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 1 803 830 27 39.74 0.24 2 803 875 72 35.68 0.04 3 803 876 73 37.79 1.02 4 803 877 74 39.18 0.48 5 803 880 77 37.81 1.02 6 803 881 78 37.77 1.01 7 803 882 79 33.66 0.45 8 804 826 22 41.84 0.50 9 804 827 23 41.81 0.52 10 804 875 71 37.81 1.01 11 804 882 78 37.77 1.01 12 805 826 21 45.05 0.67 13 805 875 70 38.98 0.42 14 805 882 77 37.81 1.01 15 805 883 78 37.80 1.01 16 805 885 80 35.44 0.09 17 806 809 3 319.62 2.12 18 806 823 17 64.05 0.24 19 806 824 18 62.34 0.61 20 806 826 20 46.20 0.10 21 806 833 27 39.73 0.24 22 806 873 67 37.79 1.00 23 806 875 69 39.77 0.25 24 807 823 16 65.39 0.36 25 807 824 17 64.09 0.24 26 808 823 15 65.39 0.36 27 808 824 16 65.38 0.36 28 809 821 12 193.41 7.90 29 809 822 13 141.34 33.80 30 809 823 14 67.78 0.53 31 809 873 64 67.49 0.70 32 809 885 76 40.32 0.20 33 809 887 78 39.08 0.43 34 810 821 11 197.24 9.80 35 810 822 12 141.44 33.81 36 811 814 3 332.94 2.56 37 811 819 8 210.21 4.20 38 811 820 9 197.82 9.87 39 811 821 10 197.35 9.83 40 811 871 60 75.48 0.84 41 811 889 78 38.97 0.41 42 812 819 7 216.86 0.93 43 812 820 8 210.21 4.21 44 812 822 10 197.84 9.87 45 813 819 6 219.53 2.27 46 813 820 7 216.86 0.94 47 814 818 4 258.85 0.46 48 814 819 5 219.53 2.26 49 814 889 75 40.45 0.18 50 814 890 76 40.31 0.21 51 814 891 77 39.08 0.45 52 815 818 3 274.19 1.27 53 815 891 76 39.62 0.32 54 816 864 48 140.75 0.01 55 816 865 49 139.56 0.03 56 816 891 75 39.80 0.27 57 817 861 44 141.44 0.26 58 817 862 45 141.27 0.18 59 817 863 46 140.85 0.01 60 817 865 48 140.74 0.02 61 818 860 42 141.50 0.26 62 818 861 43 141.44 0.26 63 818 863 45 141.28 0.18 64 819 859 40 141.84 0.28 65 819 860 41 141.71 0.31 66 819 863 44 141.53 0.24 67 819 889 70 40.43 0.17 68 820 857 37 142.98 0.53 69 820 858 38 142.18 0.18 70 820 859 39 141.84 0.28 71 821 835 14 151.82 5.58 72 821 857 36 142.99 0.52 73 821 858 37 142.20 0.18 74 821 860 39 142.17 0.17 75 821 871 50 141.19 0.14 76 821 873 52 140.53 0.09 77 821 889 68 39.27 0.40 78 822 856 34 143.31 0.65 79 822 857 35 143.00 0.52 80 823 833 10 211.22 1.28 81 823 835 12 167.44 2.07 82 823 851 28 162.85 0.21 83 823 855 32 143.77 0.51 84 823 856 33 143.38 0.64 85 823 857 34 143.37 0.65 86 823 858 35 143.38 0.65 87 823 873 50 141.21 0.15 88 825 830 5 272.71 0.58 89 825 853 28 162.99 0.07 90 826 830 4 292.06 0.96 91 826 833 7 246.91 1.58 92 826 875 49 141.19 0.17 93 828 877 49 141.45 0.30 94 829 877 48 141.45 0.30 95 830 833 3 360.56 1.76 96 830 853 23 187.16 1.46 97 830 875 45 141.55 0.33 98 830 876 46 141.50 0.31 99 830 877 47 141.44 0.31 100 831 852 21 187.32 1.53 101 831 853 22 187.21 1.47 102 831 876 45 141.53 0.32 103 831 877 46 141.44 0.31 104 831 878 47 141.44 0.31 105 832 851 19 188.53 0.93 106 832 852 20 187.33 1.53 107 832 853 21 187.21 1.47 108 832 875 43 141.57 0.34 109 832 876 44 141.51 0.33 110 833 850 17 193.58 0.74 111 833 851 18 192.42 1.00 112 833 873 40 141.66 0.33 113 833 874 41 141.62 0.34 114 833 875 42 141.56 0.35 115 834 848 14 195.81 0.16 116 834 849 15 195.53 0.12 117 834 850 16 193.43 0.82 118 834 873 39 141.66 0.34 119 834 874 40 141.65 0.34 120 834 876 42 141.53 0.35 121 835 848 13 195.84 0.14 122 835 849 14 195.71 0.20 123 835 851 16 195.41 0.06 124 835 858 23 186.90 1.60 125 835 871 36 147.27 2.37 126 835 872 37 141.74 0.31 127 835 873 38 141.69 0.32 128 836 846 10 218.36 2.10 129 836 847 11 218.05 2.23 130 836 848 12 195.85 0.14 131 836 871 35 147.27 2.37 132 836 872 36 141.81 0.34 133 837 846 9 218.42 2.10 134 837 847 10 218.33 2.10 135 837 849 12 218.31 2.10 136 837 860 23 186.02 1.19 137 837 863 26 185.83 1.26 138 837 870 33 150.68 1.21 139 837 871 34 147.30 2.35 140 838 845 7 228.66 1.61 141 838 846 8 218.43 2.10 142 838 869 31 151.45 1.46 143 838 870 32 151.02 1.29 144 839 842 3 287.08 0.27 145 839 845 6 246.98 6.88 146 839 846 7 242.90 1.97 147 839 867 28 164.77 3.77 148 839 868 29 153.18 2.00 149 839 869 30 151.46 1.45 150 840 846 6 268.80 1.70 151 840 868 28 153.55 1.82 152 840 869 29 151.61 1.38 153 840 870 30 151.61 1.38 154 840 888 48 51.63 0.04 155 842 845 3 291.52 0.13 156 842 846 4 301.10 1.95 157 843 846 3 326.20 0.72 158 849 858 9 203.69 3.52 159 851 855 4 269.51 0.56 160 851 858 7 232.25 1.59 161 852 855 3 287.80 1.81 162 860 863 3 344.57 0.98 163 860 889 29 46.04 0.12 164 863 869 6 253.47 0.44 165 863 889 26 49.44 0.16 166 863 891 28 40.16 0.20 167 864 867 3 293.19 0.51 168 864 869 5 273.39 1.50 169 864 891 27 40.97 0.02 170 865 891 26 40.96 0.02 171 866 891 25 44.09 0.18 172 867 890 23 46.38 0.04 173 867 891 24 45.09 0.68 174 868 888 20 51.29 0.10 175 868 889 21 50.40 0.48 176 868 890 22 46.45 0.06 177 869 888 19 51.51 0.01 178 869 889 20 50.78 0.29 179 869 891 22 48.66 0.73 180 870 886 16 52.78 0.25 181 870 887 17 51.80 0.05 182 870 888 18 51.49 0.02 183 871 886 15 52.75 0.23 184 871 887 16 51.83 0.06 185 872 884 12 54.15 0.89 186 872 885 13 53.23 0.46 187 872 886 14 52.73 0.23 188 873 884 11 54.15 0.89 189 873 885 12 53.22 0.45 190 874 881 7 203.96 9.66 191 874 882 8 120.83 32.23 192 874 884 10 54.14 0.88 193 875 881 6 205.86 8.71 194 875 882 7 192.88 4.16 195 876 880 4 252.69 0.09 196 876 881 5 205.86 8.71 197 877 880 3 282.86 0.52