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 15 23 8 24.80 0.60 2 16 19 3 34.42 0.20 3 16 20 4 31.43 0.33 4 17 20 3 33.88 0.07 5 17 21 4 31.43 0.33 6 18 21 3 33.95 0.42 7 18 22 4 33.84 0.36 8 19 22 3 33.22 0.79 9 19 23 4 32.83 0.87 10 20 23 3 36.77 0.32 11 20 24 4 32.82 0.86 12 21 24 3 34.24 1.58 13 21 25 4 32.82 0.87 14 21 62 41 27.61 0.64 15 24 59 35 93.04 0.83 16 24 60 36 83.45 0.35 17 25 60 35 94.73 0.14 18 25 61 36 88.42 1.28 19 25 62 37 94.66 0.15 20 25 104 79 91.45 0.24 21 26 58 32 95.92 0.09 22 26 59 33 95.75 0.05 23 26 60 34 94.94 0.21 24 26 61 35 94.90 0.23 25 26 102 76 94.88 0.20 26 26 103 77 94.86 0.21 27 26 104 78 94.12 0.03 28 27 57 30 95.90 0.08 29 27 58 31 95.92 0.09 30 27 102 75 94.86 0.21 31 28 56 28 95.97 0.07 32 28 57 29 95.93 0.09 33 28 99 71 95.75 0.15 34 28 100 72 95.91 0.09 35 28 101 73 95.00 0.24 36 28 102 74 95.70 0.07 37 29 54 25 194.50 0.18 38 29 55 26 98.77 0.21 39 29 56 27 96.10 0.09 40 29 58 29 96.08 0.07 41 30 53 23 195.00 0.00 42 30 54 24 193.63 0.31 43 30 55 25 115.36 0.57 44 31 54 23 194.95 0.02 45 31 56 25 140.47 4.13 46 33 51 18 195.00 0.00 47 34 51 17 195.00 0.00 48 37 40 3 195.00 0.00 49 39 42 3 195.00 0.00 50 46 83 37 195.00 0.00 51 47 50 3 195.00 0.00 52 47 80 33 195.00 0.00 53 47 81 34 195.00 0.00 54 48 81 33 194.99 0.01 55 54 76 22 195.00 0.00 56 57 68 11 96.06 0.10 57 57 69 12 96.09 0.09 58 57 70 13 97.05 0.52 59 61 66 5 95.95 0.09 60 61 67 6 95.92 0.10 61 61 68 7 95.87 0.09 62 63 66 3 96.06 0.10 63 64 107 43 94.95 0.21 64 65 106 41 94.94 0.21 65 65 107 42 94.81 0.21 66 66 104 38 94.94 0.21 67 66 105 39 94.92 0.22 68 66 106 40 91.89 1.02 69 67 103 36 95.94 0.09 70 67 104 37 94.88 0.20 71 67 105 38 94.61 0.12 72 67 107 40 55.11 0.06 73 68 102 34 95.90 0.08 74 68 103 35 94.95 0.21 75 68 104 36 94.78 0.21 76 69 102 33 95.92 0.08 77 69 103 34 95.90 0.08 78 69 105 36 94.95 0.21 79 70 73 3 194.99 0.01 80 70 99 29 105.10 2.33 81 70 101 31 96.01 0.13 82 70 102 32 95.92 0.08 83 71 101 30 96.12 0.08 84 71 103 32 96.10 0.09 85 71 105 34 96.00 0.08 86 72 99 27 194.62 0.12 87 72 100 28 169.49 4.40 88 72 101 29 107.11 3.24 89 73 97 24 194.99 0.01 90 73 98 25 194.94 0.03 91 73 99 26 194.64 0.13 92 73 100 27 194.62 0.12 93 74 97 23 195.00 0.01 94 74 98 24 194.97 0.01 95 74 100 26 194.94 0.03