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 1 697 702 5 764.58 1.88 2 697 703 6 757.38 1.46 3 698 703 5 757.65 1.58 4 699 703 4 813.25 1.59 5 700 703 3 876.50 3.17 6 701 815 114 97.86 1.11 7 701 816 115 88.89 0.84 8 701 817 116 88.89 0.84 9 702 705 3 849.16 0.55 10 702 817 115 98.00 1.05 11 704 707 3 866.41 3.86 12 704 708 4 866.40 3.86 13 704 716 12 113.73 1.56 14 704 717 13 113.87 1.62 15 705 708 3 866.41 3.86 16 705 716 11 232.19 60.78 17 705 798 93 113.43 1.58 18 705 817 112 113.55 1.55 19 705 818 113 113.51 1.54 20 705 819 114 108.05 0.57 21 705 821 116 111.92 1.76 22 706 709 3 875.76 0.82 23 706 936 230 67.34 0.45 24 706 937 231 67.31 0.45 25 707 711 4 864.14 1.13 26 708 711 3 864.14 1.13 27 708 712 4 827.40 0.66 28 708 713 5 824.86 0.61 29 708 714 6 772.07 1.52 30 708 715 7 757.44 1.02 31 708 716 8 753.99 2.52 32 708 726 18 114.02 1.69 33 708 819 111 113.73 1.58 34 708 824 116 113.50 1.58 35 709 821 112 113.67 1.60 36 709 823 114 113.43 1.59 37 709 824 115 113.47 1.56 38 709 872 163 70.25 1.68 39 709 933 224 71.38 1.12 40 709 937 228 69.02 1.04 41 710 868 158 70.11 1.62 42 710 871 161 70.20 1.67 43 710 872 162 70.21 1.66 44 710 937 227 69.41 1.09 45 711 714 3 1058.18 0.07 46 711 824 113 113.70 1.60 47 712 726 14 117.44 0.08 48 712 728 16 113.94 1.66 49 712 730 18 113.87 1.62 50 712 824 112 113.70 1.60 51 713 726 13 117.70 0.06 52 713 727 14 114.11 1.66 53 713 728 15 114.09 1.66 54 714 725 11 128.53 0.05 55 714 726 12 128.44 0.03 56 715 718 3 929.37 1.34 57 715 723 8 251.72 61.43 58 715 724 9 128.81 0.01 59 715 725 10 128.53 0.05 60 716 724 8 128.89 0.01 61 716 726 10 128.67 0.09 62 716 816 100 128.88 0.01 63 716 817 101 128.81 0.01 64 716 818 102 128.73 0.05 65 716 819 103 128.52 0.06 66 717 723 6 374.18 0.20 67 717 724 7 128.90 0.01 68 717 814 97 478.67 7.21 69 717 816 99 128.89 0.01 70 718 722 4 791.10 1.27 71 718 723 5 251.73 61.42 72 718 744 26 575.10 0.54 73 719 722 3 843.50 2.81 74 719 744 25 575.18 0.54 75 719 814 95 503.54 0.57 76 720 744 24 575.18 0.54 77 721 743 22 575.18 0.54 78 721 744 23 575.18 0.53 79 721 745 24 575.18 0.54 80 721 749 28 574.62 0.71 81 721 805 84 574.06 0.52 82 721 807 86 574.11 0.52 83 721 812 91 573.44 0.41 84 722 741 19 576.26 0.28 85 722 742 20 575.75 0.29 86 722 744 22 575.21 0.54 87 722 749 27 575.15 0.54 88 722 752 30 574.22 0.58 89 722 803 81 572.32 0.56 90 722 805 83 574.15 0.54 91 723 740 17 576.45 0.33 92 723 741 18 576.40 0.34 93 723 742 19 575.91 0.23 94 723 744 21 575.93 0.24 95 724 739 15 576.57 0.32 96 724 740 16 576.44 0.33 97 724 741 17 576.40 0.34 98 724 801 77 573.02 0.23 99 724 803 79 574.15 0.54 100 724 816 92 572.64 0.68 101 725 739 14 576.65 0.28 102 725 740 15 576.58 0.31 103 726 737 11 577.04 0.29 104 726 738 12 577.00 0.30 105 726 739 13 576.90 0.30 106 726 818 92 572.63 0.68 107 726 819 93 565.57 0.83 108 727 737 10 577.07 0.29 109 727 738 11 577.01 0.29 110 727 740 13 577.00 0.30 111 728 736 8 577.18 0.26 112 728 737 9 577.08 0.29 113 729 735 6 577.24 0.25 114 729 736 7 577.20 0.27 115 730 734 4 751.24 1.30 116 730 735 5 577.23 0.26 117 730 789 59 578.21 0.64 118 730 824 94 541.62 1.79 119 730 825 95 541.29 1.91 120 731 734 3 842.65 2.64 121 732 825 93 541.75 1.74 122 732 894 162 301.84 0.53 123 733 790 57 669.53 0.18 124 733 791 58 669.32 0.10 125 733 825 92 541.76 1.73 126 733 894 161 301.70 0.43 127 733 895 162 302.06 0.49 128 733 896 163 303.18 0.97 129 734 789 55 669.96 0.11 130 734 790 56 669.61 0.21 131 734 825 91 541.69 1.77 132 735 788 53 670.43 0.02 133 735 789 54 670.13 0.03 134 736 786 50 670.89 0.07 135 736 787 51 670.64 0.06 136 736 788 52 670.44 0.02 137 736 789 53 670.43 0.02 138 737 786 49 671.03 0.12 139 737 787 50 670.68 0.06 140 737 789 52 670.67 0.06 141 737 818 81 573.47 0.53 142 737 819 82 573.35 0.50 143 737 820 83 568.11 2.10 144 738 784 46 671.59 0.24 145 738 785 47 671.50 0.24 146 738 786 48 671.03 0.12 147 739 784 45 671.84 0.19 148 739 785 46 671.55 0.26 149 739 787 48 671.21 0.10 150 739 801 62 669.96 0.12 151 739 818 79 572.63 0.68 152 740 782 42 672.17 0.16 153 740 783 43 672.08 0.12 154 740 784 44 671.86 0.20 155 741 752 11 669.84 0.10 156 741 754 13 670.28 0.01 157 741 782 41 672.20 0.16 158 741 783 42 672.11 0.13 159 741 785 44 672.12 0.14 160 741 801 60 670.50 0.01 161 741 803 62 670.07 0.06 162 742 781 39 673.15 0.54 163 742 782 40 672.20 0.16 164 743 747 4 879.70 10.58 165 743 748 5 780.78 8.96 166 743 749 6 716.58 19.16 167 743 777 34 673.43 0.51 168 743 778 35 683.67 2.90 169 743 779 36 683.66 2.89 170 743 780 37 680.86 4.29 171 743 781 38 673.35 0.55 172 745 749 4 889.06 7.34 173 745 779 34 738.90 1.37 174 745 780 35 737.19 1.28 175 745 807 62 669.56 0.18 176 746 779 33 742.28 0.28 177 747 779 32 745.66 0.69 178 747 807 60 670.08 0.08 179 748 776 28 746.07 0.63 180 748 777 29 745.95 0.64 181 748 778 30 745.88 0.62 182 748 779 31 745.86 0.60 183 749 752 3 892.39 0.21 184 749 775 26 746.08 0.63 185 749 776 27 746.09 0.62 186 749 777 28 746.08 0.64 187 749 805 56 670.29 0.00 188 749 806 57 670.23 0.01 189 749 807 58 669.54 0.17 190 750 775 25 746.10 0.63 191 750 776 26 746.11 0.64 192 750 805 55 670.32 0.01 193 750 806 56 670.24 0.00 194 751 775 24 746.11 0.64 195 751 804 53 670.61 0.01 196 751 805 54 670.32 0.01 197 751 806 55 670.29 0.01 198 752 775 23 746.14 0.62 199 752 777 25 746.41 0.77 200 752 803 51 670.73 0.04 201 752 804 52 670.61 0.04 202 752 805 53 670.29 0.01 203 753 802 49 671.50 0.22 204 753 803 50 670.74 0.03 205 753 804 51 670.65 0.04 206 754 773 19 746.62 0.69 207 754 785 31 746.59 0.70 208 754 801 47 671.60 0.18 209 754 802 48 671.50 0.23 210 754 803 49 670.74 0.04 211 755 800 45 671.88 0.19 212 755 801 46 671.75 0.16 213 755 802 47 671.59 0.18 214 756 768 12 746.33 0.77 215 756 770 14 746.70 0.65 216 756 787 31 746.60 0.69 217 756 800 44 671.88 0.19 218 756 801 45 671.85 0.19 219 756 818 62 575.51 0.68 220 757 799 42 671.93 0.19 221 757 800 43 671.91 0.19 222 757 802 45 671.86 0.20 223 758 762 4 839.64 5.06 224 758 763 5 792.62 1.33 225 758 768 10 748.24 0.66 226 758 799 41 671.93 0.19 227 759 762 3 848.13 0.82 228 759 763 4 844.81 2.48 229 760 763 3 857.95 2.12 230 760 764 4 855.98 3.11 231 761 764 3 858.21 2.00 232 761 765 4 849.69 0.03 233 762 765 3 853.60 1.95 234 762 766 4 841.55 4.01 235 762 795 33 736.22 2.75 236 762 797 35 672.08 0.17 237 762 798 36 672.07 0.17 238 762 799 37 672.01 0.18 239 763 766 3 842.73 3.43 240 764 792 28 746.66 0.67 241 765 791 26 746.78 0.67 242 765 792 27 746.66 0.67 243 765 793 28 746.54 0.62 244 765 794 29 746.44 0.57 245 765 795 30 743.33 0.39 246 766 789 23 747.06 0.64 247 766 790 24 746.93 0.61 248 766 791 25 746.77 0.67 249 766 792 26 746.74 0.68 250 766 795 29 740.97 0.88 251 766 799 33 671.49 0.03 252 766 820 54 573.91 0.57 253 766 825 59 562.27 0.91 254 767 789 22 747.12 0.67 255 767 790 23 746.96 0.63 256 767 792 25 746.81 0.68 257 768 787 19 747.50 0.67 258 768 788 20 747.22 0.67 259 768 789 21 747.13 0.66 260 768 799 31 671.15 0.11 261 768 820 52 573.63 0.64 262 769 787 18 747.52 0.66 263 769 788 19 747.37 0.63 264 770 785 15 747.60 0.65 265 770 786 16 747.56 0.66 266 770 787 17 747.52 0.66 267 773 783 10 747.80 0.66 268 773 785 12 747.69 0.65 269 777 781 4 810.89 7.03 270 777 783 6 748.08 0.67 271 778 781 3 850.98 5.92 272 789 820 31 573.36 0.52 273 789 825 36 541.77 1.73 274 790 896 106 303.21 0.97 275 791 795 4 870.52 0.96 276 791 825 34 545.47 0.01 277 791 895 104 302.69 0.80 278 791 896 105 303.34 1.03 279 792 895 103 303.19 0.97 280 792 896 104 303.34 1.03 281 792 897 105 304.04 0.77 282 793 895 102 303.47 0.98 283 793 897 104 304.06 0.78 284 794 822 28 573.84 0.58 285 794 895 101 305.35 0.96 286 794 923 129 183.75 4.22 287 794 925 131 159.09 1.14 288 794 926 132 115.08 22.57 289 795 820 25 575.06 0.50 290 795 821 26 574.21 0.60 291 795 822 27 573.61 0.46 292 795 825 30 573.49 0.40 293 795 929 134 93.12 11.72 294 796 929 133 71.59 1.22 295 798 817 19 575.68 0.73 296 798 818 20 575.66 0.72 297 799 817 18 575.95 0.59 298 799 818 19 575.59 0.71 299 799 820 21 574.88 0.42 300 800 815 15 576.21 0.57 301 800 816 16 576.16 0.55 302 800 817 17 575.63 0.73 303 801 815 14 576.24 0.55 304 801 816 15 576.12 0.53 305 801 818 17 575.50 0.68 306 802 813 11 576.49 0.65 307 802 814 12 576.25 0.56 308 802 815 13 576.20 0.57 309 803 813 10 576.49 0.66 310 803 814 11 576.28 0.58 311 803 816 13 576.22 0.57 312 804 812 8 576.52 0.67 313 804 813 9 576.48 0.67 314 805 811 6 576.55 0.68 315 805 812 7 576.50 0.69 316 806 810 4 576.59 0.70 317 807 810 3 832.64 1.12 318 807 812 5 576.52 0.69 319 820 825 5 856.09 1.67 320 821 824 3 871.52 2.18 321 821 825 4 865.34 0.91 322 821 929 108 71.80 1.18 323 821 933 112 71.58 1.22 324 822 825 3 880.20 2.18 325 822 893 71 302.57 0.74 326 822 926 104 72.97 0.58 327 822 929 107 71.89 1.16 328 822 930 108 71.78 1.18 329 822 933 111 71.68 1.23 330 823 826 3 861.96 1.27 331 823 872 49 271.52 3.58 332 823 893 70 303.10 0.77 333 823 930 107 71.84 1.15 334 823 933 110 71.87 1.16 335 825 893 68 306.75 0.66 336 825 894 69 306.76 0.67 337 826 872 46 305.13 0.63 338 826 873 47 304.04 0.33 339 826 874 48 305.73 0.61 340 826 891 65 306.69 0.68 341 826 892 66 306.78 0.68 342 826 893 67 306.79 0.68 343 826 902 76 306.75 0.66 344 826 930 104 174.47 4.56 345 827 891 64 306.79 0.68 346 827 892 65 306.80 0.68 347 827 894 67 306.99 0.62 348 828 873 45 306.80 0.69 349 828 874 46 306.78 0.68 350 828 875 47 306.77 0.69 351 828 891 63 306.80 0.68 352 829 875 46 306.88 0.69 353 829 877 48 306.93 0.66 354 829 890 61 306.87 0.69 355 829 891 62 306.88 0.69 356 829 892 63 307.00 0.62 357 830 875 45 306.94 0.66 358 830 877 47 306.93 0.66 359 831 835 4 842.27 0.50 360 831 836 5 841.95 0.34 361 831 839 8 819.98 0.50 362 831 877 46 307.06 0.65 363 831 890 59 307.05 0.64 364 832 835 3 853.90 2.64 365 832 836 4 842.00 0.33 366 833 836 3 845.35 1.03 367 833 837 4 843.73 0.54 368 833 879 46 307.14 0.65 369 833 880 47 307.05 0.66 370 834 837 3 870.95 3.14 371 834 838 4 844.04 0.38 372 835 838 3 863.02 7.11 373 835 839 4 843.74 0.53 374 836 839 3 853.56 2.38 375 836 840 4 842.01 0.33 376 836 877 41 308.12 0.62 377 836 880 44 308.07 0.66 378 836 888 52 308.12 0.62 379 836 889 53 308.12 0.62 380 836 890 54 308.12 0.62 381 836 903 67 308.13 0.62 382 837 840 3 844.93 0.96 383 837 841 4 835.50 2.85 384 837 880 43 308.06 0.65 385 838 841 3 868.73 5.04 386 838 842 4 844.94 0.95 387 839 842 3 854.47 3.56 388 839 903 64 308.16 0.61 389 840 843 3 884.89 1.84 390 840 903 63 308.16 0.61 391 840 904 64 308.16 0.61 392 840 905 65 308.16 0.61 393 840 918 78 227.70 2.94 394 840 920 80 222.53 4.17 395 843 846 3 933.50 4.08 396 843 848 5 797.47 4.64 397 843 849 6 567.90 55.77 398 843 920 77 227.66 2.93 399 843 921 78 227.57 2.90 400 845 848 3 855.40 1.42 401 846 849 3 853.31 7.40 402 847 924 77 225.71 2.38 403 848 920 72 244.05 1.75 404 848 921 73 234.77 6.37 405 848 922 74 233.54 5.81 406 848 923 75 227.63 2.95 407 848 924 76 214.86 1.90 408 848 927 79 201.84 0.83 409 849 918 69 278.38 1.25 410 849 919 70 257.91 0.07 411 849 920 71 246.02 0.76 412 850 918 68 278.38 1.25 413 850 919 69 264.96 2.33 414 850 927 77 201.39 1.04 415 850 928 78 201.38 1.03 416 850 931 81 199.87 0.60 417 851 916 65 289.31 3.20 418 851 917 66 289.00 3.17 419 851 918 67 278.39 1.25 420 852 916 64 290.93 2.40 421 852 917 65 289.23 3.23 422 852 931 79 200.96 0.93 423 852 935 83 196.91 0.74 424 853 914 61 293.81 3.00 425 853 915 62 293.69 2.98 426 853 916 63 290.93 2.40 427 854 914 60 293.77 2.98 428 854 915 61 293.72 2.99 429 854 917 63 293.67 2.98 430 854 935 81 197.09 0.68 431 854 938 84 193.11 0.76 432 855 913 58 307.61 0.65 433 855 914 59 293.68 2.98 434 856 860 4 830.68 0.86 435 856 913 57 304.35 2.29 436 856 914 58 304.25 2.30 437 856 915 59 304.20 2.28 438 856 938 82 192.94 0.69 439 857 936 79 197.03 0.68 440 857 938 81 192.97 0.70 441 858 937 79 195.75 0.30 442 858 938 80 192.87 0.70 443 860 908 48 308.69 0.63 444 860 909 49 308.69 0.63 445 860 910 50 308.54 0.62 446 860 913 53 304.55 2.50 447 860 914 54 304.19 2.33 448 860 915 55 304.17 2.33 449 861 864 3 835.19 0.70 450 861 865 4 825.14 4.33 451 862 865 3 843.02 4.62 452 862 866 4 826.26 3.77 453 863 866 3 842.70 0.80 454 863 867 4 834.72 0.49 455 864 867 3 838.38 0.96 456 864 868 4 833.47 1.12 457 865 868 3 847.89 6.08 458 865 869 4 837.27 0.78 459 865 887 22 309.56 0.84 460 865 906 41 309.51 0.85 461 865 938 73 183.47 0.24 462 866 869 3 851.49 5.44 463 866 870 4 837.27 0.78 464 866 876 10 352.97 6.13 465 866 887 21 309.55 0.84 466 867 870 3 838.13 3.08 467 867 871 4 824.32 3.56 468 868 871 3 841.54 1.30 469 868 872 4 824.32 3.55 470 868 937 69 183.48 0.24 471 868 938 70 183.47 0.23 472 869 872 3 824.31 3.54 473 869 873 4 824.31 3.54 474 869 876 7 402.62 18.59 475 869 887 18 309.64 0.94 476 869 906 37 309.81 1.02 477 869 938 69 183.47 0.24 478 870 873 3 840.84 1.55 479 870 876 6 427.46 6.16 480 872 930 58 197.80 1.08 481 872 933 61 192.53 0.87 482 872 934 62 192.32 0.87 483 874 889 15 337.70 1.35 484 874 890 16 337.70 1.35 485 874 891 17 337.70 1.36 486 874 904 30 337.70 1.35 487 875 889 14 337.72 1.35 488 875 890 15 338.66 0.92 489 876 887 11 337.72 1.35 490 876 888 12 337.72 1.35 491 877 880 3 883.91 3.42 492 877 888 11 339.03 0.70 493 877 890 13 339.67 0.77 494 880 888 8 340.07 0.67 495 881 886 5 409.32 8.22 496 881 888 7 340.19 0.69 497 881 905 24 340.13 0.65 498 883 886 3 858.61 8.46 499 885 908 23 340.29 0.66 500 886 906 20 340.51 0.67 501 886 907 21 340.37 0.68 502 886 908 22 340.31 0.65 503 887 905 18 340.62 0.72 504 887 906 19 340.53 0.68 505 887 908 21 340.51 0.68 506 888 904 16 342.89 0.21 507 888 905 17 340.76 0.65 508 889 903 14 344.81 1.15 509 889 904 15 343.35 0.42 510 890 902 12 346.86 0.54 511 890 903 13 346.06 0.53 512 891 901 10 360.07 3.16 513 891 902 11 348.04 0.01 514 892 899 7 398.03 1.86 515 892 900 8 370.06 1.80 516 892 901 9 360.07 3.16 517 893 899 6 398.06 1.85 518 893 900 7 370.08 1.80 519 893 902 9 370.06 1.81 520 893 926 33 198.97 0.07 521 893 930 37 192.45 1.09 522 894 899 5 403.98 4.80 523 895 898 3 850.72 0.93 524 895 899 4 804.36 0.99 525 895 900 5 800.47 2.94 526 900 921 21 201.24 0.95 527 900 922 22 201.15 0.94 528 900 923 23 201.10 0.93 529 900 926 26 200.87 0.95 530 901 921 20 201.25 0.95 531 901 922 21 201.18 0.93 532 902 920 18 201.41 0.98 533 902 921 19 201.24 0.95 534 902 926 24 200.97 0.91 535 902 930 28 199.33 0.35 536 903 919 16 209.12 1.22 537 903 920 17 201.38 0.97 538 904 917 13 285.84 27.38 539 904 918 14 219.18 3.95 540 904 919 15 211.37 0.09 541 904 934 30 193.05 0.72 542 905 916 11 343.64 1.25 543 905 917 12 285.88 27.41 544 905 918 13 225.59 2.46 545 906 915 9 346.45 2.63 546 906 916 10 343.66 1.25 547 906 917 11 285.87 27.41 548 906 938 32 183.81 0.06 549 907 915 8 346.78 2.47 550 907 916 9 343.66 1.25 551 908 914 6 373.07 0.05 552 908 915 7 358.48 2.66 553 909 912 3 844.74 6.46 554 909 913 4 780.34 0.52 555 909 914 5 396.44 7.15 556 910 913 3 814.00 3.85 557 915 938 23 192.29 0.50 558 917 931 14 199.36 0.35 559 917 934 17 196.08 0.21 560 917 935 18 192.88 0.75 561 919 927 8 283.21 40.20 562 919 930 11 199.88 0.58 563 919 931 12 198.44 0.74 564 921 926 5 797.41 6.21 565 921 927 6 413.60 4.91 566 921 930 9 418.48 2.47 567 923 926 3 846.23 4.79 568 923 927 4 833.37 0.70 569 924 927 3 840.89 3.06 570 924 928 4 840.89 3.06 571 925 928 3 840.90 3.06 572 925 929 4 840.89 3.06 573 926 929 3 855.59 0.95 574 926 930 4 842.60 4.33 575 927 930 3 859.48 3.04 576 927 931 4 830.75 0.90 577 928 931 3 852.51 6.53 578 928 932 4 833.80 0.07 579 929 932 3 856.80 3.15 580 929 933 4 833.80 0.07 581 930 933 3 840.20 1.39 582 930 934 4 836.03 2.06 583 931 934 3 855.54 5.05 584 931 935 4 836.40 4.52 585 932 935 3 851.50 3.02 586 932 936 4 846.73 0.62 587 933 936 3 859.34 3.10 588 933 937 4 859.34 3.10 589 934 937 3 867.37 0.91 590 934 938 4 866.46 0.46 591 935 938 3 875.71 3.27