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 1 97 96 28.01 0.47 2 2 94 92 28.19 0.53 3 2 95 93 28.09 0.50 4 2 96 94 28.00 0.47 5 2 100 98 28.09 0.51 6 2 133 131 28.39 0.45 7 3 9 6 29.89 0.36 8 3 10 7 29.71 0.35 9 3 94 91 28.39 0.45 10 3 95 92 28.19 0.51 11 3 97 94 28.21 0.52 12 4 7 3 42.12 0.52 13 4 10 6 29.89 0.36 14 4 92 88 29.14 0.54 15 4 93 89 29.14 0.54 16 5 10 5 30.10 0.34 17 5 78 73 29.83 0.40 18 5 91 86 29.66 0.38 19 5 92 87 29.25 0.50 20 6 77 71 31.61 0.07 21 6 78 72 31.18 0.27 22 6 91 85 29.90 0.38 23 7 10 3 119.17 35.49 24 10 15 5 187.91 0.74 25 10 92 82 61.24 0.16 26 10 95 85 61.65 0.05 27 10 97 87 64.15 0.17 28 11 14 3 194.25 1.39 29 11 97 86 84.30 0.52 30 12 15 3 192.79 0.66 31 12 47 35 68.22 0.20 32 12 52 40 68.20 0.20 33 12 80 68 72.38 2.79 34 13 16 3 190.53 0.48 35 13 47 34 74.20 0.17 36 14 97 83 90.42 0.30 37 14 122 108 136.75 13.20 38 15 19 4 196.81 0.58 39 15 45 30 88.83 0.21 40 15 47 32 89.67 0.53 41 15 52 37 89.62 0.52 42 15 92 77 90.47 0.32 43 15 95 80 92.75 0.79 44 15 97 82 92.92 0.80 45 15 101 86 90.15 0.38 46 15 122 107 137.28 12.95 47 16 45 29 89.54 0.54 48 16 46 30 89.67 0.52 49 16 47 31 89.76 0.57 50 16 122 106 185.99 0.54 51 17 44 27 89.70 0.51 52 17 45 28 89.70 0.51 53 17 122 105 186.00 0.54 54 18 43 25 90.03 0.42 55 18 44 26 89.93 0.47 56 18 122 104 186.00 0.54 57 19 42 23 90.18 0.40 58 19 43 24 90.17 0.41 59 19 44 25 90.22 0.41 60 19 45 26 90.30 0.44 61 19 97 78 186.10 0.50 62 19 99 80 186.08 0.51 63 19 100 81 186.03 0.53 64 19 101 82 185.94 0.54 65 19 120 101 185.93 0.55 66 19 121 102 186.00 0.54 67 19 122 103 186.00 0.54 68 20 42 22 90.26 0.42 69 20 120 100 186.00 0.54 70 20 121 101 186.08 0.53 71 20 122 102 186.07 0.54 72 20 123 103 186.03 0.55 73 20 124 104 185.99 0.54 74 21 24 3 238.28 7.03 75 21 40 19 90.29 0.42 76 21 41 20 90.24 0.41 77 21 42 21 90.29 0.42 78 21 119 98 186.14 0.56 79 21 120 99 186.08 0.53 80 21 151 130 90.57 0.36 81 21 155 134 80.39 1.77 82 22 119 97 186.24 0.52 83 22 120 98 186.16 0.55 84 22 121 99 186.21 0.53 85 22 123 101 186.19 0.53 86 22 124 102 186.14 0.55 87 22 125 103 186.03 0.55 88 22 126 104 186.02 0.54 89 22 131 109 185.69 0.63 90 22 150 128 92.80 0.73 91 22 151 129 90.57 0.36 92 22 152 130 90.18 0.41 93 22 155 133 79.23 2.35 94 23 118 95 186.45 0.50 95 23 119 96 186.26 0.51 96 23 131 108 185.89 0.60 97 23 134 111 170.87 1.16 98 23 148 125 97.69 0.93 99 23 149 126 96.88 0.86 100 23 150 127 92.80 0.73 101 23 151 128 92.77 0.73 102 24 32 8 96.86 0.84 103 24 38 14 96.22 0.42 104 24 39 15 95.69 0.38 105 24 40 16 95.67 0.35 106 24 116 92 186.72 0.42 107 24 117 93 186.67 0.46 108 24 118 94 186.46 0.51 109 24 120 96 186.47 0.52 110 24 148 124 97.70 0.93 111 24 149 125 97.51 0.94 112 24 151 127 96.69 0.88 113 25 32 7 169.22 3.67 114 25 116 91 186.75 0.42 115 25 117 92 186.69 0.46 116 25 134 109 185.63 0.65 117 25 138 113 154.35 0.15 118 25 143 118 144.48 0.59 119 25 147 122 105.08 0.17 120 25 148 123 97.75 0.90 121 26 32 6 181.91 2.52 122 26 114 88 186.74 0.42 123 26 115 89 186.74 0.42 124 26 116 90 186.75 0.42 125 26 143 117 145.91 0.65 126 26 147 121 128.90 0.30 127 27 114 87 186.78 0.42 128 27 115 88 186.79 0.42 129 27 143 116 146.41 0.41 130 27 147 120 139.39 2.33 131 28 31 3 193.25 1.75 132 28 112 84 186.84 0.41 133 28 113 85 186.84 0.42 134 28 114 86 186.82 0.41 135 29 32 3 194.03 0.31 136 29 33 4 186.85 0.40 137 29 146 117 146.52 0.41 138 29 147 118 142.03 1.23 139 29 149 120 142.23 1.32 140 30 33 3 186.87 0.41 141 30 36 6 186.83 0.40 142 31 36 5 186.83 0.40 143 31 37 6 186.83 0.41 144 31 38 7 186.77 0.41 145 31 39 8 186.78 0.41 146 31 109 78 187.11 0.40 147 31 114 83 187.23 0.46 148 32 38 6 186.78 0.42 149 32 39 7 186.72 0.42 150 32 116 84 187.45 0.35 151 32 147 115 147.24 0.76 152 32 149 117 146.29 0.52 153 33 36 3 186.85 0.42 154 33 39 6 186.75 0.40 155 33 149 116 146.00 0.67 156 34 39 5 186.84 0.42 157 36 39 3 191.49 0.04 158 37 40 3 231.47 4.36 159 37 84 47 189.06 0.58 160 37 85 48 189.18 0.61 161 38 84 46 189.31 0.59 162 38 85 47 189.31 0.59 163 38 88 50 189.22 0.64 164 38 107 69 189.16 0.66 165 38 114 76 189.12 0.65 166 38 116 78 188.41 0.70 167 39 149 110 146.53 0.42 168 39 151 112 144.83 0.21 169 40 56 16 142.44 1.39 170 40 57 17 139.91 2.60 171 40 58 18 139.03 2.92 172 40 67 27 142.45 1.40 173 40 69 29 146.34 0.51 174 40 84 44 189.74 0.67 175 41 56 15 144.16 0.55 176 41 57 16 142.42 1.39 177 41 59 18 141.05 2.04 178 41 151 110 146.39 0.49 179 41 154 113 142.40 1.40 180 41 155 114 131.33 0.14 181 42 45 3 322.25 2.49 182 42 54 12 146.44 0.50 183 42 55 13 146.38 0.50 184 42 56 14 144.90 0.24 185 42 120 78 139.58 25.07 186 43 55 12 146.43 0.50 187 43 56 13 146.31 0.52 188 43 57 14 146.30 0.53 189 43 66 23 146.38 0.49 190 44 54 10 153.75 0.06 191 44 55 11 149.72 2.02 192 45 52 7 154.48 0.12 193 45 53 8 154.34 0.12 194 45 54 9 153.96 0.04 195 45 101 56 189.26 0.71 196 46 52 6 154.56 0.15 197 46 53 7 154.33 0.10 198 46 55 9 154.31 0.11 199 47 52 5 161.65 0.04 200 48 51 3 182.72 0.93 201 48 53 5 164.12 0.90 202 49 73 24 252.11 0.80 203 50 72 22 252.09 0.80 204 50 73 23 252.10 0.80 205 51 70 19 251.75 0.72 206 51 71 20 252.08 0.80 207 51 72 21 252.09 0.80 208 51 73 22 252.11 0.80 209 51 80 29 252.11 0.80 210 52 70 18 252.09 0.81 211 52 71 19 252.09 0.80 212 52 80 28 252.15 0.80 213 52 90 38 252.19 0.79 214 53 69 16 252.09 0.81 215 53 70 17 252.09 0.80 216 54 68 14 252.08 0.80 217 54 69 15 252.09 0.80 218 54 71 17 252.15 0.80 219 54 90 36 270.49 8.04 220 55 67 12 252.08 0.80 221 55 68 13 252.09 0.80 222 56 66 10 252.07 0.81 223 56 67 11 252.09 0.80 224 56 69 13 252.18 0.81 225 57 64 7 251.56 0.82 226 57 65 8 252.06 0.81 227 57 66 9 252.07 0.81 228 57 67 10 252.10 0.80 229 57 155 98 251.91 0.85 230 57 157 100 214.48 3.28 231 58 64 6 252.06 0.81 232 58 65 7 252.06 0.81 233 58 67 9 252.15 0.80 234 59 62 3 252.12 0.80 235 59 63 4 252.09 0.81 236 59 64 5 252.03 0.82 237 60 63 3 252.12 0.80