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 3 61 58 65.95 1.32 2 3 62 59 62.12 0.42 3 3 65 62 46.62 0.18 4 4 33 29 97.46 1.08 5 4 34 30 97.47 1.08 6 4 35 31 97.48 1.09 7 4 47 43 97.47 1.09 8 4 48 44 97.36 1.05 9 4 49 45 97.27 1.04 10 4 50 46 96.45 0.81 11 5 9 4 252.31 0.80 12 5 10 5 252.30 0.80 13 5 47 42 97.48 1.09 14 5 48 43 97.39 1.04 15 5 50 45 97.33 1.06 16 5 53 48 97.33 1.06 17 5 61 56 67.37 0.78 18 6 9 3 260.80 2.19 19 6 10 4 253.15 0.39 20 6 48 42 97.48 1.08 21 7 10 3 261.68 1.75 22 7 11 4 256.44 2.04 23 7 20 13 140.58 2.28 24 7 24 17 140.49 2.28 25 7 46 39 97.68 1.07 26 7 48 41 97.63 1.04 27 8 11 3 262.39 1.39 28 8 12 4 262.99 1.69 29 8 20 12 140.60 2.27 30 9 12 3 273.88 2.27 31 9 64 55 70.67 1.01 32 10 13 3 263.32 1.52 33 10 16 6 165.03 0.88 34 10 23 13 140.56 2.28 35 10 48 38 97.70 1.06 36 10 53 43 97.36 1.05 37 10 61 51 81.78 0.15 38 11 17 6 161.18 2.81 39 11 18 7 140.78 2.33 40 11 19 8 140.65 2.27 41 11 20 9 140.63 2.27 42 11 23 12 140.63 2.27 43 12 64 52 78.17 1.79 44 13 16 3 241.60 4.43 45 13 57 44 91.23 1.66 46 13 60 47 82.38 0.14 47 13 61 48 82.45 0.12 48 13 64 51 80.09 0.84 49 14 60 46 84.75 0.95 50 15 56 41 96.75 1.06 51 16 23 7 175.30 1.73 52 16 32 16 151.81 0.92 53 16 57 41 96.05 0.71 54 17 22 5 203.16 4.71 55 17 23 6 193.60 4.40 56 19 22 3 263.38 0.91 57 19 23 4 249.52 1.31 58 20 23 3 249.53 1.31 59 20 24 4 249.60 1.27 60 21 25 4 246.31 0.38 61 22 25 3 253.16 0.51 62 22 26 4 246.47 0.29 63 23 26 3 247.41 0.09 64 23 27 4 249.59 1.23 65 23 32 9 229.09 2.17 66 24 27 3 249.62 1.22 67 24 28 4 253.28 0.40 68 24 48 24 119.52 1.20 69 25 28 3 263.74 0.32 70 26 29 3 253.32 0.42 71 26 30 4 258.62 2.23 72 26 32 6 249.65 1.22 73 27 30 3 263.88 0.40 74 27 31 4 239.30 1.40 75 27 32 5 239.28 1.40 76 27 48 21 119.67 1.22 77 32 48 16 119.83 1.20 78 32 52 20 119.34 1.21 79 32 53 21 119.35 1.21 80 32 54 22 119.45 1.16 81 33 49 16 119.83 1.20 82 33 52 19 119.39 1.22 83 34 46 12 123.06 0.32 84 34 47 13 120.64 0.86 85 34 48 14 119.87 1.22 86 35 47 12 123.06 0.32 87 36 44 8 123.23 0.34 88 36 45 9 123.20 0.35 89 36 46 10 123.09 0.31 90 37 40 3 270.28 0.70 91 37 45 8 123.24 0.34 92 37 47 10 123.21 0.35 93 38 44 6 123.36 0.28 94 40 45 5 163.11 0.14 95 48 53 5 235.15 5.93 96 49 52 3 251.59 2.12 97 49 53 4 245.81 0.77 98 50 53 3 253.06 1.38 99 50 58 8 191.37 0.85 100 50 61 11 188.43 2.32 101 51 58 7 204.15 2.60 102 53 57 4 241.23 1.96 103 53 58 5 230.38 3.48 104 54 57 3 256.70 0.43 105 54 58 4 241.27 1.96 106 55 58 3 252.97 1.36 107 55 59 4 241.26 1.96 108 56 60 4 243.80 3.23 109 57 60 3 246.89 1.69 110 57 61 4 243.78 3.25 111 58 61 3 248.65 0.81 112 58 62 4 243.75 3.26 113 59 62 3 265.98 1.54 114 59 63 4 250.08 6.42 115 60 63 3 259.58 1.66 116 60 64 4 258.55 2.18 117 61 64 3 260.82 1.04 118 61 65 4 242.71 2.73 119 62 65 3 250.38 1.14 120 63 66 3 269.12 2.55 121 65 68 3 262.09 1.15 122 69 72 3 316.55 1.26 123 70 73 3 249.97 0.09 124 72 75 3 255.06 2.52