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 25.20 0.39 2 16 19 3 37.37 0.42 3 16 20 4 32.09 0.96 4 17 20 3 37.39 0.41 5 17 21 4 30.40 0.11 6 18 21 3 33.66 1.46 7 18 22 4 30.41 0.12 8 19 22 3 37.27 0.35 9 19 23 4 30.39 0.14 10 20 23 3 37.27 0.35 11 20 24 4 30.16 0.20 12 21 24 3 35.81 1.08 13 21 25 4 31.92 0.72 14 21 62 41 29.58 0.45 15 22 25 3 35.75 0.32 16 24 59 35 114.00 1.36 17 24 60 36 92.20 0.73 18 25 60 35 115.03 1.16 19 25 61 36 105.20 1.60 20 25 62 37 114.99 1.13 21 25 104 79 106.78 0.55 22 26 58 32 115.30 1.21 23 26 59 33 115.23 1.22 24 26 60 34 115.22 1.22 25 26 61 35 115.18 1.22 26 26 102 76 115.22 1.22 27 26 103 77 115.18 1.22 28 26 104 78 113.80 0.90 29 27 57 30 115.31 1.20 30 27 58 31 115.43 1.21 31 27 102 75 115.20 1.21 32 28 56 28 115.45 1.23 33 28 57 29 115.44 1.22 34 28 99 71 115.26 1.22 35 28 100 72 115.31 1.22 36 28 101 73 115.25 1.22 37 28 102 74 115.31 1.21 38 29 55 26 115.56 1.22 39 29 56 27 115.54 1.22 40 29 58 29 115.53 1.23 41 30 54 24 188.12 0.91 42 30 55 25 115.59 1.20 43 31 56 25 130.44 8.63 44 57 68 11 115.50 1.24 45 57 69 12 115.55 1.23 46 57 70 13 115.62 1.22 47 58 68 10 115.51 1.24 48 61 66 5 115.46 1.22 49 61 67 6 115.44 1.22 50 61 68 7 115.27 1.23 51 63 66 3 115.44 1.22 52 64 107 43 115.23 1.22 53 65 106 41 115.21 1.22 54 65 107 42 115.17 1.21 55 66 104 38 115.23 1.22 56 66 105 39 115.20 1.22 57 66 106 40 111.03 2.15 58 67 103 36 115.45 1.22 59 67 104 37 115.20 1.22 60 67 105 38 114.95 1.16 61 67 106 39 103.03 1.31 62 67 107 40 61.40 0.73 63 68 102 34 115.44 1.22 64 68 103 35 115.23 1.22 65 68 104 36 115.22 1.22 66 69 102 33 115.45 1.22 67 69 103 34 115.43 1.21 68 69 105 36 115.23 1.22 69 70 99 29 115.23 1.22 70 70 101 31 115.45 1.22 71 70 102 32 115.45 1.22 72 71 101 30 115.55 1.25 73 71 102 31 115.56 1.24 74 71 103 32 115.55 1.24 75 71 105 34 115.51 1.24 76 72 100 28 115.60 1.22 77 72 101 29 115.59 1.23 78 73 99 26 187.55 0.21 79 73 100 27 176.25 5.86