Nature Structural Molecular Biology April

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RESULTS......Page 13
Figure 2 Decoding efficiency of the GCC codon by tRNAAlaGGC with the conserved or nonconserved 32-38 pair.......Page 14
Figure 3 Influence of the sequence variation of the 32-38 pair in tRNAAlaGGC on misreading of GUC codon.......Page 15
Figure 4 Overexpression of the conserved or nonconserved tRNAAlaGGC in E.......Page 16
References......Page 17
Mutating A32-U38 has little effect on cognate decoding......Page 19
Figure 1 Secondary structure of E.......Page 20
Figure 2 Comparison of tRNAAlaGGC (wt) to tRNAAlaGGC (UA) on the GCC cognate and GCA near-cognate codons.......Page 21
Figure 3 Time course of peptide bond formation for tRNAAlaGGC (wt) and tRNAAlaGGC (UA) on the cognate GCC codon (taken from Fig.™2d) and the mismatched ACC and GUC codons.......Page 22
Kinetics experiments......Page 23
References......Page 24
A feedback regulatory loop involving microRNA-9 and nuclear receptor TLX in neural stem cell fate determination......Page 25
Figure 1 miR-9-directed repression of TLX expression.......Page 26
Figure 3 TLXDelta3prime UTR rescues miR-9-induced neural stem cell proliferation deficiency.......Page 27
Figure 5 In utero electroporation of miR-9 in embryonic neural stem cells.......Page 28
Figure 6 Regulation of miR-9 pri-miRNA expression by TLX.......Page 29
References......Page 30
Determining the binding specificity of TRF2TRFH......Page 32
Figure 1 The TRFH domain of TRF2 recognizes short peptide sequences.......Page 33
Figure 2 The TRF2-[YF]XL interaction is important for telomere maintenance.......Page 34
Figure 3 TRF2 specifically interacts with YXL-containing proteins PNUTS and MCPH1.......Page 35
Figure 5 MCPH1 and PNUTS regulate DNA-damage response and telomere length, respectively, at the telomeres.......Page 36
Peptide synthesis, fluorescence polarization and affinity measurements......Page 37
References......Page 38
Polyglutamine disruption of the huntingtin exon 1 N terminus triggers a complex aggregation mechanism......Page 40
Table 1 Amino acid sequences of exon 1-related peptides......Page 41
Figure 1 Aggregation kinetics of huntingtin exon 1 mimic peptides exploring various polyQ repeat lengths.......Page 42
Figure 3 State of expansion of the HTTNT peptide in solution.......Page 43
Figure 5 Proton NMR analysis of HTTNT.......Page 44
Figure 7 Time course of aggregation of HTTNTQ30P6 (F17W) by multiple analyses.......Page 45
Figure 9 Mechanism of HTTNT-mediated exon 1 aggregation.......Page 46
Proton nuclear magnetic resonance......Page 47
References......Page 48
RESULTS......Page 50
Figure 1 Fe-S cluster reconstitution on IscU followed by absorbance and CD measurements.......Page 51
Figure 3 Interaction of CyaY with IscS.......Page 52
Figure 5 Gel-filtration profiles to test the state of aggregation of CyaY under the conditions used for cluster reconstitution.......Page 53
DISCUSSION......Page 54
Figure 6 Schematic model of the molecular mechanism of frataxin in the cell.......Page 55
References......Page 56
The pathway of hepatitis C virus mRNA recruitment to the human ribosome......Page 57
Figure 1 Directed hydroxyl radical probing of 18S rRNA from BABE-Fe-eIF3j-40S-HCV IRES complexes.......Page 58
Figure 2 Toeprinting analysis of the 40S-HCV-eIF3j complexes.......Page 59
Figure 3 Effects of eIF3 and eIF2-Met-tRNAi on directed hydroxyl radical probing of 18S rRNA with BABE-Fe-eIF3j.......Page 60
Figure 4 Effects of eIF1, eIF1A, HCV and eIF3 on directed hydroxyl radical probing of 18S rRNA from BABE-Fe-eIF3j.......Page 61
Figure 6 A model for HCV IRES association with the mRNA binding channel of the 40S subunit.......Page 62
References......Page 63
Subdomain folding......Page 65
Figure 2 Cross-linking and accessibility assays for beta- and alpha-hairpins.......Page 66
Figure 3 Accessibility-dependent probability of cross-linking.......Page 67
Figure 4 T1 domain mutants.......Page 68
Dynamics of the nascent peptide-tunnel complex......Page 69
AUTHOR CONTRIBUTIONS......Page 70
References......Page 71
Acetylation by GCN5 regulates CDC6 phosphorylation in the S phase of the cell cycle......Page 72
Figure 1 CDC6 is acetylated by GCN5 on lysines 92, 105 and 109 both in vitro and in vivo.......Page 73
Figure 2 Specific CDC6 phosphorylation on Ser106 depends on GCN5-mediated CDC6 acetylation.......Page 74
Figure 3 CDC6 acetylation is cell cycle dependent.......Page 75
Figure 4 GCN5-dependent CDC6 acetylation regulates its subcellular localization.......Page 76
Figure 5 Characterization of the CDC6 K3R and S106A mutants.......Page 77
Figure 6 Model showing the regulation of CDC6 by sequential modification by acetylation and phosphorylation in early S phase.......Page 78
Statistical analysis......Page 79
References......Page 80
RESULTS......Page 81
Table 1 Steady-state kinetic parameters of the wild-type, D656A and C176A NAD+ synthetaseTB-catalyzed reactionsa......Page 82
Figure 2 Oligomeric assembly of NAD+ synthetaseGln from M.......Page 83
Figure 4 The homooctameric structure of NAD+ synthetaseGln with all eight intersubunit tunnels.......Page 84
Figure 5 The ammonia tunnel and the synthetase active site.......Page 85
Figure 6 Connecting elements between glutaminase and synthetase active sites.......Page 86
Table 3 Data collection and refinement statistics for NAD+ synthetaseTB......Page 87
References......Page 88
Precursor-product discrimination by La protein during tRNA metabolism......Page 90
Figure 1 La can bind non-UUU-3primeOH-containing RNA via contacts that are not mediated by the previously characterized RNA 3primeOH binding site in the La motif.......Page 91
Table 1 Binding properties of mutated La proteins......Page 92
Figure 4 La RRM1 loop-3 mediates UUU-3primeOH-independent tRNA binding.......Page 93
Figure 5 The La loop mutant is defective in tRNA maturation in vivo.......Page 94
Figure 6 Model of involvement of La protein in a tRNA maturation pathway.......Page 95
References......Page 96
RESULTS......Page 98
Figure 2 Hydroxyl radical footprinting of the 5prime domain in the presence and absence of proteins.......Page 99
Figure 4 Primary assembly proteins pre-organize the S16 binding site.......Page 100
Figure 5 S16 discriminates against non-native assembly intermediates.......Page 101
Figure 6 RNA conformational changes during assembly.......Page 102
Figure 7 Model for assembly of the 30S 5prime domain.......Page 103
Data analysis......Page 104
References......Page 105
Figure 1 CK2alpha phosphorylates BMAL1 in vitro.......Page 106
Figure 2 CK2alpha and BMAL1-Ser90 regulate nuclear accumulation and clock function.......Page 107
Figure 3 Circadian phosphorylation of BMAL1-Ser90 by CK2alpha in vivo.......Page 108
Figure 1 H3R2me1 does not block activity of the Set1 complex toward H3K4.......Page 109
Figure 3 H3R2 is necessary for sporulation.......Page 110
References......Page 111