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 1 205 210 5 222.56 2.49 2 205 248 43 47.02 0.23 3 205 252 47 45.59 0.94 4 205 254 49 41.34 0.65 5 206 209 3 231.87 4.05 6 206 210 4 222.97 2.68 7 207 210 3 222.98 2.68 8 207 211 4 222.99 2.67 9 208 211 3 223.50 2.92 10 208 212 4 223.09 2.63 11 208 237 29 63.87 0.07 12 209 212 3 228.21 0.59 13 209 213 4 225.34 1.50 14 209 245 36 63.37 0.07 15 209 248 39 63.40 0.09 16 209 249 40 61.82 0.83 17 210 213 3 234.00 2.85 18 210 214 4 225.33 1.46 19 211 214 3 233.97 2.87 20 211 215 4 233.97 2.87 21 212 215 3 239.19 2.12 22 212 216 4 226.65 0.80 23 212 230 18 67.28 1.18 24 212 234 22 67.74 1.29 25 212 237 25 67.88 1.32 26 212 242 30 64.19 0.45 27 212 249 37 63.41 0.09 28 213 216 3 245.70 1.12 29 213 217 4 229.61 0.73 30 213 249 36 63.32 0.14 31 213 254 41 63.26 0.15 32 213 255 42 63.07 0.06 33 213 266 53 60.23 1.33 34 213 269 56 34.91 0.36 35 213 270 57 20.75 0.14 36 214 217 3 239.08 2.19 37 214 218 4 229.61 0.73 38 214 270 56 21.04 0.66 39 215 218 3 232.35 0.64 40 215 219 4 222.55 2.79 41 215 225 10 116.36 4.80 42 215 234 19 74.49 1.62 43 216 225 9 80.37 0.34 44 216 230 14 80.28 0.30 45 216 255 39 63.34 0.12 46 216 264 48 63.37 0.10 47 216 265 49 63.11 0.07 48 216 266 50 62.04 0.46 49 217 266 49 62.04 0.43 50 217 269 52 47.23 0.34 51 217 270 53 39.80 0.33 52 219 225 6 165.74 2.10 53 221 224 3 240.77 2.74 54 221 225 4 232.13 1.54 55 221 226 5 235.34 0.06 56 221 229 8 197.98 3.24 57 222 265 43 71.93 0.04 58 223 226 3 259.98 1.35 59 223 263 40 72.91 0.51 60 224 263 39 72.94 0.51 61 224 264 40 72.76 0.44 62 224 265 41 71.93 0.04 63 225 229 4 225.58 1.42 64 225 230 5 221.93 3.24 65 225 264 39 72.77 0.45 66 226 229 3 229.62 2.88 67 226 230 4 226.87 0.81 68 226 262 36 73.21 0.48 69 226 263 37 72.90 0.49 70 227 230 3 226.87 0.81 71 227 231 4 229.37 0.45 72 227 239 12 139.08 0.29 73 227 242 15 84.52 0.93 74 227 243 16 84.48 0.91 75 227 246 19 82.64 1.02 76 227 262 35 73.33 0.54 77 227 264 37 73.07 0.55 78 228 231 3 233.68 0.85 79 228 232 4 229.38 0.45 80 229 232 3 230.62 0.69 81 229 233 4 229.40 0.45 82 230 233 3 232.78 0.18 83 230 234 4 230.25 0.88 84 230 242 12 117.33 6.94 85 231 234 3 230.36 1.03 86 231 235 4 226.84 1.70 87 231 239 8 142.18 1.26 88 232 235 3 229.97 1.02 89 234 237 3 234.77 1.43 90 237 241 4 225.39 0.21 91 237 242 5 223.30 1.25 92 238 241 3 230.02 2.52 93 238 242 4 233.08 1.56 94 239 242 3 234.41 0.90 95 239 243 4 234.15 1.04 96 240 243 3 234.15 1.04 97 240 244 4 234.16 1.04 98 241 244 3 234.16 1.04 99 241 245 4 231.30 2.48 100 242 245 3 231.31 2.48 101 242 246 4 234.90 0.69 102 243 246 3 234.91 0.69 103 243 247 4 234.91 0.69 104 244 247 3 235.30 0.53 105 244 248 4 234.92 0.70 106 245 248 3 236.16 0.10 107 245 249 4 234.31 1.03 108 246 249 3 236.18 0.10 109 246 250 4 234.33 1.04 110 246 255 9 148.42 1.51 111 246 264 18 111.05 2.41 112 247 250 3 240.27 2.14 113 247 251 4 236.20 0.12 114 248 251 3 236.22 0.10 115 248 252 4 236.21 0.11 116 249 252 3 237.10 0.34 117 249 253 4 229.38 3.52 118 249 254 5 200.80 3.04 119 249 255 6 150.26 0.59 120 250 253 3 231.22 2.58 121 250 255 5 178.31 8.92 122 253 267 14 115.37 0.89 123 254 266 12 120.64 0.46 124 254 267 13 118.98 0.17 125 254 269 15 110.12 2.40 126 255 264 9 123.78 0.72 127 255 265 10 123.17 0.48 128 255 266 11 120.64 0.47 129 256 264 8 130.72 1.25 130 256 265 9 123.22 0.48 131 256 266 10 123.17 0.48 132 256 267 11 123.03 0.45 133 257 260 3 245.52 0.79 134 257 261 4 171.38 12.04 135 257 263 6 138.02 1.93 136 257 264 7 130.72 1.25 137 258 263 5 172.12 11.67 138 258 265 7 131.91 0.67 139 259 263 4 207.59 3.83 140 260 263 3 234.78 1.59 141 261 264 3 280.05 0.89 142 266 269 3 241.61 2.98