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 91 129 38 25.73 2.87 2 92 99 7 155.13 0.03 3 92 124 32 39.63 0.10 4 92 125 33 39.16 0.12 5 93 125 32 47.44 0.85 6 94 125 31 47.48 0.86 7 95 99 4 155.16 0.02 8 95 100 5 155.15 0.02 9 95 103 8 152.28 0.59 10 95 122 27 55.38 1.00 11 95 125 30 47.56 0.91 12 95 129 34 46.09 1.55 13 95 130 35 46.02 1.54 14 95 133 38 41.54 0.18 15 96 99 3 156.47 0.53 16 96 100 4 155.40 0.03 17 97 100 3 157.69 0.07 18 97 101 4 155.40 0.03 19 98 101 3 157.87 1.26 20 98 102 4 159.68 2.16 21 99 102 3 164.55 1.92 22 99 103 4 159.68 2.17 23 99 122 23 56.77 1.69 24 99 125 26 56.11 1.36 25 100 103 3 160.19 1.90 26 100 104 4 156.46 0.56 27 100 133 33 45.44 1.57 28 100 138 38 28.21 0.03 29 101 104 3 156.46 0.56 30 101 105 4 155.75 0.86 31 102 105 3 156.73 0.38 32 102 106 4 155.74 0.87 33 102 122 20 56.89 1.73 34 103 106 3 156.40 1.21 35 103 107 4 155.19 1.11 36 103 115 12 70.97 1.17 37 103 118 15 65.91 2.78 38 103 122 19 56.88 1.74 39 103 134 31 45.83 1.72 40 104 107 3 158.83 0.04 41 104 108 4 153.97 0.47 42 104 134 30 45.84 1.72 43 104 138 34 30.70 1.12 44 105 108 3 153.94 0.46 45 105 109 4 153.94 0.47 46 106 109 3 153.93 0.46 47 106 110 4 153.76 0.54 48 106 111 5 153.75 0.54 49 106 118 12 67.17 2.29 50 106 121 15 67.16 2.27 51 106 122 16 67.15 2.27 52 107 111 4 122.94 3.15 53 107 112 5 111.28 2.68 54 107 115 8 107.07 1.17 55 107 118 11 76.94 1.04 56 107 134 27 53.31 1.42 57 110 114 4 163.49 0.75 58 110 117 7 127.01 1.53 59 110 118 8 112.58 1.60 60 110 121 11 102.37 3.52 61 111 114 3 208.66 0.51 62 113 118 5 158.66 1.01 63 114 117 3 161.83 0.58 64 114 118 4 158.66 1.01 65 115 118 3 158.66 1.01 66 115 119 4 158.65 1.01 67 115 127 12 63.70 1.14 68 115 130 15 62.76 1.61 69 115 131 16 62.76 1.61 70 115 134 19 62.76 1.61 71 115 135 20 62.78 1.60 72 116 119 3 159.47 1.41 73 116 120 4 159.45 1.41 74 117 120 3 159.46 1.42 75 117 121 4 160.73 2.06 76 118 121 3 160.71 2.07 77 118 122 4 160.69 2.08 78 118 130 12 64.27 1.01 79 119 122 3 160.69 2.08 80 119 125 6 93.53 6.69 81 119 126 7 70.73 0.84 82 119 127 8 69.66 1.38 83 119 130 11 64.83 1.03 84 120 123 3 165.83 0.41 85 122 125 3 163.01 0.44 86 122 130 8 84.56 3.58 87 125 129 4 142.96 2.91 88 125 130 5 142.49 2.69 89 126 129 3 160.47 0.29 90 126 130 4 145.30 2.35 91 127 130 3 152.97 1.49 92 127 131 4 150.93 3.18 93 128 131 3 158.99 1.03 94 128 132 4 151.00 3.18 95 129 132 3 159.00 1.04 96 129 133 4 151.69 2.83 97 130 133 3 161.21 0.07 98 130 134 4 157.12 0.10 99 131 134 3 160.47 0.30 100 131 135 4 147.91 4.71 101 132 135 3 157.10 0.11 102 132 136 4 147.91 4.71 103 133 137 4 143.22 2.44 104 133 138 5 119.61 6.42 105 134 138 4 117.92 5.58 106 134 139 5 109.24 1.24 107 134 140 6 117.92 5.58 108 134 141 7 109.23 1.24 109 135 139 4 130.72 9.50