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 81.01 0.34 2 13 45 32 79.56 1.01 3 13 46 33 79.36 1.04 4 14 44 30 81.11 0.39 5 14 45 31 79.63 0.99 6 14 46 32 79.64 0.99 7 14 47 33 79.56 1.01 8 14 55 41 79.64 0.99 9 14 111 97 79.64 0.99 10 14 112 98 79.58 0.99 11 14 113 99 79.55 1.00 12 15 43 28 81.11 0.40 13 15 44 29 81.39 0.26 14 15 111 96 79.64 0.99 15 16 41 25 81.71 0.33 16 16 42 26 81.62 0.33 17 16 43 27 81.55 0.30 18 16 108 92 81.06 0.42 19 16 109 93 81.47 0.26 20 16 111 95 80.59 0.52 21 17 41 24 81.79 0.34 22 17 42 25 81.66 0.33 23 17 44 27 81.65 0.33 24 18 41 23 81.84 0.35 25 18 42 24 81.86 0.35 26 19 39 20 82.84 0.69 27 19 40 21 82.59 0.60 28 19 41 22 81.92 0.36 29 19 42 23 81.92 0.36 30 20 37 17 83.16 0.65 31 20 38 18 82.95 0.65 32 20 39 19 82.86 0.69 33 21 26 5 129.10 0.21 34 21 37 16 85.23 0.38 35 21 38 17 83.10 0.67 36 21 40 19 82.89 0.67 37 22 25 3 134.07 0.96 38 22 26 4 129.49 0.39 39 22 37 15 85.24 0.38 40 23 26 3 134.07 0.96 41 23 27 4 129.12 0.21 42 23 28 5 124.94 0.34 43 23 29 6 122.55 0.54 44 23 32 9 118.94 2.10 45 23 35 12 104.23 0.82 46 23 36 13 96.19 2.88 47 23 37 14 88.73 0.81 48 23 38 15 88.76 0.82 49 24 27 3 129.20 0.18 50 24 29 5 125.66 0.03 51 28 31 3 137.24 0.52 52 28 32 4 127.02 1.39 53 31 91 60 128.50 0.71 54 31 92 61 128.51 0.70 55 32 35 3 221.33 0.54 56 32 89 57 125.48 0.10 57 32 90 58 126.34 0.21 58 32 91 59 126.36 0.23 59 33 90 57 123.06 0.29 60 33 91 58 125.53 0.13 61 33 92 59 128.43 0.69 62 34 89 55 119.14 2.21 63 34 90 56 119.20 2.21 64 35 38 3 162.31 1.54 65 35 88 53 119.12 2.21 66 35 89 54 119.13 2.21 67 38 87 49 117.91 2.40 68 43 79 36 81.62 0.33 69 43 80 37 81.62 0.33 70 43 81 38 81.78 0.34 71 44 79 35 81.61 0.33 72 45 79 34 81.56 0.32 73 46 76 30 81.80 0.35 74 47 51 4 152.75 3.32 75 47 77 30 81.59 0.32 76 47 78 31 81.42 0.24 77 47 79 32 80.98 0.33 78 48 51 3 204.33 2.43 79 48 55 7 119.19 2.19 80 48 65 17 91.41 2.02 81 48 76 28 81.76 0.34 82 49 65 16 91.44 2.00 83 49 66 17 91.41 2.02 84 49 69 20 84.06 0.20 85 51 55 4 155.66 2.29 86 51 57 6 118.56 2.29 87 51 61 10 105.59 1.03 88 51 62 11 92.45 2.12 89 51 65 14 91.45 2.00 90 51 113 62 119.26 2.17 91 52 55 3 158.99 0.63 92 55 113 58 118.79 2.17 93 56 82 26 81.64 0.32 94 56 83 27 81.89 0.35 95 56 111 55 119.00 2.12 96 56 112 56 92.84 2.17 97 56 113 57 113.28 2.09 98 56 114 58 103.14 2.98 99 57 61 4 152.76 1.13 100 57 62 5 150.21 1.41 101 57 113 56 92.71 2.19 102 57 114 57 92.42 2.08 103 58 61 3 164.47 1.35 104 58 62 4 154.66 0.95 105 58 114 56 91.56 1.94 106 59 62 3 180.11 6.46 107 59 63 4 156.34 1.79 108 60 63 3 170.42 1.97 109 60 64 4 159.88 0.03 110 61 64 3 165.24 0.62 111 61 65 4 158.19 0.81 112 61 77 16 79.52 1.01 113 61 113 52 91.36 2.03 114 61 114 53 83.45 0.56 115 62 65 3 171.55 1.85 116 62 66 4 168.30 3.47 117 63 66 3 177.81 2.91 118 63 67 4 160.72 0.32 119 64 67 3 171.25 0.38 120 64 68 4 165.92 2.29 121 64 74 10 81.66 0.32 122 64 75 11 81.62 0.31 123 64 76 12 81.49 0.33 124 65 68 3 176.41 2.96 125 65 69 4 165.91 2.29 126 66 69 3 175.00 3.65 127 66 70 4 175.40 3.46 128 67 70 3 187.73 3.30 129 67 71 4 163.34 1.07 130 67 74 7 85.78 1.74 131 68 71 3 171.10 4.95 132 68 72 4 142.49 0.48 133 68 74 6 81.72 0.33 134 68 75 7 81.67 0.32 135 68 76 8 81.55 0.30 136 71 74 3 194.72 2.32 137 77 113 36 79.65 0.99 138 77 114 37 79.62 0.99 139 78 112 34 81.58 0.31 140 78 113 35 79.62 0.99 141 78 114 36 79.55 1.00 142 79 111 32 81.42 0.24 143 79 112 33 79.64 0.99 144 79 113 34 79.63 0.99 145 80 111 31 81.56 0.29 146 80 112 32 81.00 0.34 147 80 114 34 79.64 0.99 148 81 84 3 248.46 1.61 149 81 108 27 79.64 0.99 150 81 110 29 81.69 0.32 151 81 111 30 81.61 0.33 152 82 110 28 81.78 0.34 153 82 111 29 81.75 0.35 154 82 112 30 81.65 0.33 155 82 114 32 81.61 0.33 156 83 108 25 82.69 0.72 157 83 109 26 81.95 0.35 158 83 110 27 81.88 0.36 159 84 105 21 82.15 0.20 160 84 107 23 82.77 0.71 161 84 108 24 82.69 0.73 162 84 109 25 81.98 0.35 163 85 105 20 82.20 0.20 164 85 106 21 83.01 0.61 165 85 107 22 82.85 0.68 166 85 109 24 82.79 0.70 167 86 103 17 111.92 3.98 168 86 104 18 85.25 0.55 169 86 105 19 82.98 0.58 170 87 102 15 118.71 2.31 171 87 103 16 118.63 2.31 172 87 106 19 83.05 0.61 173 87 107 20 83.14 0.66 174 88 100 12 118.95 2.23 175 88 101 13 118.92 2.23 176 88 102 14 118.72 2.31 177 89 100 11 118.99 2.21 178 89 101 12 118.95 2.23 179 89 103 14 118.86 2.25 180 89 106 17 118.91 2.22 181 90 98 8 118.98 2.22 182 90 99 9 119.00 2.21 183 90 100 10 119.00 2.22 184 91 97 6 135.19 1.57 185 91 98 7 126.21 1.39 186 91 99 8 119.00 2.21 187 91 101 10 119.05 2.21 188 91 103 12 119.09 2.21 189 92 96 4 147.52 4.05 190 92 97 5 134.98 1.47 191 92 98 6 127.02 1.79 192 93 96 3 208.81 8.88 193 93 97 4 151.13 3.56 194 93 99 6 127.71 2.12 195 103 106 3 247.74 0.12 196 108 111 3 245.72 1.57