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 5 8 3 253.66 1.79 2 5 9 4 246.05 1.64 3 6 9 3 246.51 1.85 4 6 10 4 241.55 0.24 5 6 11 5 241.54 0.25 6 6 45 39 95.81 0.18 7 6 46 40 95.58 0.14 8 6 49 43 95.20 0.24 9 7 10 3 254.56 2.17 10 7 11 4 241.54 0.30 11 7 12 5 241.55 0.30 12 7 53 46 95.27 0.21 13 8 11 3 257.90 0.50 14 8 12 4 240.77 2.22 15 9 12 3 245.15 0.03 16 9 13 4 243.82 0.70 17 9 32 23 96.65 0.43 18 9 37 28 96.86 0.50 19 10 13 3 253.96 0.03 20 10 14 4 243.19 0.39 21 10 28 18 96.56 0.46 22 10 29 19 96.56 0.47 23 10 32 22 96.67 0.42 24 10 46 36 96.13 0.32 25 10 49 39 96.09 0.33 26 10 50 40 95.97 0.34 27 10 53 43 95.64 0.18 28 11 14 3 243.58 0.59 29 11 53 42 95.50 0.25 30 11 58 47 86.52 0.05 31 12 15 3 267.12 2.43 32 13 16 3 234.82 2.12 33 13 17 4 224.74 2.92 34 13 28 15 96.66 0.42 35 13 31 18 96.79 0.48 36 14 28 14 96.71 0.43 37 14 53 39 96.11 0.34 38 14 59 45 85.55 0.43 39 14 73 59 40.70 0.48 40 15 73 58 42.90 0.38 41 17 23 6 149.13 0.18 42 19 22 3 262.32 1.70 43 21 70 49 54.86 0.34 44 21 71 50 54.81 0.33 45 21 72 51 54.79 0.32 46 22 70 48 54.79 0.34 47 23 26 3 254.22 0.12 48 23 27 4 185.31 0.91 49 23 28 5 183.62 1.76 50 23 59 36 99.39 0.72 51 23 71 48 54.80 0.33 52 24 71 47 54.80 0.33 53 25 29 4 216.43 2.00 54 25 50 25 103.10 1.21 55 25 71 46 54.80 0.33 56 26 30 4 242.99 1.02 57 27 30 3 251.94 1.83 58 27 31 4 248.25 0.01 59 28 31 3 254.25 2.35 60 28 32 4 253.62 2.67 61 28 50 22 103.77 0.99 62 28 53 25 103.77 0.99 63 28 59 31 102.97 0.68 64 29 32 3 262.73 1.89 65 29 39 10 107.59 0.99 66 29 46 17 103.84 1.02 67 29 47 18 104.00 1.09 68 29 50 21 103.77 0.99 69 30 39 9 107.64 0.97 70 32 37 5 140.24 1.91 71 32 39 7 107.75 0.94 72 32 46 14 105.25 1.11 73 33 37 4 140.24 1.91 74 33 38 5 107.73 0.95 75 33 39 6 107.75 0.94 76 37 42 5 194.33 0.68 77 37 45 8 194.32 0.67 78 38 41 3 256.73 0.04 79 38 42 4 232.94 5.46 80 38 45 7 204.99 1.20 81 39 43 4 196.46 0.39 82 39 45 6 201.53 2.93 83 39 46 7 194.31 0.67 84 40 43 3 234.88 1.17 85 42 45 3 257.87 1.77 86 43 46 3 257.78 1.80 87 43 47 4 245.32 0.58 88 44 47 3 261.88 0.96 89 44 48 4 245.74 0.79 90 45 48 3 251.27 0.99 91 45 49 4 245.25 0.70 92 46 49 3 253.95 0.35 93 46 50 4 243.26 1.00 94 47 50 3 253.95 0.35 95 47 51 4 231.90 4.69 96 48 51 3 245.90 0.33 97 48 52 4 235.01 3.12 98 49 52 3 244.65 0.29 99 49 53 4 232.91 2.06 100 50 53 3 235.18 3.13 101 50 54 4 235.88 3.54 102 50 55 5 235.87 3.54 103 51 55 4 235.86 3.55 104 52 55 3 248.62 0.39 105 52 56 4 231.83 2.97 106 53 56 3 257.39 2.73 107 53 57 4 243.03 3.18 108 53 58 5 217.59 1.26 109 53 59 6 208.81 5.63 110 54 57 3 263.17 4.35 111 54 59 5 199.46 0.96 112 54 60 6 199.46 0.96 113 54 61 7 181.15 0.04 114 54 71 17 142.93 0.57 115 57 60 3 233.44 3.17 116 57 74 17 133.06 5.01 117 58 73 15 141.35 0.93 118 58 74 16 131.38 5.86 119 59 71 12 148.81 2.04 120 59 73 14 141.34 0.93 121 60 71 11 149.00 2.02 122 60 72 12 148.97 2.02 123 60 73 13 147.29 1.33 124 60 74 14 144.01 0.30 125 60 75 15 133.54 4.88 126 61 69 8 149.38 2.02 127 61 70 9 149.17 1.99 128 61 71 10 149.00 2.02 129 61 72 11 149.14 1.99 130 62 68 6 151.15 1.77 131 62 69 7 149.39 2.02 132 62 70 8 149.39 2.02 133 62 72 10 149.35 2.02 134 63 69 6 149.42 2.02 135 64 68 4 196.47 2.94 136 64 69 5 156.89 1.12 137 65 68 3 263.94 3.84