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 1 660 778 118 53.86 4.91 2 660 779 119 53.90 4.95 3 660 781 121 53.95 4.96 4 660 782 122 61.62 4.65 5 660 783 123 62.38 4.37 6 660 795 135 57.23 6.29 7 660 796 136 54.23 4.95 8 660 797 137 54.36 5.00 9 660 830 170 57.91 3.24 10 660 831 171 53.44 4.72 11 660 835 175 53.45 4.72 12 661 782 121 62.67 4.23 13 661 783 122 62.67 4.23 14 661 784 123 62.96 4.36 15 661 785 124 63.91 3.64 16 661 828 167 62.95 4.08 17 661 829 168 62.66 4.21 18 661 830 169 62.11 4.49 19 661 832 171 62.37 4.36 20 661 856 195 62.59 4.26 21 661 857 196 62.63 4.24 22 662 797 135 62.84 4.14 23 662 828 166 63.00 4.06 24 662 829 167 62.66 4.21 25 663 796 133 63.09 4.42 26 663 797 134 62.69 4.21 27 664 776 112 84.16 1.52 28 664 795 131 95.81 0.07 29 664 796 132 77.26 0.29 30 664 797 133 189.32 1.51 31 664 798 134 241.49 3.65 32 665 793 128 138.72 0.97 33 665 794 129 148.69 6.13 34 665 795 130 138.44 11.26 35 666 670 4 153.93 6.54 36 666 671 5 148.42 6.58 37 666 778 112 138.56 1.05 38 666 794 128 163.59 0.79 39 666 795 129 193.86 3.08 40 667 670 3 171.25 0.07 41 668 712 44 140.16 0.48 42 669 710 41 142.53 0.73 43 669 720 51 156.38 0.80 44 669 758 89 142.26 0.66 45 671 674 3 238.55 14.77 46 671 776 105 141.04 0.40 47 671 778 107 152.47 0.71 48 672 757 85 156.33 0.83 49 672 758 86 156.31 0.83 50 672 759 87 155.77 0.70 51 672 760 88 151.41 0.25 52 673 687 14 149.63 0.34 53 673 688 15 148.49 0.09 54 673 760 87 156.16 0.90 55 673 761 88 152.47 0.78 56 673 762 89 146.40 0.96 57 673 776 103 156.55 1.01 58 673 839 166 155.88 0.73 59 673 841 168 156.41 1.01 60 674 685 11 156.80 0.96 61 674 686 12 156.55 1.06 62 674 778 104 156.72 0.97 63 674 779 105 156.79 0.96 64 674 780 106 158.88 0.70 65 674 794 120 166.13 1.04 66 674 839 165 156.33 0.93 67 675 685 10 157.08 0.89 68 675 686 11 156.77 0.97 69 675 687 12 156.66 1.02 70 675 688 13 156.68 1.02 71 675 694 19 156.78 0.97 72 675 707 32 159.02 0.85 73 675 708 33 159.09 0.83 74 675 709 34 158.41 1.02 75 675 780 105 159.01 0.70 76 676 682 6 159.62 0.83 77 676 684 8 159.17 0.83 78 676 707 31 159.25 0.83 79 676 708 32 159.18 0.86 80 676 711 35 159.27 0.85 81 676 714 38 159.53 0.78 82 676 780 104 159.02 0.71 83 677 682 5 159.69 0.83 84 677 683 6 159.65 0.84 85 677 684 7 159.36 0.91 86 677 685 8 159.19 0.82 87 677 694 17 159.13 0.79 88 677 696 19 159.15 0.80 89 677 700 23 159.64 0.82 90 677 705 28 159.62 0.82 91 677 706 29 159.62 0.81 92 677 707 30 159.28 0.81 93 677 747 70 159.24 0.83 94 678 681 3 163.41 0.78 95 678 682 4 159.72 0.83 96 678 683 5 160.35 0.52 97 678 705 27 159.63 0.82 98 678 706 28 159.62 0.81 99 678 708 30 159.56 0.78 100 679 683 4 164.44 0.67 101 679 702 23 164.35 0.96 102 679 704 25 160.62 0.67 103 682 714 32 285.94 1.99 104 687 762 75 214.50 1.91 105 688 761 73 245.83 2.58 106 688 762 74 233.99 1.19 107 689 762 73 244.98 3.19 108 689 764 75 196.60 0.88 109 689 875 186 61.04 2.44 110 689 879 190 31.17 0.41 111 690 879 189 36.14 2.08 112 693 879 186 31.14 0.41 113 693 882 189 19.52 0.45 114 695 875 180 61.02 2.44 115 712 792 80 157.47 0.58 116 712 793 81 156.85 0.62 117 712 794 82 155.94 0.89 118 713 792 79 157.43 0.58 119 713 793 80 157.17 0.67 120 714 792 78 157.43 0.58 121 715 792 77 157.59 0.66 122 728 882 154 19.49 0.46 123 730 874 144 79.14 0.50 124 730 878 148 55.30 2.88 125 730 882 152 20.34 0.04 126 732 871 139 109.78 2.06 127 732 874 142 81.40 0.62 128 733 874 141 94.53 0.58 129 739 819 80 199.96 18.66 130 740 819 79 165.81 1.74 131 741 816 75 165.72 1.72 132 741 818 77 165.75 1.74 133 741 819 78 165.75 1.75 134 742 818 76 165.62 1.76 135 742 871 129 132.57 2.58 136 743 866 123 156.72 0.79 137 744 866 122 156.65 0.74 138 744 871 127 97.77 0.66 139 744 874 130 76.35 0.87 140 744 875 131 62.79 3.33 141 746 874 128 75.19 0.29 142 746 875 129 61.02 2.44 143 746 878 132 47.95 0.80 144 748 882 134 18.07 0.24 145 762 846 84 286.07 1.56 146 763 845 82 277.26 5.58 147 763 846 83 257.93 3.38 148 764 845 81 236.83 3.33 149 764 846 82 195.67 2.38 150 764 868 104 246.89 3.38 151 764 872 108 78.30 1.08 152 764 875 111 61.19 2.50 153 764 876 112 61.03 2.44 154 765 845 80 193.83 2.77 155 765 846 81 172.74 1.56 156 765 847 82 166.99 4.36 157 765 868 103 286.24 1.58 158 765 869 104 115.06 3.31 159 765 872 107 78.52 1.19 160 767 847 80 158.13 0.55 161 768 847 79 157.07 0.43 162 769 773 4 168.13 0.38 163 769 801 32 138.71 0.98 164 769 847 78 157.77 0.47 165 770 773 3 179.33 0.11 166 770 801 31 139.11 0.98 167 771 801 30 139.11 0.98 168 771 802 31 139.13 0.99 169 771 803 32 139.16 0.97 170 772 800 28 139.11 0.98 171 772 801 29 139.15 0.98 172 773 800 27 139.22 0.96 173 773 801 28 139.24 0.96 174 774 798 24 139.15 0.99 175 774 799 25 139.21 0.96 176 774 800 26 139.22 0.96 177 775 798 23 139.20 0.96 178 775 799 24 139.21 0.96 179 775 801 26 147.85 0.12 180 776 796 20 138.76 1.16 181 776 797 21 139.08 1.01 182 776 798 22 139.13 0.99 183 777 796 19 137.89 1.39 184 777 797 20 138.65 1.01 185 777 799 22 139.35 0.91 186 777 822 45 159.47 0.81 187 777 865 88 158.09 0.52 188 778 794 16 139.32 0.92 189 778 795 17 139.08 1.01 190 778 796 18 138.56 1.05 191 779 794 15 139.28 0.94 192 779 795 16 139.10 0.99 193 780 790 10 157.59 1.31 194 780 791 11 156.59 1.05 195 780 792 12 156.52 1.05 196 780 793 13 151.80 0.32 197 780 794 14 139.28 0.94 198 781 790 9 158.12 1.08 199 781 791 10 157.61 1.30 200 781 833 52 285.91 1.70 201 781 835 54 285.85 1.03 202 782 787 5 159.69 0.84 203 782 788 6 159.02 0.70 204 782 789 7 158.88 0.76 205 782 790 8 158.13 1.07 206 782 832 50 208.69 3.83 207 782 833 51 278.00 2.10 208 783 789 6 159.01 0.70 209 783 791 8 158.81 0.74 210 783 795 12 139.25 0.96 211 784 787 3 168.56 0.32 212 784 788 4 159.58 0.84 213 784 789 5 159.47 0.79 214 785 856 71 157.04 1.24 215 785 857 72 157.03 1.23 216 785 858 73 157.00 1.21 217 790 833 43 158.86 0.75 218 791 795 4 167.05 2.70 219 797 829 32 139.12 1.01 220 797 830 33 138.59 1.07 221 798 824 26 139.25 0.95 222 799 823 24 138.94 1.07 223 799 824 25 139.25 0.95 224 800 822 22 183.53 3.02 225 800 823 23 139.21 0.96 226 800 824 24 143.09 0.62 227 801 820 19 213.34 3.15 228 801 821 20 198.96 4.32 229 801 822 21 183.53 3.02 230 801 842 41 149.02 0.70 231 802 821 19 204.40 7.02 232 802 822 20 198.95 4.32 233 802 823 21 198.95 4.32 234 802 825 23 183.62 3.00 235 802 862 60 155.50 0.56 236 806 825 19 270.06 9.19 237 810 860 50 158.16 0.51 238 810 861 51 158.15 0.52 239 810 862 52 158.15 0.52 240 811 852 41 165.12 1.56 241 811 853 42 162.77 0.77 242 811 854 43 162.74 0.78 243 811 861 50 158.18 0.51 244 811 862 51 158.18 0.51 245 811 864 53 157.10 0.80 246 814 852 38 165.66 1.71 247 815 852 37 165.71 1.73 248 815 864 49 158.12 0.54 249 817 867 50 157.44 0.73 250 817 870 53 156.36 0.88 251 818 866 48 157.46 0.73 252 818 867 49 157.05 0.84 253 818 870 52 155.08 1.06 254 818 871 53 152.93 0.43 255 819 852 33 165.83 1.79 256 819 864 45 157.85 0.69 257 819 865 46 157.23 0.83 258 819 867 48 156.84 0.86 259 820 840 20 159.33 0.82 260 820 847 27 158.68 1.12 261 820 848 28 158.72 1.11 262 820 864 44 157.84 0.68 263 820 865 45 157.16 0.83 264 820 866 46 156.97 0.92 265 820 867 47 156.78 0.88 266 821 862 41 157.93 0.67 267 821 863 42 157.84 0.68 268 821 864 43 156.87 0.86 269 822 862 40 157.94 0.67 270 822 863 41 157.84 0.68 271 822 865 43 157.12 1.00 272 824 829 5 258.29 9.16 273 825 859 34 159.72 0.89 274 825 860 35 159.55 0.83 275 825 862 37 158.53 1.04 276 826 859 33 159.72 0.89 277 827 857 30 163.06 0.58 278 827 858 31 162.29 0.24 279 827 859 32 159.74 0.88 280 828 857 29 165.38 1.75 281 829 857 28 180.40 5.78 282 830 857 27 248.84 16.30 283 830 863 33 156.75 0.99 284 831 865 34 156.59 0.88 285 840 865 25 158.14 0.54 286 846 868 22 120.50 0.60 287 847 866 19 158.16 0.55 288 847 867 20 156.36 0.87 289 847 868 21 120.48 0.59 290 847 869 22 109.88 2.04 291 848 865 17 158.13 0.54 292 848 866 18 157.36 0.47 293 848 868 20 113.01 1.57 294 849 865 16 157.58 0.58 295 849 866 17 156.38 0.86 296 849 868 19 113.16 1.50 297 850 865 15 157.25 0.52 298 851 864 13 158.09 0.53 299 851 865 14 157.55 0.38 300 851 866 15 157.24 0.51 301 852 863 11 158.11 0.52 302 852 864 12 157.93 0.46 303 853 864 11 157.87 0.42 304 854 861 7 179.50 0.69 305 858 861 3 285.27 1.04 306 868 872 4 286.26 0.49 307 868 875 7 61.65 2.75 308 869 872 3 81.56 0.24 309 871 874 3 72.75 1.64 310 871 875 4 62.77 3.31 311 872 875 3 62.79 3.31 312 872 876 4 62.76 3.31 313 873 876 3 67.20 5.50 314 873 877 4 61.16 2.52 315 874 877 3 62.84 2.52 316 874 878 4 60.27 2.71 317 875 878 3 62.84 2.52 318 875 879 4 40.76 4.38 319 876 879 3 42.86 3.35 320 876 880 4 31.20 0.40 321 877 880 3 44.15 6.08 322 877 881 4 31.19 0.39 323 878 881 3 44.73 5.79 324 878 882 4 28.87 0.24 325 879 882 3 23.43 2.25