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 10 8 136.62 0.23 2 3 6 3 155.08 1.06 3 3 7 4 152.22 2.48 4 4 7 3 155.51 1.28 5 4 8 4 155.08 1.06 6 4 118 114 23.45 0.39 7 5 8 3 155.81 0.71 8 5 9 4 155.09 1.06 9 5 116 111 27.45 0.59 10 5 117 112 24.41 0.70 11 5 118 113 24.40 0.69 12 6 9 3 155.44 0.94 13 6 10 4 152.17 2.50 14 7 10 3 152.81 2.25 15 7 11 4 148.72 1.16 16 8 11 3 155.75 0.78 17 8 12 4 148.71 1.17 18 8 13 5 145.09 0.65 19 8 54 46 81.04 6.55 20 8 108 100 34.81 0.47 21 8 117 109 35.90 0.04 22 8 118 110 35.82 0.04 23 8 119 111 34.23 0.76 24 8 120 112 34.73 0.44 25 9 12 3 151.85 0.41 26 9 13 4 142.25 0.77 27 9 33 24 111.67 1.21 28 9 51 42 91.72 1.11 29 10 33 23 111.67 1.21 30 10 35 25 111.66 1.21 31 11 35 24 111.64 1.22 32 11 44 33 110.81 0.85 33 11 46 35 110.58 0.75 34 12 41 29 113.64 0.22 35 12 44 32 111.28 1.05 36 12 45 33 110.59 0.75 37 12 46 34 110.58 0.75 38 12 47 35 110.55 0.74 39 12 120 108 38.02 0.48 40 13 33 20 115.50 0.10 41 13 47 34 110.59 0.75 42 13 49 36 110.57 0.75 43 13 50 37 110.47 0.77 44 13 51 38 109.09 1.19 45 13 54 41 94.74 0.29 46 14 17 3 162.13 0.02 47 14 25 11 115.78 0.25 48 14 29 15 115.61 0.15 49 14 33 19 115.52 0.10 50 14 46 32 111.62 1.22 51 14 47 33 111.27 1.05 52 14 48 34 110.64 0.79 53 15 48 33 111.25 1.06 54 15 49 34 110.64 0.79 55 15 50 35 110.62 0.78 56 17 48 31 115.25 0.07 57 18 48 30 115.67 0.24 58 18 80 62 115.73 0.26 59 19 48 29 115.77 0.27 60 19 80 61 115.76 0.27 61 19 101 82 115.83 0.27 62 20 25 5 115.95 0.24 63 20 48 28 115.83 0.24 64 20 82 62 115.86 0.25 65 20 99 79 115.88 0.26 66 20 101 81 115.84 0.27 67 21 25 4 125.02 0.80 68 22 25 3 148.37 2.86 69 22 99 77 143.28 0.30 70 23 99 76 144.33 0.23 71 25 46 21 176.10 1.17 72 25 48 23 165.72 1.12 73 25 82 57 167.58 0.23 74 25 99 74 185.15 1.58 75 26 82 56 246.27 0.46 76 26 97 71 212.81 0.18 77 26 98 72 212.81 0.17 78 26 99 73 193.11 0.68 79 27 96 69 223.99 0.68 80 27 97 70 219.47 0.70 81 29 46 17 227.72 0.59 82 30 36 6 326.98 3.45 83 30 41 11 228.10 0.66 84 30 44 14 228.04 0.64 85 30 46 16 227.88 0.57 86 30 97 67 227.72 0.59 87 31 36 5 326.99 3.46 88 33 46 13 227.86 0.58 89 35 41 6 257.62 15.31 90 35 44 9 228.13 0.66 91 35 46 11 228.11 0.66 92 36 40 4 313.24 5.50 93 36 95 59 327.38 2.60 94 36 97 61 303.30 3.39 95 40 86 46 228.12 0.64 96 42 85 43 228.09 0.62 97 42 86 44 228.09 0.62 98 43 84 41 228.02 0.61 99 43 85 42 228.02 0.62 100 44 83 39 228.05 0.64 101 44 84 40 227.94 0.59 102 45 81 36 228.08 0.62 103 45 82 37 228.01 0.62 104 45 83 38 227.93 0.59 105 45 120 75 38.86 0.29 106 46 81 35 228.01 0.62 107 46 82 36 227.97 0.60 108 46 84 38 227.93 0.59 109 47 54 7 334.14 0.60 110 47 79 32 228.06 0.63 111 47 80 33 228.01 0.62 112 47 81 34 227.93 0.59 113 47 106 59 231.58 31.77 114 47 120 73 38.99 0.35 115 48 80 32 227.96 0.60 116 48 81 33 227.93 0.59 117 48 82 34 227.93 0.59 118 49 79 30 227.97 0.60 119 49 80 31 227.95 0.60 120 53 79 26 227.59 0.70 121 54 79 25 225.43 0.04 122 54 117 63 51.87 0.78 123 55 117 62 52.28 0.98 124 57 73 16 227.74 0.62 125 57 74 17 227.73 0.62 126 57 75 18 217.22 0.35 127 57 79 22 212.33 0.12 128 58 73 15 227.72 0.62 129 58 115 57 55.91 2.08 130 58 116 58 54.62 1.51 131 58 117 59 54.57 1.51 132 60 74 14 227.75 0.61 133 60 75 15 227.56 0.64 134 60 76 16 220.71 0.19 135 61 73 12 227.93 0.59 136 61 74 13 227.72 0.60 137 61 76 15 227.61 0.63 138 62 70 8 233.47 0.89 139 62 72 10 228.03 0.63 140 62 73 11 227.94 0.59 141 63 72 9 228.05 0.63 142 63 73 10 228.05 0.62 143 63 74 11 228.04 0.62 144 63 107 44 228.09 0.58 145 64 72 8 248.83 0.51 146 65 109 44 227.59 0.68 147 65 121 56 53.16 1.25 148 66 121 55 53.18 1.25 149 66 122 56 53.17 1.25 150 71 109 38 227.67 0.65 151 71 110 39 227.66 0.65 152 71 111 40 227.60 0.68 153 71 115 44 154.02 0.89 154 72 107 35 227.86 0.60 155 72 108 36 227.75 0.61 156 72 109 37 227.55 0.68 157 72 121 49 52.70 1.08 158 73 107 34 227.79 0.60 159 73 108 35 227.75 0.61 160 73 110 37 227.23 0.83 161 73 115 42 134.08 3.33 162 74 105 31 227.94 0.60 163 74 106 32 227.78 0.61 164 74 107 33 227.53 0.69 165 74 124 50 40.19 0.12 166 75 79 4 220.77 4.29 167 75 105 30 227.78 0.61 168 75 106 31 227.75 0.62 169 76 105 29 227.76 0.62 170 77 105 28 227.18 0.81 171 78 103 25 227.75 0.62 172 78 104 26 217.33 1.06 173 78 105 27 212.80 0.16 174 79 103 24 222.58 1.39 175 79 104 25 214.17 0.51 176 79 106 27 210.58 0.76 177 80 101 21 227.77 0.61 178 80 102 22 227.21 0.84 179 80 103 23 212.76 0.18 180 81 101 20 217.34 1.08 181 81 102 21 214.19 0.49 182 81 104 23 209.30 0.12 183 81 106 25 172.87 0.94 184 81 123 42 38.98 0.23 185 82 99 17 227.75 0.62 186 82 100 18 214.20 0.48 187 82 101 19 212.77 0.18 188 83 98 15 227.78 0.61 189 83 99 16 222.22 0.67 190 83 100 17 212.77 0.18 191 84 97 13 227.75 0.61 192 84 98 14 213.92 0.35 193 85 97 12 227.75 0.61 194 85 98 13 227.48 0.57 195 86 90 4 310.56 11.91 196 86 96 10 227.92 0.61 197 86 97 11 227.80 0.62 198 87 90 3 330.77 0.47 199 87 96 9 228.00 0.62 200 87 97 10 227.90 0.63 201 87 98 11 227.87 0.62 202 90 94 4 325.42 1.97 203 90 95 5 228.21 0.62 204 90 96 6 228.19 0.61 205 91 95 4 295.40 1.76 206 104 123 19 39.23 0.12 207 104 124 20 38.86 0.30 208 105 123 18 39.54 0.04 209 105 124 19 39.22 0.12 210 106 120 14 51.68 0.75 211 106 122 16 40.33 0.11 212 106 123 17 39.68 0.12 213 107 120 13 51.85 0.83 214 107 121 14 49.51 1.44 215 107 122 15 42.29 0.73 216 107 124 17 40.24 0.14 217 108 117 9 54.58 1.53 218 108 119 11 53.03 1.19 219 108 120 12 51.94 0.79 220 108 121 13 51.62 0.73 221 109 117 8 54.63 1.53 222 109 118 9 54.58 1.52 223 109 119 10 53.37 1.32 224 110 115 5 129.21 5.25 225 110 116 6 56.10 1.00 226 110 117 7 54.62 1.51 227 111 115 4 129.78 5.29 228 111 116 5 92.19 11.94 229 111 118 7 54.81 1.62 230 112 115 3 145.84 0.15