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 3 101 98 219.08 0.05 2 4 22 18 219.16 0.03 3 4 23 19 219.30 0.06 4 4 24 20 219.31 0.06 5 4 28 24 219.34 0.06 6 4 29 25 219.33 0.06 7 4 90 86 219.12 0.04 8 4 91 87 219.19 0.04 9 4 92 88 219.28 0.06 10 4 100 96 219.25 0.05 11 4 101 97 219.16 0.03 12 4 102 98 219.03 0.03 13 4 103 99 218.97 0.06 14 5 22 17 219.24 0.04 15 5 23 18 219.31 0.05 16 6 20 14 219.26 0.06 17 6 21 15 219.29 0.04 18 6 22 16 219.31 0.05 19 6 37 31 219.31 0.05 20 6 88 82 219.16 0.03 21 6 89 83 219.24 0.05 22 6 90 84 219.30 0.05 23 6 102 96 219.25 0.05 24 6 103 97 219.15 0.02 25 6 104 98 219.13 0.03 26 6 105 99 219.12 0.02 27 7 20 13 219.31 0.06 28 7 21 14 219.33 0.06 29 7 105 98 219.15 0.03 30 8 103 95 219.33 0.06 31 8 104 96 219.27 0.05 32 8 105 97 219.15 0.03 33 8 106 98 219.15 0.03 34 9 105 96 219.25 0.05 35 9 106 97 219.15 0.03 36 10 18 8 219.56 0.18 37 10 20 10 219.38 0.04 38 10 105 95 219.31 0.06 39 10 106 96 219.27 0.06 40 10 107 97 219.15 0.02 41 10 108 98 219.14 0.02 42 11 18 7 219.66 0.16 43 11 108 97 219.15 0.02 44 11 110 99 219.13 0.03 45 12 80 68 265.79 0.36 46 12 108 96 219.27 0.06 47 12 109 97 219.14 0.03 48 12 110 98 219.13 0.03 49 13 16 3 267.69 0.49 50 13 80 67 288.69 4.20 51 13 109 96 219.22 0.04 52 13 110 97 219.13 0.03 53 14 80 66 291.66 2.72 54 14 81 67 299.45 5.37 55 14 82 68 308.56 1.63 56 14 109 95 219.28 0.04 57 14 110 96 219.25 0.06 58 14 111 97 219.13 0.02 59 14 112 98 219.09 0.01 60 15 79 64 405.59 0.67 61 15 80 65 414.67 2.66 62 16 79 63 417.32 1.33 63 16 80 64 417.32 1.34 64 17 77 60 417.32 1.33 65 17 78 61 417.33 1.33 66 17 79 62 417.34 1.33 67 17 80 63 417.32 1.34 68 18 76 58 417.33 1.33 69 18 77 59 417.33 1.33 70 18 107 89 219.27 0.04 71 19 75 56 417.33 1.33 72 19 76 57 417.33 1.33 73 20 105 85 219.41 0.04 74 20 107 87 219.15 0.01 75 27 94 67 412.36 1.12 76 28 94 66 321.93 3.60 77 28 100 72 220.80 0.19 78 38 101 63 220.26 0.01 79 80 109 29 219.28 0.04 80 82 109 27 219.33 0.03 81 82 112 30 214.13 1.11 82 82 174 92 40.51 2.45 83 83 174 91 35.47 0.06 84 84 107 23 219.45 0.04 85 85 107 22 219.45 0.04 86 85 108 23 219.43 0.04 87 85 109 24 219.40 0.03 88 85 170 85 35.41 0.02 89 86 106 20 219.65 0.01 90 86 107 21 219.56 0.02 91 87 105 18 219.70 0.03 92 87 106 19 219.60 0.04 93 88 104 16 219.70 0.03 94 88 105 17 219.60 0.04 95 88 107 19 219.42 0.03 96 89 102 13 220.00 0.01 97 89 103 14 219.95 0.01 98 89 104 15 219.61 0.05 99 90 101 11 220.03 0.01 100 90 102 12 220.00 0.01 101 91 99 8 220.57 0.10 102 91 100 9 220.33 0.00 103 91 101 10 220.15 0.04 104 92 99 7 220.72 0.17 105 92 100 8 220.34 0.01 106 93 97 4 261.72 0.71 107 93 98 5 221.00 0.18 108 93 99 6 220.83 0.21 109 94 98 4 224.41 1.73 110 94 99 5 221.00 0.18 111 94 100 6 220.97 0.18 112 95 98 3 280.73 1.21 113 109 112 3 292.66 1.06 114 112 144 32 87.96 0.09 115 112 174 62 88.44 0.21 116 113 144 31 88.18 0.18 117 114 144 30 88.14 0.17 118 114 145 31 88.16 0.17 119 114 201 87 87.73 0.01 120 114 202 88 87.98 0.17 121 115 142 27 88.89 0.18 122 115 143 28 88.45 0.20 123 115 144 29 88.45 0.21 124 115 175 60 88.85 0.20 125 115 201 86 88.12 0.20 126 116 201 85 88.08 0.22 127 116 204 88 87.86 0.33 128 117 140 23 89.07 0.17 129 117 141 24 89.08 0.18 130 117 143 26 88.89 0.18 131 117 148 31 88.62 0.23 132 117 199 82 87.97 0.17 133 117 201 84 88.49 0.21 134 118 139 21 94.02 0.25 135 118 140 22 91.62 1.03 136 118 141 23 89.23 0.16 137 119 138 19 95.83 1.16 138 119 139 20 94.02 0.26 139 119 140 21 92.92 0.38 140 119 199 80 89.17 0.14 141 119 206 87 88.30 0.28 142 119 208 89 85.78 0.10 143 120 137 17 97.11 1.42 144 120 138 18 96.42 1.40 145 120 139 19 95.78 1.14 146 121 136 15 97.22 1.42 147 121 137 16 96.98 1.49 148 121 138 17 96.43 1.40 149 121 152 31 97.17 1.43 150 121 195 74 97.20 1.43 151 121 197 76 96.44 1.39 152 121 208 87 88.23 0.29 153 121 209 88 87.93 0.44 154 121 210 89 84.31 0.83 155 122 136 14 97.22 1.42 156 122 137 15 97.17 1.42 157 122 139 17 97.09 1.44 158 123 189 66 117.78 0.88 159 123 210 87 87.95 0.43 160 123 214 91 46.69 0.44 161 124 128 4 245.50 2.78 162 124 129 5 240.91 0.72 163 124 134 10 104.80 1.48 164 124 135 11 98.53 1.28 165 124 136 12 98.43 1.24 166 124 189 65 117.87 0.84 167 124 214 90 58.92 0.75 168 125 128 3 253.67 1.28 169 125 129 4 245.51 2.79 170 125 216 91 36.81 1.72 171 126 129 3 253.81 0.20 172 126 130 4 252.59 0.77 173 126 216 90 39.65 2.83 174 127 130 3 253.77 0.18 175 127 131 4 252.47 0.82 176 128 131 3 265.79 5.79 177 128 132 4 248.47 2.81 178 128 133 5 240.53 0.72 179 128 134 6 237.27 0.69 180 128 135 7 237.27 0.69 181 129 132 3 242.43 1.28 182 129 133 4 240.99 0.72 183 129 134 5 240.72 0.62 184 129 186 57 240.91 0.52 185 129 189 60 251.62 3.16 186 129 216 87 56.52 0.45 187 136 152 16 419.62 0.92 188 136 210 74 87.95 0.43 189 138 199 61 323.69 1.08 190 150 180 30 419.47 0.84 191 152 182 30 419.29 0.94 192 153 207 54 89.02 0.14 193 189 210 21 88.85 0.12 194 189 211 22 88.72 0.10 195 189 212 23 88.46 0.18 196 189 214 25 88.07 0.40 197 192 212 20 88.80 0.12 198 193 211 18 88.73 0.09 199 193 212 19 88.73 0.09 200 194 209 15 88.85 0.13 201 194 210 16 88.72 0.08 202 194 211 17 88.47 0.18 203 194 212 18 88.49 0.17 204 195 209 14 88.72 0.08 205 195 210 15 88.67 0.08 206 196 207 11 88.90 0.14 207 196 208 12 88.72 0.08 208 196 209 13 88.05 0.39 209 197 207 10 88.71 0.08 210 197 208 11 88.50 0.17 211 198 205 7 88.99 0.14 212 198 206 8 88.84 0.13 213 198 207 9 88.69 0.07 214 199 205 6 88.97 0.12 215 199 206 7 88.76 0.09 216 200 204 4 182.62 28.17 217 200 205 5 88.70 0.07 218 201 204 3 248.53 2.40