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 1 773 821 48 60.08 1.93 2 774 777 3 241.69 1.25 3 774 778 4 230.87 0.94 4 775 778 3 232.59 1.67 5 775 779 4 227.98 0.53 6 776 779 3 231.57 1.44 7 776 780 4 231.60 1.45 8 777 780 3 241.43 0.72 9 777 781 4 249.52 0.03 10 777 812 35 94.06 2.27 11 777 814 37 83.34 1.31 12 777 817 40 82.55 1.72 13 778 781 3 249.52 0.03 14 778 782 4 244.91 2.27 15 778 814 36 92.59 3.00 16 778 817 39 82.87 1.61 17 778 821 43 78.44 0.25 18 778 822 44 76.72 0.61 19 778 825 47 76.67 0.60 20 779 782 3 252.09 1.31 21 779 783 4 253.39 0.66 22 779 825 46 76.73 0.62 23 780 783 3 270.56 1.79 24 780 784 4 254.06 0.99 25 780 812 32 94.23 2.27 26 781 784 3 250.25 0.41 27 781 785 4 241.81 0.72 28 781 808 27 98.67 0.50 29 781 814 33 94.14 2.31 30 782 785 3 247.14 1.95 31 782 786 4 240.16 0.10 32 782 825 43 78.52 1.20 33 782 829 47 76.70 0.61 34 782 834 52 55.13 1.17 35 783 786 3 240.05 0.06 36 783 787 4 237.44 1.35 37 784 787 3 237.72 1.50 38 784 788 4 233.40 0.63 39 784 808 24 101.14 0.03 40 784 809 25 101.19 0.04 41 784 812 28 101.19 0.05 42 785 788 3 249.03 0.06 43 785 789 4 233.62 3.54 44 785 800 15 100.67 0.10 45 785 804 19 100.56 0.15 46 785 822 37 93.17 2.81 47 785 825 40 92.25 3.07 48 785 826 41 78.67 1.18 49 786 789 3 238.88 0.91 50 786 790 4 229.14 2.69 51 786 834 48 56.45 1.81 52 786 845 59 37.03 0.27 53 787 790 3 229.68 3.06 54 787 791 4 221.45 2.54 55 788 791 3 231.59 3.40 56 788 792 4 216.49 0.35 57 788 795 7 159.31 2.42 58 788 800 12 122.88 1.61 59 788 803 15 109.62 4.09 60 788 804 16 103.95 1.28 61 789 793 4 204.31 4.32 62 789 794 5 179.48 4.42 63 789 795 6 158.50 2.81 64 789 800 11 134.77 2.04 65 789 835 46 57.25 1.42 66 789 843 54 42.73 1.05 67 789 845 56 40.40 0.12 68 790 845 55 40.42 0.12 69 792 795 3 296.02 1.49 70 794 838 44 48.80 1.99 71 794 842 48 42.91 0.98 72 794 843 49 42.74 1.06 73 794 844 50 42.31 1.05 74 795 799 4 234.04 0.71 75 795 800 5 226.65 2.08 76 795 803 8 222.52 1.64 77 795 842 47 42.76 1.06 78 795 843 48 42.73 1.05 79 796 799 3 243.88 1.47 80 796 800 4 236.16 0.35 81 796 841 45 42.95 1.16 82 796 842 46 42.55 1.17 83 797 800 3 238.91 1.02 84 797 801 4 236.94 0.04 85 797 819 22 99.09 0.30 86 797 822 25 98.98 0.35 87 797 823 26 98.93 0.33 88 797 826 29 98.81 0.33 89 797 843 46 42.58 1.19 90 798 801 3 236.94 0.04 91 798 802 4 238.62 0.89 92 799 802 3 238.62 0.89 93 799 803 4 235.59 2.40 94 800 803 3 240.60 0.10 95 800 804 4 233.90 1.46 96 800 822 22 98.96 0.34 97 800 826 26 98.80 0.33 98 800 843 43 42.59 1.12 99 801 804 3 240.61 0.10 100 801 805 4 238.91 1.05 101 801 814 13 106.92 1.86 102 801 817 16 100.88 0.12 103 801 818 17 100.16 0.43 104 801 819 18 99.28 0.18 105 801 822 21 98.96 0.34 106 802 805 3 240.94 0.04 107 802 806 4 240.94 0.04 108 803 806 3 251.59 0.45 109 803 807 4 237.18 1.91 110 804 807 3 240.92 0.04 111 804 808 4 228.86 0.83 112 804 814 10 113.90 1.62 113 804 822 18 98.95 0.33 114 805 814 9 106.89 1.88 115 808 812 4 233.84 0.77 116 808 813 5 218.59 5.32 117 808 814 6 167.35 5.67 118 809 812 3 243.71 1.19 119 809 813 4 233.84 0.77 120 810 813 3 232.13 0.07 121 810 815 5 205.38 5.70 122 814 817 3 220.75 3.45 123 814 822 8 193.83 6.85 124 817 821 4 223.50 3.79 125 817 822 5 222.85 3.46 126 818 821 3 238.18 2.02 127 818 822 4 226.54 2.27 128 819 822 3 229.97 0.58 129 819 823 4 225.94 1.97 130 820 823 3 231.18 0.04 131 820 824 4 230.41 0.35 132 821 824 3 241.47 0.49 133 821 825 4 232.40 0.67 134 822 825 3 242.48 0.53 135 822 826 4 237.38 3.07 136 823 826 3 242.48 0.53 137 823 827 4 230.66 0.29 138 824 827 3 242.92 0.74 139 824 828 4 232.41 0.59 140 825 828 3 235.13 0.76 141 825 829 4 232.44 0.58 142 826 829 3 238.14 0.35 143 826 830 4 232.43 0.58 144 826 835 9 130.44 1.07 145 826 843 17 42.62 1.20 146 827 830 3 239.22 2.81 147 827 831 4 229.39 2.09 148 827 843 16 78.11 16.41 149 828 831 3 228.31 1.49 150 828 832 4 228.30 1.49 151 829 832 3 238.39 3.23 152 829 834 5 165.47 0.45 153 829 835 6 132.88 0.14 154 830 835 5 132.88 0.14 155 833 846 13 78.12 16.40 156 834 845 11 80.26 16.88 157 834 846 12 78.13 16.40 158 835 843 8 115.95 2.60 159 835 844 9 111.12 1.97 160 835 845 10 80.07 17.35 161 835 846 11 79.68 17.16 162 836 843 7 124.58 1.71 163 836 844 8 111.37 2.08 164 836 846 10 80.73 17.02 165 837 841 4 231.47 0.07 166 837 842 5 141.75 0.77 167 837 843 6 124.58 1.71 168 838 841 3 250.11 1.51 169 838 842 4 148.75 2.12 170 838 844 6 130.68 1.07