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 8 138.79 1.77 2 3 6 3 151.31 3.73 3 3 7 4 145.15 1.38 4 4 7 3 153.30 2.73 5 4 8 4 148.24 2.29 6 4 118 114 23.37 0.29 7 5 8 3 151.46 3.66 8 5 9 4 149.04 2.69 9 5 116 111 24.39 0.73 10 5 117 112 23.88 0.48 11 5 118 113 23.43 0.26 12 6 9 3 154.73 0.15 13 6 10 4 148.42 3.00 14 7 10 3 149.80 2.31 15 7 11 4 146.94 2.90 16 8 11 3 155.27 0.12 17 8 12 4 146.88 2.93 18 8 13 5 145.66 3.54 19 8 54 46 56.70 6.17 20 8 108 100 34.97 0.36 21 8 117 109 35.41 0.14 22 8 118 110 34.97 0.36 23 8 119 111 34.92 0.34 24 8 120 112 34.48 0.56 25 9 12 3 156.32 0.41 26 9 13 4 140.24 0.93 27 9 33 24 118.88 0.29 28 9 51 42 86.01 1.44 29 10 33 23 118.86 0.29 30 10 34 24 118.95 0.25 31 10 35 25 118.94 0.25 32 11 35 24 118.89 0.28 33 11 41 30 119.05 0.19 34 11 44 33 116.05 0.01 35 11 46 35 115.27 0.36 36 12 41 29 119.45 0.26 37 12 44 32 116.84 0.38 38 12 45 33 115.29 0.37 39 12 46 34 115.27 0.36 40 12 47 35 115.26 0.37 41 12 120 108 35.99 0.23 42 13 33 20 119.72 0.20 43 13 47 34 115.28 0.37 44 13 49 36 115.25 0.38 45 13 50 37 115.16 0.41 46 13 51 38 106.68 1.15 47 13 54 41 99.08 1.54 48 14 17 3 164.44 0.32 49 14 25 11 119.23 0.48 50 14 29 15 119.68 0.24 51 14 33 19 119.77 0.20 52 14 46 32 118.55 0.43 53 14 47 33 116.06 0.01 54 14 48 34 115.28 0.38 55 15 49 34 115.25 0.39 56 15 50 35 115.18 0.41 57 15 51 36 115.19 0.41 58 17 48 31 118.93 0.28 59 18 48 30 119.03 0.32 60 18 80 62 119.09 0.35 61 19 48 29 119.27 0.28 62 19 101 82 119.42 0.35 63 20 25 5 119.89 0.20 64 20 48 28 119.73 0.21 65 20 82 62 119.72 0.23 66 20 99 79 119.83 0.21 67 20 101 81 119.69 0.24 68 22 25 3 145.43 1.88 69 22 99 77 149.49 1.78 70 23 99 76 149.49 1.78 71 24 28 4 336.01 0.41 72 25 29 4 336.84 0.01 73 25 46 21 182.65 0.53 74 25 48 23 165.42 0.17 75 25 82 57 170.71 0.18 76 25 99 74 185.56 0.30 77 26 30 4 335.14 0.83 78 26 82 56 238.06 0.32 79 26 97 71 216.08 0.01 80 26 98 72 214.84 0.62 81 26 99 73 205.09 1.83 82 27 96 69 228.16 0.39 83 27 97 70 223.16 1.12 84 29 46 17 228.69 0.34 85 30 35 5 332.39 1.82 86 30 36 6 330.49 0.88 87 30 41 11 229.12 0.32 88 30 44 14 229.00 0.33 89 30 46 16 228.90 0.29 90 30 97 67 228.41 0.37 91 31 36 5 333.28 1.38 92 33 46 13 228.88 0.38 93 35 41 6 278.94 5.90 94 35 44 9 229.13 0.32 95 35 46 11 229.13 0.32 96 36 40 4 335.11 0.13 97 36 95 59 336.02 0.29 98 36 97 61 336.01 0.29 99 40 86 46 229.13 0.33 100 42 85 43 229.09 0.33 101 42 86 44 229.09 0.33 102 43 84 41 228.99 0.33 103 43 85 42 229.00 0.33 104 44 83 39 229.00 0.33 105 44 84 40 228.93 0.35 106 45 81 36 229.04 0.32 107 45 82 37 228.99 0.34 108 45 83 38 228.88 0.34 109 45 120 75 37.03 0.37 110 46 81 35 228.97 0.34 111 46 82 36 228.94 0.35 112 46 84 38 228.86 0.34 113 47 54 7 336.90 0.50 114 47 79 32 229.06 0.33 115 47 80 33 228.97 0.34 116 47 81 34 228.88 0.34 117 47 106 59 196.34 17.73 118 47 120 73 37.72 0.62 119 48 80 32 228.95 0.34 120 48 81 33 228.88 0.34 121 48 82 34 228.86 0.35 122 49 79 30 228.96 0.34 123 49 80 31 228.93 0.34 124 53 79 26 228.66 0.38 125 54 79 25 226.68 0.51 126 54 117 63 62.43 3.75 127 55 116 61 66.14 5.61 128 55 117 62 62.44 3.76 129 57 73 16 228.75 0.36 130 57 74 17 228.69 0.38 131 57 75 18 216.07 0.01 132 57 79 22 212.87 0.38 133 58 73 15 228.68 0.38 134 58 115 57 67.23 5.29 135 58 116 58 67.13 5.32 136 58 117 59 67.09 5.34 137 60 73 13 228.87 0.33 138 60 74 14 228.78 0.34 139 60 75 15 228.34 0.33 140 60 76 16 218.30 0.51 141 61 73 12 228.92 0.33 142 61 74 13 228.79 0.35 143 61 76 15 228.34 0.33 144 62 70 8 241.96 0.33 145 62 72 10 229.02 0.33 146 62 73 11 228.93 0.33 147 63 72 9 229.03 0.34 148 63 73 10 229.02 0.33 149 63 74 11 229.01 0.33 150 63 107 44 229.09 0.33 151 64 72 8 246.32 1.85 152 65 109 44 228.69 0.37 153 65 121 56 63.22 3.87 154 66 121 55 63.31 3.91 155 66 122 56 63.31 3.91 156 71 109 38 228.76 0.36 157 71 110 39 228.71 0.38 158 71 111 40 228.66 0.39 159 71 115 44 156.53 1.43 160 72 107 35 228.84 0.35 161 72 108 36 228.76 0.36 162 72 109 37 228.62 0.36 163 72 121 49 62.93 4.00 164 73 107 34 228.81 0.35 165 73 108 35 228.70 0.38 166 73 110 37 228.34 0.33 167 73 115 42 131.73 3.38 168 74 105 31 228.90 0.34 169 74 106 32 228.81 0.35 170 74 107 33 228.35 0.33 171 74 124 50 38.38 0.72 172 75 79 4 222.22 3.08 173 75 105 30 228.81 0.35 174 75 106 31 228.69 0.38 175 76 105 29 228.75 0.36 176 77 105 28 227.30 0.25 177 78 103 25 228.69 0.38 178 78 104 26 216.09 0.01 179 78 105 27 214.77 0.64 180 79 103 24 221.21 0.37 181 79 104 25 216.05 0.02 182 79 106 27 208.44 0.14 183 80 101 21 228.76 0.37 184 80 102 22 228.02 0.46 185 80 103 23 214.80 0.61 186 81 101 20 216.39 0.02 187 81 102 21 214.84 0.62 188 81 104 23 208.88 0.35 189 81 106 25 168.62 0.05 190 81 123 42 36.83 0.29 191 82 99 17 228.69 0.38 192 82 100 18 216.23 0.06 193 82 101 19 214.77 0.62 194 83 98 15 228.75 0.38 195 83 99 16 218.22 1.05 196 83 100 17 214.80 0.62 197 84 97 13 228.62 0.35 198 84 98 14 216.09 0.01 199 85 97 12 228.72 0.39 200 85 98 13 228.58 0.41 201 86 90 4 264.18 4.33 202 86 96 10 228.93 0.33 203 86 97 11 228.80 0.39 204 87 90 3 334.73 0.97 205 87 96 9 229.00 0.33 206 87 97 10 228.94 0.34 207 87 98 11 228.91 0.33 208 90 94 4 334.75 0.93 209 90 95 5 229.18 0.33 210 90 96 6 229.13 0.33 211 104 123 19 37.38 0.34 212 104 124 20 36.98 0.29 213 105 123 18 37.40 0.34 214 105 124 19 37.18 0.35 215 106 120 14 61.70 3.73 216 106 122 16 40.48 1.31 217 106 123 17 37.83 0.54 218 107 120 13 61.78 3.72 219 107 121 14 58.73 5.17 220 107 122 15 41.86 0.62 221 107 124 17 38.91 0.91 222 108 117 9 66.94 5.40 223 108 119 11 64.22 4.71 224 108 120 12 62.13 3.90 225 108 121 13 61.64 3.71 226 109 117 8 67.11 5.36 227 109 118 9 66.95 5.40 228 109 119 10 66.37 5.36 229 110 115 5 101.62 11.68 230 110 116 6 67.53 5.17 231 110 117 7 67.12 5.34 232 110 118 8 67.09 5.34 233 111 115 4 131.73 3.38 234 111 116 5 101.62 11.68 235 111 118 7 67.72 5.03 236 112 115 3 149.59 0.75