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Protein structure modeling

Protein structure modeling. June 4, 2002 Quiz#4 Writing Assignments-Average=80/100 Homework Correction on Quiz #2 answer Learning objectives-Learn how to use Deep View to create models of proteins-human and hen lysozyme. Quiz #2 CORRECTION. M E Q V L I V C - -

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Protein structure modeling

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  1. Protein structure modeling • June 4, 2002 • Quiz#4 • Writing Assignments-Average=80/100 • Homework • Correction on Quiz #2 answer • Learning objectives-Learn how to use Deep View to create models of proteins-human and hen lysozyme.

  2. Quiz #2 CORRECTION M E Q V L I V C - - M E E - - I V C N D PATH SCORES 5 4 3 3 2 1 SIM SCORES 5 5 2-4 0 4 4 9-4 0 GAP EXT PEN -1-1 -1-1 PATH SCORE TOTAL=18 SIMILARITY SCORE TOTAL=17

  3. Homework #17 Conf: 987644588777886268899874177645567666752132024612455531345666 Pred: CCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHCCCHHHHHHHHCCCCCC AA: MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP 10 20 30 40 50 60 Conf: 433467778865688888888878786878788888788887665640588862378652 Pred: CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCC AA: DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK 70 80 90 100 110 120 Conf: 266631631344344201446568996377667844788762044167889987378865 Pred: EEEEECCCCHHHHHHHCCCCCCEEEEECCCCCCCCEEEEEEEECCHHHHHHHHHHCCCCC AA: SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE 130 140 150 160 170 180 Conf: 578888887755136641466531002578851589851479977641565666653134 Pred: CCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHCC AA: RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS 190 200 210 220 230 240 Conf: 445888763068999980899845301048999844798653024665421478887788 Pred: CCCCCCCCCCEEEEEEEECCCCCEEECCEEEEEEECCCCCCCHHHHHHHHCCCCCCCCCC AA: SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP. . . 250 260 270 280 290 300

  4. HELIX 1 1 SER A 166 HIS A 168 5 1TSR 168 HELIX 2 2 PRO A 177 GLU A 180 1 1TSR 169 HELIX 3 3 PRO A 278 GLU A 287 1 1TSR 170 HELIX 4 4 GLN B 167 THR B 170 5 1TSR 171 HELIX 5 5 PRO B 177 ARG B 181 1 1TSR 172 HELIX 6 6 PRO B 278 GLU B 287 1 1TSR 173 HELIX 7 7 GLY C 105 TYR C 107 5 1TSR 174 HELIX 8 8 SER C 166 MET C 169 1 1TSR 175 HELIX 9 9 PRO C 177 ARG C 181 1 1TSR 176 HELIX 10 10 PRO C 278 GLU C 285 1 1TSR 177 SHEET 1 A 4 ARG A 110 GLY A 112 0 1TSR 178 SHEET 2 A 4 CYS A 141 TRP A 146 -1 N TRP A 146 O ARG A 110 1TSR 179 SHEET 3 A 4 THR A 230 TYR A 236 -1 N TYR A 234 O CYS A 141 1TSR 180 SHEET 4 A 4 ILE A 195 GLU A 198 -1 N GLU A 198 O HIS A 233 1TSR 181 SHEET 1 B 7 CYS A 124 SER A 127 0 1TSR 182 SHEET 2 B 7 LYS A 132 CYS A 135 -1 N PHE A 134 O THR A 125 1TSR 183 SHEET 3 B 7 LEU A 264 VAL A 274 1 N GLU A 271 O MET A 133 1TSR 184 SHEET 4 B 7 ILE A 251 GLU A 258 -1 N LEU A 257 O LEU A 265 1TSR 185 SHEET 5 B 7 ARG A 156 TYR A 163 -1 N ILE A 162 O LEU A 252 1TSR 186 SHEET 6 B 7 HIS A 214 PRO A 219 -1 N VAL A 218 O VAL A 157 1TSR 187 SHEET 7 B 7 GLU A 204 ASP A 207 -1 N LEU A 206 O SER A 215 1TSR 188 SHEET 1 C 4 ARG B 110 GLY B 112 0 1TSR 189 SHEET 2 C 4 CYS B 141 TRP B 146 -1 N TRP B 146 O ARG B 110 1TSR 190 SHEET 3 C 4 THR B 230 TYR B 236 -1 N TYR B 234 O CYS B 141 1TSR 191 SHEET 4 C 4 ILE B 195 GLU B 198 -1 N GLU B 198 O HIS B 233 1TSR 192 SHEET 1 D 7 CYS B 124 SER B 127 0 1TSR 193 SHEET 2 D 7 LYS B 132 CYS B 135 -1 N PHE B 134 O THR B 125 1TSR 194 SHEET 3 D 7 LEU B 264 VAL B 274 1 N GLU B 271 O MET B 133 1TSR 195 SHEET 4 D 7 ILE B 251 GLU B 258 -1 N LEU B 257 O LEU B 265 1TSR 196 SHEET 5 D 7 ARG B 156 TYR B 163 -1 N ILE B 162 O LEU B 252 1TSR 197 SHEET 6 D 7 HIS B 214 PRO B 219 -1 N VAL B 218 O VAL B 157 1TSR 198 SHEET 7 D 7 GLU B 204 ASP B 207 -1 N LEU B 206 O SER B 215 1TSR 199 SHEET 1 E 4 ARG C 110 PHE C 113 0 1TSR 200 SHEET 2 E 4 CYS C 141 TRP C 146 -1 N TRP C 146 O ARG C 110 1TSR 201 SHEET 3 E 4 THR C 230 TYR C 236 -1 N TYR C 234 O CYS C 141 1TSR 202 SHEET 4 E 4 ILE C 195 VAL C 197 -1 N ARG C 196 O ASN C 235 1TSR 203 SHEET 1 F 7 THR C 125 SER C 127 0 1TSR 204 SHEET 2 F 7 LYS C 132 GLN C 136 -1 N PHE C 134 O THR C 125 1TSR 205 SHEET 3 F 7 LEU C 264 CYS C 275 1 N GLU C 271 O MET C 133 1TSR 206 SHEET 4 F 7 ILE C 251 GLU C 258 -1 N LEU C 257 O LEU C 265 1TSR 207 SHEET 5 F 7 ARG C 156 TYR C 163 -1 N ILE C 162 O LEU C 252 1TSR 208 SHEET 6 F 7 HIS C 214 PRO C 219 -1 N VAL C 218 O VAL C 157 1TSR 209 SHEET 7 F 7 GLU C 204 ASP C 207 -1 N LEU C 206 O SER C 215 1TSR 210

  5. Answers to HW#17 Using polypeptide A we get the following percentage of correct assignments: 5/14 x 100 = 36% Using non-overlapping structure assignments of polypeptides A,B and C we get the following percentage of correct assignments: 33/55 X 100 = 60% Assuming coil (C) for areas not assigned in crystal structure (PDB) between aa 105 and aa 287 we get the following percentage of correct assignments: 116/184 X 100 = 63%

  6. Tertiary structure modeling • Use hen lysozyme as a template to create human lysozyme structure model

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