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 8 31 23 30.02 0.18 2 8 32 24 28.90 0.43 3 8 33 25 25.95 0.11 4 8 34 26 28.06 0.47 5 10 34 24 58.56 14.32 6 11 16 5 224.44 5.03 7 11 17 6 191.28 7.67 8 11 34 23 58.48 14.29 9 12 16 4 241.66 2.85 10 13 16 3 253.72 0.14 11 13 17 4 235.87 0.05 12 14 17 3 244.71 4.37 13 14 18 4 240.47 2.04 14 15 18 3 253.72 0.14 15 15 19 4 243.74 2.21 16 15 78 63 39.11 0.14 17 15 81 66 33.73 0.17 18 15 82 67 25.73 0.34 19 16 19 3 250.99 0.15 20 16 20 4 239.82 1.27 21 16 34 18 110.03 2.44 22 16 74 58 42.84 0.29 23 16 75 59 42.96 0.33 24 16 78 62 39.27 0.17 25 17 20 3 250.90 0.21 26 17 21 4 250.90 0.20 27 18 21 3 249.48 0.51 28 18 22 4 249.47 0.51 29 18 54 36 90.56 1.51 30 18 58 40 89.78 1.64 31 18 59 41 89.86 1.59 32 19 22 3 252.67 0.74 33 19 23 4 243.67 0.54 34 19 51 32 90.67 1.46 35 19 55 36 89.93 1.58 36 19 74 55 57.04 1.22 37 19 77 58 46.52 2.07 38 19 78 59 46.52 2.08 39 19 81 62 46.43 2.03 40 20 23 3 250.84 0.17 41 20 24 4 247.18 1.21 42 20 32 12 127.45 1.28 43 20 74 54 57.80 1.02 44 21 24 3 257.55 3.98 45 21 25 4 240.77 1.91 46 22 25 3 241.62 2.33 47 22 26 4 237.31 0.29 48 22 50 28 91.37 1.14 49 22 51 29 90.95 1.32 50 22 54 32 90.58 1.51 51 23 27 4 212.47 6.66 52 23 29 6 197.88 7.21 53 23 32 9 148.05 6.92 54 23 36 13 122.42 1.72 55 23 37 14 113.03 1.06 56 23 38 15 111.88 1.52 57 23 51 28 90.81 1.40 58 23 73 50 80.72 0.62 59 23 74 51 74.86 0.56 60 24 28 4 188.75 2.50 61 24 29 5 156.35 2.82 62 24 30 6 156.33 2.81 63 24 31 7 156.31 2.81 64 24 32 8 150.01 5.95 65 25 28 3 228.68 2.04 66 26 47 21 92.05 1.24 67 26 50 24 91.76 1.16 68 26 51 25 91.78 1.16 69 27 38 11 111.95 1.56 70 27 47 20 92.19 1.21 71 27 48 21 92.08 1.26 72 27 51 24 92.05 1.25 73 29 32 3 272.50 1.88 74 32 36 4 240.50 0.55 75 32 74 42 81.67 0.21 76 33 36 3 248.56 0.17 77 33 74 41 81.70 0.20 78 34 73 39 81.90 0.11 79 34 74 40 81.65 0.20 80 34 75 41 81.64 0.20 81 35 73 38 81.89 0.12 82 35 75 40 81.67 0.21 83 36 40 4 245.49 2.50 84 36 73 37 81.88 0.12 85 37 40 3 248.07 1.21 86 37 72 35 81.95 0.12 87 38 48 10 92.03 1.29 88 38 51 13 92.10 1.27 89 38 68 30 89.21 1.82 90 38 72 34 81.95 0.12 91 38 73 35 81.83 0.14 92 38 77 39 80.34 0.12 93 39 43 4 238.62 3.21 94 45 48 3 252.09 0.30 95 45 49 4 248.04 2.33 96 45 69 24 89.44 1.72 97 46 49 3 248.63 2.62 98 46 50 4 248.05 2.33 99 47 50 3 251.47 0.61 100 47 51 4 252.07 0.91 101 48 51 3 252.08 0.91 102 48 52 4 252.09 0.90 103 48 68 20 89.30 1.78 104 49 52 3 252.09 0.90 105 49 53 4 252.14 0.88 106 49 65 16 89.41 1.70 107 49 68 19 89.31 1.77 108 50 53 3 252.15 0.87 109 50 54 4 252.13 0.86 110 51 54 3 252.12 0.86 111 51 55 4 252.12 0.86 112 52 55 3 252.08 0.84 113 52 56 4 245.78 2.29 114 52 63 11 92.42 0.25 115 52 68 16 89.30 1.76 116 53 56 3 251.42 0.65 117 53 57 4 244.96 1.97 118 54 57 3 253.80 0.07 119 54 58 4 235.85 1.55 120 55 58 3 242.80 1.85 121 55 59 4 235.80 1.52 122 55 61 6 200.44 4.92 123 55 63 8 129.07 3.00 124 55 77 22 61.80 0.33 125 55 81 26 51.77 0.60 126 56 59 3 238.39 2.81 127 56 60 4 215.82 0.62 128 59 81 22 51.76 0.58 129 61 81 20 57.55 1.07 130 62 80 18 89.74 11.84 131 63 67 4 246.68 0.00 132 63 68 5 238.97 2.61 133 63 77 14 105.95 4.02 134 63 80 17 89.39 14.11 135 64 67 3 248.69 1.01 136 64 68 4 246.69 0.01 137 65 68 3 246.47 0.12 138 65 69 4 246.47 0.12 139 66 69 3 246.56 0.08 140 66 70 4 246.25 0.23 141 67 70 3 246.16 2.77 142 67 71 4 242.47 0.93 143 67 80 13 149.96 2.72 144 68 71 3 246.16 2.77 145 68 72 4 228.38 7.87 146 68 77 9 171.58 0.19 147 69 72 3 247.91 1.90 148 71 76 5 200.97 2.64 149 71 77 6 202.53 1.50 150 71 80 9 173.91 0.96 151 72 77 5 240.53 0.38 152 73 76 3 243.84 1.84 153 73 77 4 241.38 0.81 154 74 77 3 247.61 0.58 155 74 78 4 241.38 0.81 156 75 78 3 247.39 2.31 157 75 79 4 243.36 1.55 158 76 79 3 244.62 0.93 159 76 80 4 244.67 0.90 160 77 80 3 246.81 1.97 161 77 81 4 242.62 0.14 162 78 81 3 244.72 0.91 163 78 82 4 242.49 0.21 164 79 82 3 244.87 0.62 165 79 83 4 236.52 2.73 166 80 83 3 259.50 0.75