Nature Structural Molecular Biology April

Table of contents :
largecover……Page 1
masthead……Page 2
toc……Page 3
nsmb0409-345……Page 5
nsmb0409-346……Page 6
nsmb0409-348……Page 8
nsmb0409-350……Page 10
nsmb0409-352……Page 12
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