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 27 26 229.69 0.20 2 1 28 27 229.66 0.21 3 1 73 72 229.62 0.21 4 1 74 73 229.69 0.20 5 1 75 74 229.69 0.20 6 1 78 77 229.69 0.20 7 1 79 78 229.64 0.20 8 1 80 79 212.11 1.84 9 2 25 23 229.71 0.19 10 2 26 24 229.71 0.19 11 2 80 78 229.62 0.20 12 3 23 20 229.70 0.19 13 3 24 21 229.71 0.19 14 3 25 22 229.72 0.19 15 3 71 68 229.62 0.21 16 3 73 70 229.69 0.20 17 3 80 77 229.67 0.18 18 3 81 78 229.58 0.18 19 3 82 79 197.01 0.23 20 4 23 19 229.72 0.18 21 4 24 20 229.73 0.18 22 4 26 22 229.75 0.18 23 4 82 78 229.62 0.20 24 5 8 3 249.86 0.59 25 5 22 17 229.72 0.18 26 5 23 18 229.72 0.18 27 5 82 77 229.68 0.19 28 5 84 79 207.02 1.28 29 6 21 15 229.71 0.18 30 6 22 16 229.73 0.18 31 6 84 78 229.69 0.19 32 7 10 3 251.53 0.42 33 7 11 4 214.04 8.73 34 7 21 14 229.74 0.18 35 7 84 77 229.71 0.18 36 8 82 74 229.75 0.18 37 9 83 74 229.74 0.18 38 9 84 75 229.72 0.18 39 9 85 76 229.72 0.18 40 10 84 74 229.73 0.18 41 10 85 75 229.72 0.18 42 10 87 77 229.71 0.18 43 11 19 8 229.76 0.18 44 11 21 10 229.80 0.20 45 11 84 73 229.75 0.18 46 11 85 74 229.74 0.18 47 11 86 75 229.72 0.18 48 11 87 76 229.71 0.18 49 12 87 75 229.72 0.18 50 12 88 76 229.71 0.18 51 12 89 77 229.71 0.18 52 12 177 165 60.55 0.61 53 13 19 6 230.30 0.45 54 13 61 48 250.97 0.35 55 13 87 74 229.74 0.18 56 13 88 75 229.71 0.18 57 13 89 76 229.71 0.18 58 14 17 3 252.84 0.04 59 14 61 47 281.85 5.23 60 14 89 75 229.70 0.17 61 15 61 46 287.63 2.33 62 15 62 47 262.06 2.33 63 15 63 48 270.99 2.13 64 15 88 73 229.74 0.18 65 15 89 74 229.69 0.17 66 15 90 75 211.53 0.24 67 16 60 44 401.93 0.35 68 16 61 45 404.63 0.04 69 21 84 63 229.89 0.12 70 21 86 65 229.37 0.03 71 25 28 3 400.19 1.29 72 35 84 49 230.27 0.10 73 36 81 45 230.62 0.06 74 58 86 28 229.88 0.13 75 61 88 27 229.75 0.18 76 62 88 26 229.84 0.14 77 63 88 25 229.86 0.14 78 63 119 56 90.84 15.43 79 63 147 84 90.94 15.45 80 63 149 86 90.95 15.37 81 65 86 21 229.99 0.12 82 66 86 20 230.06 0.12 83 66 88 22 229.78 0.12 84 66 119 53 90.84 15.43 85 66 147 81 90.94 15.45 86 67 85 18 230.08 0.11 87 67 86 19 230.04 0.12 88 68 84 16 230.27 0.10 89 68 85 17 229.94 0.04 90 69 83 14 230.28 0.09 91 69 84 15 230.27 0.09 92 69 86 17 229.95 0.05 93 70 81 11 230.50 0.09 94 70 82 12 230.29 0.09 95 70 83 13 230.00 0.06 96 71 81 10 230.36 0.10 97 71 82 11 230.27 0.10 98 72 79 7 230.67 0.06 99 72 80 8 230.64 0.06 100 72 81 9 230.35 0.07 101 73 79 6 230.66 0.05 102 73 80 7 230.65 0.05 103 74 78 4 230.74 0.04 104 74 79 5 230.66 0.04 105 75 78 3 234.16 1.67 106 88 119 31 90.78 15.39 107 89 119 30 90.76 15.40 108 89 120 31 90.67 15.44 109 89 175 86 62.30 1.42 110 89 177 88 61.50 0.92 111 90 117 27 92.97 14.29 112 90 118 28 90.78 15.40 113 90 119 29 91.00 15.35 114 90 149 59 94.24 13.87 115 90 175 85 62.48 1.33 116 91 115 24 94.50 13.48 117 91 118 27 92.03 14.83 118 91 124 33 90.96 15.37 119 91 173 82 65.59 1.61 120 91 175 84 62.57 1.29 121 91 185 94 61.49 0.84 122 91 186 95 60.91 0.67 123 91 187 96 55.72 0.23 124 92 116 24 94.92 13.61 125 92 117 25 94.83 13.66 126 92 187 95 60.91 0.68 127 93 115 22 94.84 13.56 128 93 116 23 95.01 13.56 129 93 117 24 94.95 13.62 130 93 187 94 61.41 0.89 131 94 187 93 61.45 0.86 132 95 113 18 101.53 10.27 133 95 114 19 99.31 11.42 134 95 115 20 97.64 12.25 135 95 171 76 90.31 6.87 136 95 173 78 69.35 0.80 137 95 187 92 61.83 0.71 138 95 188 93 61.29 0.76 139 95 189 94 60.77 0.70 140 96 112 16 103.53 9.35 141 96 113 17 101.58 10.29 142 96 114 18 99.95 11.12 143 97 111 14 103.58 9.34 144 97 112 15 103.53 9.35 145 97 113 16 101.59 10.29 146 97 169 72 102.84 9.45 147 97 170 73 103.26 9.44 148 97 171 74 101.57 10.29 149 97 189 92 61.82 0.70 150 97 190 93 61.80 0.70 151 97 191 94 60.70 0.73 152 98 110 12 104.14 9.14 153 98 111 13 103.81 9.23 154 98 112 14 103.53 9.35 155 99 109 10 104.83 8.81 156 99 110 11 104.13 9.15 157 99 111 12 104.04 9.12 158 99 169 70 104.03 9.12 159 99 191 92 61.94 0.66 160 100 109 9 104.83 8.81 161 100 110 10 104.15 9.14 162 101 109 8 108.83 6.92 163 102 109 7 120.42 1.24 164 103 109 6 125.61 1.16 165 103 160 57 255.46 2.67 166 103 165 62 245.87 1.67 167 103 193 90 61.97 0.65 168 103 194 91 61.91 0.63 169 103 195 92 61.55 0.64 170 104 107 3 254.88 1.61 171 104 160 56 280.71 1.23 172 105 160 55 280.72 1.23 173 105 162 57 266.64 0.46 174 106 159 53 291.24 1.32 175 106 160 54 309.35 1.43 176 111 128 17 403.76 1.87 177 120 177 57 401.19 0.09 178 123 175 52 404.73 0.97 179 123 176 53 403.73 0.63 180 123 179 56 401.25 0.12 181 124 175 51 403.86 0.57 182 125 174 49 404.09 0.65 183 158 193 35 61.94 0.63 184 164 193 29 62.05 0.64 185 165 193 28 62.05 0.64 186 165 194 29 62.02 0.66 187 165 195 30 61.93 0.62 188 166 192 26 62.09 0.64 189 166 193 27 62.05 0.64 190 167 192 25 62.06 0.65 191 167 193 26 62.03 0.65 192 168 190 22 62.11 0.63 193 168 191 23 62.04 0.65 194 168 192 24 61.91 0.64 195 169 190 21 62.03 0.65 196 169 191 22 61.97 0.65 197 169 193 24 61.75 0.68 198 170 188 18 62.11 0.64 199 170 189 19 62.05 0.64 200 170 190 20 61.94 0.66 201 171 188 17 62.02 0.65 202 171 189 18 62.00 0.66 203 172 186 14 62.11 0.64 204 172 187 15 62.08 0.62 205 172 188 16 61.94 0.66 206 173 186 13 62.08 0.62 207 173 187 14 62.03 0.64 208 174 184 10 62.12 0.62 209 174 185 11 62.10 0.63 210 174 186 12 61.98 0.62 211 175 184 9 62.09 0.61 212 175 185 10 62.06 0.62 213 176 181 5 129.38 1.68 214 176 182 6 88.87 12.72 215 176 184 8 62.08 0.62 216 177 185 8 62.09 0.61 217 178 181 3 199.75 27.16