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 1 549 753 204 167.06 0.57 2 550 751 201 169.41 0.09 3 550 752 202 168.62 0.04 4 551 753 202 169.13 0.14 5 555 753 198 200.76 1.75 6 556 699 143 203.99 0.52 7 557 681 124 203.81 0.55 8 557 699 142 206.18 1.59 9 557 748 191 203.91 0.50 10 557 753 196 203.87 0.52 11 558 681 123 203.93 0.51 12 558 699 141 206.19 1.58 13 558 701 143 203.91 0.51 14 559 701 142 203.99 0.49 15 560 701 141 203.99 0.49 16 560 729 169 203.44 0.67 17 564 692 128 212.81 0.18 18 565 692 127 212.81 0.18 19 565 699 134 210.38 0.47 20 565 700 135 206.22 1.56 21 566 692 126 212.77 0.17 22 566 698 132 210.49 0.42 23 566 699 133 210.36 0.46 24 567 692 125 212.73 0.18 25 567 693 126 212.05 0.06 26 567 696 129 211.65 0.07 27 567 697 130 211.50 0.10 28 567 698 131 210.49 0.29 29 568 697 129 211.25 0.04 30 568 698 130 210.54 0.24 31 568 699 131 210.46 0.20 32 573 681 108 209.62 0.26 33 573 683 110 209.83 0.20 34 573 697 124 211.02 0.14 35 573 699 126 209.84 0.21 36 573 746 173 208.25 0.27 37 573 753 180 208.27 0.29 38 575 744 169 207.88 0.22 39 575 746 171 208.36 0.23 40 575 753 178 208.48 0.29 41 576 683 107 209.90 0.17 42 576 684 108 210.50 0.25 43 576 685 109 211.19 0.06 44 576 697 121 211.18 0.06 45 576 744 168 207.88 0.22 46 577 685 108 211.22 0.07 47 578 685 107 211.21 0.07 48 586 685 99 211.67 0.09 49 586 740 154 205.24 0.93 50 588 740 152 205.16 0.94 51 588 741 153 206.03 0.52 52 589 740 151 191.12 7.08 53 589 741 152 206.85 0.63 54 589 742 153 207.56 0.32 55 589 743 154 207.73 0.24 56 590 742 152 207.23 0.46 57 590 743 153 207.62 0.34 58 590 744 154 207.97 0.21 59 591 744 153 207.88 0.22 60 591 755 164 208.19 0.24 61 593 755 162 208.17 0.29 62 593 784 191 45.11 0.77 63 593 788 195 27.49 0.91 64 594 788 194 27.46 0.89 65 597 787 190 39.48 0.55 66 597 788 191 30.29 0.15 67 597 791 194 24.05 1.24 68 599 755 156 208.32 0.19 69 599 758 159 207.86 0.26 70 599 777 178 76.48 0.18 71 599 783 184 58.40 0.35 72 599 784 185 49.98 1.05 73 600 742 142 207.28 0.50 74 600 758 158 207.94 0.21 75 601 741 140 207.81 0.24 76 601 742 141 207.62 0.34 77 601 758 157 208.02 0.23 78 601 759 158 207.95 0.21 79 601 760 159 206.59 0.49 80 603 741 138 207.91 0.20 81 604 741 137 207.81 0.21 82 604 742 138 207.90 0.20 83 620 685 65 211.41 0.08 84 621 685 64 211.61 0.06 85 621 696 75 211.40 0.07 86 621 697 76 211.02 0.02 87 622 685 63 211.76 0.04 88 622 695 73 211.79 0.06 89 622 696 74 211.52 0.07 90 623 685 62 211.78 0.05 91 623 695 72 211.79 0.06 92 639 783 144 63.19 0.18 93 639 787 148 44.38 0.42 94 639 791 152 35.44 0.12 95 640 783 143 68.32 2.00 96 641 780 139 75.10 0.15 97 641 783 142 67.97 1.84 98 642 783 141 70.69 1.01 99 643 780 137 88.27 1.42 100 644 721 77 209.22 0.88 101 644 723 79 209.22 0.88 102 644 724 80 209.22 0.88 103 644 780 136 88.28 1.42 104 646 775 129 94.28 0.53 105 647 758 111 208.04 0.22 106 647 775 128 94.17 0.48 107 647 780 133 74.88 0.04 108 647 783 136 68.01 1.83 109 648 783 135 63.41 0.29 110 649 783 134 59.38 0.17 111 649 784 135 51.06 0.67 112 649 787 138 43.96 0.48 113 649 788 139 39.62 0.48 114 651 791 140 24.80 0.93 115 665 746 81 167.24 0.48 116 665 755 90 167.08 0.57 117 666 752 86 168.63 0.04 118 666 753 87 168.36 0.07 119 666 754 88 166.79 0.43 120 666 755 89 166.79 0.42 121 667 754 87 168.36 0.07 122 667 755 88 167.24 0.48 123 667 777 110 75.17 0.20 124 667 781 114 55.30 0.99 125 667 784 117 44.97 0.33 126 668 672 4 199.09 1.66 127 668 754 86 168.64 0.03 128 668 755 87 168.41 0.09 129 668 756 88 168.28 0.04 130 668 777 109 75.52 0.35 131 668 778 110 73.34 0.49 132 668 781 113 57.92 0.20 133 669 672 3 203.99 0.45 134 669 778 109 75.18 0.22 135 670 778 108 75.18 0.23 136 670 781 111 63.25 0.39 137 670 782 112 59.76 0.57 138 671 778 107 75.14 0.24 139 671 779 108 75.12 0.25 140 672 756 84 172.37 1.23 141 672 778 106 75.15 0.25 142 673 776 103 89.12 0.14 143 674 678 4 204.19 0.69 144 674 680 6 204.03 0.62 145 674 704 30 203.63 0.82 146 674 725 51 196.28 0.73 147 674 747 73 203.31 0.75 148 674 756 82 178.51 0.47 149 674 776 102 86.06 1.67 150 675 678 3 204.68 0.47 151 675 704 29 203.87 0.84 152 676 704 28 203.87 0.85 153 676 705 29 203.77 0.88 154 676 706 30 203.72 0.91 155 676 709 33 207.84 1.16 156 677 703 26 208.57 1.39 157 677 704 27 208.47 1.43 158 678 703 25 211.74 0.14 159 678 704 26 209.03 1.45 160 678 747 69 227.02 0.28 161 679 702 23 316.96 0.27 162 679 703 24 233.84 10.91 163 680 702 22 318.19 0.33 164 680 704 24 310.42 3.54 165 680 745 65 223.74 2.00 166 680 746 66 314.60 2.03 167 681 745 64 255.71 0.10 168 682 738 56 145.07 0.62 169 682 739 57 145.77 0.29 170 682 744 62 250.21 2.85 171 682 745 63 315.50 1.46 172 682 759 77 194.00 0.70 173 682 774 92 94.27 0.53 174 683 739 56 145.05 0.64 175 684 739 55 145.05 0.63 176 684 740 56 169.53 0.42 177 685 740 55 169.68 0.36 178 686 739 53 169.63 0.36 179 686 740 54 173.06 1.91 180 687 761 74 277.08 16.54 181 700 738 38 145.07 0.62 182 702 738 36 152.61 2.50 183 702 774 72 97.08 0.72 184 705 771 66 99.67 0.34 185 707 776 69 97.09 0.71 186 710 771 61 104.01 1.17 187 715 769 54 119.89 0.99 188 715 770 55 117.28 0.73 189 715 771 56 117.98 0.39 190 716 770 54 118.27 0.29 191 716 771 55 118.17 0.29 192 716 773 57 110.00 1.02 193 720 773 53 99.67 0.34 194 722 776 54 97.12 0.73 195 722 779 57 93.79 0.64 196 723 775 52 97.11 0.73 197 723 776 53 97.00 0.76 198 723 779 56 87.12 0.71 199 723 780 57 87.00 0.78 200 724 763 39 223.19 7.88 201 724 773 49 99.61 0.32 202 724 774 50 97.75 0.42 203 724 775 51 97.08 0.72 204 724 776 52 96.89 0.78 205 725 773 48 98.22 0.36 206 725 774 49 97.09 0.72 207 725 776 51 94.20 0.51 208 726 771 45 99.69 0.34 209 726 772 46 99.64 0.33 210 726 773 47 98.00 0.27 211 727 771 44 99.67 0.34 212 727 772 45 99.61 0.32 213 727 774 47 97.09 0.71 214 728 771 43 99.64 0.33 215 729 733 4 318.69 0.52 216 730 769 39 116.64 0.48 217 730 771 41 101.02 0.33 218 731 768 37 129.98 1.75 219 731 769 38 117.59 0.51 220 732 768 36 130.97 1.33 221 733 768 35 130.50 1.56 222 734 766 32 166.83 1.01 223 734 767 33 165.03 0.92 224 734 768 34 139.40 1.67 225 735 766 31 305.16 1.48 226 735 767 32 147.00 0.79 227 735 768 33 145.91 1.33 228 736 766 30 314.36 2.15 229 740 743 3 196.53 1.91 230 741 761 20 266.73 2.70 231 743 759 16 272.50 2.15 232 745 757 12 239.12 1.66 233 745 774 29 94.23 0.51 234 746 755 9 291.75 1.90 235 746 756 10 281.42 2.25 236 747 756 9 229.38 0.10 237 755 777 22 75.20 0.20 238 756 776 20 76.48 0.18 239 756 777 21 75.80 0.10 240 757 774 17 94.12 0.47 241 757 775 18 93.86 0.57 242 757 777 20 76.39 0.19 243 758 774 16 94.25 0.52 244 758 775 17 93.86 0.57 245 758 777 19 76.84 0.01 246 759 774 15 94.28 0.53 247 760 763 3 318.70 0.36 248 760 775 15 94.28 0.53 249 761 764 3 318.09 0.09 250 761 765 4 303.69 1.43 251 763 773 10 99.72 0.36 252 763 774 11 99.71 0.36 253 763 775 12 99.71 0.36 254 764 772 8 99.77 0.38 255 764 773 9 99.73 0.36 256 765 772 7 99.75 0.37 257 766 770 4 114.35 0.70 258 766 771 5 100.83 0.88 259 766 772 6 99.76 0.38 260 767 770 3 117.34 0.78 261 775 780 5 105.95 0.28 262 776 779 3 117.01 1.04 263 776 780 4 115.30 0.18 264 777 780 3 115.30 0.18 265 777 781 4 105.59 2.41 266 777 784 7 57.87 0.20 267 778 781 3 116.97 0.17 268 780 783 3 108.26 3.60 269 780 784 4 102.19 0.91 270 781 784 3 103.25 1.09 271 781 785 4 102.28 0.96 272 782 785 3 106.62 1.21 273 782 786 4 101.75 1.22 274 783 786 3 105.29 2.06 275 783 787 4 101.89 1.16 276 784 787 3 107.98 1.29 277 784 788 4 102.67 0.76 278 785 788 3 105.45 0.59 279 785 789 4 105.44 0.59 280 786 789 3 123.50 2.64 281 786 790 4 105.45 0.59 282 787 791 4 65.45 17.07