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 2 98 96 58.38 0.12 2 2 106 104 58.42 0.14 3 2 107 105 58.41 0.13 4 3 24 21 58.54 0.14 5 3 25 22 58.56 0.15 6 3 26 23 58.60 0.15 7 3 27 24 58.55 0.14 8 4 23 19 58.50 0.14 9 4 24 20 58.54 0.15 10 4 27 23 58.62 0.14 11 4 106 102 58.55 0.15 12 4 107 103 58.49 0.14 13 5 23 18 58.55 0.15 14 5 107 102 58.53 0.14 15 5 109 104 58.45 0.14 16 6 21 15 58.55 0.15 17 6 22 16 58.54 0.15 18 6 23 17 58.60 0.14 19 6 36 30 58.54 0.14 20 6 95 89 58.52 0.14 21 6 96 90 58.53 0.14 22 6 108 102 58.55 0.15 23 6 109 103 58.52 0.15 24 6 110 104 58.51 0.15 25 6 111 105 58.23 0.07 26 7 20 13 58.58 0.14 27 7 21 14 58.59 0.14 28 7 111 104 58.51 0.15 29 8 19 11 58.66 0.10 30 8 20 12 58.58 0.14 31 8 21 13 58.63 0.14 32 9 18 9 88.45 0.69 33 9 20 11 58.73 0.11 34 10 18 8 88.45 0.69 35 10 19 9 71.70 6.38 36 10 113 103 58.52 0.15 37 10 114 104 58.51 0.15 38 11 17 6 92.23 1.45 39 11 18 7 92.07 1.40 40 11 114 103 58.51 0.15 41 11 116 105 47.05 1.53 42 12 16 4 92.28 1.44 43 12 17 5 92.23 1.45 44 12 18 6 92.23 1.45 45 12 83 71 92.24 1.46 46 12 86 74 103.59 0.48 47 12 113 101 58.58 0.16 48 12 114 102 58.52 0.15 49 12 115 103 58.02 0.04 50 12 116 104 57.39 0.27 51 13 16 3 104.74 1.38 52 13 88 75 126.86 1.74 53 13 115 102 58.50 0.15 54 13 116 103 58.45 0.15 55 13 117 104 58.02 0.04 56 14 86 72 132.31 0.70 57 14 87 73 132.34 0.69 58 14 88 74 135.32 0.80 59 15 86 71 162.84 4.58 60 16 84 68 146.40 0.84 61 17 83 66 197.19 24.40 62 17 84 67 148.24 0.08 63 18 81 63 258.61 0.04 64 18 82 64 258.54 0.01 65 18 83 65 227.75 9.12 66 18 112 94 58.68 0.21 67 18 113 95 58.50 0.15 68 18 114 96 58.52 0.15 69 20 111 91 62.98 2.37 70 20 112 92 61.67 1.73 71 20 113 93 58.45 0.13 72 22 107 85 77.59 0.57 73 23 107 84 79.07 0.02 74 24 107 83 79.27 0.04 75 27 107 80 102.83 0.14 76 32 100 68 255.97 1.12 77 33 100 67 257.42 0.40 78 34 98 64 257.76 0.23 79 34 99 65 258.77 0.14 80 34 107 73 78.84 0.10 81 35 99 64 257.63 0.29 82 36 111 75 67.39 0.79 83 52 99 47 255.41 0.23 84 83 113 30 61.34 1.56 85 86 115 29 59.09 0.44 86 87 115 28 61.61 1.70 87 88 115 27 61.62 1.70 88 88 117 29 61.30 1.55 89 89 115 26 62.87 2.25 90 90 115 25 63.13 2.39 91 91 113 22 63.27 2.43 92 91 114 23 63.15 2.39 93 91 115 24 63.13 2.39 94 92 112 20 63.28 2.43 95 92 113 21 63.24 2.43 96 93 110 17 63.51 2.45 97 93 111 18 63.40 2.44 98 93 112 19 63.23 2.44 99 94 110 16 63.48 2.47 100 94 111 17 63.32 2.47 101 94 112 18 63.16 2.47 102 94 113 19 63.27 2.46 103 95 109 14 69.83 2.00 104 95 110 15 63.40 2.51 105 96 107 11 76.36 0.06 106 97 104 7 80.46 0.34 107 97 107 10 77.60 0.58 108 98 103 5 94.31 0.45 109 98 104 6 80.45 0.34 110 98 106 8 79.05 0.02 111 98 107 9 78.83 0.10 112 99 104 5 86.56 3.39 113 100 103 3 120.36 0.58 114 100 104 4 108.93 0.78 115 102 106 4 238.42 6.75 116 103 106 3 222.32 1.29