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 92 96 4 155.62 1.89 2 92 98 6 151.19 1.79 3 92 99 7 130.62 1.72 4 92 125 33 37.38 0.75 5 93 125 32 38.45 0.97 6 95 99 4 154.56 0.75 7 95 100 5 153.96 0.42 8 95 103 8 146.00 0.30 9 95 122 27 53.00 0.06 10 95 125 30 51.09 0.40 11 95 129 34 37.73 0.58 12 95 130 35 37.69 0.59 13 95 133 38 36.97 0.39 14 96 99 3 157.57 0.76 15 96 100 4 154.00 0.40 16 97 100 3 157.41 0.04 17 97 101 4 154.00 0.40 18 98 101 3 155.69 0.18 19 98 102 4 155.70 0.18 20 99 102 3 163.11 1.20 21 99 103 4 156.69 0.30 22 99 122 23 53.65 0.38 23 99 125 26 53.62 0.38 24 100 103 3 160.94 2.27 25 100 104 4 156.79 1.06 26 100 133 33 37.44 0.48 27 100 138 38 24.17 0.55 28 101 104 3 156.87 1.10 29 101 105 4 156.56 1.25 30 102 105 3 162.94 1.99 31 102 106 4 156.49 1.23 32 102 122 20 55.43 0.49 33 103 106 3 156.49 1.23 34 103 107 4 156.48 1.23 35 103 118 15 55.59 0.41 36 103 122 19 55.45 0.48 37 103 134 31 40.37 1.90 38 104 107 3 158.93 0.01 39 104 108 4 156.48 1.24 40 104 134 30 43.01 0.61 41 104 138 34 25.16 0.14 42 105 108 3 154.83 2.05 43 105 109 4 145.49 2.10 44 106 109 3 154.71 0.65 45 106 110 4 144.90 2.38 46 106 118 12 56.55 0.05 47 106 121 15 55.84 0.33 48 106 122 16 56.56 0.04 49 107 110 3 152.81 0.07 50 107 111 4 127.42 5.33 51 107 112 5 102.56 6.49 52 107 115 8 86.78 1.39 53 107 118 11 67.73 1.85 54 107 134 27 52.94 0.43 55 107 141 34 24.18 0.53 56 110 114 4 159.77 3.36 57 110 117 7 103.76 3.53 58 110 121 11 95.04 0.15 59 112 115 3 214.77 0.83 60 112 134 22 54.09 0.09 61 112 141 29 23.92 0.68 62 113 118 5 155.81 0.30 63 114 117 3 161.63 0.48 64 114 118 4 158.26 1.20 65 115 118 3 156.47 0.30 66 115 119 4 153.13 1.03 67 115 127 12 54.95 0.18 68 115 130 15 54.83 0.18 69 115 131 16 54.80 0.18 70 115 134 19 54.80 0.19 71 115 135 20 54.83 0.18 72 116 119 3 162.44 0.08 73 116 120 4 158.72 1.76 74 117 120 3 160.80 0.73 75 117 121 4 160.02 2.41 76 118 121 3 162.65 1.10 77 118 122 4 158.71 1.76 78 118 130 12 54.93 0.21 79 119 122 3 162.09 1.38 80 119 123 4 153.31 2.50 81 119 126 7 56.69 0.43 82 119 127 8 56.07 0.73 83 119 130 11 54.96 0.19 84 120 123 3 166.78 0.96 85 122 125 3 163.94 0.70 86 125 129 4 138.64 1.54 87 125 130 5 134.60 0.48 88 126 129 3 159.91 0.10 89 126 130 4 154.37 0.70 90 127 130 3 158.09 1.17 91 127 131 4 154.37 0.69 92 128 131 3 160.81 1.02 93 128 132 4 154.38 0.69 94 129 132 3 159.31 0.27 95 129 133 4 154.38 0.68 96 130 133 3 162.53 1.30 97 130 134 4 159.31 0.28 98 131 134 3 162.53 1.30 99 131 135 4 146.02 1.66 100 132 135 3 154.05 1.42 101 132 136 4 151.18 0.93 102 133 137 4 141.53 3.90 103 133 138 5 121.34 2.48 104 134 138 4 104.77 3.54 105 134 139 5 104.17 3.24 106 134 140 6 104.42 3.37 107 134 141 7 104.17 3.24