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 23 31 8 25.51 0.14 2 24 27 3 36.54 0.90 3 24 28 4 32.29 1.20 4 25 28 3 32.31 1.21 5 25 29 4 32.29 1.19 6 26 29 3 32.29 1.20 7 26 30 4 30.31 0.21 8 27 30 3 35.39 0.80 9 27 31 4 30.22 0.26 10 28 31 3 36.66 0.16 11 28 32 4 33.24 0.28 12 29 32 3 37.49 0.17 13 29 33 4 29.68 0.02 14 29 70 41 30.17 0.28 15 32 67 35 112.17 0.54 16 32 68 36 86.98 0.42 17 33 67 34 112.29 0.53 18 33 68 35 112.27 0.53 19 33 69 36 73.01 1.12 20 33 70 37 111.50 0.28 21 33 112 79 84.53 0.42 22 34 66 32 112.35 0.54 23 34 67 33 112.31 0.53 24 34 69 35 112.27 0.53 25 34 110 76 112.28 0.53 26 34 111 77 112.28 0.53 27 34 112 78 105.57 0.93 28 35 64 29 112.41 0.53 29 35 65 30 112.31 0.53 30 35 66 31 112.32 0.52 31 35 110 75 112.28 0.53 32 36 63 27 112.45 0.53 33 36 64 28 112.40 0.53 34 36 65 29 112.33 0.53 35 36 107 71 112.37 0.54 36 36 110 74 112.30 0.53 37 37 62 25 193.25 1.54 38 37 63 26 112.48 0.54 39 37 64 27 112.44 0.53 40 37 66 29 112.44 0.53 41 38 62 24 193.25 1.54 42 38 63 25 113.80 1.17 43 39 64 25 156.22 4.53 44 65 76 11 112.39 0.53 45 65 77 12 112.42 0.54 46 65 78 13 112.52 0.53 47 66 76 10 112.38 0.53 48 67 76 9 112.38 0.53 49 69 74 5 112.39 0.53 50 69 75 6 112.37 0.53 51 69 76 7 112.33 0.53 52 71 74 3 112.38 0.53 53 72 115 43 112.31 0.53 54 73 114 41 112.30 0.53 55 73 115 42 112.12 0.48 56 74 112 38 112.31 0.53 57 74 113 39 112.28 0.53 58 74 114 40 94.48 0.30 59 74 115 41 74.92 0.03 60 75 112 37 112.29 0.52 61 75 113 38 112.28 0.53 62 75 115 40 56.38 0.91 63 76 110 34 112.33 0.52 64 76 111 35 112.31 0.53 65 76 112 36 112.28 0.53 66 77 110 33 112.37 0.53 67 77 111 34 112.33 0.53 68 77 113 36 112.31 0.53 69 78 107 29 112.56 0.58 70 78 109 31 112.44 0.53 71 78 110 32 112.40 0.53 72 79 109 30 112.49 0.54 73 79 111 32 112.44 0.53 74 79 113 34 112.41 0.54 75 80 108 28 112.65 0.60 76 80 109 29 112.53 0.55 77 81 106 25 195.90 0.04 78 81 107 26 130.24 6.33 79 81 108 27 112.67 0.59