In an α helix:A) the hydrogen bonds are at right angles tothe axis of the helix.B) the hydrogen bonds occur between mainchain atoms in the helix.C) runs of Glu residues tend to stabilize thestructure .D) every turn of the helix contains fiveresidues.E) Pro residues are often found centrallylocated.B and T Fig. 2-2Fig. 4-4LehnFig. 4-4LehnBox 4-1LehnB and T Fig. 2-2Fig. 4-5 LehnFig. 4-2 LehnFig. 4-6LehnAlpha helix stability affected by:Electrostatic repulsion or attraction between charged side chainsRepulsion between bulky side chainsInteractions between residues 3 - 4 apartWhether or not pro/gly presentAmino acids at ends interacting with inherent dipole of helixB and TFig. 2-4Fig. 4-7 LehnFig. 4-7 LehnFig. 4-8 LehnFig. 4-16LehnI want to understand the structure ofa cellular protein. I could:A) observe the protein, in cells, through themicroscope and diagram the structure.B) use electron microscopy to visualizeisolated proteins.C) chemically analyze the protein tounderstand the peptide bonding pattern .D) use a computer program to predictsecondary structure from the primarystructure.E) model the structure physically.A cartoon of a protein kinase,showing secondary structure.Huse and Kuriyan, 2002Protein Kinase Domain Alignments (all of the N lobe, part of the C lobe) < 1> P loop <-- 2--> <-- 3--><- B-> A002101_Rsk3 43 ISNHVKEGFEKADPSQFELLKVLGQGSYGKVFLVRKVTGSDAGQLYAMKVLKKATLKVRD A001562_Msk1 32 RTANLTGHAEKVGIENFELLKVLGTGAYGKVFLVRKISGHDAGKLYAMKVLKKATIVQKA A001298_Jnk3 48 FYSVEVGDSTFTVLKRYQNLKPIGSGAQG------IVCAAYDAVLDRNVAIKKLSRPFQN A001296_Jnk1 10 FYSVEIGDSTFTVLKRYQNLKPIGSGAQG------IVCAAYDAILERNVAIKKLSRPFQN A001454_Map4k3 1 -MNPGFDLSRRNPQEDFELIQRIGSGTYG------DVYKARNVNTGELAAIKVIKLEPGE A001144_Hpk1 1 MALVDPDIFNKDPREHYDLLQRLGGGTYG------EVFKARDKVSKDLVALKMVKMEPDD A001506_Mek2 56 AFLTQKAKVGELKDDDFERISELGAGNGG------VVTKARHRPSGFIMARKLIHLEIKP A001561_Mrcka 61 KPFTSKVKQMRLHREDFEILKVIGRGAFG---EVAVVKLKNADKVFAMKILNKWEMLKRA (K72 in PKA) <--- C------> <- 4-> <- 5-> <--- D---> A002101_Rsk3 103 R--VRSKMERDILAEVN-HPFIVKLHYAFQTEGKLYLILDFLRGGDLFTR---LSKEVMF A001562_Msk1 92 KTTEHTRTERQVLEHIRQSPFLVTLHYAFQTETKLHLILDYINGGELFTH---LSQRERF A001298_Jnk3 102 QTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMEL A001296_Jnk1 64 QTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMEL A001454_Map4k3 54 D--FAVVQQEIIMMKDCKHPNIVAYFGSYLRRDKLWICMEFCGGGSLQDIY---HVTGPL A001144_Hpk1 55 D--VATLQKEILMLKTCRHANIVAYHGSYLWLQKLWICMEFCGAGSLQDIY---QVTGSL A001506_Mek2 110 -AVRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVL---KEAKRI A001561_Mrcka 118 ETACFREERDVLVNGD--SKWITTLHYAFQDDNNLYLVMDYYVGGDLLTLLS--KFEDRL (E91 in PKA) <--------- E--------> < 6> <- 7-> <- 8-> < 9>------ A002101_Rsk3 157 TEEDVKFYLAELALALDHLHGL-GIIYRDLKPENILLDEEGHIKITDFGLSKEAT-DHDK A001562_Msk1 149 TEHEVQIYVGEIVLALEHLHKL-GIIYRDIKLENILLDSNGHVVLTDFGLSKEFVADETE A001298_Jnk3 162 DHERMSYLLYQMLCGIKHLHSA-GIIHRDLKPSNIVVKSDCTLKILDFGLARTAG--TSF A001296_Jnk1 124 DHERMSYLLYQMLCGIKHLHSA-GIIHRDLKPSNIVVKSDCTLKILDFGLARTAG--TSF A001454_Map4k3 109 SELQIAYVSRETLQGLYYLHSK-GKMHRDIKGANILLTDNGHVKLADFGVSAQIT-ATIA A001144_Hpk1 110 SELQISYVCREVLQGLAYLHSE-KKIHRDIKGANILINDCGEVKLADFGISAQIG-ATLA A001506_Mek2 166 PEDILGKVSIAVLRGLAYLREKHQIMHRDVKPSNILVNSRGEIKLCDFGVSGQLI---DS A001561_Mrcka 174 PEEMARFYLAEMVIAIDSVHQL-HYVHRDIKPDNILMDMNGHIRLADFGSCLKLMEDGTV (D166, N171 in PKA) (D184 in PKA) activation loop <------ F------> A002101_Rsk3 215 RAYSFCGTIEYMAPEVVNR-----RGHTQSADWWSFGVLMFEMLTGS-LPFQGKDRK--- A001562_Msk1 208 RAYSFCGTIEYMAPDIVRGG---DSGHDKAVDWWSLGVLMYELLTGA-SPFTVDGEKNSQ A001298_Jnk3 219 MMTPYVVTRYYRAPEVILG-----MGYKENVDIWSVGCIMGEMVRHK-ILFPGRD----- A001296_Jnk1 181 MMTPYVVTRYYRAPEVILG-----MGYKENVDLWSVGCIMGEMVCHK-ILFPGRD----- A001454_Map4k3 167 KRKSFIGTPYWMAPEVAAVER--KGGYNQLCDLWAVGITAIELAELQPPMFDLHPMRALF A001144_Hpk1 168 RRLSFIGTPYWMAPEVAAVAL--KGGYNELCDIWSLGITAIELAELQPPLFDVHPLRVLF A001506_Mek2 223 MANSFVGTRSYMSPERLQG-----THYSVQSDIWSMGLSLVELAIGR---YPIPP----- A001561_Mrcka 233 QSSVAVGTPDYISPEILQAMEDGKGRYGPECDWWSLGVCMYEMLYGETPFYAESLVETYG Not shown: ~50 amino acids comprising G, H, I and connecting loops between these helices.Box 4-4 LehnFig. 18-11 B and TFig. 4-11 LehnFig. 4-11LehnBox 4-2 LehnFig. 14-1 B and TFig. 4-12 LehnFig. 4-13LehnOsteogenesis imperfectaGroup of genetic bone disorders: One of brittle bone diseases Most patients have mutations in genesFor Type I pro-collagenSingle glycine replaced by largerR groupFig. 4-14 LehnFig. 4-14LehnFig. 4-3 LehnFig. 4-9Fig.
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