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 16 19 3 197.00 1.67 2 16 20 4 186.91 0.24 3 17 21 4 186.97 0.29 4 17 47 30 46.02 0.35 5 17 50 33 45.94 0.31 6 17 51 34 45.90 0.32 7 17 54 37 45.91 0.32 8 18 21 3 189.33 0.88 9 18 22 4 186.98 0.29 10 19 22 3 188.43 0.43 11 19 23 4 187.88 0.09 12 19 37 18 84.12 5.15 13 20 23 3 197.89 1.27 14 20 24 4 185.45 1.12 15 20 33 13 91.76 2.58 16 20 37 17 84.62 4.91 17 20 47 27 46.33 0.24 18 20 51 31 46.20 0.21 19 21 24 3 185.46 1.12 20 21 25 4 185.44 1.12 21 21 51 30 46.24 0.23 22 21 55 34 45.95 0.32 23 21 63 42 45.83 0.29 24 21 64 43 45.74 0.32 25 21 67 46 39.84 0.17 26 22 25 3 190.02 0.41 27 22 26 4 189.97 0.39 28 23 26 3 188.67 0.48 29 23 27 4 188.27 0.47 30 23 28 5 148.16 1.74 31 23 33 10 117.76 6.21 32 23 36 13 97.78 1.28 33 23 37 14 97.78 1.28 34 24 27 3 179.84 0.12 35 24 28 4 147.87 1.73 36 24 33 9 125.42 2.40 37 24 51 27 46.39 0.24 38 24 60 36 45.97 0.35 39 24 63 39 45.88 0.32 40 24 64 40 45.75 0.32 41 25 64 39 45.77 0.33 42 25 67 42 40.56 0.18 43 25 68 43 39.87 0.12 44 26 75 49 11.98 0.03 45 28 32 4 184.57 0.05 46 28 33 5 178.81 2.93 47 28 36 8 133.87 3.79 48 29 33 4 186.22 0.79 49 30 33 3 188.58 1.96 50 30 34 4 186.22 0.79 51 30 41 11 87.67 6.32 52 30 44 14 84.58 4.86 53 30 48 18 84.22 5.03 54 31 34 3 189.15 1.67 55 31 35 4 186.22 0.79 56 31 41 10 88.72 5.90 57 32 35 3 188.57 1.96 58 32 36 4 186.21 0.78 59 33 36 3 188.53 1.98 60 33 37 4 184.50 0.04 61 33 38 5 184.47 0.02 62 33 44 11 87.67 6.40 63 34 38 4 141.93 4.14 64 34 39 5 122.02 0.38 65 34 40 6 122.01 0.38 66 34 41 7 117.69 1.73 67 37 44 7 153.28 15.95 68 40 43 3 197.59 1.86 69 40 44 4 195.52 2.89 70 41 44 3 198.18 1.57 71 41 45 4 196.44 2.44 72 42 45 3 198.18 1.56 73 42 46 4 196.47 2.42 74 43 46 3 204.97 0.20 75 43 47 4 191.61 0.03 76 44 47 3 191.61 0.03 77 44 48 4 190.56 0.56 78 45 48 3 193.19 0.75 79 45 49 4 190.60 0.54 80 46 49 3 197.00 1.21 81 46 50 4 190.60 0.54 82 47 50 3 190.60 0.54 83 47 51 4 188.13 0.69 84 48 51 3 188.50 0.87 85 48 52 4 189.84 0.17 86 48 59 11 90.64 8.53 87 48 60 12 90.03 8.77 88 49 52 3 197.38 2.93 89 49 53 4 190.52 0.59 90 50 53 3 190.07 0.82 91 50 54 4 189.32 0.44 92 51 54 3 193.05 1.43 93 51 55 4 189.32 0.44 94 51 60 9 99.52 4.33 95 51 63 12 99.34 4.29 96 52 55 3 197.76 0.94 97 52 56 4 177.16 0.53 98 52 57 5 153.93 2.96 99 52 58 6 106.73 2.15 100 52 59 7 99.58 4.33 101 52 60 8 99.55 4.33 102 52 63 11 90.64 8.68 103 55 63 8 105.44 1.45 104 55 66 11 105.33 1.40 105 57 62 5 170.35 1.91 106 57 63 6 154.04 10.05 107 57 66 9 112.10 3.93 108 58 62 4 174.82 0.78 109 59 62 3 190.87 2.44 110 59 63 4 183.68 1.16 111 60 63 3 187.19 0.58 112 60 64 4 184.77 0.61 113 61 64 3 190.38 1.02 114 61 65 4 187.97 2.21 115 62 65 3 198.15 2.00 116 62 66 4 189.12 1.64 117 63 66 3 191.41 1.38 118 63 67 4 186.99 0.47 119 64 67 3 198.10 0.21 120 64 68 4 184.81 0.61 121 65 68 3 182.16 0.71 122 65 69 4 183.56 0.01 123 65 71 6 150.35 5.45 124 66 69 3 189.06 0.44 125 68 71 3 214.34 2.41 126 68 73 5 187.02 0.57 127 68 74 6 185.38 0.26 128 68 75 7 173.54 4.58