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 13 44 31 78.44 0.67 2 13 45 32 77.72 0.99 3 13 46 33 76.31 0.66 4 14 44 30 78.61 0.58 5 14 45 31 77.78 0.99 6 14 46 32 77.78 0.99 7 14 47 33 77.71 0.99 8 14 55 41 77.78 0.99 9 14 111 97 77.78 0.99 10 14 112 98 77.73 0.98 11 14 113 99 77.70 0.98 12 15 43 28 79.66 0.06 13 15 44 29 79.88 0.17 14 15 111 96 77.77 0.99 15 16 41 25 80.25 0.18 16 16 42 26 80.17 0.17 17 16 108 92 80.14 0.20 18 16 109 93 80.07 0.12 19 16 111 95 78.36 0.70 20 17 41 24 80.28 0.19 21 17 42 25 80.20 0.17 22 17 44 27 80.18 0.16 23 18 41 23 80.30 0.18 24 18 42 24 80.30 0.18 25 19 39 20 80.45 0.21 26 19 40 21 80.40 0.21 27 19 41 22 80.35 0.21 28 19 42 23 80.36 0.21 29 20 37 17 82.17 0.49 30 20 38 18 80.58 0.18 31 20 39 19 80.45 0.22 32 21 26 5 130.29 0.92 33 21 37 16 82.19 0.49 34 21 38 17 81.75 0.33 35 21 40 19 80.44 0.22 36 22 25 3 134.87 1.83 37 22 26 4 131.51 0.32 38 22 37 15 82.19 0.49 39 23 26 3 131.51 0.32 40 23 27 4 128.21 1.96 41 23 28 5 123.05 0.22 42 23 29 6 119.70 0.77 43 23 32 9 108.23 1.33 44 23 35 12 84.98 0.98 45 23 36 13 82.32 0.54 46 23 37 14 82.23 0.52 47 23 38 15 82.24 0.52 48 24 27 3 128.22 1.96 49 24 29 5 123.07 0.23 50 27 30 3 145.70 0.03 51 28 31 3 139.75 2.02 52 28 32 4 125.98 0.25 53 29 32 3 126.88 0.15 54 31 91 60 127.59 1.59 55 31 92 61 129.38 2.02 56 31 103 72 178.47 3.62 57 32 35 3 226.10 3.12 58 32 89 57 123.38 0.09 59 32 90 58 123.70 0.13 60 32 91 59 123.71 0.13 61 33 90 57 123.28 0.07 62 33 91 58 123.36 0.10 63 33 92 59 126.42 1.01 64 34 89 55 110.20 0.47 65 34 90 56 115.62 0.18 66 35 88 53 106.83 0.20 67 35 89 54 106.92 0.15 68 38 87 49 84.02 0.64 69 43 79 36 80.17 0.16 70 43 80 37 80.17 0.16 71 43 81 38 80.26 0.17 72 44 79 35 80.16 0.16 73 45 79 34 80.12 0.14 74 46 76 30 80.29 0.17 75 47 76 29 80.22 0.14 76 47 77 30 80.17 0.16 77 47 78 31 80.05 0.15 78 47 79 32 78.25 0.78 79 48 51 3 185.72 1.74 80 48 52 4 114.48 0.75 81 48 55 7 96.45 0.55 82 48 65 17 82.81 0.32 83 49 65 16 82.81 0.32 84 49 66 17 82.81 0.32 85 49 69 20 82.53 0.39 86 51 62 11 82.81 0.32 87 51 65 14 82.83 0.30 88 51 66 15 82.78 0.30 89 52 55 3 168.13 1.24 90 55 111 56 92.09 1.55 91 55 112 57 85.26 0.89 92 55 113 58 85.36 0.94 93 56 82 26 80.23 0.16 94 56 112 56 85.08 0.84 95 56 113 57 85.08 0.83 96 56 114 58 85.08 0.83 97 57 61 4 157.41 3.15 98 57 62 5 149.70 1.50 99 57 113 56 84.89 0.91 100 57 114 57 84.10 0.52 101 58 61 3 183.72 0.43 102 58 62 4 151.93 0.41 103 58 113 55 84.19 0.56 104 58 114 56 82.56 0.39 105 59 62 3 178.78 2.90 106 59 63 4 156.90 2.08 107 60 63 3 167.88 1.57 108 60 64 4 151.91 0.40 109 61 64 3 183.77 0.47 110 61 65 4 164.11 4.16 111 61 77 16 79.61 0.02 112 61 113 52 82.53 0.38 113 61 114 53 81.09 0.15 114 62 65 3 167.24 2.60 115 62 66 4 164.11 4.16 116 63 66 3 169.34 1.55 117 63 67 4 169.33 1.55 118 64 67 3 169.71 1.37 119 64 68 4 169.31 1.54 120 64 74 10 98.55 1.26 121 64 75 11 94.06 1.47 122 64 76 12 80.17 0.16 123 65 68 3 171.69 0.78 124 65 69 4 163.88 3.12 125 65 76 11 80.17 0.15 126 65 77 12 80.15 0.15 127 66 69 3 189.93 6.08 128 66 70 4 171.46 0.66 129 67 70 3 199.06 1.51 130 67 71 4 150.81 0.82 131 67 74 7 101.55 0.24 132 68 71 3 168.66 4.57 133 68 72 4 132.41 0.78 134 68 74 6 98.61 1.24 135 68 75 7 98.57 1.26 136 68 76 8 88.25 3.90 137 71 74 3 210.07 5.01 138 77 113 36 78.45 0.66 139 78 112 34 80.15 0.16 140 78 113 35 77.73 0.98 141 78 114 36 77.64 0.96 142 79 111 32 79.74 0.10 143 79 112 33 77.78 0.99 144 79 113 34 77.75 0.98 145 80 111 31 79.98 0.18 146 80 112 32 78.52 0.70 147 80 114 34 77.78 0.99 148 81 108 27 78.22 1.22 149 81 110 29 80.21 0.16 150 81 111 30 80.11 0.15 151 82 110 28 80.29 0.18 152 82 111 29 80.23 0.15 153 82 112 30 80.18 0.16 154 82 114 32 80.09 0.15 155 83 108 25 80.42 0.20 156 83 109 26 80.31 0.17 157 83 110 27 80.30 0.17 158 84 105 21 81.94 0.28 159 84 107 23 80.58 0.17 160 84 108 24 80.53 0.17 161 85 105 20 82.73 0.33 162 85 106 21 82.56 0.32 163 85 107 22 80.65 0.14 164 85 109 24 80.56 0.15 165 86 102 16 86.92 0.23 166 86 103 17 83.13 0.18 167 86 104 18 82.89 0.30 168 86 106 20 82.75 0.34 169 87 102 15 95.95 0.91 170 87 103 16 85.41 0.80 171 87 106 19 82.88 0.29 172 87 107 20 82.87 0.29 173 88 100 12 114.14 0.04 174 88 101 13 103.71 0.35 175 88 102 14 95.95 0.91 176 89 99 10 120.80 1.08 177 89 100 11 114.92 0.31 178 89 101 12 110.80 1.08 179 89 103 14 101.80 0.67 180 89 106 17 93.98 1.57 181 90 98 8 124.67 0.53 182 90 99 9 120.80 1.08 183 90 100 10 119.17 0.41 184 91 97 6 137.53 0.97 185 91 98 7 125.06 0.33 186 91 99 8 123.03 0.07 187 91 101 10 123.01 0.07 188 91 103 12 120.77 1.09 189 92 96 4 137.52 0.97 190 92 97 5 137.53 0.97 191 92 98 6 126.42 1.01 192 93 96 3 191.31 2.79 193 93 97 4 141.10 2.76 194 93 99 6 132.02 1.77 195 103 106 3 249.12 0.29 196 108 111 3 247.31 0.73