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 1002 1104 99 107.94 2.98 2 1003 1029 26 213.52 0.06 3 1003 1102 96 108.00 2.98 4 1003 1103 97 108.02 2.98 5 1003 1168 139 95.26 0.65 6 1003 1172 143 78.80 0.78 7 1004 1028 24 213.56 0.07 8 1004 1029 25 213.53 0.07 9 1004 1101 94 108.01 2.98 10 1004 1102 95 108.01 2.98 11 1004 1168 138 100.92 0.10 12 1005 1027 22 213.66 0.04 13 1005 1028 23 213.63 0.04 14 1005 1100 92 110.55 1.85 15 1005 1101 93 108.88 2.68 16 1005 1164 133 108.00 2.98 17 1005 1167 136 104.67 1.42 18 1005 1168 137 101.69 0.06 19 1005 1171 140 93.75 0.01 20 1006 1026 20 213.87 0.06 21 1006 1027 21 213.67 0.04 22 1006 1098 89 113.59 1.36 23 1006 1099 90 112.72 1.76 24 1006 1100 91 111.09 1.58 25 1006 1101 92 111.72 1.76 26 1006 1102 93 112.05 1.92 27 1006 1113 104 112.73 1.75 28 1007 1024 17 214.96 0.42 29 1007 1025 18 214.90 0.42 30 1007 1063 53 207.51 1.08 31 1007 1067 57 206.65 1.03 32 1007 1098 88 113.69 1.32 33 1007 1099 89 112.75 1.75 34 1007 1160 127 112.73 1.75 35 1008 1024 16 214.96 0.42 36 1008 1025 17 214.93 0.43 37 1008 1027 19 214.94 0.43 38 1008 1097 86 114.53 1.18 39 1008 1098 87 113.70 1.31 40 1009 1024 15 215.15 0.41 41 1009 1070 58 207.49 1.09 42 1009 1071 59 206.74 1.08 43 1009 1073 61 206.66 1.09 44 1009 1074 62 206.44 1.19 45 1009 1096 84 115.62 0.69 46 1009 1097 85 114.53 1.19 47 1010 1022 12 216.14 0.31 48 1010 1023 13 215.81 0.17 49 1010 1095 82 123.48 1.86 50 1010 1096 83 116.06 0.64 51 1011 1021 10 216.70 0.48 52 1011 1022 11 216.15 0.31 53 1011 1074 60 206.44 1.19 54 1011 1078 64 205.50 1.66 55 1011 1094 80 127.57 0.42 56 1011 1095 81 124.06 1.70 57 1012 1020 8 216.91 0.46 58 1012 1021 9 216.74 0.49 59 1012 1078 63 206.01 1.42 60 1012 1092 77 141.94 0.04 61 1012 1093 78 141.35 0.23 62 1012 1094 79 132.07 2.62 63 1013 1020 7 217.46 0.20 64 1013 1078 62 206.06 1.39 65 1013 1092 76 141.95 0.04 66 1013 1093 77 141.62 0.12 67 1014 1017 3 528.89 0.97 68 1014 1018 4 491.20 2.17 69 1014 1019 5 245.82 4.92 70 1014 1020 6 218.54 0.70 71 1015 1089 71 143.80 0.03 72 1015 1090 72 143.24 0.23 73 1015 1091 73 143.21 0.24 74 1015 1092 74 142.99 0.22 75 1020 1075 52 206.52 1.31 76 1020 1078 55 206.03 1.41 77 1020 1079 56 206.01 1.41 78 1021 1038 17 372.78 0.74 79 1022 1036 14 372.92 0.74 80 1022 1037 15 372.84 0.73 81 1022 1038 16 372.81 0.74 82 1022 1071 46 207.39 1.08 83 1022 1074 49 206.44 1.19 84 1023 1035 12 373.08 0.72 85 1023 1036 13 372.92 0.74 86 1023 1037 14 372.85 0.74 87 1024 1035 11 373.08 0.72 88 1024 1036 12 372.93 0.74 89 1024 1067 40 207.47 1.08 90 1024 1070 43 207.51 1.10 91 1024 1071 44 206.66 1.09 92 1025 1032 7 373.53 0.72 93 1025 1034 9 373.12 0.71 94 1025 1035 10 373.08 0.72 95 1026 1032 6 373.53 0.72 96 1026 1033 7 373.41 0.77 97 1026 1034 8 373.12 0.71 98 1027 1031 4 373.56 0.72 99 1027 1032 5 373.54 0.72 100 1027 1033 6 373.53 0.72 101 1028 1031 3 521.12 2.32 102 1028 1033 5 373.59 0.71 103 1028 1168 114 101.86 0.03 104 1028 1171 117 99.06 0.98 105 1028 1172 118 91.78 0.47 106 1028 1179 125 50.00 1.52 107 1029 1209 154 45.27 3.54 108 1030 1209 153 45.26 3.54 109 1030 1210 154 45.20 3.56 110 1030 1211 155 45.20 3.56 111 1030 1241 183 45.27 3.54 112 1031 1051 17 372.78 0.74 113 1031 1178 121 53.53 0.29 114 1031 1179 122 51.56 0.76 115 1031 1209 152 47.41 2.49 116 1032 1049 14 372.77 0.74 117 1032 1051 16 372.76 0.74 118 1033 1045 12 372.76 0.75 119 1033 1049 13 372.67 0.72 120 1033 1051 15 372.66 0.73 121 1033 1052 16 371.61 0.80 122 1033 1171 112 101.70 0.01 123 1034 1043 9 372.79 0.74 124 1034 1044 10 372.76 0.75 125 1034 1045 11 372.69 0.74 126 1034 1063 26 207.64 1.09 127 1034 1171 111 101.81 0.03 128 1035 1040 5 513.97 1.19 129 1035 1043 8 372.75 0.77 130 1035 1044 9 372.70 0.74 131 1036 1040 4 509.44 0.48 132 1036 1042 6 372.81 0.74 133 1036 1043 7 372.65 0.76 134 1036 1067 28 207.58 1.10 135 1036 1068 29 207.56 1.09 136 1037 1040 3 516.01 0.94 137 1040 1044 4 558.96 1.80 138 1043 1064 18 207.61 1.11 139 1045 1052 4 530.73 1.76 140 1045 1054 6 349.04 11.38 141 1045 1060 12 207.82 1.07 142 1045 1171 100 101.92 0.01 143 1049 1052 3 535.20 0.48 144 1049 1054 5 495.62 6.22 145 1050 1054 4 498.26 4.90 146 1051 1054 3 585.87 2.15 147 1051 1175 101 99.10 0.96 148 1051 1178 104 83.45 0.15 149 1051 1179 105 83.45 0.15 150 1052 1171 96 101.94 0.01 151 1052 1174 99 99.97 0.54 152 1052 1175 100 96.75 1.97 153 1053 1058 5 385.68 40.41 154 1053 1174 98 100.37 0.38 155 1055 1058 3 442.17 26.98 156 1055 1060 5 294.94 4.96 157 1058 1061 3 599.57 3.64 158 1058 1170 89 112.48 1.03 159 1058 1174 93 105.92 2.02 160 1059 1062 3 536.50 3.12 161 1059 1170 88 112.49 1.04 162 1060 1063 3 512.15 2.44 163 1060 1064 4 512.15 2.44 164 1060 1167 84 113.06 1.05 165 1060 1170 87 112.49 1.04 166 1060 1171 88 112.28 0.97 167 1060 1174 91 105.92 2.03 168 1061 1064 3 509.69 1.20 169 1061 1065 4 510.34 0.07 170 1062 1065 3 533.41 0.14 171 1062 1066 4 514.18 1.82 172 1062 1163 78 113.63 1.25 173 1063 1066 3 518.27 0.21 174 1063 1067 4 514.20 1.83 175 1063 1167 81 112.81 0.94 176 1063 1171 85 111.92 0.89 177 1064 1067 3 516.34 1.89 178 1064 1068 4 514.20 1.83 179 1065 1068 3 534.27 1.24 180 1065 1069 4 514.15 1.85 181 1066 1069 3 520.73 2.44 182 1066 1070 4 510.31 3.58 183 1066 1160 71 113.86 1.25 184 1067 1070 3 521.83 2.16 185 1067 1071 4 511.35 0.21 186 1068 1071 3 521.85 2.15 187 1068 1072 4 517.94 3.02 188 1069 1072 3 519.62 2.18 189 1069 1073 4 518.26 2.86 190 1070 1073 3 529.40 2.71 191 1070 1097 27 123.61 1.79 192 1070 1099 29 122.50 2.27 193 1070 1160 67 114.14 1.26 194 1071 1074 3 550.56 1.08 195 1072 1075 3 548.50 0.05 196 1073 1077 4 473.50 0.51 197 1073 1097 24 124.12 1.72 198 1074 1077 3 511.59 2.44 199 1074 1078 4 494.59 1.31 200 1074 1079 5 494.59 1.31 201 1075 1079 4 489.49 6.92 202 1076 1080 4 502.91 0.21 203 1077 1080 3 520.16 0.83 204 1077 1081 4 507.41 2.04 205 1077 1095 18 141.88 0.04 206 1078 1081 3 515.06 1.79 207 1078 1082 4 511.77 0.14 208 1078 1093 15 142.23 0.09 209 1078 1094 16 142.00 0.03 210 1078 1095 17 139.87 0.58 211 1078 1118 40 141.97 0.05 212 1079 1082 3 522.23 0.85 213 1079 1083 4 515.04 1.78 214 1080 1083 3 515.04 1.77 215 1080 1084 4 515.04 1.77 216 1081 1084 3 514.85 1.68 217 1081 1085 4 511.78 0.14 218 1081 1095 14 142.22 0.07 219 1081 1118 37 142.22 0.07 220 1081 1123 42 142.25 0.08 221 1082 1086 4 482.79 3.32 222 1082 1087 5 385.56 43.95 223 1082 1089 7 253.34 6.83 224 1082 1093 11 142.88 0.24 225 1082 1118 36 142.37 0.14 226 1083 1086 3 496.75 2.81 227 1083 1089 6 272.34 0.88 228 1085 1118 33 143.80 0.09 229 1085 1123 38 143.75 0.09 230 1087 1090 3 635.68 0.48 231 1087 1093 6 267.99 3.39 232 1087 1118 31 233.64 1.90 233 1088 1091 3 563.35 1.61 234 1100 1164 41 612.40 4.57 235 1101 1165 41 657.90 5.61 236 1101 1168 44 509.17 0.02 237 1103 1168 42 528.00 2.08 238 1163 1167 4 604.09 1.79 239 1164 1167 3 530.27 3.18 240 1164 1168 4 518.62 2.10 241 1165 1168 3 519.80 1.55 242 1165 1169 4 516.02 3.41 243 1166 1169 3 520.01 1.65 244 1166 1170 4 514.61 2.70 245 1167 1170 3 509.23 0.01 246 1167 1171 4 509.12 0.00 247 1168 1171 3 516.20 3.54 248 1168 1172 4 507.74 0.69 249 1169 1173 4 505.29 0.04 250 1170 1173 3 506.33 2.42 251 1170 1174 4 501.76 1.78 252 1171 1174 3 501.94 1.69 253 1171 1175 4 496.26 4.52 254 1171 1179 8 383.28 43.30 255 1172 1176 4 483.77 0.55 256 1172 1179 7 383.22 43.33 257 1172 1180 8 284.42 6.05 258 1173 1176 3 508.42 1.57 259 1175 1178 3 534.23 0.70 260 1175 1179 4 476.91 0.35 261 1176 1179 3 519.01 0.18 262 1176 1180 4 470.18 0.12 263 1177 1181 4 473.11 1.58 264 1178 1181 3 505.03 2.51 265 1178 1209 31 410.68 1.25 266 1178 1239 59 438.55 1.33 267 1181 1209 28 459.13 2.40 268 1182 1209 27 459.44 2.55 269 1182 1264 80 451.25 0.89 270 1182 1265 81 446.70 0.18 271 1183 1207 24 460.25 2.79 272 1183 1208 25 459.88 2.73 273 1183 1209 26 459.49 2.53 274 1183 1263 78 453.56 0.14 275 1184 1208 24 459.94 2.71 276 1184 1263 77 453.53 0.13 277 1184 1265 79 453.05 0.24 278 1184 1266 80 453.00 0.26 279 1185 1205 20 460.86 2.65 280 1185 1206 21 460.84 2.65 281 1185 1208 23 460.44 2.76 282 1185 1213 28 459.98 2.53 283 1185 1261 74 454.21 0.12 284 1185 1263 76 453.76 0.14 285 1185 1266 79 453.28 0.32 286 1186 1205 19 460.89 2.65 287 1186 1206 20 460.88 2.65 288 1187 1204 17 460.93 2.64 289 1187 1205 18 460.91 2.65 290 1187 1261 72 454.50 0.19 291 1187 1270 81 453.12 0.28 292 1187 1272 83 444.57 0.82 293 1188 1204 16 461.00 2.62 294 1188 1206 18 461.24 2.56 295 1188 1275 85 292.74 3.41 296 1189 1201 12 461.50 2.60 297 1189 1202 13 461.42 2.60 298 1189 1203 14 461.17 2.54 299 1189 1217 28 461.36 2.58 300 1189 1272 81 453.08 0.27 301 1189 1274 83 371.76 10.69 302 1189 1275 84 346.43 23.34 303 1190 1200 10 461.72 2.66 304 1190 1201 11 461.56 2.62 305 1190 1202 12 461.46 2.59 306 1191 1199 8 462.72 3.08 307 1191 1201 10 461.56 2.62 308 1191 1251 58 463.14 3.20 309 1191 1254 61 462.74 3.16 310 1191 1274 81 453.05 0.25 311 1192 1199 7 462.76 3.10 312 1192 1200 8 461.76 2.64 313 1193 1199 6 462.79 3.11 314 1193 1251 56 463.14 3.19 315 1194 1197 3 521.38 5.39 316 1194 1198 4 463.21 3.18 317 1194 1199 5 463.20 3.17 318 1194 1200 6 463.20 3.17 319 1194 1248 52 463.22 3.18 320 1197 1251 52 694.50 0.25 321 1198 1251 51 695.00 0.00 322 1201 1217 16 690.47 0.12 323 1203 1215 12 694.94 0.01 324 1203 1272 67 453.10 0.28 325 1215 1245 28 691.78 1.59 326 1217 1247 28 695.00 0.21 327 1255 1273 18 453.37 0.31 328 1255 1274 19 453.36 0.31 329 1258 1271 13 453.37 0.32 330 1258 1273 15 453.06 0.29 331 1259 1270 11 453.37 0.31 332 1259 1271 12 453.18 0.31 333 1259 1272 13 453.11 0.28 334 1260 1270 10 453.31 0.33 335 1260 1271 11 453.11 0.29 336 1261 1266 5 467.62 0.37 337 1261 1269 8 453.31 0.33 338 1261 1270 9 453.11 0.29 339 1261 1272 11 453.11 0.29 340 1262 1266 4 479.95 5.80 341 1262 1269 7 453.24 0.34 342 1263 1266 3 518.23 0.41 343 1266 1270 4 507.40 1.95 344 1273 1276 3 547.93 2.31