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 8 12 4 231.34 1.05 2 8 13 5 222.03 0.26 3 8 47 39 33.47 0.35 4 9 12 3 241.26 1.88 5 9 13 4 238.74 2.65 6 10 13 3 241.81 1.10 7 10 14 4 221.96 0.27 8 10 63 53 33.41 0.39 9 10 66 56 33.41 0.40 10 11 14 3 242.55 0.73 11 11 66 55 33.45 0.38 12 11 70 59 33.41 0.41 13 12 16 4 227.35 1.96 14 13 16 3 227.35 1.96 15 13 17 4 226.03 2.62 16 13 43 30 35.27 1.12 17 13 47 34 35.40 1.09 18 14 17 3 232.24 0.49 19 14 18 4 227.36 1.96 20 14 40 26 35.26 1.12 21 14 43 29 35.29 1.12 22 14 63 49 35.36 1.07 23 14 66 52 35.41 1.08 24 14 67 53 35.33 1.10 25 15 18 3 230.30 0.49 26 15 19 4 225.48 2.87 27 15 20 5 208.61 2.92 28 15 70 55 35.43 1.08 29 15 72 57 35.30 1.09 30 16 19 3 229.93 0.68 31 17 39 22 35.23 1.14 32 17 43 26 35.46 1.08 33 18 35 17 35.05 1.23 34 18 72 54 35.41 1.07 35 20 33 13 35.30 1.09 36 20 72 52 35.44 1.08 37 25 30 5 206.69 2.54 38 26 30 4 200.28 0.66 39 27 30 3 239.72 2.40 40 33 72 39 98.86 1.08 41 33 73 40 98.98 1.02 42 34 73 39 98.98 1.02 43 34 75 41 98.84 1.08 44 35 39 4 225.03 0.52 45 35 40 5 213.25 1.22 46 35 72 37 99.25 1.11 47 35 73 38 99.23 1.10 48 35 74 39 99.11 1.09 49 35 75 40 99.12 1.08 50 36 39 3 233.33 0.85 51 36 40 4 226.09 0.01 52 36 74 38 99.20 1.09 53 36 75 39 99.12 1.08 54 37 40 3 234.40 0.41 55 37 41 4 221.93 0.84 56 37 60 23 102.56 0.12 57 37 64 27 102.20 0.17 58 37 74 37 99.23 1.11 59 37 75 38 99.23 1.11 60 37 76 39 99.00 1.02 61 38 41 3 240.88 0.90 62 38 42 4 221.59 1.02 63 39 42 3 229.16 1.80 64 39 43 4 228.22 2.28 65 40 43 3 232.47 0.15 66 40 44 4 229.15 1.81 67 40 60 20 102.47 0.16 68 40 63 23 102.31 0.14 69 40 67 27 101.97 0.31 70 40 74 34 99.23 1.11 71 41 44 3 229.15 1.81 72 41 45 4 229.15 1.81 73 41 56 15 118.87 0.08 74 41 60 19 102.55 0.12 75 42 45 3 230.16 1.04 76 42 46 4 230.16 1.04 77 43 46 3 230.31 0.97 78 43 47 4 230.21 1.06 79 44 47 3 233.94 0.50 80 44 48 4 230.19 1.05 81 44 59 15 107.34 1.41 82 44 60 16 103.47 0.53 83 44 63 19 102.42 0.13 84 45 48 3 230.77 0.78 85 45 49 4 241.61 1.39 86 45 56 11 129.96 2.04 87 46 49 3 302.16 1.56 88 46 50 4 242.40 1.51 89 47 50 3 236.71 1.89 90 47 51 4 236.69 1.90 91 48 51 3 239.85 0.33 92 48 53 5 170.35 0.00 93 48 54 6 170.35 0.00 94 48 55 7 149.64 1.72 95 48 56 8 141.95 0.98 96 48 59 11 130.65 0.38 97 51 59 8 147.93 0.60 98 51 62 11 147.93 0.60 99 53 58 5 165.67 0.11 100 53 59 6 166.64 0.36 101 53 62 9 160.71 2.61 102 54 58 4 225.38 2.71 103 55 58 3 229.45 1.19 104 55 59 4 225.39 2.71 105 56 59 3 223.62 3.59 106 56 60 4 210.40 2.32 107 57 61 4 221.19 2.14 108 58 61 3 228.56 1.47 109 58 62 4 228.63 1.46 110 59 62 3 233.72 0.55 111 59 63 4 228.62 1.46 112 60 63 3 228.61 1.47 113 60 64 4 228.22 1.27 114 61 64 3 234.86 2.05 115 61 65 4 228.22 1.26 116 62 66 4 215.78 0.43 117 63 66 3 227.26 2.76 118 63 67 4 213.56 0.67 119 64 67 3 222.50 2.75 120 64 68 4 213.54 0.66 121 65 68 3 228.75 0.39 122 65 69 4 208.02 2.10 123 66 70 4 207.81 2.08 124 67 72 5 144.86 0.84 125 67 73 6 142.44 2.04 126 68 71 3 231.02 3.52 127 68 72 4 167.44 4.17 128 68 73 5 142.35 2.04