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 25 28 3 40.98 1.45 2 25 29 4 37.16 0.18 3 26 29 3 38.15 0.04 4 26 30 4 37.27 0.24 5 27 30 3 38.15 0.03 6 27 31 4 37.49 0.35 7 28 31 3 41.68 1.72 8 28 32 4 37.27 0.24 9 29 32 3 45.42 0.15 10 29 33 4 37.35 0.18 11 30 33 3 45.74 0.32 12 30 34 4 35.09 0.75 13 30 70 40 33.96 0.21 14 30 71 41 33.95 0.21 15 31 34 3 37.84 0.57 16 33 68 35 116.92 2.66 17 33 69 36 110.97 0.18 18 34 69 35 116.98 2.68 19 34 70 36 111.86 0.27 20 34 113 79 111.92 0.24 21 35 67 32 117.17 2.65 22 35 68 33 117.05 2.68 23 35 69 34 117.05 2.68 24 35 70 35 117.03 2.69 25 35 111 76 117.05 2.68 26 35 112 77 117.01 2.68 27 35 113 78 116.79 2.57 28 36 66 30 117.16 2.65 29 36 67 31 117.17 2.64 30 36 111 75 117.03 2.68 31 37 64 27 117.25 2.65 32 37 65 28 117.21 2.65 33 37 66 29 117.19 2.65 34 37 108 71 117.17 2.66 35 37 109 72 117.17 2.66 36 37 111 74 117.06 2.69 37 38 64 26 117.30 2.64 38 38 65 27 117.26 2.66 39 38 67 29 117.25 2.65 40 39 64 25 120.70 0.94 41 40 65 25 180.69 9.63 42 66 77 11 117.22 2.65 43 66 78 12 117.25 2.65 44 66 79 13 117.30 2.65 45 67 77 10 117.22 2.65 46 68 77 9 117.22 2.65 47 70 75 5 117.23 2.65 48 70 76 6 117.19 2.65 49 70 77 7 117.17 2.65 50 72 75 3 117.20 2.65 51 73 116 43 117.06 2.68 52 74 115 41 117.05 2.68 53 74 116 42 117.02 2.68 54 75 113 38 117.06 2.68 55 75 114 39 117.05 2.69 56 75 115 40 116.97 2.68 57 76 113 37 117.05 2.68 58 76 114 38 117.02 2.67 59 76 116 40 62.36 0.21 60 77 111 34 117.19 2.65 61 77 112 35 117.05 2.68 62 77 113 36 117.05 2.68 63 78 111 33 117.20 2.65 64 78 112 34 117.19 2.65 65 78 114 36 117.05 2.68 66 79 108 29 117.25 2.65 67 79 110 31 117.25 2.65 68 79 111 32 117.20 2.65 69 80 110 30 117.28 2.65 70 80 111 31 117.28 2.65 71 80 112 32 117.25 2.65 72 80 114 34 117.23 2.65 73 81 109 28 177.49 6.46 74 81 110 29 140.91 2.06 75 82 108 26 194.72 2.58 76 82 109 27 182.59 7.77