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 50 47 94.44 1.21 2 3 61 58 72.09 1.15 3 4 33 29 97.20 2.06 4 4 34 30 97.20 2.11 5 4 35 31 97.28 2.08 6 4 47 43 97.17 2.14 7 4 48 44 97.09 2.10 8 4 49 45 96.87 2.21 9 4 50 46 96.66 2.31 10 5 9 4 252.86 0.42 11 5 10 5 248.56 1.73 12 5 47 42 97.28 2.10 13 5 48 43 97.11 2.11 14 5 50 45 97.09 2.10 15 5 53 48 96.94 2.10 16 5 61 56 74.50 0.07 17 6 9 3 255.62 0.96 18 6 10 4 250.62 0.70 19 6 48 42 97.30 2.10 20 7 10 3 255.40 3.04 21 7 11 4 249.78 1.12 22 7 20 13 116.02 10.48 23 7 24 17 115.03 10.68 24 7 46 39 97.57 2.08 25 7 48 41 97.43 2.08 26 8 11 3 255.63 2.93 27 8 12 4 259.94 1.10 28 8 20 12 116.06 10.49 29 9 64 55 72.70 0.97 30 10 13 3 259.32 0.69 31 10 16 6 160.87 2.16 32 10 23 13 116.12 10.62 33 10 48 38 97.56 2.07 34 10 53 43 97.04 2.09 35 11 17 6 155.48 0.03 36 11 18 7 118.59 9.38 37 11 19 8 116.17 10.52 38 11 20 9 116.08 10.48 39 11 23 12 116.23 10.57 40 12 64 52 81.81 1.03 41 13 16 3 259.46 1.38 42 13 57 44 94.79 1.42 43 13 60 47 88.64 1.55 44 13 61 48 88.69 1.54 45 13 64 51 82.73 0.58 46 14 60 46 94.44 1.30 47 15 56 41 96.70 2.06 48 16 23 7 173.40 0.79 49 16 32 16 150.80 2.16 50 16 57 41 94.85 1.39 51 17 22 5 193.99 0.49 52 17 23 6 188.80 2.89 53 19 22 3 262.74 0.45 54 19 23 4 250.89 0.30 55 20 23 3 254.12 1.31 56 20 24 4 249.75 0.26 57 21 25 4 254.28 2.11 58 22 25 3 258.54 0.01 59 22 26 4 250.24 1.84 60 23 26 3 261.11 1.28 61 23 27 4 251.47 1.25 62 23 32 9 212.41 2.49 63 23 48 25 126.44 0.45 64 24 27 3 258.81 2.42 65 24 28 4 261.20 1.23 66 24 48 24 126.48 0.42 67 25 28 3 266.94 0.01 68 26 29 3 258.09 0.34 69 26 30 4 258.09 0.34 70 26 32 6 250.33 1.86 71 27 30 3 258.62 0.07 72 27 31 4 250.33 1.86 73 27 32 5 245.77 0.42 74 27 48 21 126.58 0.44 75 32 48 16 127.56 0.90 76 32 52 20 126.44 0.42 77 32 53 21 126.45 0.42 78 32 54 22 126.46 0.42 79 33 48 15 127.59 0.89 80 33 49 16 126.69 0.46 81 33 52 19 126.61 0.42 82 34 46 12 128.31 0.58 83 34 47 13 128.19 0.61 84 34 48 14 127.58 0.90 85 35 46 11 128.40 0.56 86 35 47 12 128.22 0.61 87 36 44 8 141.41 0.26 88 36 45 9 134.05 3.21 89 37 40 3 269.69 0.40 90 37 45 8 143.93 1.72 91 37 47 10 134.05 3.20 92 38 42 4 220.22 5.56 93 38 43 5 171.66 0.20 94 38 44 6 148.18 3.10 95 39 42 3 270.65 0.88 96 40 45 5 191.89 0.45 97 41 45 4 235.33 6.19 98 48 53 5 225.15 3.17 99 49 52 3 252.21 0.70 100 49 53 4 247.62 2.39 101 50 53 3 256.54 0.98 102 50 58 8 206.94 4.54 103 50 61 11 200.69 1.42 104 51 58 7 220.03 1.59 105 53 57 4 246.09 0.82 106 53 58 5 242.36 0.55 107 53 61 8 234.60 3.48 108 54 57 3 261.14 1.17 109 54 58 4 254.09 0.82 110 55 58 3 256.26 0.27 111 55 59 4 254.09 0.82 112 56 59 3 265.21 1.45 113 56 60 4 251.70 1.30 114 57 60 3 257.80 0.51 115 57 61 4 250.77 0.83 116 58 61 3 256.86 0.84 117 58 62 4 252.17 1.51 118 59 62 3 274.58 2.79 119 59 63 4 255.22 0.03 120 60 63 3 255.23 0.03 121 60 64 4 254.78 0.25 122 61 64 3 263.00 0.32 123 61 65 4 252.31 1.02 124 62 65 3 252.31 1.02 125 63 66 3 271.85 0.26 126 65 68 3 277.88 2.83 127 69 72 3 389.60 1.53 128 71 74 3 279.74 4.58