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 4 207 203 163.00 0.20 2 8 207 199 183.46 0.78 3 9 157 148 165.94 0.64 4 10 137 127 183.31 0.71 5 10 157 147 177.32 2.74 6 14 157 143 221.83 3.73 7 14 158 144 214.96 1.24 8 14 159 145 214.88 1.25 9 15 135 120 227.94 0.68 10 15 159 144 214.88 1.25 11 15 187 172 184.03 0.52 12 15 188 173 183.96 0.48 13 16 187 171 184.00 0.50 14 16 188 172 183.97 0.49 15 17 187 170 184.06 0.51 16 17 188 171 183.99 0.49 17 17 189 172 184.00 0.49 18 17 222 205 109.34 0.82 19 18 143 125 223.04 2.74 20 18 188 170 184.06 0.50 21 18 189 171 184.02 0.49 22 18 192 174 183.99 0.48 23 19 157 138 234.33 2.38 24 19 158 139 230.75 3.92 25 19 188 169 184.06 0.50 26 19 192 173 184.02 0.49 27 20 156 136 236.40 2.33 28 20 157 137 236.27 2.31 29 21 154 133 241.27 4.73 30 21 155 134 236.47 2.33 31 21 156 135 236.40 2.33 32 21 157 136 236.40 2.33 33 22 155 133 238.38 3.27 34 22 156 134 237.19 2.68 35 22 157 135 236.44 2.32 36 27 137 110 241.73 4.91 37 27 139 112 241.96 5.00 38 27 155 128 242.13 4.93 39 27 157 130 241.96 5.00 40 27 200 173 201.98 2.98 41 27 207 180 203.44 3.58 42 29 207 178 202.03 2.95 43 30 139 109 241.97 5.00 44 30 141 111 243.06 5.19 45 30 155 125 242.93 5.23 46 30 198 168 195.18 1.64 47 32 141 109 243.58 5.28 48 40 141 101 243.69 5.32 49 40 194 154 193.46 1.83 50 42 194 152 192.27 1.29 51 42 195 153 194.10 2.00 52 43 194 151 189.61 0.65 53 43 195 152 192.89 1.60 54 43 196 153 194.23 2.00 55 43 197 154 194.42 1.96 56 44 196 152 193.09 1.51 57 45 198 153 195.53 1.50 58 47 238 191 39.69 0.24 59 47 242 195 29.87 1.68 60 51 241 190 32.97 1.89 61 51 242 191 29.87 1.68 62 51 245 194 23.45 0.27 63 53 209 156 197.88 0.85 64 53 212 159 195.73 1.53 65 54 196 142 193.99 1.94 66 54 212 158 195.87 1.53 67 55 196 141 194.30 2.08 68 55 212 157 195.96 1.54 69 55 213 158 195.84 1.53 70 57 195 138 195.72 1.53 71 57 213 156 197.67 0.81 72 57 214 157 195.72 1.43 73 58 195 137 195.21 1.62 74 58 196 138 195.56 1.52 75 70 141 71 243.82 5.27 76 71 141 70 243.83 5.26 77 71 154 83 243.72 5.31 78 71 155 84 243.63 5.33 79 72 153 81 243.84 5.28 80 72 154 82 243.73 5.30 81 73 141 68 243.86 5.28 82 73 153 80 243.86 5.28 83 74 153 79 243.88 5.29 84 89 237 148 56.41 0.50 85 89 241 152 39.98 0.39 86 89 245 156 31.69 2.58 87 90 237 147 60.27 0.99 88 91 234 143 67.46 0.91 89 91 237 146 56.84 0.72 90 98 177 79 229.42 10.13 91 98 180 82 229.62 10.00 92 99 180 81 229.41 9.98 93 99 215 116 197.71 0.77 94 100 177 77 229.27 10.06 95 100 179 79 229.35 10.00 96 100 180 80 229.35 10.00 97 101 179 78 229.34 10.00 98 101 234 133 67.49 0.91 99 102 214 112 195.66 1.55 100 103 212 109 197.47 0.81 101 103 234 131 66.59 0.95 102 103 237 134 56.55 0.58 103 104 237 133 56.55 0.58 104 105 237 132 55.66 0.27 105 105 238 133 49.33 2.71 106 105 241 136 36.92 0.46 107 107 245 138 28.16 2.04 108 121 200 79 162.59 0.33 109 121 207 86 162.62 0.33 110 121 208 87 162.60 0.33 111 121 209 88 162.56 0.33 112 122 206 84 162.65 0.34 113 122 207 85 162.59 0.34 114 122 208 86 161.97 0.39 115 122 209 87 160.78 0.22 116 123 208 85 162.60 0.33 117 123 209 86 162.53 0.35 118 123 231 108 66.84 0.84 119 123 235 112 53.72 0.68 120 123 238 115 39.66 0.23 121 124 128 4 162.67 0.33 122 124 130 6 162.65 0.35 123 124 208 84 162.69 0.32 124 124 209 85 162.63 0.34 125 124 231 107 66.88 0.83 126 124 232 108 66.53 0.82 127 124 235 111 54.96 0.14 128 125 128 3 186.95 1.61 129 125 232 107 66.84 0.85 130 125 235 110 56.02 0.66 131 126 232 106 66.83 0.85 132 126 235 109 56.27 0.54 133 126 236 110 56.02 0.66 134 128 232 104 66.84 0.84 135 130 162 32 182.78 1.03 136 130 201 71 183.51 0.60 137 130 208 78 184.22 0.47 138 130 210 80 182.03 0.69 139 130 232 102 67.11 0.84 140 131 134 3 194.52 0.28 141 131 162 31 183.21 0.83 142 132 162 30 183.22 0.83 143 132 163 31 182.79 1.04 144 132 164 32 182.81 1.03 145 133 161 28 227.66 10.66 146 133 162 29 210.86 14.65 147 134 160 26 250.88 3.08 148 134 161 27 236.67 6.16 149 134 162 28 227.68 10.66 150 135 159 24 309.49 1.03 151 135 160 25 251.10 2.98 152 135 161 26 240.21 7.92 153 136 160 24 251.22 2.94 154 136 162 26 250.87 2.81 155 136 199 63 201.21 0.24 156 136 200 64 248.15 3.60 157 137 199 62 202.62 0.95 158 138 192 54 183.52 0.24 159 138 193 55 183.97 0.46 160 138 198 60 197.75 0.84 161 138 199 61 310.34 1.08 162 138 228 90 96.92 0.51 163 139 193 54 184.00 0.46 164 140 192 52 184.05 0.49 165 140 193 53 185.53 1.08 166 140 194 54 189.52 0.58 167 141 192 51 185.65 1.01 168 141 194 53 189.73 0.58 169 142 191 49 185.66 1.01 170 142 192 50 185.77 0.98 171 142 193 51 189.62 0.64 172 142 194 52 189.73 0.58 173 143 191 48 185.88 1.04 174 143 192 49 185.90 1.04 175 145 191 46 189.76 0.58 176 145 193 48 242.18 25.78 177 145 194 49 244.68 24.53 178 146 220 74 189.84 0.64 179 156 192 36 183.94 0.48 180 157 192 35 183.49 0.26 181 158 192 34 183.94 0.48 182 160 186 26 310.49 1.10 183 160 188 28 233.79 24.11 184 160 190 30 217.97 17.05 185 163 225 62 97.62 0.29 186 165 230 65 97.39 0.29 187 171 223 52 121.98 1.39 188 171 224 53 109.12 0.43 189 171 225 54 108.12 0.07 190 172 224 52 111.53 1.62 191 172 225 53 109.12 0.43 192 172 227 55 106.42 0.54 193 176 227 51 97.62 0.29 194 178 230 52 97.29 0.31 195 179 229 50 97.03 0.27 196 179 230 51 84.62 0.70 197 179 233 54 67.53 0.91 198 179 234 55 67.50 0.91 199 180 227 47 97.53 0.28 200 180 228 48 97.41 0.29 201 180 230 50 83.65 0.35 202 181 226 45 97.61 0.29 203 181 227 46 97.45 0.28 204 181 228 47 97.41 0.28 205 181 229 48 97.20 0.26 206 181 230 49 83.63 0.35 207 182 225 43 97.62 0.29 208 182 226 44 97.56 0.29 209 182 227 45 97.45 0.28 210 182 228 46 97.44 0.28 211 183 225 42 97.61 0.29 212 183 226 43 97.48 0.28 213 183 228 45 97.45 0.28 214 184 225 41 97.60 0.28 215 185 222 37 108.03 0.10 216 185 223 38 107.78 0.09 217 185 224 39 106.49 0.51 218 185 225 40 97.63 0.28 219 187 222 35 107.99 0.14 220 188 222 34 107.98 0.14 221 189 220 31 306.59 0.46 222 189 222 33 107.95 0.16 223 190 228 38 97.56 0.31 224 194 197 3 190.29 0.35 225 199 211 12 282.94 7.74 226 199 228 29 85.80 0.86 227 200 210 10 291.24 4.28 228 201 210 9 233.71 0.65 229 209 231 22 66.86 0.84 230 210 231 21 66.86 0.84 231 211 228 17 85.25 1.14 232 211 229 18 80.09 1.71 233 211 231 20 66.99 0.78 234 212 228 16 85.25 1.14 235 212 229 17 83.00 0.26 236 212 231 19 68.71 0.28 237 213 227 14 97.44 0.29 238 213 228 15 89.71 0.91 239 214 227 13 97.44 0.29 240 214 228 14 96.97 0.17 241 215 226 11 97.62 0.30 242 215 227 12 97.57 0.29 243 216 226 10 97.62 0.30 244 217 220 3 229.88 4.58 245 217 221 4 184.93 0.96 246 217 224 7 106.78 0.68 247 221 224 3 107.98 0.14 248 230 233 3 108.67 0.99 249 230 234 4 102.41 2.15 250 231 234 3 103.27 2.58 251 231 235 4 77.89 10.10 252 232 235 3 110.84 1.21 253 234 237 3 107.28 0.57 254 234 238 4 60.23 2.78 255 235 238 3 100.75 0.90 256 235 239 4 58.60 3.71 257 236 239 3 104.75 2.71 258 236 240 4 75.17 12.03 259 237 240 3 107.10 3.93 260 237 241 4 71.34 13.95 261 238 241 3 107.06 3.95 262 238 242 4 71.36 13.97 263 239 242 3 71.37 13.97 264 239 243 4 68.99 15.16 265 240 243 3 110.44 0.20 266 240 244 4 90.95 7.57 267 241 244 3 110.44 0.20 268 241 245 4 68.38 15.46 269 242 245 3 114.67 1.25