29 152 712 898 186 134.66 19.55 153 713 716 3 838.55 1.71 154 713 717 4 835.37 2.83 155 714 717 3 834.12 1.01 156 714 718 4 827.97 0.85 157 715 718 3 837.19 0.53 158 715 719 4 828.49 1.11 159 715 737 22 346.06 86.08 160 715 744 29 346.10 86.10 161 715 745 30 346.11 86.11 162 716 719 3 848.33 6.10 163 716 720 4 834.51 1.89 164 716 737 21 350.74 83.75 165 717 720 3 849.71 3.69 166 717 721 4 840.33 1.01 167 718 721 3 850.14 3.47 168 718 722 4 840.32 1.01 169 718 744 26 353.08 82.67 170 718 808 90 353.08 82.66 171 718 809 91 353.08 82.66 172 718 812 94 353.07 82.66 173 719 722 3 849.70 3.69 174 719 725 6 585.30 8.91 175 719 737 18 353.09 82.64 176 719 812 93 353.07 82.66 177 720 725 5 608.70 2.79 178 720 726 6 585.29 8.90 179 722 725 3 848.76 2.78 180 722 809 87 353.43 82.50 181 722 812 90 353.47 82.50 182 722 813 91 353.45 82.49 183 722 834 112 241.71 26.61 184 723 830 107 242.51 27.01 185 723 834 111 241.71 26.61 186 724 727 3 837.76 0.15 187 724 830 106 242.51 27.01 188 725 728 3 850.85 2.25 189 725 733 8 545.64 12.22 190 725 736 11 518.79 0.47 191 725 737 12 518.75 0.49 192 725 812 87 355.44 81.52 193 725 813 88 355.01 81.73 194 725 830 105 242.92 26.80 195 726 733 7 663.58 4.92 196 727 826 99 261.32 24.57 197 728 732 4 810.94 5.49 198 728 733 5 794.32 2.57 199 728 813 85 365.45 76.51 200 728 826 98 261.32 24.57 201 728 827 99 261.31 24.57 202 728 830 102 254.41 21.12 203 729 732 3 844.35 5.33 204 729 733 4 829.51 2.70 205 729 822 93 274.91 23.16 206 729 823 94 267.42 26.89 207 730 733 3 835.47 0.28 208 730 734 4 835.47 0.28 209 731 734 3 846.27 1.28 210 731 735 4 821.45 5.76 211 731 822 91 275.26 23.04 212 732 735 3 842.62 4.83 213 732 736 4 833.62 0.35 214 732 821 89 275.23 23.05 215 732 822 90 275.19 23.00 216 732 823 91 282.36 19.37 217 733 736 3 870.21 7.50 218 733 737 4 844.50 3.88 219 734 737 3 853.74 0.73 220 734 738 4 837.40 0.32 221 735 738 3 843.45 2.71 222 735 739 4 840.11 1.67 223 735 821 86 283.29 19.03 224 736 739 3 846.90 0.97 225 736 740 4 840.11 1.67 226 736 812 76 381.92 68.40 227 736 816 80 381.69 68.30 228 736 821 85 286.62 17.30 229 736 827 91 270.92 12.83 230 737 740 3 846.91 0.97 231 737 741 4 814.82 8.93 232 737 812 75 382.00 68.36 233 738 741 3 865.27 1.54 234 738 898 160 187.03 45.81 235 738 902 164 170.59 47.10 236 739 815 76 389.96 64.33 237 739 817 78 389.93 64.22 238 739 902 163 177.38 50.50 239 739 905 166 169.25 47.77 240 739 906 167 166.84 47.61 241 739 911 172 150.53 55.48 242 740 743 3 838.32 2.64 243 740 744 4 833.76 0.35 244 740 811 71 390.16 64.40 245 740 812 72 390.12 64.38 246 740 815 75 389.81 64.23 247 741 744 3 848.09 3.81 248 741 745 4 836.65 1.79 249 741 898 157 190.55 47.51 250 741 899 158 193.29 48.95 251 741 903 162 179.71 50.44 252 742 745 3 854.37 4.92 253 742 746 4 838.00 1.12 254 742 870 128 249.25 15.54 255 742 873 131 239.86 20.28 256 742 874 132 239.81 20.30 257 742 877 135 237.66 27.21 258 743 746 3 854.37 4.92 259 743 747 4 821.08 1.00 260 743 811 68 399.78 59.72 261 743 866 123 250.25 15.01 262 743 870 127 249.27 15.54 263 744 747 3 846.94 4.38 264 744 748 4 821.22 1.07 265 744 808 64 399.79 59.72 266 744 811 67 399.78 59.72 267 744 812 68 399.77 59.72 268 745 748 3 834.36 0.64 269 745 749 4 830.38 1.03 270 746 749 3 836.57 1.74 271 746 750 4 832.76 0.15 272 746 787 41 448.55 77.52 273 746 790 44 448.56 77.51 274 746 869 123 255.59 18.53 275 746 873 127 246.13 23.41 276 747 750 3 845.45 1.39 277 747 751 4 837.57 2.56 278 747 790 43 448.54 77.53 279 747 794 47 448.59 77.49 280 747 804 57 406.33 56.54 281 747 807 60 406.04 56.62 282 747 808 61 406.04 56.62 283 747 811 64 406.01 56.62 284 747 866 119 256.44 18.10 285 748 751 3 840.69 1.00 286 748 752 4 836.90 2.89 287 748 804 56 406.28 56.56 288 748 808 60 406.05 56.61 289 749 752 3 853.44 7.36 290 749 753 4 827.73 1.70 291 749 762 13 450.76 78.11 292 749 763 14 450.76 78.11 293 749 764 15 450.70 78.09 294 749 787 38 448.74 77.55 295 750 753 3 840.80 2.30 296 750 754 4 823.69 0.34 297 750 791 41 448.63 77.50 298 750 794 44 448.64 77.50 299 751 754 3 838.22 0.24 300 751 755 4 831.53 3.58 301 751 794 43 448.64 77.50 302 751 799 48 406.79 56.57 303 751 800 49 406.66 56.51 304 751 801 50 406.63 56.50 305 751 804 53 406.29 56.55 306 752 755 3 831.53 3.58 307 752 756 4 823.32 5.75 308 752 763 11 451.14 77.96 309 752 764 12 451.15 77.96 310 753 756 3 842.38 4.93 311 753 757 4 823.31 5.76 312 753 758 5 788.01 3.92 313 753 759 6 568.35 19.85 314 753 761 8 558.94 24.49 315 753 762 9 541.47 32.80 316 753 763 10 451.14 77.95 317 753 791 38 449.29 77.27 318 754 758 4 677.54 27.88 319 754 759 5 568.54 19.95 320 754 791 37 449.29 77.27 321 754 794 40 449.22 77.23 322 754 795 41 449.20 77.23 323 756 763 7 557.03 25.14 324 757 760 3 835.33 0.29 325 757 761 4 811.75 12.07 326 757 763 6 557.08 25.12 327 759 788 29 449.43 77.23 328 759 791 32 449.38 77.25 329 759 792 33 449.36 77.23 330 760 788 28 450.08 77.06 331 761 769 8 531.18 38.20 332 761 770 9 452.31 77.61 333 761 771 10 452.31 77.61 334 761 775 14 452.30 77.62 335 762 769 7 531.19 38.20 336 762 770 8 452.31 77.61 337 762 775 13 452.32 77.61 338 762 784 22 450.43 76.91 339 762 787 25 450.20 76.98 340 762 788 26 450.29 76.84 341 763 766 3 893.04 0.76 342 763 769 6 552.63 27.48 343 764 768 4 776.15 21.59 344 764 770 6 568.07 19.80 345 764 787 23 450.52 76.81 346 765 768 3 804.90 9.76 347 765 769 4 776.14 21.59 348 768 774 6 824.85 0.13 349 769 774 5 824.87 0.12 350 770 774 4 824.87 0.12 351 770 775 5 819.06 2.96 352 770 778 8 765.15 0.57 353 770 784 14 543.22 30.51 354 771 774 3 846.83 0.84 355 771 775 4 824.88 0.12 356 772 775 3 851.02 2.94 357 772 776 4 834.51 1.40 358 772 781 9 574.09 17.34 359 773 776 3 845.36 0.12 360 773 777 4 824.88 0.12 361 774 777 3 838.75 2.81 362 774 778 4 820.00 2.35 363 775 778 3 860.95 0.49 364 775 780 5 748.41 4.62 365 775 781 6 573.53 17.08 366 775 784 9 567.00 18.66 367 775 788 13 571.86 16.26 368 776 779 3 849.63 6.16 369 776 781 5 574.77 17.02 370 778 876 98 305.93 52.57 371 779 876 97 305.97 52.55 372 779 887 108 271.82 69.93 373 780 783 3 848.93 3.72 374 780 784 4 833.04 2.19 375 780 787 7 832.89 2.12 376 780 873 93 314.46 48.30 377 780 876 96 305.96 52.56 378 781 784 3 843.63 1.30 379 781 785 4 833.03 2.19 380 782 785 3 839.49 0.77 381 782 786 4 841.72 0.34 382 783 786 3 843.75 0.56 383 783 787 4 841.73 0.34 384 783 872 89 314.60 48.30 385 783 873 90 314.55 48.35 386 783 876 93 305.96 52.70 387 784 787 3 843.68 0.58 388 784 788 4 839.80 1.30 389 785 788 3 839.81 1.29 390 785 789 4 839.81 1.28 391 786 789 3 834.39 1.44 392 786 790 4 832.96 2.16 393 786 868 82 315.71 48.17 394 786 869 83 315.29 48.36 395 786 872 86 315.32 48.41 396 787 790 3 834.40 1.44 397 787 791 4 841.77 2.25 398 787 869 82 315.35 48.39 399 787 873 86 312.69 49.83 400 788 791 3 841.77 2.25 401 788 792 4 841.78 2.26 402 789 792 3 833.44 6.44 403 789 793 4 848.90 1.30 404 789 796 7 803.48 3.89 405 790 793 3 848.91 1.30 406 790 794 4 848.90 1.30 407 790 862 72 319.95 46.20 408 790 865 75 319.24 46.55 409 790 866 76 316.31 48.04 410 790 869 79 315.79 48.33 411 791 794 3 867.16 6.17 412 792 795 3 848.97 1.27 413 792 796 4 827.88 0.64 414 793 796 3 840.75 1.87 415 793 797 4 813.01 4.00 416 793 862 69 319.97 46.20 417 794 798 4 763.20 0.35 418 794 799 5 685.66 19.78 419 794 804 10 563.37 22.26 420 794 862 68 320.27 46.35 421 795 798 3 828.91 3.06 422 797 855 58 334.19 53.09 423 797 858 61 333.62 52.93 424 797 862 65 333.33 52.82 425 798 855 57 337.00 54.45 426 799 803 4 818.93 0.67 427 799 804 5 808.92 4.33 428 799 807 8 773.64 5.73 429 799 855 56 336.97 54.48 430 799 859 60 334.13 53.22 431 799 862 63 334.12 53.22 432 800 803 3 832.92 1.61 433 800 804 4 813.28 6.45 434 801 804 3 825.64 1.41 435 801 805 4 820.28 2.96 436 802 805 3 839.12 3.46 437 802 806 4 837.74 5.37 438 802 841 39 365.02 41.77 439 803 806 3 842.76 2.87 440 803 807 4 847.18 0.66 441 803 841 38 365.01 41.77 442 803 855 52 337.65 54.77 443 803 859 56 337.26 54.80 444 804 807 3 847.26 0.62 445 804 808 4 847.25 0.61 446 805 808 3 847.34 0.66 447 805 809 4 847.25 0.61 448 806 809 3 847.27 0.62 449 806 810 4 845.90 0.06 450 806 834 28 372.30 38.73 451 806 837 31 370.93 39.16 452 806 838 32 370.20 39.47 453 806 841 35 365.31 41.90 454 807 810 3 845.91 0.06 455 807 811 4 845.91 0.06 456 807 838 31 370.19 39.47 457 807 859 52 337.40 54.90 458 807 862 55 337.36 54.90 459 807 863 56 337.16 54.97 460 808 811 3 846.00 0.07 461 808 812 4 845.93 0.03 462 809 812 3 852.46 3.29 463 809 813 4 845.93 0.03 464 809 834 25 372.31 38.73 465 810 813 3 850.95 2.50 466 810 814 4 845.88 0.01 467 810 831 21 372.74 38.76 468 810 834 24 372.31 38.73 469 810 835 25 372.30 38.73 470 810 838 28 371.20 39.27 471 810 863 53 337.20 54.97 472 810 916 106 228.83 99.98 473 811 814 3 845.60 0.14 474 811 863 52 336.85 55.15 475 811 866 55 336.53 55.25 476 811 867 56 336.54 55.26 477 813 827 14 373.57 38.50 478 813 830 17 373.38 38.56 479 813 831 18 372.79 38.85 480 813 834 21 372.69 38.90 481 814 831 17 372.88 38.83 482 814 867 53 336.53 55.25 483 814 913 99 230.58 99.52 484 814 914 100 230.18 99.58 485 815 906 91 251.78 90.08 486 815 911 96 235.18 97.81 487 815 912 97 233.53 98.36 488 815 913 98 231.03 99.30 489 815 914 99 230.58 99.52 490 816 821 5 449.30 63.98 491 816 824 8 398.66 38.80 492 816 827 11 394.02 38.48 493 816 911 95 235.19 97.81 494 816 912 96 235.12 97.80 495 816 914 98 233.22 98.44 496 817 820 3 834.56 5.39 497 817 821 4 807.86 6.11 498 817 910 93 239.57 95.85 499 817 911 94 235.33 97.75 500 818 909 91 248.25 91.78 501 818 910 92 241.50 94.74 502 818 912 94 239.41 95.77 503 820 824 4 794.60 4.41 504 821 824 3 809.48 3.03 505 821 827 6 794.66 1.82 506 823 826 3 874.31 1.73 507 823 827 4 841.44 0.94 508 824 827 3 841.44 0.94 509 824 828 4 841.43 0.93 510 825 828 3 851.77 2.77 511 825 829 4 841.41 0.93 512 826 829 3 857.15 0.80 513 826 830 4 826.96 0.36 514 827 830 3 841.33 0.93 515 827 831 4 821.96 2.14 516 827 914 87 232.93 98.66 517 828 831 3 841.33 0.93 518 828 832 4 841.37 0.88 519 829 832 3 841.38 0.88 520 829 833 4 841.38 0.88 521 830 833 3 841.41 0.89 522 830 834 4 841.49 0.93 523 831 834 3 849.44 3.04 524 831 835 4 841.50 0.93 525 831 914 83 230.30 99.61 526 831 916 85 229.19 100.12 527 832 835 3 850.31 2.44 528 832 836 4 841.48 0.94 529 833 836 3 844.36 2.56 530 833 837 4 841.30 1.02 531 834 837 3 857.27 7.13 532 834 838 4 841.12 0.94 533 835 838 3 849.02 0.74 534 835 839 4 841.19 0.77 535 835 856 21 337.86 55.09 536 835 916 81 227.15 99.77 537 836 839 3 849.02 0.74 538 836 840 4 846.61 1.95 539 837 840 3 840.82 5.13 540 837 841 4 834.88 2.16 541 838 841 3 841.40 4.54 542 838 842 4 828.03 5.58 543 838 859 21 337.47 54.90 544 838 863 25 337.44 54.88 545 839 842 3 833.72 8.39 546 839 843 4 808.31 3.38 547 839 856 17 338.01 55.02 548 840 843 3 811.62 1.13 549 840 844 4 807.55 3.00 550 841 844 3 823.76 2.85 551 842 846 4 817.13 2.23 552 842 852 10 339.54 55.64 553 842 855 13 339.48 55.62 554 842 856 14 339.43 55.65 555 842 859 17 338.06 54.98 556 843 846 3 852.71 1.25 557 843 852 9 339.88 55.80 558 846 851 5 787.70 6.42 559 846 852 6 443.17 71.94 560 846 855 9 411.43 83.14 561 848 851 3 848.45 1.94 562 848 852 4 838.07 7.12 563 849 852 3 846.30 3.01 564 850 853 3 863.51 5.16 565 850 854 4 821.13 0.85 566 851 854 3 844.03 4.13 567 851 855 4 815.01 3.83 568 852 855 3 852.02 0.79 569 852 856 4 824.02 2.82 570 853 856 3 852.02 0.79 571 853 857 4 818.39 3.72 572 854 857 3 840.16 5.15 573 854 858 4 818.40 3.73 574 855 858 3 838.14 6.15 575 855 859 4 830.66 2.40 576 856 859 3 855.80 4.58 577 856 860 4 830.67 2.41 578 857 860 3 840.57 3.02 579 857 861 4 829.22 3.14 580 857 917 60 225.52 99.23 581 858 861 3 836.91 4.55 582 858 862 4 830.69 2.40 583 859 862 3 835.95 5.03 584 859 863 4 830.68 2.40 585 860 863 3 852.62 1.88 586 860 864 4 836.74 0.66 587 860 916 56 226.43 99.39 588 860 917 57 226.38 99.37 589 861 864 3 842.46 0.90 590 861 865 4 831.35 2.03 591 861 917 56 226.38 99.37 592 862 865 3 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