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 7 5 29.09 0.42 2 2 15 13 21.48 0.96 3 2 16 14 21.49 0.96 4 2 52 50 21.48 0.96 5 2 53 51 21.48 0.96 6 2 108 106 23.12 0.15 7 2 109 107 21.48 0.96 8 2 110 108 21.48 0.96 9 3 6 3 37.77 0.24 10 3 7 4 32.44 0.12 11 3 17 14 28.92 0.36 12 3 107 104 28.75 0.26 13 3 108 105 23.12 0.14 14 4 7 3 35.11 0.28 15 4 8 4 151.75 7.34 16 4 17 13 29.43 0.29 17 4 107 103 32.34 0.36 18 7 17 10 183.34 0.91 19 8 19 11 156.39 0.74 20 12 52 40 122.21 1.97 21 13 46 33 122.59 1.79 22 13 47 34 122.52 1.81 23 14 46 32 122.48 1.81 24 14 47 33 121.75 1.90 25 14 49 35 122.14 1.90 26 14 52 38 121.94 1.99 27 15 45 30 122.47 1.79 28 15 46 31 121.72 1.89 29 15 47 32 121.73 1.90 30 15 48 33 121.70 1.90 31 15 52 37 121.73 1.90 32 15 109 94 121.73 1.90 33 15 110 95 121.72 1.90 34 15 111 96 121.42 1.92 35 16 44 28 121.73 1.90 36 16 45 29 122.19 1.67 37 16 52 36 121.73 1.90 38 16 109 93 120.67 1.55 39 17 42 25 122.67 1.75 40 17 43 26 122.55 1.76 41 17 106 89 122.28 1.70 42 17 107 90 122.20 1.76 43 17 108 91 121.73 1.90 44 17 109 92 121.67 1.90 45 18 42 24 122.68 1.75 46 18 43 25 122.59 1.76 47 18 45 27 122.59 1.74 48 19 42 23 122.69 1.75 49 20 40 20 122.86 1.73 50 20 41 21 122.75 1.72 51 20 42 22 122.71 1.74 52 20 43 23 122.72 1.74 53 21 38 17 123.28 1.70 54 21 39 18 123.23 1.71 55 21 40 19 123.01 1.66 56 22 27 5 144.09 0.70 57 22 28 6 141.03 1.04 58 22 38 16 123.28 1.70 59 22 39 17 123.28 1.70 60 22 41 19 123.12 1.71 61 23 26 3 158.22 1.33 62 23 27 4 148.83 1.19 63 23 28 5 142.90 0.12 64 23 37 14 123.32 1.69 65 23 38 15 123.30 1.70 66 24 28 4 144.09 0.70 67 24 29 5 141.09 1.02 68 24 30 6 140.62 0.95 69 24 33 9 125.92 0.48 70 24 36 12 123.41 1.71 71 24 37 13 123.38 1.71 72 24 38 14 123.38 1.71 73 24 39 15 123.38 1.70 74 24 104 80 123.37 1.71 75 25 29 4 141.07 1.01 76 25 30 5 141.02 1.03 77 25 31 6 140.80 1.02 78 26 29 3 150.32 0.46 79 30 33 3 157.19 0.58 80 30 101 71 145.11 1.72 81 30 104 74 126.67 0.07 82 32 88 56 159.03 1.62 83 32 90 58 159.15 1.57 84 33 88 55 147.88 0.49 85 33 90 57 155.08 0.32 86 34 37 3 196.94 2.64 87 34 89 55 149.31 0.23 88 34 90 56 153.68 0.21 89 34 91 57 159.01 1.64 90 35 88 53 139.50 1.49 91 35 89 54 140.74 0.95 92 36 87 51 139.30 1.58 93 36 88 52 139.49 1.49 94 39 86 47 126.59 0.16 95 44 78 34 122.67 1.75 96 44 79 35 122.68 1.75 97 44 80 36 122.74 1.76 98 45 78 33 122.68 1.75 99 46 78 32 122.67 1.75 100 48 76 28 122.68 1.75 101 48 77 29 122.59 1.78 102 48 78 30 122.38 1.77 103 49 52 3 219.97 5.88 104 50 60 10 124.01 1.57 105 50 63 13 123.38 1.73 106 50 64 14 123.40 1.72 107 50 67 17 123.34 1.71 108 51 54 3 225.94 4.69 109 52 111 59 124.42 1.58 110 53 110 57 124.41 1.57 111 53 111 58 124.39 1.58 112 54 59 5 138.59 4.42 113 54 60 6 129.47 0.18 114 54 111 57 124.31 1.60 115 55 59 4 168.13 0.71 116 55 110 55 124.32 1.61 117 55 111 56 124.31 1.60 118 55 112 57 123.92 1.56 119 56 59 3 200.54 3.39 120 56 60 4 186.59 4.15 121 57 60 3 194.10 3.28 122 57 61 4 181.66 1.26 123 58 61 3 206.59 4.25 124 58 62 4 181.66 1.26 125 59 62 3 209.06 3.79 126 59 63 4 188.72 2.27 127 59 111 52 123.97 1.56 128 59 112 53 123.36 1.68 129 60 63 3 205.97 2.24 130 60 64 4 188.73 2.27 131 61 64 3 206.75 4.33 132 61 65 4 181.25 0.88 133 62 65 3 189.26 4.09 134 62 66 4 179.05 1.98 135 62 74 12 125.96 0.14 136 62 75 13 122.69 1.75 137 62 76 14 122.64 1.76 138 63 66 3 192.12 1.83 139 63 67 4 179.22 1.90 140 63 76 13 122.64 1.76 141 64 67 3 190.08 0.65 142 64 68 4 188.26 1.55 143 65 68 3 240.72 5.19 144 65 69 4 181.16 2.85 145 65 71 6 170.66 0.06 146 65 72 7 144.40 1.26 147 65 74 9 126.59 0.12 148 66 69 3 217.31 4.54 149 66 70 4 168.89 0.94 150 66 72 6 138.27 1.81 151 66 73 7 134.32 0.16 152 66 74 8 126.56 0.14 153 66 75 9 125.98 0.13 154 67 70 3 199.38 4.42 155 69 72 3 221.79 0.62 156 70 73 3 245.26 3.73 157 76 111 35 121.73 1.90 158 76 112 36 121.71 1.90 159 77 110 33 122.59 1.79 160 77 111 34 121.72 1.90 161 77 112 35 121.50 1.88 162 78 109 31 122.56 1.79 163 78 110 32 121.73 1.90 164 78 111 33 121.72 1.90 165 79 109 30 122.59 1.78 166 79 110 31 122.56 1.79 167 79 112 33 121.73 1.90 168 80 106 26 122.75 1.78 169 80 108 28 122.68 1.75 170 80 109 29 122.59 1.78 171 81 108 27 122.72 1.76 172 81 109 28 122.70 1.75 173 81 110 29 122.68 1.75 174 82 106 24 123.14 1.70 175 82 107 25 122.86 1.75 176 82 108 26 122.81 1.77 177 83 103 20 122.78 1.82 178 83 105 22 123.27 1.70 179 83 106 23 123.16 1.69 180 83 107 24 123.03 1.72 181 84 103 19 123.39 1.69 182 84 104 20 123.38 1.69 183 84 105 21 123.30 1.70 184 84 107 23 123.27 1.70 185 85 100 15 126.70 0.03 186 85 101 16 126.62 0.06 187 85 102 17 124.04 1.20 188 85 103 18 123.42 1.68 189 85 104 19 123.39 1.69 190 86 100 14 126.70 0.02 191 86 101 15 126.67 0.03 192 86 104 18 123.42 1.69 193 87 99 12 132.91 0.90 194 87 100 13 126.70 0.02 195 88 98 10 140.47 1.08 196 88 99 11 138.66 1.07 197 88 101 13 135.48 0.24 198 89 96 7 154.65 0.51 199 89 97 8 153.62 0.24 200 89 98 9 140.77 0.93 201 90 96 6 154.69 0.49 202 90 97 7 154.59 0.54 203 90 99 9 154.52 0.55 204 91 94 3 267.97 0.65 205 91 95 4 181.09 0.48 206 91 96 5 154.69 0.49 207 91 97 6 156.50 0.40 208 92 95 3 267.50 0.88 209 92 97 5 191.89 4.25