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 8 136.79 0.95 2 3 6 3 145.80 1.49 3 3 7 4 146.75 1.01 4 4 7 3 152.62 2.22 5 4 8 4 147.02 0.88 6 4 118 114 24.12 0.06 7 5 8 3 156.77 2.38 8 5 9 4 146.75 1.01 9 5 116 111 26.02 0.07 10 5 117 112 25.24 0.46 11 5 118 113 25.15 0.41 12 6 9 3 147.05 0.90 13 6 10 4 146.69 0.99 14 7 10 3 149.13 2.54 15 7 11 4 145.70 1.49 16 8 11 3 148.22 0.17 17 8 12 4 145.30 1.56 18 8 13 5 140.38 0.16 19 8 54 46 72.59 1.97 20 8 108 100 35.56 1.01 21 8 117 109 36.80 0.42 22 8 118 110 35.57 1.01 23 8 119 111 35.56 1.01 24 8 120 112 35.56 1.01 25 9 12 3 152.44 2.28 26 9 13 4 139.50 0.24 27 9 33 24 116.10 0.70 28 9 51 42 85.70 2.19 29 10 33 23 116.05 0.71 30 10 34 24 116.13 0.69 31 10 35 25 116.23 0.64 32 11 35 24 116.33 0.59 33 11 41 30 116.40 0.62 34 11 44 33 115.20 0.45 35 11 46 35 115.15 0.45 36 12 41 29 118.07 0.14 37 12 44 32 115.20 0.45 38 12 45 33 115.16 0.45 39 12 46 34 115.15 0.45 40 12 47 35 115.12 0.44 41 12 120 108 38.70 0.96 42 13 33 20 118.33 0.18 43 13 47 34 115.16 0.45 44 13 49 36 115.12 0.45 45 13 50 37 115.12 0.44 46 13 51 38 110.48 0.73 47 13 54 41 94.44 1.61 48 14 25 11 118.29 0.12 49 14 29 15 118.29 0.15 50 14 33 19 118.34 0.18 51 14 46 32 115.85 0.67 52 14 47 33 115.34 0.51 53 14 48 34 115.14 0.46 54 15 48 33 115.20 0.45 55 15 49 34 115.19 0.44 56 15 50 35 115.12 0.46 57 17 48 31 118.12 0.07 58 18 48 30 118.21 0.12 59 18 80 62 118.23 0.12 60 19 48 29 118.25 0.12 61 19 80 61 118.26 0.12 62 19 101 82 118.29 0.14 63 20 25 5 118.55 0.18 64 20 48 28 118.39 0.15 65 20 82 62 118.32 0.12 66 20 99 79 119.25 0.54 67 20 101 81 118.35 0.12 68 21 25 4 143.81 0.43 69 22 25 3 177.30 2.19 70 22 99 77 146.35 1.89 71 23 99 76 146.36 1.89 72 24 27 3 233.61 0.58 73 24 28 4 233.58 0.57 74 25 28 3 233.62 0.57 75 25 29 4 233.52 0.59 76 25 46 21 223.88 0.19 77 25 48 23 171.13 0.91 78 25 82 57 319.06 1.31 79 25 99 74 186.57 1.84 80 26 29 3 233.60 0.56 81 26 30 4 233.16 0.72 82 26 97 71 216.30 0.23 83 26 99 73 201.45 2.39 84 27 31 4 316.44 0.43 85 27 96 69 231.19 0.03 86 27 97 70 224.05 3.60 87 30 35 5 322.20 0.34 88 30 97 67 254.06 3.00 89 40 86 46 319.78 0.17 90 42 85 43 264.68 14.92 91 42 86 44 290.17 2.18 92 43 84 41 234.19 0.29 93 43 85 42 254.47 9.84 94 44 83 39 234.18 0.30 95 44 84 40 233.62 0.57 96 45 82 37 318.71 1.41 97 45 83 38 233.66 0.56 98 45 120 75 39.55 0.73 99 46 82 36 237.09 2.03 100 46 84 38 233.64 0.57 101 47 54 7 191.25 0.95 102 47 81 34 233.64 0.57 103 47 106 59 157.33 0.76 104 47 120 73 39.68 0.78 105 48 80 32 233.68 0.57 106 48 81 33 233.64 0.57 107 48 82 34 233.64 0.57 108 48 101 53 320.67 0.62 109 49 53 4 221.77 0.49 110 49 54 5 216.99 0.56 111 49 79 30 233.98 0.48 112 49 80 31 233.68 0.57 113 50 53 3 229.53 0.89 114 50 54 4 221.77 0.49 115 51 54 3 227.06 0.18 116 51 55 4 220.13 0.83 117 52 55 3 228.34 1.28 118 52 56 4 217.30 0.40 119 53 56 3 225.78 0.00 120 53 57 4 224.72 0.53 121 53 79 26 233.47 0.57 122 54 57 3 231.58 0.24 123 54 79 25 225.00 0.43 124 54 117 63 53.34 2.79 125 55 58 3 232.38 0.81 126 55 117 62 57.76 0.58 127 57 73 16 233.55 0.58 128 57 74 17 233.50 0.57 129 57 75 18 218.30 0.24 130 57 79 22 210.86 0.81 131 58 73 15 233.50 0.57 132 58 115 57 60.95 0.40 133 58 116 58 60.70 0.46 134 58 117 59 60.75 0.49 135 60 73 13 233.62 0.58 136 60 74 14 233.51 0.57 137 60 75 15 232.94 0.42 138 60 76 16 218.30 0.24 139 61 73 12 233.66 0.58 140 61 74 13 233.56 0.59 141 61 76 15 233.34 0.62 142 62 72 10 261.44 2.64 143 62 73 11 233.67 0.58 144 63 72 9 320.90 0.01 145 63 73 10 271.69 1.21 146 63 74 11 235.00 0.06 147 63 107 44 321.44 0.26 148 65 121 56 59.45 0.52 149 66 121 55 59.98 0.72 150 66 122 56 59.50 0.49 151 71 109 38 233.55 0.58 152 71 110 39 233.50 0.57 153 71 111 40 233.47 0.56 154 71 115 44 159.99 1.23 155 72 107 35 233.62 0.57 156 72 108 36 233.55 0.58 157 72 109 37 233.34 0.61 158 72 121 49 55.94 1.85 159 73 107 34 233.58 0.58 160 73 108 35 233.50 0.57 161 73 110 37 232.51 0.64 162 73 115 42 132.13 0.12 163 74 105 31 233.66 0.57 164 74 106 32 233.58 0.58 165 74 107 33 232.88 0.57 166 74 124 50 42.86 1.24 167 75 105 30 233.58 0.58 168 75 106 31 233.50 0.57 169 76 105 29 233.55 0.58 170 77 105 28 232.42 0.80 171 78 103 25 233.53 0.58 172 78 104 26 218.44 1.03 173 78 105 27 216.18 0.21 174 79 103 24 221.22 0.36 175 79 104 25 216.99 0.56 176 79 106 27 204.12 1.05 177 80 101 21 233.58 0.58 178 80 102 22 230.08 0.47 179 80 103 23 215.81 0.24 180 81 101 20 219.94 0.92 181 81 102 21 216.41 0.27 182 81 104 23 207.70 0.74 183 81 106 25 170.41 0.39 184 81 123 42 39.80 0.66 185 82 99 17 233.53 0.58 186 82 100 18 217.00 0.55 187 82 101 19 215.91 0.07 188 83 98 15 233.58 0.58 189 83 99 16 223.00 0.54 190 83 100 17 216.30 0.21 191 84 97 13 233.39 0.64 192 84 98 14 220.38 0.79 193 85 97 12 233.56 0.58 194 85 98 13 233.26 0.68 195 86 96 10 233.63 0.59 196 86 97 11 233.59 0.58 197 87 96 9 233.68 0.58 198 87 97 10 233.64 0.59 199 87 98 11 233.63 0.59 200 90 95 5 321.72 0.14 201 90 96 6 290.18 2.57 202 104 123 19 40.63 0.61 203 104 124 20 40.27 0.70 204 105 123 18 41.70 1.14 205 105 124 19 40.54 0.57 206 106 120 14 53.06 2.90 207 106 122 16 42.95 1.20 208 106 123 17 41.73 1.15 209 107 120 13 53.44 2.71 210 107 121 14 52.68 2.75 211 107 122 15 42.95 1.20 212 107 124 17 42.41 0.96 213 108 117 9 60.45 0.63 214 108 119 11 55.97 1.93 215 108 120 12 53.30 2.79 216 108 121 13 53.04 2.90 217 109 117 8 60.77 0.51 218 109 118 9 60.73 0.49 219 109 119 10 59.44 0.38 220 110 115 5 66.70 1.40 221 110 116 6 60.97 0.42 222 110 117 7 60.77 0.51 223 110 118 8 60.77 0.50 224 111 115 4 114.52 15.38 225 111 116 5 65.23 0.67 226 111 118 7 60.81 0.50 227 112 115 3 149.87 1.30