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 8 135.60 0.70 2 3 6 3 151.88 0.46 3 3 7 4 145.94 0.57 4 4 7 3 151.94 0.48 5 4 8 4 145.94 0.57 6 4 118 114 22.64 0.31 7 5 8 3 148.86 2.02 8 5 9 4 145.93 0.57 9 5 116 111 26.01 1.61 10 5 117 112 24.33 0.79 11 5 118 113 23.91 0.93 12 6 9 3 152.00 0.46 13 6 10 4 145.44 0.48 14 7 10 3 151.04 1.27 15 7 11 4 145.44 0.47 16 8 11 3 152.88 0.67 17 8 12 4 144.15 0.24 18 8 13 5 144.12 0.26 19 8 54 46 69.17 0.59 20 8 108 100 34.91 0.49 21 8 117 109 36.07 0.09 22 8 118 110 35.88 0.01 23 8 119 111 34.88 0.51 24 8 120 112 34.80 0.47 25 9 12 3 153.13 0.33 26 9 13 4 144.07 0.29 27 9 33 24 117.17 0.88 28 9 51 42 87.95 0.77 29 10 33 23 117.16 0.89 30 10 34 24 117.19 0.88 31 10 35 25 117.19 0.88 32 11 35 24 117.20 0.88 33 11 41 30 117.23 0.85 34 11 44 33 114.53 0.35 35 11 46 35 114.50 0.35 36 12 41 29 117.32 0.83 37 12 44 32 116.83 0.83 38 12 45 33 114.52 0.35 39 12 46 34 114.50 0.35 40 12 47 35 114.50 0.35 41 12 120 108 38.01 0.48 42 13 33 20 118.82 0.75 43 13 47 34 114.51 0.36 44 13 49 36 114.50 0.35 45 13 50 37 114.42 0.39 46 13 51 38 108.42 0.72 47 13 54 41 104.80 1.01 48 14 17 3 169.15 2.24 49 14 25 11 118.90 0.71 50 14 29 15 118.83 0.75 51 14 33 19 118.84 0.74 52 14 46 32 116.92 0.81 53 14 47 33 116.18 1.16 54 14 48 34 114.52 0.36 55 15 48 33 114.53 0.36 56 15 49 34 114.53 0.36 57 15 50 35 114.49 0.36 58 17 48 31 117.79 0.45 59 18 48 30 117.87 0.48 60 18 80 62 118.62 0.79 61 19 48 29 118.71 0.78 62 19 101 82 118.87 0.71 63 20 25 5 124.01 3.18 64 20 48 28 118.92 0.70 65 20 82 62 118.92 0.70 66 20 99 79 119.00 0.67 67 20 101 81 118.91 0.70 68 21 25 4 124.09 3.15 69 22 25 3 150.03 1.36 70 22 99 77 148.96 2.07 71 23 99 76 149.34 1.88 72 24 28 4 332.88 0.67 73 25 46 21 186.55 1.89 74 25 48 23 165.64 1.03 75 25 82 57 173.04 0.85 76 25 99 74 178.28 0.45 77 26 30 4 334.48 0.17 78 26 82 56 241.10 1.26 79 26 97 71 215.24 0.17 80 26 98 72 215.15 0.17 81 26 99 73 195.31 0.28 82 27 96 69 229.06 1.32 83 27 97 70 216.26 0.34 84 29 46 17 229.46 1.39 85 30 36 6 325.14 1.98 86 30 41 11 229.87 1.41 87 30 44 14 229.81 1.42 88 30 46 16 229.66 1.46 89 30 97 67 229.51 1.45 90 31 36 5 320.64 0.29 91 33 46 13 229.72 1.46 92 35 41 6 301.36 0.45 93 35 44 9 229.85 1.43 94 35 46 11 229.81 1.42 95 36 40 4 324.68 4.59 96 36 95 59 333.43 1.46 97 36 97 61 331.67 0.58 98 40 86 46 229.93 1.40 99 42 85 43 229.84 1.45 100 42 86 44 229.84 1.45 101 43 83 40 229.84 1.44 102 43 84 41 229.73 1.45 103 43 85 42 229.78 1.45 104 44 83 39 229.78 1.44 105 44 84 40 229.72 1.45 106 45 81 36 229.83 1.44 107 45 82 37 229.77 1.44 108 45 83 38 229.69 1.46 109 45 120 75 38.86 0.29 110 46 81 35 229.77 1.44 111 46 82 36 229.73 1.45 112 46 84 38 229.69 1.46 113 47 79 32 229.84 1.44 114 47 80 33 229.78 1.44 115 47 81 34 229.69 1.46 116 47 106 59 230.41 32.36 117 47 120 73 39.28 0.21 118 48 80 32 229.72 1.45 119 48 81 33 229.69 1.46 120 48 82 34 229.68 1.46 121 49 79 30 229.73 1.45 122 49 80 31 229.70 1.46 123 53 79 26 229.34 1.57 124 54 79 25 225.43 0.03 125 54 117 63 54.60 2.82 126 55 117 62 54.09 2.57 127 57 73 16 229.61 1.46 128 57 74 17 229.51 1.50 129 57 75 18 218.20 0.84 130 57 79 22 212.80 0.35 131 58 73 15 229.51 1.50 132 58 115 57 61.77 1.49 133 58 116 58 57.88 3.02 134 58 117 59 57.83 3.02 135 60 73 13 229.67 1.46 136 60 74 14 229.63 1.46 137 60 75 15 228.58 1.15 138 60 76 16 222.41 0.72 139 61 73 12 229.69 1.45 140 61 74 13 229.66 1.46 141 61 76 15 229.10 1.38 142 62 70 8 248.11 3.33 143 62 72 10 229.77 1.43 144 62 73 11 229.69 1.45 145 63 72 9 229.78 1.44 146 63 73 10 229.78 1.44 147 63 74 11 229.76 1.44 148 63 107 44 229.86 1.37 149 64 72 8 250.88 2.56 150 65 109 44 229.38 1.56 151 65 121 56 56.26 2.77 152 66 121 55 56.71 2.56 153 66 122 56 56.26 2.77 154 71 109 38 229.54 1.50 155 71 110 39 229.45 1.54 156 71 111 40 229.34 1.57 157 71 115 44 160.24 3.62 158 72 107 35 229.69 1.46 159 72 108 36 229.62 1.46 160 72 109 37 229.34 1.57 161 72 121 49 55.96 2.89 162 73 107 34 229.63 1.46 163 73 108 35 229.56 1.49 164 73 110 37 228.24 1.31 165 73 115 42 136.84 1.95 166 74 105 31 229.69 1.46 167 74 106 32 229.63 1.46 168 74 107 33 229.28 1.45 169 74 124 50 40.36 0.22 170 75 79 4 214.84 0.10 171 75 105 30 229.61 1.47 172 75 106 31 229.56 1.49 173 76 105 29 229.56 1.49 174 77 105 28 229.00 1.62 175 78 103 25 229.55 1.49 176 78 104 26 218.16 0.82 177 78 105 27 215.33 0.07 178 79 103 24 223.86 0.14 179 79 104 25 215.39 0.10 180 79 106 27 208.70 1.53 181 80 101 21 229.59 1.47 182 80 102 22 228.45 1.46 183 80 103 23 215.31 0.07 184 81 101 20 217.04 0.26 185 81 102 21 215.38 0.10 186 81 104 23 209.18 0.14 187 81 106 25 167.47 1.45 188 81 123 42 38.96 0.21 189 82 99 17 229.56 1.48 190 82 100 18 216.06 0.16 191 82 101 19 215.02 0.21 192 83 98 15 229.65 1.45 193 83 99 16 220.61 1.49 194 83 100 17 215.14 0.18 195 84 97 13 229.48 1.48 196 84 98 14 215.97 0.20 197 85 97 12 229.57 1.48 198 85 98 13 229.13 1.38 199 86 90 4 326.18 4.10 200 86 96 10 229.71 1.43 201 86 97 11 229.66 1.45 202 87 96 9 229.75 1.44 203 87 97 10 229.70 1.45 204 87 98 11 229.69 1.46 205 89 96 7 230.00 1.40 206 90 95 5 230.03 1.40 207 90 96 6 230.00 1.40 208 104 123 19 39.68 0.12 209 104 124 20 39.02 0.11 210 105 123 18 39.72 0.14 211 105 124 19 39.02 0.02 212 106 120 14 53.17 2.12 213 106 122 16 40.84 0.00 214 106 123 17 39.69 0.12 215 107 120 13 53.19 2.12 216 107 121 14 49.97 1.55 217 107 122 15 40.86 0.01 218 107 124 17 40.38 0.23 219 108 117 9 57.82 3.02 220 108 119 11 55.98 2.90 221 108 120 12 53.18 2.12 222 108 121 13 52.92 2.23 223 109 117 8 57.91 3.06 224 109 118 9 57.80 3.01 225 109 119 10 56.77 3.02 226 110 115 5 65.15 0.03 227 110 116 6 61.73 1.26 228 110 117 7 57.83 3.02 229 110 118 8 57.83 3.02 230 111 115 4 105.25 17.23 231 111 116 5 65.13 0.01 232 111 118 7 58.00 3.06 233 112 115 3 145.84 0.15