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 1 118 117 60.06 0.46 2 2 24 22 77.73 7.91 3 2 25 23 77.78 7.88 4 2 27 25 71.59 4.79 5 2 32 30 67.66 2.87 6 2 103 101 67.53 2.93 7 2 118 116 60.35 0.60 8 3 24 21 77.84 7.91 9 3 25 22 77.84 7.91 10 4 22 18 78.15 8.11 11 4 23 19 78.21 8.10 12 4 24 20 77.84 7.91 13 4 29 25 77.85 7.91 14 4 101 97 77.44 7.88 15 4 102 98 74.11 6.11 16 4 103 99 72.67 5.36 17 4 118 114 60.85 0.54 18 4 119 115 60.66 0.51 19 4 120 116 60.13 0.53 20 5 22 17 78.33 8.16 21 5 23 18 78.33 8.14 22 5 121 116 60.43 0.62 23 6 21 15 78.39 8.18 24 6 22 16 78.37 8.17 25 6 36 30 78.36 8.19 26 6 99 93 78.40 8.26 27 6 100 94 78.31 8.21 28 6 101 95 78.34 8.19 29 6 120 114 60.85 0.54 30 6 121 115 60.80 0.55 31 6 122 116 60.44 0.62 32 6 123 117 60.05 0.52 33 7 20 13 78.48 8.22 34 7 21 14 78.48 8.21 35 7 123 116 60.62 0.53 36 8 18 10 78.67 8.31 37 8 19 11 78.55 8.25 38 8 20 12 78.49 8.22 39 9 18 9 79.09 8.29 40 9 20 11 78.50 8.21 41 9 123 114 60.83 0.54 42 9 124 115 60.70 0.57 43 9 125 116 60.44 0.61 44 10 18 8 79.11 8.29 45 10 124 114 60.84 0.54 46 10 125 115 60.45 0.62 47 10 126 116 60.44 0.61 48 11 126 115 60.44 0.61 49 11 128 117 60.43 0.62 50 12 16 4 140.09 0.36 51 12 91 79 141.99 0.90 52 12 126 114 60.83 0.54 53 12 127 115 60.45 0.61 54 12 128 116 60.44 0.62 55 13 16 3 152.69 2.89 56 13 127 114 60.79 0.54 57 13 128 115 60.62 0.53 58 14 91 77 163.81 2.67 59 14 93 79 172.60 0.79 60 14 127 113 60.79 0.54 61 14 128 114 60.75 0.54 62 14 129 115 60.40 0.61 63 15 90 75 226.77 6.05 64 15 91 76 274.07 1.68 65 18 125 107 60.80 0.55 66 20 123 103 60.81 0.55 67 20 125 105 60.44 0.61 68 32 105 73 244.98 5.12 69 32 118 86 85.17 12.68 70 33 106 73 179.36 3.35 71 33 107 74 152.12 0.95 72 33 116 83 85.25 12.67 73 34 103 69 280.15 2.63 74 34 116 82 85.24 12.67 75 35 116 81 85.22 12.65 76 37 112 75 85.61 12.52 77 37 113 76 85.36 12.58 78 37 116 79 85.28 12.62 79 37 119 82 75.25 7.69 80 45 113 68 85.51 12.47 81 45 119 74 82.38 11.17 82 47 111 64 85.78 12.42 83 50 116 66 85.25 12.67 84 53 105 52 273.99 2.79 85 53 106 53 184.33 3.14 86 64 110 46 95.84 7.40 87 64 111 47 95.83 7.40 88 88 125 37 60.80 0.54 89 91 127 36 60.77 0.54 90 92 127 35 60.80 0.54 91 93 127 34 60.80 0.54 92 93 129 36 60.77 0.54 93 95 127 32 60.79 0.55 94 96 125 29 60.90 0.56 95 96 126 30 60.80 0.54 96 96 127 31 60.72 0.54 97 97 124 27 60.93 0.56 98 97 125 28 60.85 0.55 99 98 122 24 61.00 0.58 100 98 123 25 60.91 0.55 101 98 124 26 60.81 0.55 102 99 122 23 60.91 0.56 103 99 123 24 60.84 0.54 104 99 125 26 60.75 0.53 105 100 119 19 69.16 4.64 106 100 120 20 68.72 4.46 107 100 121 21 66.22 3.21 108 100 122 22 60.77 0.55 109 101 119 18 69.12 4.66 110 101 120 19 68.80 4.50 111 102 116 14 85.18 12.63 112 102 118 16 76.33 8.23 113 102 119 17 69.11 4.67 114 103 116 13 85.21 12.66 115 103 117 14 85.16 12.64 116 103 118 15 80.38 10.29 117 104 107 3 227.69 0.62 118 104 108 4 168.76 0.98 119 104 110 6 131.94 1.02 120 104 116 12 85.24 12.67 121 104 117 13 85.20 12.66 122 105 117 12 85.24 12.68 123 109 112 3 157.38 0.83 124 112 116 4 150.63 0.29 125 113 116 3 159.85 0.10 126 113 119 6 124.79 0.12 127 116 119 3 180.04 0.42