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 10 94 84 62.51 0.35 2 10 95 85 61.90 0.60 3 12 16 4 188.03 1.14 4 12 44 32 62.03 0.43 5 12 90 78 62.63 0.31 6 12 98 86 62.57 0.33 7 13 42 29 61.41 0.74 8 13 43 30 61.40 0.74 9 13 44 31 62.04 0.43 10 14 41 27 61.84 0.63 11 14 42 28 61.84 0.63 12 15 40 25 61.87 0.62 13 15 41 26 61.88 0.61 14 15 120 105 130.40 0.51 15 16 39 23 62.47 0.38 16 16 40 24 62.38 0.39 17 16 41 25 62.52 0.36 18 16 42 26 62.59 0.33 19 16 96 80 130.41 0.52 20 16 97 81 130.39 0.52 21 16 98 82 129.41 0.06 22 16 118 102 129.41 0.06 23 16 119 103 130.35 0.51 24 16 120 104 130.43 0.52 25 17 39 22 62.53 0.35 26 17 40 23 62.57 0.34 27 17 118 101 130.42 0.52 28 17 119 102 130.66 0.64 29 17 121 104 131.00 0.70 30 17 150 133 62.57 0.33 31 18 21 3 225.86 4.49 32 18 37 19 62.52 0.35 33 18 38 20 62.55 0.34 34 18 39 21 62.56 0.34 35 18 117 99 130.69 0.62 36 18 118 100 130.71 0.63 37 18 149 131 62.66 0.32 38 18 150 132 62.57 0.33 39 19 117 98 131.24 0.68 40 19 124 105 131.28 0.70 41 19 148 129 62.91 0.35 42 19 149 130 62.68 0.33 43 19 150 131 62.57 0.33 44 20 116 96 131.41 0.66 45 20 117 97 131.31 0.67 46 20 124 104 131.38 0.69 47 20 129 109 131.34 0.68 48 20 132 112 131.24 0.64 49 20 146 126 69.81 0.14 50 20 147 127 67.46 0.81 51 20 149 129 62.79 0.29 52 21 29 8 123.01 3.10 53 21 35 14 66.12 1.09 54 21 115 94 131.44 0.64 55 21 116 95 131.44 0.65 56 21 132 111 131.40 0.65 57 21 145 124 82.48 1.43 58 21 146 125 69.84 0.13 59 21 147 126 69.79 0.14 60 21 149 128 66.70 0.44 61 22 114 92 131.46 0.63 62 22 115 93 131.45 0.64 63 22 132 110 131.43 0.66 64 22 136 114 123.11 0.45 65 22 141 119 111.83 1.20 66 22 145 123 79.34 0.12 67 22 146 124 69.84 0.14 68 23 26 3 175.39 0.71 69 23 29 6 140.92 0.47 70 23 113 90 131.51 0.62 71 23 114 91 131.48 0.64 72 23 141 118 112.40 0.92 73 23 145 122 89.77 1.97 74 24 112 88 131.54 0.61 75 24 113 89 131.52 0.62 76 24 141 117 112.42 0.90 77 25 28 3 170.56 0.72 78 25 112 87 131.56 0.62 79 26 29 3 168.28 0.42 80 26 30 4 158.33 0.79 81 26 145 119 111.49 1.26 82 27 30 3 166.31 1.08 83 27 33 6 140.85 0.44 84 28 33 5 140.06 0.84 85 28 34 6 139.99 0.86 86 28 35 7 136.02 1.12 87 28 106 78 132.84 0.48 88 28 112 84 132.44 0.66 89 29 33 4 147.64 2.91 90 29 35 6 136.03 1.12 91 29 36 7 135.97 1.10 92 30 33 3 156.88 0.04 93 30 36 6 135.99 1.10 94 31 36 5 152.16 0.65 95 31 152 121 99.06 1.01 96 32 36 4 156.71 0.05 97 32 58 26 89.94 0.70 98 32 59 27 89.93 0.70 99 32 60 28 89.93 0.70 100 32 61 29 87.67 0.42 101 33 36 3 175.83 3.19 102 34 37 3 200.74 0.82 103 34 82 48 133.92 0.43 104 34 83 49 133.84 0.48 105 35 83 48 134.10 0.51 106 35 86 51 134.03 0.51 107 35 104 69 133.56 0.44 108 35 114 79 132.49 0.70 109 36 149 113 111.45 1.08 110 36 152 116 109.75 1.53 111 37 55 18 110.55 1.19 112 37 56 19 110.08 1.24 113 37 57 20 103.22 1.64 114 38 55 17 110.55 1.19 115 38 56 18 110.49 1.20 116 38 149 111 111.73 1.21 117 38 152 114 110.84 1.07 118 38 153 115 103.17 1.67 119 39 42 3 267.32 3.23 120 39 53 14 111.87 1.22 121 39 55 16 110.56 1.18 122 39 118 79 98.00 18.07 123 40 54 14 111.75 1.19 124 40 55 15 111.70 1.18 125 40 56 16 111.72 1.17 126 40 153 113 111.76 1.20 127 40 155 115 104.78 1.02 128 40 156 116 87.96 3.60 129 40 157 117 44.51 15.14 130 41 53 12 116.31 0.97 131 41 54 13 111.86 1.22 132 42 51 9 123.52 1.05 133 42 52 10 118.00 0.96 134 42 53 11 116.58 0.84 135 42 98 56 135.80 1.55 136 43 51 8 123.53 1.05 137 43 52 9 118.45 1.19 138 44 50 6 132.56 0.07 139 44 51 7 127.19 0.12 140 44 78 34 148.80 1.12 141 44 90 46 150.88 0.10 142 45 48 3 170.16 0.31 143 45 49 4 148.10 1.25 144 45 50 5 136.03 1.66 145 46 49 3 158.91 3.95 146 49 71 22 234.78 2.02 147 49 72 23 234.78 2.02 148 50 69 19 234.75 2.00 149 50 70 20 234.78 2.02 150 50 71 21 234.78 2.02 151 50 72 22 234.81 2.02 152 50 78 28 234.81 2.02 153 51 68 17 234.80 2.02 154 51 69 18 234.80 2.02 155 51 70 19 234.78 2.02 156 51 78 27 234.84 2.02 157 51 88 37 234.83 2.02 158 52 68 16 234.80 2.02 159 52 69 17 234.80 2.02 160 53 66 13 234.80 2.02 161 53 67 14 234.80 2.02 162 53 68 15 234.81 2.02 163 53 70 17 234.84 2.02 164 53 88 35 252.86 4.05 165 54 65 11 234.79 2.02 166 54 66 12 234.80 2.02 167 54 67 13 234.81 2.02 168 55 65 10 234.80 2.02 169 55 66 11 234.81 2.02 170 55 68 13 234.84 2.02 171 55 82 27 293.55 14.17 172 56 63 7 233.18 1.28 173 56 64 8 234.79 2.02 174 56 65 9 234.81 2.02 175 56 155 99 173.35 1.11 176 56 156 100 168.88 0.65 177 57 62 5 234.81 2.02 178 57 63 6 234.79 2.02 179 57 64 7 234.81 2.02 180 57 66 9 234.84 2.02 181 57 82 25 313.64 4.18 182 58 61 3 234.83 2.02 183 58 62 4 234.81 2.02 184 58 63 5 234.81 2.02 185 58 154 96 234.81 2.02 186 58 155 97 234.81 2.02 187 59 62 3 234.83 2.02 188 59 64 5 234.84 2.02 189 122 150 28 318.73 3.89