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 8 13 5 54.40 0.06 2 8 14 6 58.22 0.69 3 9 13 4 70.08 0.10 4 10 13 3 75.70 2.90 5 10 14 4 70.98 0.89 6 11 14 3 77.60 1.96 7 11 23 12 61.64 0.91 8 11 121 110 60.41 0.27 9 11 127 116 60.38 0.28 10 11 128 117 60.40 0.29 11 12 122 110 60.48 0.25 12 12 123 111 60.45 0.26 13 12 124 112 60.44 0.27 14 12 125 113 60.40 0.29 15 12 126 114 60.40 0.28 16 13 122 109 60.47 0.25 17 14 121 107 60.49 0.23 18 14 122 108 60.50 0.24 19 15 23 8 158.65 0.19 20 15 121 106 67.44 0.29 21 16 21 5 180.41 0.74 22 16 23 7 180.07 0.70 23 16 129 113 180.08 0.71 24 18 21 3 180.47 0.70 25 19 22 3 229.89 0.37 26 22 201 179 186.41 0.62 27 22 209 187 283.38 0.03 28 23 201 178 180.44 0.73 29 23 202 179 180.41 0.74 30 23 203 180 180.19 0.65 31 24 130 106 283.50 0.00 32 24 200 176 180.47 0.72 33 24 202 178 180.19 0.65 34 24 209 185 180.46 0.72 35 25 199 174 180.49 0.71 36 25 200 175 180.41 0.74 37 25 202 177 174.99 0.21 38 26 197 171 208.61 1.72 39 26 198 172 180.47 0.72 40 26 199 173 180.26 0.68 41 26 202 176 177.88 0.77 42 27 167 140 283.49 0.01 43 27 169 142 281.49 0.03 44 27 171 144 242.25 17.56 45 27 197 170 180.47 0.72 46 27 198 171 180.41 0.74 47 28 196 168 180.47 0.72 48 28 197 169 180.24 0.67 49 29 171 142 180.43 0.72 50 29 196 167 180.40 0.73 51 29 229 200 144.24 0.04 52 29 232 203 143.72 0.01 53 29 233 204 143.40 0.12 54 30 193 163 199.96 0.96 55 30 194 164 180.47 0.72 56 31 193 162 180.47 0.72 57 31 194 163 180.41 0.73 58 31 232 201 144.12 0.03 59 31 233 202 144.06 0.01 60 32 88 56 283.48 0.00 61 32 190 158 180.59 0.72 62 32 192 160 180.47 0.72 63 32 193 161 180.06 0.71 64 33 111 78 283.50 0.00 65 33 190 157 180.47 0.72 66 33 191 158 180.47 0.72 67 33 192 159 180.19 0.65 68 34 38 4 144.55 0.04 69 34 41 7 144.37 0.03 70 34 86 52 283.50 0.01 71 34 88 54 189.15 1.72 72 34 112 78 283.50 0.00 73 34 189 155 180.25 0.84 74 34 191 157 180.39 0.74 75 35 38 3 144.72 0.04 76 35 187 152 180.18 0.85 77 35 191 156 179.75 0.62 78 38 188 150 171.53 1.73 79 38 189 151 144.55 0.04 80 41 86 45 144.38 0.01 81 41 87 46 144.37 0.04 82 42 107 65 143.50 0.14 83 43 85 42 144.32 0.01 84 43 86 43 144.24 0.06 85 43 154 111 144.41 0.01 86 43 155 112 144.40 0.02 87 44 85 41 144.06 0.02 88 44 86 42 144.05 0.01 89 44 105 61 141.81 0.66 90 44 106 62 142.29 0.43 91 44 107 63 142.68 0.36 92 44 112 68 142.49 0.34 93 44 157 113 143.00 0.46 94 45 84 39 144.05 0.02 95 45 85 40 144.05 0.02 96 45 105 60 137.73 0.50 97 45 157 112 142.86 0.47 98 45 158 113 142.81 0.47 99 45 159 114 142.62 0.53 100 46 84 38 144.27 0.04 101 46 85 39 144.18 0.03 102 46 153 107 144.38 0.01 103 46 155 109 142.91 0.49 104 46 156 110 142.93 0.49 105 46 157 111 142.81 0.47 106 46 158 112 142.81 0.47 107 47 83 36 144.35 0.07 108 47 84 37 144.34 0.01 109 48 82 34 144.66 0.22 110 48 83 35 144.37 0.06 111 48 103 55 142.30 0.43 112 48 241 193 283.16 0.15 113 48 242 194 279.91 0.81 114 49 81 32 154.76 5.25 115 49 82 33 147.25 1.47 116 50 80 30 161.68 8.68 117 50 81 31 160.59 8.13 118 51 79 28 161.84 8.75 119 51 80 29 161.69 8.67 120 52 77 25 161.99 8.77 121 52 78 26 161.96 8.76 122 52 79 27 161.89 8.76 123 53 77 24 161.99 8.76 124 53 78 25 161.99 8.76 125 54 58 4 283.50 0.01 126 55 77 22 161.99 8.76 127 57 65 8 283.49 0.01 128 57 70 13 270.27 1.21 129 60 64 4 283.50 0.00 130 63 67 4 283.50 0.00 131 72 75 3 283.50 0.00 132 76 96 20 281.13 0.76 133 77 95 18 283.12 0.10 134 78 94 16 283.20 0.14 135 78 95 17 283.08 0.09 136 79 93 14 283.49 0.01 137 79 94 15 283.48 0.01 138 80 93 13 283.49 0.01 139 81 103 22 283.50 0.00 140 83 241 158 137.41 0.83 141 84 89 5 283.50 0.00 142 86 112 26 283.49 0.01 143 89 151 62 283.50 0.00 144 94 97 3 283.50 0.01 145 96 142 46 283.50 0.00 146 98 199 101 185.09 0.20 147 103 240 137 112.49 1.40 148 103 241 138 105.88 0.18 149 104 164 60 283.49 0.01 150 104 238 134 141.82 0.60 151 104 239 135 137.12 0.31 152 104 240 136 123.67 2.73 153 104 241 137 108.42 0.84 154 105 238 133 141.82 0.65 155 105 239 134 141.71 0.61 156 105 241 136 135.60 0.18 157 106 237 131 142.65 0.26 158 106 238 132 141.84 0.66 159 108 237 129 144.05 0.10 160 113 233 120 144.11 0.03 161 113 238 125 141.81 0.65 162 115 166 51 283.47 0.01 163 115 238 123 141.67 0.58 164 117 167 50 283.50 0.00 165 120 167 47 283.50 0.00 166 120 202 82 174.45 0.07 167 121 202 81 179.90 0.79 168 121 203 82 179.71 0.71 169 131 134 3 283.50 0.00 170 134 137 3 283.50 0.00 171 135 209 74 283.38 0.03 172 139 199 60 283.38 0.04 173 139 209 70 283.44 0.01 174 139 211 72 283.46 0.02 175 142 199 57 283.18 0.01 176 144 197 53 283.41 0.04 177 145 182 37 283.50 0.00 178 146 195 49 283.50 0.01 179 148 185 37 283.50 0.00 180 158 241 83 142.74 0.46 181 159 239 80 142.92 0.42 182 159 240 81 142.34 0.39 183 159 241 82 141.94 0.58 184 159 242 83 141.94 0.58 185 160 240 80 142.11 0.49 186 160 242 82 141.88 0.58 187 162 240 78 141.88 0.59 188 164 238 74 141.86 0.58 189 167 202 35 170.28 1.70 190 168 202 34 179.66 0.69 191 169 198 29 283.50 0.00 192 169 201 32 180.38 0.75 193 169 202 33 176.39 0.62 194 169 210 41 268.98 6.77 195 171 229 58 143.27 0.18 196 171 230 59 142.53 0.01 197 172 205 33 283.37 0.04 198 172 230 58 142.53 0.02 199 173 228 55 143.25 0.18 200 176 212 36 283.50 0.00 201 177 211 34 283.50 0.00 202 179 199 20 283.49 0.00 203 179 211 32 283.50 0.00 204 180 197 17 283.49 0.01 205 185 193 8 283.50 0.00 206 187 190 3 283.50 0.00 207 194 232 38 144.02 0.03 208 196 229 33 144.03 0.03 209 196 232 36 142.94 0.35 210 212 226 14 143.43 0.29 211 212 227 15 143.44 0.28 212 215 223 8 150.68 2.95 213 215 224 9 144.42 0.01 214 216 221 5 179.93 0.53 215 216 222 6 175.02 2.95 216 216 223 7 165.77 0.16 217 216 225 9 150.69 2.95 218 216 227 11 144.47 0.01 219 217 220 3 281.05 0.90 220 217 221 4 181.79 1.46 221 217 222 5 179.81 0.56 222 218 221 3 246.16 1.47 223 229 232 3 213.94 0.85 224 233 238 5 275.38 2.00 225 234 237 3 282.06 0.09 226 234 238 4 279.82 0.58 227 235 238 3 281.84 0.31