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 22 25 3 255.50 2.88 2 22 26 4 229.74 1.55 3 23 27 4 252.30 0.54 4 23 58 35 105.66 0.34 5 24 64 40 101.81 1.05 6 24 68 44 101.75 1.07 7 25 28 3 255.95 1.83 8 25 29 4 250.62 0.18 9 26 29 3 261.95 1.24 10 26 30 4 250.65 0.19 11 26 54 28 116.95 2.23 12 26 57 31 116.87 2.19 13 27 30 3 255.31 2.08 14 27 31 4 253.50 1.23 15 27 50 23 117.09 2.19 16 27 54 27 116.95 2.23 17 27 58 31 116.95 2.23 18 27 60 33 114.22 2.75 19 27 64 37 110.53 3.15 20 27 65 38 105.34 0.57 21 28 31 3 256.87 1.31 22 28 32 4 253.50 1.24 23 28 68 40 105.19 0.55 24 28 72 44 103.53 1.38 25 29 32 3 254.60 0.68 26 29 33 4 250.37 0.33 27 30 33 3 254.59 0.68 28 30 34 4 250.20 0.24 29 30 50 20 117.25 2.15 30 30 54 24 117.23 2.15 31 31 34 3 255.27 0.36 32 31 35 4 250.19 0.24 33 31 46 15 119.56 1.10 34 31 50 19 117.40 2.10 35 31 65 34 110.56 3.14 36 31 68 37 107.03 1.39 37 31 69 38 105.26 0.53 38 31 72 41 105.22 0.55 39 31 78 47 88.28 1.32 40 32 35 3 252.41 1.06 41 32 36 4 246.24 1.59 42 32 72 40 103.56 1.39 43 32 90 58 65.56 0.60 44 33 36 3 250.41 0.33 45 33 37 4 250.41 0.33 46 34 37 3 259.26 0.84 47 34 38 4 250.25 0.41 48 34 41 7 211.31 1.12 49 34 46 12 148.44 2.07 50 34 49 15 123.88 1.11 51 34 50 16 121.73 0.06 52 34 53 19 121.70 0.04 53 35 38 3 250.41 0.33 54 35 39 4 242.84 0.09 55 35 41 6 216.78 6.38 56 35 46 11 157.66 0.88 57 35 78 43 88.28 1.32 58 35 88 53 72.17 1.31 59 35 89 54 71.06 1.17 60 35 90 55 65.51 0.58 61 36 39 3 253.69 0.80 62 36 90 54 66.59 0.47 63 38 41 3 277.17 3.09 64 38 49 11 180.37 1.29 65 39 89 50 71.66 1.30 66 39 90 51 70.33 1.14 67 40 81 41 88.20 1.34 68 40 87 47 72.33 1.29 69 40 88 48 72.20 1.31 70 40 89 49 71.67 1.30 71 41 45 4 240.99 4.15 72 41 46 5 234.51 0.95 73 41 49 8 234.04 1.15 74 41 88 47 72.18 1.32 75 42 45 3 246.41 1.44 76 42 46 4 234.62 0.96 77 42 86 44 72.42 1.24 78 42 87 45 72.18 1.32 79 43 46 3 247.40 1.94 80 43 47 4 242.99 3.16 81 43 66 23 114.55 2.81 82 43 69 26 114.50 2.79 83 43 86 43 72.23 1.29 84 43 88 45 72.18 1.32 85 44 47 3 250.57 0.39 86 44 48 4 243.69 3.79 87 45 48 3 256.58 3.36 88 45 49 4 250.56 0.35 89 46 49 3 253.74 1.24 90 46 50 4 244.19 2.83 91 46 69 23 114.30 2.71 92 46 88 42 72.17 1.32 93 47 50 3 253.74 1.24 94 47 51 4 236.87 0.35 95 47 62 15 114.86 2.65 96 47 65 18 114.56 2.81 97 48 51 3 253.76 0.51 98 48 52 4 236.88 0.35 99 49 52 3 253.75 0.52 100 49 53 4 239.91 1.86 101 50 53 3 246.30 1.48 102 50 54 4 239.83 1.90 103 50 65 15 114.52 2.83 104 51 55 4 247.24 5.11 105 51 60 9 115.62 2.50 106 51 65 14 114.67 2.75 107 52 55 3 261.51 2.02 108 54 58 4 232.12 0.60 109 54 60 6 146.89 4.58 110 55 58 3 250.71 0.69 111 55 60 5 163.13 1.32 112 61 64 3 269.42 1.94 113 61 65 4 245.59 0.24 114 62 65 3 245.62 0.21 115 62 66 4 243.81 1.12 116 63 66 3 254.15 1.80 117 63 67 4 248.29 1.07 118 64 67 3 255.66 2.60 119 64 68 4 248.30 1.07 120 65 68 3 251.49 0.52 121 65 69 4 248.78 0.83 122 66 69 3 253.07 0.27 123 66 70 4 251.67 0.61 124 67 70 3 253.44 0.70 125 67 71 4 254.93 1.45 126 68 71 3 258.50 0.24 127 68 72 4 255.51 1.26 128 69 72 3 257.63 0.21 129 69 73 4 253.00 0.01 130 69 78 9 150.84 0.94 131 69 88 19 72.16 1.31 132 70 73 3 262.45 0.64 133 70 74 4 253.02 0.01 134 70 80 10 150.81 0.94 135 71 74 3 260.75 1.49 136 71 75 4 250.28 1.38 137 72 75 3 255.41 1.19 138 72 76 4 250.27 1.38 139 72 77 5 183.16 5.41 140 72 78 6 168.36 1.21 141 73 76 3 255.41 1.19 142 73 78 5 150.91 0.93 143 73 79 6 150.90 0.93 144 73 80 7 150.91 0.93 145 73 88 15 72.23 1.31 146 76 91 15 68.75 1.94 147 76 92 16 65.54 0.59 148 77 90 13 71.27 1.13 149 77 91 14 68.70 1.97 150 77 92 15 65.09 0.41 151 78 89 11 71.50 1.23 152 78 90 12 69.16 1.74 153 78 91 13 65.89 0.58 154 79 88 9 72.22 1.31 155 79 89 10 72.11 1.31 156 79 91 12 69.92 1.46 157 80 85 5 131.56 0.67 158 80 87 7 72.31 1.32 159 80 88 8 72.23 1.31 160 80 89 9 72.22 1.31 161 81 84 3 257.38 1.92 162 81 87 6 97.27 11.14 163 81 89 8 72.28 1.30 164 84 87 3 266.76 0.10 165 85 88 3 287.29 0.73