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 3 49 46 60.69 6.57 2 3 72 69 30.67 0.30 3 3 75 72 30.31 0.14 4 3 76 73 29.59 0.47 5 4 7 3 274.79 2.91 6 4 8 4 262.24 2.53 7 5 8 3 279.82 0.40 8 5 9 4 262.19 2.52 9 5 24 19 63.28 3.86 10 5 28 23 51.11 2.14 11 5 68 63 42.27 0.30 12 5 72 67 37.42 0.96 13 6 9 3 270.39 1.55 14 6 10 4 273.94 3.35 15 7 10 3 279.85 0.41 16 7 11 4 274.84 2.91 17 8 11 3 274.84 2.91 18 8 12 4 274.83 2.91 19 8 49 41 79.64 11.06 20 8 72 64 47.70 0.59 21 9 12 3 274.83 2.91 22 9 13 4 273.37 3.64 23 9 22 13 120.08 1.46 24 9 24 15 66.84 2.10 25 10 13 3 275.47 2.59 26 10 14 4 275.03 2.81 27 11 14 3 273.94 0.29 28 11 15 4 259.57 3.25 29 11 45 34 80.21 11.23 30 11 48 37 80.25 11.22 31 11 52 41 80.49 11.37 32 12 15 3 273.94 0.29 33 12 16 4 254.88 0.93 34 12 24 12 120.81 1.09 35 12 32 20 82.33 8.75 36 12 37 25 83.86 9.34 37 12 42 30 80.23 11.21 38 12 45 33 80.22 11.23 39 12 68 56 59.61 0.94 40 13 16 3 258.12 0.34 41 13 17 4 233.07 2.65 42 13 18 5 202.27 2.65 43 13 22 9 127.59 2.99 44 13 37 24 83.92 9.33 45 15 41 26 83.41 9.64 46 15 44 29 83.35 9.67 47 15 45 30 83.36 9.67 48 16 37 21 83.89 9.35 49 16 41 25 83.40 9.64 50 18 22 4 183.08 5.62 51 18 37 19 88.09 7.29 52 22 37 15 105.46 4.56 53 23 26 3 273.87 0.09 54 23 27 4 265.14 1.06 55 24 27 3 276.61 1.46 56 24 28 4 265.11 1.07 57 24 68 44 96.85 2.95 58 25 28 3 289.00 0.91 59 27 30 3 273.61 0.24 60 27 35 8 178.08 1.12 61 27 68 41 101.45 1.74 62 28 67 39 102.78 1.69 63 28 68 40 101.08 1.55 64 28 69 41 100.23 1.60 65 29 67 38 102.80 1.70 66 29 69 40 102.54 1.58 67 30 34 4 267.97 2.55 68 30 35 5 258.37 1.80 69 30 68 38 103.12 1.79 70 31 34 3 270.63 1.22 71 31 35 4 268.06 2.50 72 31 66 35 103.17 1.81 73 31 67 36 103.12 1.79 74 32 35 3 267.98 2.54 75 32 36 4 263.88 0.50 76 32 37 5 214.00 1.89 77 32 42 10 196.48 3.11 78 32 66 34 103.23 1.79 79 32 67 35 103.23 1.78 80 32 68 36 104.17 1.31 81 32 71 39 104.16 1.33 82 33 37 4 267.97 2.54 83 37 41 4 267.41 1.30 84 37 42 5 266.47 0.83 85 38 41 3 270.25 0.12 86 38 42 4 266.49 0.83 87 39 42 3 267.98 1.57 88 39 43 4 266.49 0.82 89 40 43 3 268.36 1.76 90 40 44 4 271.34 0.27 91 41 44 3 271.36 0.26 92 41 45 4 271.38 0.24 93 42 45 3 273.91 1.51 94 42 46 4 271.38 0.24 95 42 62 20 113.44 1.73 96 42 71 29 110.89 2.20 97 43 46 3 271.39 0.24 98 43 47 4 271.38 0.24 99 43 58 15 113.51 1.68 100 43 59 16 113.52 1.68 101 43 62 19 113.52 1.69 102 44 47 3 280.72 1.90 103 44 48 4 271.37 0.24 104 45 48 3 274.00 2.00 105 45 49 4 268.55 0.71 106 46 49 3 270.37 0.20 107 46 50 4 270.36 0.20 108 46 57 11 128.77 1.26 109 46 58 12 128.50 1.12 110 47 50 3 271.35 0.82 111 47 51 4 267.44 0.15 112 48 51 3 270.21 1.07 113 48 52 4 267.80 0.33 114 49 52 3 281.00 1.34 115 49 53 4 268.41 1.71 116 49 57 8 185.25 11.48 117 49 71 22 89.48 13.86 118 49 75 26 89.17 13.88 119 50 53 3 272.69 0.44 120 50 54 4 236.90 13.73 121 50 55 5 190.30 8.97 122 50 56 6 190.30 8.97 123 50 58 8 188.80 9.71 124 55 75 20 89.34 13.93 125 56 61 5 255.37 3.42 126 57 61 4 257.13 2.53 127 57 62 5 255.34 3.42 128 57 71 14 99.92 11.30 129 57 74 17 89.43 13.88 130 57 75 18 89.45 13.88 131 58 61 3 279.94 3.02 132 58 62 4 263.56 1.38 133 59 62 3 266.60 0.14 134 59 63 4 255.39 3.43 135 60 63 3 273.10 1.52 136 61 64 3 271.85 0.89 137 61 65 4 264.56 1.15 138 62 65 3 268.91 3.60 139 62 71 9 141.97 0.34 140 65 70 5 246.04 1.12 141 67 70 3 271.37 0.46 142 67 71 4 268.20 0.91 143 68 71 3 268.20 0.91 144 68 72 4 268.75 0.63 145 69 72 3 270.23 0.11 146 69 73 4 257.23 1.97 147 70 73 3 265.48 2.16 148 70 74 4 257.24 1.97 149 71 74 3 279.19 4.70 150 71 75 4 269.69 1.10 151 72 75 3 279.10 4.74 152 72 76 4 256.63 1.73 153 73 76 3 263.81 1.88 154 73 77 4 256.61 1.72 155 74 77 3 264.29 1.65 156 74 78 4 258.81 2.52