Slide 1

AR3436A report 1.Sim CN NOESY, aromatic NOESY, CCH-TOCSY were reprocessed and analyzed to evaluate the assignment and structure. 2.Oliver's assignment corrections are confirmed (~100), and additional assignment corrections are found as well (~20). The new assignment has > 120 shifts with (H>0.045ppm, C, N>0.45ppm) compared to the deposited shifts. 3.New assignment and submitted PDB NOESY peak lists (or submitted casd- NMR peak lists) still gave opened structure as deposited one. 4.Sim CN NOESY and aromatic NOESY were re-picked and the new NOESY peak lists and new assignment gave closed structure as CS-Rosetta structure, by CYANA or ASDP. 5.The new peak lists with previous deposited assignment also gave closed structures, by CYANA or ASDP 6.The opened deposited structure became closed after consRosetta refinement, with old constraints and defined loop region. Slide 2 Additional Assignment Update RESIDUE NAMEOLDNew diff H > 0.045 ppm diff C/N > 0.45ppm Leu17CG=26.35 HG=1.584 CG=26.867 HG=1.685 HIS18HB2=3.20HB2=3.299 THR20QG2=- HA=4.970 HB=4.865 QG2=1.243 HA=4.913 HB=4.794 Phe33CE=128.10CE=130.66 Lys45HE2=2.826 HE3=2.884 TRP47CH2=121.70 HH2=7.144 CZ3=124.10 HZ3=7.190 CH2=123.388 HH2=7.228 CZ3=121.381 HZ3=7.147 Lys48QD=1.447HD3=1.394 Lys49QD=1.669HD2=1.666 HD3=1.740 Leu59HG=0.747HG=1.264 SER73HB2=4.00HB2=4.05 ASP74HA=4.858HA=4.806 Phe88HA=4.653 CZ? HZ? HA=4.607 CZ=130.962 HZ=7.656 HIS91HD2=6.38HD2=7.051 Slide 3 AR3436A Peak Lists Updated 1. AR3436A has different sets of peak lists available From Rajee 1)CasdNMR: 15N: 577peaks ali: 1402 peaks, aro: 97 peaks 2)HarvestDB: 15N: 581peaks ali: 1399 peaks, aro: 98 peaks (similar to casd NMR) 3)July 23th 2009: 15N: 788peaks ali: 1796 peaks, aro: 166 peaks; find in mani_home/nmrdata/AR3436A/AR3436A_structure, not available to public? New peak lists: 15N: 1041 peaks ali: 3451 peaks, aro: 328 peaks 2.Calculation done for July 23th 2009 peaks, old shift Casd peaks, new shifts July 23th 2009 peaks, new shifts New peaks, new shifts ConsRosetta of deposited PDB Slide 4 Newcy vs. Newasdp vs. Deposited The structure is closed with new peak lists and chemical shift Slide 5 Newpeakonly vs. Newshiftonly vs. Deposit The cyana structure is closed with new peak lists and old chemical shift The cyana structure is open with old peak lists and new chemical shift Slide 6 Newpeakonlyasdp vs. Newasdp vs. Deposit The asdp structure is closed with new peak lists and old chemical shift Slide 7 Deposit vs. casdpeak vs. New Old casd peaks with new assignment, the hole became slightly smaller Slide 8 Deposit vs. oldpeakoldshift vs. New Old complete July2009 peaks with old assignment, the hole became smaller Slide 9 Deposit vs. 723peaknewshift vs. New Old complete July 23th 2009 peaks with new assignment, the hole became smaller Slide 10 Deposit vs. Newpeakoldshift vs. New New peaks with old assignment, the hole became as small as new peak new assignment (magenta) Slide 11 AR3436A Report Updated 1.New assignment and submitted PDB NOESY peak lists (or submitted casd-NMR peak lists) still gave relative opened structure, but the hole is smaller than that of the deposited structure. 2.New assignment and old July 23th 2009 peak lists (or submitted casd-NMR peak lists) still gave relative opened structure, but the hole is smaller than those of the deposited structure and 1. 3.Old assignment and old July 23th 2009 peak lists (or submitted casd- NMR peak lists) still gave relative opened structure, but the hole is smaller than those of the deposited structure, 1 and 2. 4.Sim CN NOESY and aromatic NOESY were re-picked and the new NOESY peak lists and new assignment gave closed structure as CS- Rosetta structure, by CYANA or ASDP. 5.The new peak lists with previous deposited assignment gave relative closed structures, but the hole size is similar to 4. Slide 12 Comparing of the Hole Size CA distance (A)F27 C50S28--K49 New peaks, new shifts (magenta)6.9-8.19.6-10.8 New peaks, old shifts (blue)7.56-8.678.6-10.1 July2009peak, old shifts (lavender)8.6-21.311.3-20.0 July2009peak, new shifts (purple)12.2-19.715.1-21.4 Casd peaks, new shifts (dark yellow)11.8-24.913.7-25.1 Deposit (yellow)15.0-23.118.0-25.0 Slide 13 Newcy vs. consRos_dep vs. Deposit The opened deposit structure is closed after refinement with constraint Rosetta Slide 14 Different Loop Region Definition affect consRos Refinement A, Deposited; B, without loop; C: loop 1-14, 25-27, 29-30, 35-36, 50-54, 73-72, 83-87, 95-97, defined as no-ordered residues by psvs; D: loop 1-14, 22-28, 51- 56, 63-67, 85-97, F: New cns structure