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 1 549 752 199 169.84 0.01 2 549 753 200 168.93 0.21 3 550 751 197 171.95 0.14 4 550 752 198 171.12 0.07 5 551 753 198 171.83 0.25 6 555 753 194 193.18 0.26 7 556 699 139 211.31 0.95 8 557 681 124 199.37 0.46 9 557 699 138 211.36 0.94 10 557 753 192 203.93 1.57 11 558 681 123 210.65 0.65 12 558 699 137 211.33 0.95 13 558 700 138 211.28 0.95 14 558 701 139 210.30 0.81 15 559 701 138 211.31 0.96 16 560 701 137 211.31 0.96 17 560 734 170 167.71 0.34 18 562 734 168 167.76 0.34 19 563 734 167 167.78 0.33 20 564 698 130 212.04 1.09 21 564 734 166 167.80 0.34 22 564 738 170 162.88 1.95 23 565 698 129 211.85 1.14 24 565 699 130 211.81 1.15 25 565 700 131 211.34 0.94 26 565 738 169 158.10 0.36 27 566 698 128 211.82 1.16 28 566 699 129 211.77 1.14 29 567 696 125 211.90 1.16 30 567 697 126 211.86 1.15 31 567 698 127 211.81 1.16 32 568 697 125 211.69 1.09 33 568 698 126 211.36 0.95 34 568 699 127 211.18 0.94 35 573 681 108 194.54 0.04 36 573 683 110 195.80 0.04 37 573 697 120 211.18 0.94 38 573 699 122 198.10 0.80 39 573 746 169 193.88 0.15 40 573 753 176 194.25 0.01 41 575 746 167 194.03 0.10 42 575 753 174 194.31 0.00 43 576 683 107 196.18 0.09 44 576 684 108 196.60 0.06 45 576 685 109 210.82 0.70 46 576 697 117 209.97 0.93 47 576 744 164 193.58 0.12 48 577 685 108 210.97 1.02 49 578 685 107 211.18 1.01 50 586 685 99 212.21 1.07 51 586 687 101 212.69 1.28 52 586 740 150 192.73 0.14 53 588 740 148 192.13 0.12 54 588 741 149 192.72 0.13 55 589 740 147 175.66 0.30 56 589 741 148 192.62 0.07 57 589 742 149 192.94 0.20 58 589 743 150 193.36 0.01 59 590 742 148 192.63 0.07 60 590 743 149 192.96 0.20 61 590 744 150 193.78 0.04 62 591 744 149 193.56 0.12 63 591 755 160 194.02 0.09 64 593 755 158 193.78 0.10 65 593 784 187 46.58 0.09 66 593 788 191 34.02 0.62 67 594 788 190 34.45 0.83 68 597 787 186 42.98 0.30 69 597 788 187 34.49 0.82 70 597 791 190 29.25 0.05 71 599 755 152 194.31 0.01 72 599 758 155 193.46 0.04 73 599 777 174 79.02 1.41 74 599 784 181 47.12 0.17 75 600 742 138 192.63 0.06 76 600 758 154 193.65 0.12 77 601 742 137 193.50 0.10 78 601 758 153 193.93 0.07 79 601 759 154 193.71 0.07 80 603 741 134 193.78 0.06 81 603 761 154 193.05 0.21 82 604 741 133 193.55 0.10 83 604 742 134 193.74 0.04 84 620 685 65 212.09 1.12 85 621 685 64 212.31 1.23 86 621 696 71 212.09 1.12 87 621 697 72 211.29 0.92 88 622 685 63 212.34 1.24 89 622 695 69 212.41 1.20 90 622 696 70 212.09 1.12 91 623 685 62 212.40 1.20 92 623 687 64 212.88 1.32 93 623 693 66 212.76 1.30 94 623 694 67 212.77 1.29 95 623 695 68 212.68 1.33 96 639 783 140 58.00 0.34 97 639 787 144 46.52 0.12 98 639 791 148 38.64 1.28 99 640 783 139 67.75 0.37 100 641 780 135 78.03 1.16 101 641 783 138 67.12 0.69 102 642 783 137 73.81 2.99 103 643 780 133 89.11 0.76 104 644 721 73 196.16 0.22 105 644 723 75 196.21 0.23 106 644 780 132 90.94 0.14 107 646 775 125 92.27 0.01 108 647 758 107 193.93 0.07 109 647 775 124 92.23 0.01 110 647 780 129 77.25 1.30 111 649 783 130 55.52 0.31 112 649 784 131 47.23 0.13 113 649 787 134 44.33 0.03 114 651 791 136 33.30 0.83 115 665 755 86 168.97 0.17 116 666 752 82 171.34 0.05 117 666 753 83 170.54 0.20 118 666 754 84 168.93 0.18 119 666 755 85 168.90 0.19 120 667 754 83 170.55 0.20 121 667 777 106 78.17 1.10 122 667 781 110 54.36 0.86 123 667 784 113 46.34 0.04 124 667 788 117 35.70 0.21 125 668 672 4 204.46 0.06 126 668 754 82 171.16 0.09 127 668 755 83 171.01 0.02 128 668 756 84 169.28 0.29 129 668 777 105 78.18 1.10 130 668 778 106 77.09 0.87 131 668 781 109 55.74 0.22 132 669 672 3 210.65 1.26 133 669 778 105 78.17 1.10 134 670 778 104 78.20 1.09 135 670 781 107 64.82 0.90 136 670 782 108 60.52 0.29 137 671 778 103 78.23 1.09 138 671 779 104 78.19 1.10 139 672 756 80 172.83 0.14 140 672 778 102 78.21 1.10 141 673 776 99 91.80 0.03 142 674 678 4 206.11 0.69 143 674 704 26 198.53 0.25 144 674 747 69 193.69 0.01 145 674 756 78 176.88 0.66 146 674 776 98 91.81 0.02 147 675 678 3 209.97 0.67 148 675 704 25 199.73 0.12 149 676 704 24 203.28 0.81 150 676 705 25 198.74 0.37 151 676 706 26 198.11 0.66 152 677 703 22 210.87 0.74 153 677 704 23 208.94 0.84 154 678 703 21 212.16 1.16 155 678 704 22 211.44 0.81 156 678 747 65 227.76 2.14 157 679 701 18 321.42 1.90 158 679 702 19 275.41 22.73 159 679 703 20 212.34 1.09 160 680 701 17 323.88 0.77 161 680 702 18 296.31 13.60 162 680 704 20 266.94 26.95 163 680 745 61 221.50 0.38 164 680 746 62 307.00 4.09 165 681 701 16 324.89 0.26 166 681 745 60 250.15 2.63 167 682 736 50 157.41 0.10 168 682 738 52 157.41 0.10 169 682 739 53 157.50 0.06 170 682 744 58 257.62 1.25 171 682 745 59 321.89 0.14 172 682 774 88 92.43 0.01 173 683 739 52 157.42 0.10 174 683 744 57 322.35 0.35 175 684 738 50 157.42 0.10 176 684 739 51 157.44 0.10 177 684 740 52 169.66 1.25 178 685 738 49 159.18 0.75 179 685 740 51 175.56 0.29 180 686 737 47 159.90 0.39 181 686 738 48 165.10 0.82 182 686 739 49 175.56 0.30 183 686 740 50 179.16 2.10 184 687 740 49 184.47 0.52 185 698 738 40 157.40 0.10 186 700 736 36 157.37 0.07 187 700 738 38 157.49 0.06 188 702 736 34 157.34 0.08 189 702 766 64 127.59 1.23 190 702 774 72 107.65 0.49 191 705 771 66 107.98 0.43 192 707 776 69 107.78 0.43 193 710 771 61 115.22 1.35 194 716 770 54 120.61 0.19 195 716 771 55 120.53 0.18 196 716 773 57 115.34 0.66 197 720 773 53 108.02 0.45 198 722 776 54 107.81 0.42 199 722 779 57 104.67 0.19 200 723 775 52 107.81 0.42 201 723 776 53 107.77 0.43 202 723 779 56 90.34 1.83 203 723 780 57 90.34 1.83 204 724 763 39 321.12 1.54 205 724 773 49 107.95 0.42 206 724 774 50 107.84 0.44 207 724 775 51 107.78 0.43 208 724 776 52 107.36 0.23 209 725 773 48 107.84 0.44 210 725 774 49 107.79 0.43 211 725 776 51 105.37 0.18 212 726 771 45 107.99 0.44 213 726 772 46 107.89 0.42 214 726 773 47 107.78 0.43 215 727 766 39 127.59 1.23 216 727 771 44 107.89 0.42 217 727 772 45 107.84 0.44 218 727 774 47 107.78 0.43 219 728 766 38 127.59 1.23 220 728 771 43 107.87 0.43 221 729 733 4 323.99 0.74 222 729 771 42 107.95 0.45 223 730 769 39 122.64 0.87 224 730 771 41 113.45 0.42 225 731 768 37 132.32 1.30 226 731 769 38 122.88 0.94 227 732 768 36 132.32 1.30 228 733 768 35 127.17 1.03 229 735 766 31 321.25 1.71 230 735 767 32 124.81 0.17 231 735 768 33 124.76 0.18 232 736 766 30 192.07 15.35 233 740 743 3 188.70 0.39 234 743 759 16 324.67 0.12 235 745 757 12 230.16 0.11 236 745 774 29 92.29 0.01 237 746 755 9 324.47 0.13 238 746 756 10 303.21 2.19 239 747 756 9 243.38 2.13 240 755 777 22 78.18 1.10 241 756 776 20 80.48 1.02 242 756 777 21 78.19 1.10 243 757 774 17 92.24 0.01 244 757 775 18 91.91 0.03 245 757 777 20 78.30 1.05 246 758 774 16 92.28 0.01 247 758 775 17 92.01 0.06 248 758 777 19 80.36 1.06 249 759 774 15 92.31 0.01 250 760 763 3 195.40 0.52 251 760 764 4 175.90 9.22 252 763 773 10 107.70 0.39 253 764 772 8 107.83 0.45 254 765 772 7 107.82 0.45 255 766 770 4 111.00 0.67 256 766 771 5 107.92 0.43 257 766 772 6 107.87 0.43 258 767 770 3 112.91 0.22 259 775 780 5 108.90 0.19 260 776 779 3 120.27 4.38 261 776 780 4 115.00 1.81 262 777 780 3 115.00 1.81 263 777 781 4 90.05 11.71 264 777 784 7 53.37 1.28 265 778 781 3 115.00 1.81 266 780 783 3 113.93 2.35 267 780 784 4 82.86 13.35 268 781 784 3 108.55 0.66 269 781 785 4 82.44 13.55 270 782 785 3 113.75 1.94 271 782 786 4 82.40 13.54 272 783 786 3 113.58 2.03 273 783 787 4 80.67 14.39 274 784 787 3 112.35 1.65 275 784 788 4 100.00 3.67 276 785 788 3 113.66 2.25 277 785 789 4 75.77 15.79 278 786 789 3 113.80 2.33 279 786 790 4 70.81 18.27 280 787 790 3 115.10 1.68 281 787 791 4 69.27 19.02 282 788 791 3 113.56 2.29