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 4 71 67 14.26 0.24 2 5 20 15 20.14 1.19 3 6 20 14 22.59 0.07 4 6 21 15 22.62 0.08 5 6 24 18 22.61 0.08 6 7 17 10 125.41 1.25 7 7 18 11 74.86 23.82 8 7 21 14 26.68 0.04 9 9 18 9 133.11 2.60 10 12 52 40 81.73 0.17 11 13 52 39 82.83 0.69 12 13 54 41 88.75 0.39 13 14 18 4 226.78 5.09 14 14 21 7 162.83 3.84 15 14 22 8 157.47 1.15 16 14 52 38 88.78 0.40 17 14 53 39 88.78 0.40 18 14 54 40 88.92 0.36 19 14 55 41 89.09 0.37 20 15 18 3 243.38 1.88 21 15 22 7 194.74 7.12 22 15 54 39 89.23 0.44 23 15 55 40 89.09 0.37 24 16 22 6 220.37 6.08 25 16 44 28 88.82 0.32 26 16 47 31 89.00 0.34 27 16 48 32 89.33 0.45 28 16 53 37 89.40 0.42 29 16 55 39 89.34 0.45 30 16 56 40 89.36 0.46 31 16 57 41 89.34 0.46 32 16 59 43 89.14 0.38 33 16 60 44 88.67 0.23 34 16 64 48 88.59 0.25 35 16 65 49 88.59 0.25 36 16 68 52 87.94 0.18 37 18 21 3 252.38 0.46 38 18 22 4 234.96 3.31 39 19 22 3 249.53 0.24 40 19 23 4 242.94 0.70 41 19 67 48 88.69 0.23 42 19 68 49 88.66 0.23 43 19 71 52 88.65 0.23 44 20 23 3 249.08 0.30 45 20 24 4 242.06 1.14 46 20 71 51 88.66 0.24 47 20 74 54 88.24 0.29 48 20 75 55 73.23 1.28 49 21 24 3 249.85 0.08 50 21 25 4 242.06 1.14 51 22 25 3 245.85 0.76 52 22 26 4 242.06 1.14 53 22 47 25 91.93 0.26 54 22 50 28 92.48 0.43 55 22 68 46 88.84 0.29 56 23 26 3 247.12 1.68 57 23 27 4 244.51 2.40 58 23 68 45 88.90 0.29 59 23 71 48 88.81 0.28 60 23 72 49 88.66 0.24 61 24 27 3 249.67 0.18 62 24 28 4 239.43 2.44 63 24 71 47 88.84 0.27 64 24 75 51 63.86 0.65 65 25 28 3 250.06 0.01 66 25 29 4 247.14 1.46 67 25 50 25 92.56 0.47 68 26 29 3 247.14 1.47 69 26 30 4 241.16 4.45 70 26 43 17 92.58 0.48 71 26 46 20 92.59 0.48 72 26 47 21 92.54 0.47 73 26 50 24 92.64 0.44 74 26 68 42 89.48 0.42 75 26 72 46 88.82 0.28 76 27 30 3 247.78 1.15 77 27 31 4 213.24 2.23 78 27 72 45 88.85 0.28 79 27 75 48 82.23 0.22 80 27 76 49 63.60 0.78 81 28 31 3 251.36 0.17 82 30 33 3 248.78 1.35 83 30 46 16 93.02 0.61 84 30 72 42 91.64 0.83 85 33 38 5 234.02 3.12 86 33 46 13 153.32 2.01 87 33 72 39 92.27 1.01 88 34 37 3 256.42 0.28 89 34 38 4 240.63 0.89 90 35 38 3 247.01 3.82 91 35 69 34 92.52 0.89 92 35 72 37 92.50 0.90 93 35 73 38 92.26 1.01 94 35 76 41 89.45 0.81 95 36 73 37 92.52 0.89 96 38 43 5 232.83 0.24 97 38 46 8 224.30 4.49 98 38 72 34 105.00 2.69 99 39 42 3 243.69 1.17 100 39 43 4 240.36 0.82 101 40 43 3 241.68 0.16 102 40 44 4 240.34 0.81 103 40 62 22 116.18 2.40 104 40 65 25 115.93 2.29 105 40 66 26 115.95 2.29 106 40 69 29 115.84 2.24 107 41 44 3 246.85 0.41 108 41 45 4 241.67 0.16 109 42 45 3 252.36 3.06 110 42 46 4 244.12 1.07 111 43 46 3 252.37 3.05 112 43 47 4 243.74 1.26 113 43 65 22 116.22 2.37 114 43 68 25 116.19 2.38 115 43 69 26 116.13 2.35 116 43 72 29 116.12 2.35 117 44 47 3 252.37 3.05 118 44 48 4 243.73 1.26 119 44 57 13 116.56 2.36 120 44 60 16 116.31 2.41 121 44 65 21 116.23 2.38 122 45 48 3 245.05 0.60 123 45 49 4 243.72 1.27 124 46 49 3 246.14 0.77 125 46 50 4 243.34 1.44 126 46 72 26 116.17 2.36 127 47 50 3 245.89 0.90 128 47 53 6 167.52 1.60 129 47 65 18 116.26 2.38 130 47 68 21 116.22 2.37 131 48 53 5 165.62 0.65 132 48 57 9 116.87 2.50 133 50 53 3 225.12 6.08 134 53 57 4 270.30 0.43 135 56 59 3 251.34 0.35 136 57 60 3 263.68 1.03 137 59 64 5 239.52 1.67 138 60 64 4 236.80 0.32 139 60 65 5 236.79 0.32 140 61 64 3 242.02 2.88 141 61 65 4 241.96 2.90 142 62 65 3 242.22 2.77 143 62 66 4 241.96 2.90 144 63 66 3 247.69 0.03 145 63 67 4 241.96 2.90 146 64 67 3 247.28 0.23 147 64 68 4 243.86 1.95 148 65 68 3 241.38 0.70 149 65 69 4 239.83 0.07 150 66 69 3 240.94 0.26 151 66 70 4 239.09 1.35 152 67 70 3 248.93 1.75 153 67 71 4 239.09 1.34 154 68 71 3 245.37 1.45 155 68 72 4 239.09 1.34 156 69 72 3 242.42 0.32 157 69 73 4 242.44 0.33 158 70 73 3 241.28 0.91 159 70 74 4 239.81 1.64 160 71 74 3 241.94 0.58 161 71 75 4 239.83 1.65 162 72 75 3 245.09 0.84 163 72 76 4 239.76 1.67 164 73 76 3 239.77 1.68