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 1 550 751 201 179.91 0.07 2 550 752 202 175.58 1.96 3 551 753 202 179.78 0.14 4 555 753 198 204.80 0.55 5 556 699 143 216.91 3.68 6 557 681 124 209.40 0.01 7 557 699 142 217.36 3.87 8 557 753 196 209.29 0.05 9 558 681 123 209.65 0.04 10 558 699 141 217.12 3.75 11 558 700 142 215.69 3.06 12 558 701 143 209.63 0.04 13 559 701 142 215.70 3.06 14 560 701 141 215.71 3.06 15 561 729 168 208.36 0.14 16 561 732 171 194.19 0.81 17 561 733 172 180.01 0.12 18 561 734 173 179.97 0.14 19 562 734 172 180.00 0.15 20 563 734 171 179.97 0.14 21 564 698 134 224.31 0.55 22 564 738 174 176.66 1.76 23 565 699 134 220.11 2.53 24 565 738 173 176.28 1.64 25 566 698 132 220.24 2.46 26 566 699 133 220.11 2.53 27 567 689 122 220.69 2.43 28 567 692 125 220.74 2.42 29 567 693 126 220.64 2.39 30 567 696 129 220.65 2.38 31 567 697 130 220.53 2.35 32 567 698 131 220.49 2.34 33 568 697 129 224.50 0.34 34 568 698 130 220.47 2.33 35 568 699 131 220.46 2.33 36 573 681 108 222.53 0.79 37 573 683 110 222.97 0.57 38 573 697 124 224.58 0.04 39 573 699 126 224.00 0.07 40 573 746 173 218.20 0.82 41 573 753 180 218.43 0.96 42 575 744 169 217.66 0.71 43 575 746 171 218.77 0.99 44 575 753 178 218.78 0.98 45 576 683 107 223.55 0.31 46 576 684 108 224.34 0.23 47 576 685 109 224.72 0.28 48 576 697 121 224.68 0.23 49 576 744 168 217.59 0.59 50 578 685 107 224.75 0.28 51 586 685 99 225.29 0.07 52 586 740 154 216.77 0.92 53 588 740 152 216.68 0.89 54 588 741 153 216.84 0.91 55 588 761 173 216.78 0.92 56 589 740 151 197.56 6.76 57 589 741 152 217.19 0.73 58 589 742 153 217.24 0.72 59 589 743 154 217.45 0.62 60 590 742 152 217.19 0.73 61 590 743 153 217.45 0.63 62 590 744 154 217.79 0.67 63 591 744 153 217.78 0.68 64 591 755 164 218.00 0.70 65 593 755 162 217.83 0.66 66 593 784 191 51.93 0.08 67 593 788 195 40.99 0.66 68 594 788 194 40.98 0.66 69 597 787 190 49.23 0.70 70 597 788 191 41.77 0.28 71 597 791 194 32.80 1.61 72 599 755 156 218.12 0.77 73 599 758 159 217.52 0.56 74 599 777 178 84.52 0.40 75 599 784 185 53.17 0.54 76 600 742 142 217.22 0.71 77 600 758 158 217.78 0.68 78 601 741 140 217.45 0.62 79 601 742 141 217.46 0.62 80 601 758 157 217.89 0.69 81 601 759 158 217.81 0.67 82 603 761 158 217.09 0.67 83 604 741 137 217.47 0.64 84 604 742 138 217.61 0.64 85 604 761 157 216.74 0.84 86 620 685 65 225.25 0.07 87 621 685 64 225.37 0.01 88 621 695 74 225.44 0.01 89 621 696 75 225.22 0.03 90 621 697 76 225.12 0.01 91 622 694 72 225.58 0.00 92 622 695 73 225.44 0.01 93 622 696 74 225.22 0.03 94 623 685 62 225.41 0.01 95 623 695 72 225.47 0.00 96 639 783 144 72.10 0.27 97 639 787 148 51.64 0.09 98 639 791 152 43.12 0.55 99 640 783 143 73.36 0.57 100 641 780 139 83.95 0.58 101 641 783 142 72.33 0.17 102 642 783 141 83.40 0.78 103 643 780 137 95.21 0.92 104 644 721 77 218.83 1.73 105 644 723 79 218.82 1.73 106 644 780 136 96.27 0.39 107 646 721 75 219.08 1.60 108 646 775 129 102.03 0.32 109 647 758 111 217.88 0.68 110 647 775 128 100.33 1.17 111 647 780 133 83.91 0.56 112 647 783 136 73.22 0.48 113 648 783 135 72.11 0.27 114 649 783 134 66.25 0.42 115 649 784 135 59.22 0.05 116 649 787 138 51.25 0.05 117 649 788 139 49.22 0.70 118 651 791 140 39.00 0.09 119 665 755 90 169.75 0.96 120 666 752 86 174.28 2.62 121 666 753 87 172.85 2.52 122 666 754 88 167.82 1.26 123 666 755 89 167.82 1.27 124 667 754 87 172.40 2.13 125 667 755 88 168.95 1.25 126 667 777 110 83.88 0.56 127 667 781 114 65.66 0.14 128 667 784 117 51.92 0.08 129 668 672 4 209.95 0.26 130 668 754 86 174.27 2.62 131 668 755 87 173.66 2.31 132 668 756 88 172.26 2.20 133 668 777 109 83.94 0.55 134 668 778 110 83.02 0.40 135 668 781 113 66.25 0.42 136 669 672 3 216.27 0.70 137 669 778 109 83.92 0.55 138 670 778 108 83.94 0.54 139 670 781 111 74.21 0.97 140 670 782 112 70.00 1.51 141 671 778 107 83.98 0.56 142 671 779 108 83.92 0.54 143 672 756 84 181.85 0.66 144 672 778 106 83.91 0.54 145 673 776 103 99.95 1.15 146 674 678 4 210.03 0.30 147 674 704 30 207.69 0.78 148 674 756 82 182.59 1.02 149 674 776 102 100.08 1.08 150 675 678 3 216.12 0.46 151 675 704 29 208.81 0.27 152 676 704 28 207.97 0.68 153 676 705 29 207.80 0.74 154 676 706 30 207.78 0.74 155 677 703 26 217.31 3.92 156 677 704 27 217.28 3.93 157 678 703 25 222.16 1.53 158 678 704 26 218.53 3.32 159 678 747 69 244.69 0.47 160 679 701 22 324.57 2.54 161 679 703 24 224.29 0.46 162 680 702 22 318.96 5.34 163 680 704 24 229.12 0.76 164 680 745 65 233.11 2.52 165 680 746 66 317.85 1.57 166 681 745 64 258.82 2.93 167 682 736 54 175.21 2.16 168 682 738 56 175.19 2.15 169 682 739 57 175.19 2.16 170 682 744 62 259.43 2.81 171 682 774 92 100.91 1.40 172 683 739 56 175.19 2.15 173 684 738 54 174.99 2.12 174 684 739 55 175.24 2.02 175 684 740 56 179.93 0.11 176 685 738 53 176.25 1.62 177 685 740 55 180.00 0.15 178 686 737 51 176.27 1.63 179 686 738 52 176.29 1.64 180 686 740 54 180.20 0.06 181 687 737 50 176.41 1.69 182 687 738 51 176.46 1.69 183 698 738 40 174.98 2.09 184 699 738 39 175.02 2.07 185 700 736 36 175.18 2.17 186 700 738 38 175.20 2.16 187 702 736 34 174.99 2.07 188 702 766 64 144.18 0.28 189 702 774 72 113.58 0.24 190 705 771 66 115.18 0.09 191 707 776 69 110.60 1.28 192 710 771 61 127.68 1.66 193 714 769 55 146.22 1.24 194 714 770 56 146.22 1.24 195 715 769 54 143.28 0.10 196 715 770 55 143.03 0.11 197 716 770 54 140.63 0.78 198 716 771 55 140.63 0.78 199 716 773 57 133.68 0.03 200 720 773 53 115.14 0.08 201 722 776 54 110.14 1.57 202 722 779 57 100.19 1.14 203 723 775 52 109.68 0.18 204 723 776 53 102.00 0.48 205 723 779 56 91.45 0.92 206 723 780 57 91.44 0.91 207 724 773 49 114.81 0.18 208 724 774 50 110.98 1.17 209 724 775 51 103.00 0.03 210 724 776 52 101.31 0.68 211 725 773 48 113.77 0.38 212 725 774 49 110.23 1.52 213 725 776 51 101.23 0.71 214 726 771 45 115.20 0.09 215 726 772 46 115.14 0.08 216 727 766 39 144.34 0.33 217 727 771 44 115.16 0.08 218 727 772 45 115.12 0.07 219 727 774 47 110.81 1.24 220 728 766 38 144.31 0.35 221 728 771 43 115.15 0.08 222 729 768 39 143.46 0.07 223 729 769 40 143.34 0.04 224 730 769 39 143.35 0.07 225 730 771 41 137.34 0.09 226 731 769 38 144.14 0.29 227 732 768 36 144.34 0.36 228 733 768 35 144.13 0.26 229 734 768 34 144.92 0.11 230 735 766 31 325.85 1.06 231 735 767 32 145.30 0.83 232 735 768 33 145.29 0.83 233 736 766 30 284.76 2.00 234 737 767 30 294.24 0.97 235 740 743 3 211.85 0.79 236 741 761 20 329.73 1.20 237 745 757 12 246.62 2.35 238 745 774 29 100.34 1.17 239 747 756 9 237.36 0.32 240 755 777 22 83.90 0.57 241 756 776 20 86.65 0.66 242 756 777 21 83.90 0.57 243 757 774 17 100.34 1.17 244 757 775 18 99.86 1.02 245 757 777 20 84.00 0.58 246 758 774 16 100.34 1.17 247 758 775 17 100.17 1.15 248 758 777 19 86.64 0.67 249 759 764 5 147.33 0.67 250 759 774 15 100.35 1.17 251 760 763 3 220.94 1.34 252 760 764 4 173.92 2.63 253 760 773 13 112.99 0.12 254 760 774 14 103.63 0.29 255 763 772 9 115.17 0.09 256 763 773 10 115.13 0.08 257 764 772 8 115.14 0.08 258 764 773 9 115.13 0.08 259 764 774 10 114.94 0.17 260 765 772 7 115.16 0.09 261 766 770 4 123.48 3.77 262 766 771 5 115.21 0.09 263 766 772 6 115.16 0.08 264 767 770 3 124.76 3.13 265 767 771 4 115.56 0.12 266 775 780 5 100.28 7.71 267 776 779 3 119.95 0.64 268 776 780 4 115.98 0.19 269 777 780 3 101.92 6.89 270 777 781 4 100.03 7.58 271 777 784 7 66.27 0.42 272 778 781 3 116.27 0.04 273 780 783 3 115.78 0.28 274 780 784 4 91.72 12.30 275 781 784 3 116.09 0.12 276 781 785 4 91.72 12.30 277 782 785 3 93.72 10.86 278 782 786 4 90.34 12.54 279 783 786 3 90.61 14.01 280 783 787 4 115.65 0.12 281 784 787 3 117.25 0.69 282 784 788 4 117.56 0.53 283 785 788 3 117.58 0.53 284 785 789 4 117.56 0.53 285 786 789 3 83.17 16.68 286 786 790 4 80.52 18.00 287 787 790 3 80.40 18.06 288 787 791 4 42.82 0.72 289 788 791 3 121.23 2.49