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 1 548 752 204 173.16 0.63 2 549 752 203 172.40 1.00 3 549 753 204 170.24 0.17 4 550 751 201 173.77 0.41 5 550 752 202 173.38 0.56 6 551 753 202 173.58 0.49 7 555 572 17 329.50 0.01 8 555 753 198 196.16 0.94 9 556 699 143 202.29 2.02 10 557 681 124 201.97 2.11 11 557 699 142 202.78 1.92 12 557 753 196 202.27 2.04 13 558 681 123 202.28 2.04 14 558 699 141 202.78 1.92 15 558 701 143 202.28 2.04 16 559 562 3 329.50 0.00 17 559 701 142 202.30 2.04 18 560 701 141 202.30 2.04 19 560 729 169 201.96 2.11 20 561 729 168 201.97 2.01 21 561 731 170 197.75 2.06 22 561 732 171 183.66 0.12 23 561 733 172 171.09 1.25 24 561 734 173 170.44 0.96 25 562 734 172 171.05 1.26 26 563 734 171 170.44 0.95 27 564 738 174 170.27 0.90 28 565 699 134 203.00 1.92 29 565 738 173 169.22 0.50 30 566 698 132 205.37 0.89 31 566 699 133 202.98 1.93 32 567 696 129 207.13 1.73 33 567 697 130 206.66 1.50 34 567 698 131 205.68 1.03 35 568 697 129 206.68 1.50 36 568 698 130 206.65 1.49 37 568 699 131 205.78 1.05 38 569 572 3 329.50 0.00 39 573 681 108 207.75 1.22 40 573 683 110 207.80 1.21 41 573 697 124 208.39 1.28 42 573 699 126 207.97 1.25 43 573 746 173 205.22 1.50 44 573 753 180 205.38 1.60 45 575 744 169 203.83 2.00 46 575 746 171 205.50 1.65 47 575 753 178 205.51 1.65 48 576 683 107 208.16 1.24 49 576 684 108 208.30 1.26 50 576 685 109 209.06 1.26 51 576 697 121 208.90 1.31 52 576 744 168 203.28 2.28 53 577 685 108 209.06 1.27 54 578 685 107 209.07 1.26 55 581 585 4 329.50 0.00 56 586 685 99 210.10 1.40 57 586 740 154 202.86 2.21 58 588 740 152 202.58 2.35 59 588 741 153 202.99 2.27 60 588 761 173 202.99 2.27 61 589 740 151 198.44 3.83 62 589 741 152 203.03 2.27 63 589 742 153 203.06 2.27 64 589 743 154 203.16 2.31 65 590 742 152 203.03 2.27 66 590 743 153 203.11 2.25 67 590 744 154 203.38 2.23 68 591 744 153 203.27 2.27 69 591 755 164 205.34 1.66 70 593 755 162 205.16 1.59 71 593 784 191 47.81 0.12 72 593 788 195 37.97 0.02 73 594 788 194 36.70 0.10 74 597 787 190 42.27 0.28 75 597 788 191 37.41 0.26 76 597 791 194 30.27 0.07 77 599 755 156 205.37 1.67 78 599 758 159 203.28 2.30 79 599 777 178 82.50 0.35 80 599 784 185 53.17 1.88 81 600 742 142 203.05 2.27 82 600 758 158 203.41 2.24 83 601 742 141 203.11 2.29 84 601 758 157 203.74 2.35 85 603 761 158 203.00 2.28 86 604 741 137 203.05 2.27 87 604 761 157 203.00 2.28 88 605 608 3 329.50 0.00 89 612 634 22 329.50 0.00 90 620 685 65 209.99 1.38 91 621 685 64 210.00 1.39 92 621 695 74 210.16 1.36 93 621 696 75 209.90 1.34 94 621 697 76 208.62 1.24 95 622 694 72 210.22 1.36 96 622 695 73 210.16 1.35 97 622 696 74 209.98 1.39 98 623 685 62 210.06 1.38 99 623 695 72 210.15 1.36 100 639 783 144 68.48 1.31 101 639 787 148 47.65 0.12 102 639 791 152 40.93 0.22 103 640 783 143 71.87 0.35 104 641 647 6 329.50 0.00 105 641 780 139 82.33 0.31 106 641 783 142 71.87 0.35 107 642 783 141 81.10 0.10 108 643 780 137 90.24 0.18 109 644 723 79 205.02 1.53 110 644 780 136 90.22 0.20 111 646 775 129 94.81 0.38 112 647 758 111 203.74 2.36 113 647 775 128 94.14 0.07 114 647 780 133 82.34 0.28 115 647 783 136 71.64 0.16 116 649 783 134 62.36 0.61 117 649 784 135 53.18 1.88 118 649 787 138 43.56 0.01 119 651 791 140 29.72 0.20 120 665 755 90 171.16 0.47 121 666 752 86 173.40 0.55 122 666 753 87 172.22 0.87 123 666 754 88 170.15 0.23 124 666 755 89 170.25 0.17 125 667 754 87 172.21 0.88 126 667 755 88 170.98 0.53 127 667 777 110 82.31 0.29 128 667 781 114 57.17 0.01 129 667 784 117 47.88 0.06 130 667 785 118 46.80 0.51 131 667 788 121 40.84 0.06 132 668 754 86 173.39 0.56 133 668 755 87 173.13 0.59 134 668 756 88 171.01 0.54 135 668 777 109 82.29 0.30 136 668 778 110 80.15 0.54 137 668 781 113 58.66 0.65 138 669 672 3 203.15 2.22 139 669 778 109 82.27 0.32 140 670 778 108 82.16 0.26 141 670 781 111 65.02 0.01 142 671 778 107 82.17 0.24 143 671 779 108 82.09 0.29 144 672 756 84 175.43 0.30 145 672 778 106 82.12 0.28 146 673 776 103 93.50 0.01 147 674 678 4 202.81 1.99 148 674 704 30 200.47 2.98 149 674 756 82 178.44 1.78 150 675 678 3 202.83 2.00 151 675 704 29 201.81 2.48 152 676 704 28 201.81 2.48 153 676 705 29 200.59 3.04 154 676 706 30 200.55 3.02 155 677 703 26 202.61 2.18 156 677 704 27 202.93 1.95 157 678 703 25 209.47 1.66 158 678 704 26 206.84 2.48 159 678 747 69 242.33 0.43 160 679 701 22 323.50 1.84 161 679 702 23 226.99 8.25 162 679 703 24 210.12 1.38 163 680 701 21 324.77 2.21 164 680 702 22 307.49 2.42 165 680 704 24 248.15 2.36 166 680 745 65 231.19 2.50 167 680 746 66 311.39 1.34 168 681 701 20 329.06 0.21 169 681 745 64 256.70 0.07 170 682 700 18 329.50 0.00 171 682 702 20 329.48 0.01 172 682 736 54 159.44 0.01 173 682 738 56 159.46 0.01 174 682 739 57 164.91 2.43 175 682 744 62 273.49 3.19 176 682 745 63 327.66 0.71 177 682 774 92 94.92 0.32 178 683 739 56 164.78 2.50 179 683 744 61 328.61 0.24 180 684 738 54 160.12 1.15 181 684 739 55 163.49 0.12 182 684 740 56 170.59 0.97 183 685 738 53 167.96 1.04 184 685 740 55 175.44 1.28 185 686 737 51 169.16 0.45 186 686 738 52 170.18 0.90 187 686 739 53 171.49 0.69 188 686 740 54 175.79 1.11 189 687 737 50 170.22 0.90 190 687 738 51 170.51 0.81 191 690 694 4 329.50 0.00 192 698 738 40 158.63 0.40 193 700 738 38 164.67 2.60 194 702 727 25 329.50 0.00 195 702 736 34 163.81 2.21 196 702 774 72 102.61 0.20 197 705 771 66 104.28 0.08 198 707 776 69 102.94 0.34 199 710 771 61 111.62 0.39 200 714 770 56 131.58 1.71 201 715 730 15 329.50 0.00 202 715 770 55 125.37 0.82 203 715 771 56 125.37 0.82 204 716 771 55 125.02 0.65 205 716 773 57 124.62 0.71 206 720 724 4 329.50 0.00 207 720 773 53 103.44 0.35 208 722 776 54 102.99 0.37 209 722 779 57 97.79 0.28 210 723 775 52 103.03 0.35 211 723 776 53 102.99 0.37 212 723 779 56 94.52 0.41 213 723 780 57 94.52 0.41 214 724 773 49 103.39 0.36 215 724 774 50 103.14 0.39 216 724 775 51 102.95 0.35 217 724 776 52 102.76 0.34 218 725 773 48 103.26 0.40 219 725 774 49 103.03 0.35 220 725 776 51 99.89 0.79 221 726 771 45 103.44 0.35 222 726 772 46 103.27 0.41 223 726 773 47 103.01 0.38 224 727 771 44 103.26 0.42 225 727 772 45 103.19 0.40 226 727 774 47 102.95 0.35 227 728 771 43 103.22 0.41 228 729 733 4 320.19 1.34 229 729 769 40 124.76 0.76 230 730 769 39 124.95 0.68 231 730 771 41 124.14 1.05 232 731 769 38 125.48 0.88 233 732 769 37 125.48 0.92 234 733 768 35 125.46 0.91 235 733 769 36 125.41 0.91 236 734 768 34 125.45 0.91 237 735 766 31 318.47 2.33 238 735 767 32 138.44 0.21 239 735 768 33 125.48 0.90 240 736 766 30 315.29 2.01 241 740 743 3 201.27 0.99 242 741 761 20 328.80 0.25 243 742 759 17 329.50 0.00 244 743 759 16 306.14 0.62 245 745 757 12 258.67 4.76 246 745 774 29 94.76 0.38 247 746 755 9 328.20 0.32 248 747 754 7 329.50 0.00 249 747 756 9 230.02 1.91 250 755 777 22 82.31 0.29 251 756 776 20 82.53 0.36 252 756 777 21 82.32 0.30 253 757 774 17 94.17 0.09 254 757 775 18 93.80 0.07 255 757 777 20 82.36 0.30 256 758 774 16 94.77 0.38 257 758 775 17 94.04 0.05 258 758 777 19 84.00 0.95 259 759 764 5 135.67 0.48 260 759 774 15 94.78 0.38 261 760 763 3 231.87 3.81 262 760 764 4 153.69 0.17 263 760 773 13 102.34 0.26 264 760 774 14 96.14 0.88 265 762 765 3 325.86 1.45 266 763 772 9 103.22 0.45 267 763 773 10 103.19 0.47 268 764 773 9 103.14 0.45 269 766 770 4 117.33 0.82 270 766 771 5 113.05 0.46 271 766 772 6 103.23 0.43 272 767 770 3 124.73 0.66 273 775 780 5 108.20 0.81 274 776 779 3 121.39 0.38 275 776 780 4 112.48 0.86 276 777 780 3 116.45 2.85 277 777 781 4 108.20 0.81 278 777 784 7 58.51 0.73 279 778 781 3 112.47 0.87 280 780 783 3 112.07 1.61 281 780 784 4 64.59 0.71 282 781 784 3 85.33 9.42 283 781 785 4 85.36 9.44 284 782 785 3 104.60 0.17 285 782 786 4 85.37 9.44 286 783 786 3 112.92 1.18 287 783 787 4 107.41 1.57 288 784 787 3 107.41 1.57 289 784 788 4 107.41 1.57 290 785 788 3 117.50 3.48 291 785 789 4 104.84 0.32 292 786 789 3 104.80 0.34 293 786 790 4 104.80 0.34 294 787 790 3 105.98 0.94 295 787 791 4 74.48 14.81 296 788 791 3 105.98 0.94