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 2 14 12 20.73 0.01 2 2 38 36 33.17 0.62 3 2 39 37 32.62 0.39 4 3 10 7 36.06 0.84 5 3 11 8 33.63 0.64 6 3 38 35 34.65 1.12 7 4 9 5 149.13 5.71 8 4 10 6 75.39 18.75 9 4 11 7 33.63 0.64 10 4 13 9 33.59 0.65 11 4 29 25 36.50 0.61 12 4 32 28 35.01 1.28 13 4 33 29 34.65 1.12 14 4 36 32 34.80 1.19 15 4 38 34 34.66 1.12 16 5 9 4 149.13 5.71 17 5 10 5 84.86 23.07 18 6 9 3 171.53 0.10 19 6 11 5 149.13 5.71 20 6 28 22 39.12 0.59 21 6 29 23 38.80 0.73 22 6 32 26 38.77 0.73 23 7 26 19 44.81 2.22 24 7 28 21 40.49 0.07 25 7 29 22 40.47 0.06 26 9 24 15 64.12 0.24 27 11 19 8 88.59 12.48 28 11 21 10 64.27 0.32 29 11 24 13 64.28 0.32 30 11 29 18 64.30 0.32 31 12 19 7 88.61 12.47 32 12 20 8 64.27 0.32 33 12 21 9 64.30 0.32 34 13 17 4 134.06 1.49 35 13 18 5 88.62 12.48 36 13 19 6 88.64 12.46 37 13 20 7 88.61 12.46 38 13 33 20 86.05 1.12 39 13 36 23 89.84 0.33 40 13 38 25 94.23 2.52 41 13 39 26 94.20 2.52 42 14 17 3 152.90 4.14 43 14 18 4 132.57 0.74 44 14 20 6 88.69 12.45 45 14 110 96 64.39 0.31 46 15 39 24 94.30 2.56 47 16 39 23 94.30 2.56 48 16 104 88 92.80 1.94 49 17 33 16 93.27 2.04 50 17 39 22 94.31 2.57 51 17 104 87 92.86 1.92 52 18 99 81 94.31 2.58 53 18 100 82 94.32 2.58 54 18 103 85 92.87 1.92 55 18 104 86 92.87 1.92 56 18 108 90 89.31 0.44 57 18 109 91 83.47 0.20 58 18 110 92 82.50 0.00 59 18 111 93 82.48 0.00 60 19 22 3 164.08 1.73 61 19 25 6 123.99 3.21 62 19 29 10 110.01 10.14 63 19 33 14 94.48 2.46 64 19 107 88 89.68 0.38 65 19 109 90 88.56 0.62 66 20 109 89 89.44 0.49 67 20 110 90 89.45 0.50 68 21 24 3 172.02 2.33 69 22 25 3 174.80 0.95 70 22 58 36 100.83 4.80 71 22 61 39 100.48 5.18 72 22 62 40 101.05 4.90 73 22 107 85 94.48 2.46 74 22 109 87 89.72 0.48 75 23 58 35 101.50 4.69 76 24 29 5 168.62 0.65 77 25 29 4 168.62 0.65 78 25 30 5 165.01 1.15 79 25 33 8 156.99 0.42 80 25 54 29 106.74 2.33 81 25 58 33 105.00 3.20 82 25 105 80 105.06 3.18 83 25 106 81 104.95 3.15 84 25 107 82 101.06 3.71 85 26 29 3 168.78 0.70 86 26 30 4 168.63 0.64 87 27 30 3 170.47 1.52 88 27 31 4 171.35 0.71 89 27 51 24 108.17 1.53 90 28 31 3 173.88 1.97 91 28 32 4 171.37 0.71 92 29 32 3 169.19 1.80 93 29 33 4 169.09 1.85 94 30 33 3 172.71 0.06 95 30 34 4 169.16 1.84 96 30 46 16 108.64 1.36 97 30 51 21 108.48 1.45 98 30 105 75 108.34 1.55 99 31 34 3 172.72 0.07 100 31 35 4 172.73 0.06 101 31 46 15 108.66 1.36 102 31 51 20 108.51 1.46 103 32 35 3 174.41 0.72 104 32 36 4 169.00 1.91 105 33 36 3 171.88 0.37 106 33 104 71 108.58 1.52 107 33 105 72 108.50 1.48 108 33 107 74 108.50 1.47 109 34 43 9 119.65 2.74 110 34 44 10 108.83 1.29 111 34 46 12 108.84 1.29 112 34 105 71 108.58 1.50 113 35 43 8 114.22 0.03 114 36 39 3 184.66 1.17 115 36 40 4 160.09 3.17 116 36 104 68 109.28 1.28 117 37 40 3 167.68 0.61 118 37 42 5 152.66 7.83 119 37 43 6 138.18 1.64 120 39 96 57 335.39 0.28 121 39 104 65 123.78 0.26 122 40 104 64 161.35 0.73 123 44 101 57 206.24 1.53 124 44 105 61 194.56 0.37 125 46 105 59 204.61 1.33 126 53 102 49 206.27 1.54 127 54 105 51 205.84 1.75 128 54 106 52 196.89 0.78 129 57 102 45 333.72 0.32 130 57 103 46 226.03 8.20 131 57 106 49 205.84 1.75 132 57 108 51 204.52 1.73 133 58 106 48 205.84 1.75 134 58 107 49 205.84 1.75 135 58 108 50 205.45 1.79 136 61 108 47 205.79 1.74 137 61 109 48 205.78 1.74 138 66 112 46 154.86 0.38 139 67 103 36 334.38 0.54 140 67 108 41 205.52 1.85 141 67 111 44 154.87 0.38 142 67 112 45 130.56 1.28 143 67 113 46 128.19 1.56 144 67 114 47 127.61 1.37 145 68 114 46 127.28 1.28 146 69 113 44 127.30 1.30 147 69 114 45 127.20 1.30 148 69 115 46 127.14 1.27 149 70 114 44 127.14 1.28 150 70 115 45 126.85 1.18 151 94 101 7 205.84 1.75 152 94 102 8 205.77 1.74 153 94 105 11 200.40 0.33 154 95 101 6 205.81 1.74 155 96 100 4 205.73 1.74 156 96 101 5 205.55 1.80 157 97 100 3 205.84 1.75 158 97 101 4 205.72 1.75 159 97 102 5 205.58 1.81 160 98 102 4 205.57 1.81 161 98 103 5 205.56 1.81 162 98 114 16 125.35 0.69 163 99 103 4 205.66 1.75 164 99 104 5 205.55 1.80 165 99 111 12 127.23 1.30 166 99 114 15 125.25 0.74 167 100 104 4 205.65 1.74 168 101 104 3 205.62 1.73 169 101 105 4 201.07 0.56 170 102 105 3 200.44 0.87 171 102 106 4 198.75 1.72 172 103 106 3 200.16 1.01 173 103 107 4 194.88 1.78 174 103 108 5 181.71 2.79 175 103 111 8 127.58 1.12 176 103 114 11 126.56 1.27 177 104 107 3 196.75 2.71 178 111 114 3 179.22 0.65