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 40 32 64.94 0.27 2 8 44 36 47.91 0.12 3 8 48 40 46.14 0.30 4 9 12 3 181.72 0.55 5 9 13 4 181.72 0.55 6 10 13 3 190.53 2.35 7 10 14 4 181.89 0.64 8 11 14 3 184.84 0.15 9 11 15 4 181.93 0.66 10 11 37 26 87.96 1.07 11 11 38 27 87.92 1.06 12 12 15 3 192.93 0.98 13 12 16 4 184.73 0.23 14 12 38 26 87.91 1.06 15 12 39 27 87.92 1.06 16 12 40 28 87.92 1.06 17 13 16 3 194.25 0.33 18 13 17 4 188.94 2.33 19 14 17 3 193.27 0.17 20 14 18 4 190.91 0.69 21 15 18 3 196.65 1.73 22 15 19 4 186.44 1.54 23 15 34 19 88.48 0.80 24 15 38 23 88.47 0.82 25 16 19 3 190.92 0.69 26 16 20 4 185.09 0.42 27 16 34 18 88.50 0.78 28 16 38 22 88.53 0.79 29 16 45 29 87.78 0.91 30 16 48 32 86.38 0.21 31 16 49 33 86.36 0.21 32 17 20 3 189.10 1.59 33 17 21 4 185.16 0.38 34 17 48 31 87.39 0.71 35 17 52 35 83.71 1.07 36 18 21 3 183.16 0.61 37 18 22 4 183.09 0.58 38 19 22 3 187.33 1.74 39 19 23 4 185.42 0.59 40 19 26 7 134.34 3.08 41 19 30 11 90.28 0.41 42 19 34 15 88.56 0.78 43 19 49 30 87.84 0.75 44 20 23 3 185.50 0.56 45 20 48 28 88.16 0.62 46 20 49 29 87.40 0.69 47 20 52 32 86.34 0.23 48 20 53 33 83.84 1.01 49 20 56 36 69.17 0.93 50 22 30 8 158.55 1.45 51 23 26 3 225.00 1.16 52 23 49 26 88.23 0.64 53 24 49 25 88.18 0.61 54 24 53 29 86.47 0.21 55 24 56 32 83.61 1.10 56 25 53 28 87.03 0.06 57 26 30 4 175.40 1.87 58 26 31 5 163.71 1.11 59 26 34 8 163.71 1.11 60 26 45 19 88.73 0.80 61 26 49 23 88.50 0.78 62 27 30 3 194.80 0.83 63 27 31 4 180.55 1.09 64 28 31 3 195.31 1.08 65 28 32 4 184.64 0.95 66 28 42 14 88.92 0.86 67 29 32 3 184.65 0.95 68 29 33 4 184.62 0.95 69 30 33 3 186.78 0.13 70 30 34 4 183.81 0.80 71 31 34 3 188.80 0.05 72 31 35 4 183.81 0.80 73 31 42 11 88.94 0.85 74 31 45 14 88.84 0.83 75 31 46 15 88.82 0.83 76 32 35 3 189.88 0.48 77 32 36 4 183.78 0.79 78 32 42 10 88.98 0.88 79 33 36 3 189.60 0.35 80 33 37 4 185.56 1.67 81 34 37 3 195.19 1.64 82 34 38 4 180.00 1.00 83 34 45 11 88.92 0.86 84 35 38 3 191.25 3.61 85 35 39 4 174.57 1.54 86 35 40 5 130.57 6.12 87 35 42 7 96.75 3.04 88 35 45 10 88.92 0.86 89 36 39 3 180.15 4.33 90 38 45 7 155.49 2.75 91 40 44 4 184.12 2.36 92 40 45 5 176.53 1.43 93 41 44 3 195.08 1.34 94 42 45 3 188.93 0.04 95 42 46 4 189.46 0.31 96 43 46 3 189.47 0.32 97 43 47 4 189.37 0.35 98 44 47 3 190.43 0.17 99 44 48 4 189.37 0.35 100 45 48 3 191.71 0.82 101 45 49 4 183.97 2.33 102 46 49 3 186.03 1.27 103 46 50 4 189.01 0.23 104 47 50 3 191.97 0.68 105 47 51 4 188.00 1.63 106 48 51 3 191.41 0.96 107 48 52 4 188.08 1.66 108 49 52 3 189.72 0.83 109 49 53 4 190.46 0.51 110 50 53 3 197.34 0.59 111 50 54 4 190.46 0.51 112 51 54 3 189.77 0.85 113 51 55 4 188.53 1.47 114 52 55 3 188.53 1.47 115 52 56 4 188.51 1.45 116 52 59 7 179.88 2.39 117 53 56 3 184.52 0.56 118 53 57 4 184.50 0.56 119 54 58 4 187.01 1.01 120 55 59 4 186.23 0.66 121 56 59 3 193.71 0.10 122 56 60 4 187.41 0.81 123 57 60 3 191.47 1.22 124 57 61 4 189.27 0.12 125 57 64 7 138.72 1.54 126 57 67 10 17.64 1.68 127 58 61 3 201.11 0.31 128 60 64 4 170.69 1.12 129 61 64 3 182.40 1.68 130 61 65 4 172.66 0.14 131 62 65 3 203.37 0.82 132 63 66 3 283.78 2.69 133 64 67 3 198.75 0.07