Nature Structural Molecular Biology February

Table of contents :
largecover……Page 1
masthead……Page 2
toc……Page 3
nsmb0209-99……Page 6
nsmb0209-100……Page 7
nsmb0209-104……Page 0
nsmb0209-106……Page 13
nsmb.1550……Page 14
Structural characterization of Tip20p and Dsl1p, subunits of the Dsl1p vesicle tethering complex……Page 21
Figure 1 X-ray crystal structures of S…….Page 22
Figure 2 The Tip20p and Dsl1p subunits of the Dsl1p complex form stoichiometric heterodimers…….Page 23
Figure 4 Reconstitution of the heterotrimeric Dsl1p complex…….Page 24
Figure 5 ER SNAREs Sec20p and Use1p bind Dsl1p complex via different subunits…….Page 25
Figure 6 Schematic model for the tethering of Golgi-derived retrograde trafficking vesicles to the ER via bivalent attachment of the Dsl1p complex to the ER SNAREs Use1p and Sec20p…….Page 26
Protein production……Page 27
Table 1 Data collection, phasing and refinement statistics……Page 28
References……Page 29
Mapping of interactions with near base pair precision……Page 31
Figure 2 Histone-DNA interaction map within a nucleosome core particle…….Page 32
Figure 4 Mechanical unzipping (left) to mimic motor enzyme progression into a nucleosome (right)…….Page 33
Implications for transcription……Page 34
References……Page 35
CLIP-seq for mapping functional RNA elements……Page 37
Figure 1 CLIP-seq of FOX2 in hESCs…….Page 38
Figure 2 Genomic mapping and analysis of FOX2 CLIP-seq reads…….Page 39
Figure 3 Clustering of FOX2 CLIP-seq reads around regulated splicing events…….Page 40
Figure 4 RNA map of FOX2-regulated alternative splicing…….Page 41
Figure 5 FOX2 is important for hESC survival…….Page 42
Analysis of cross-linking immunoprecipitation reads……Page 43
References……Page 44
RESULTS……Page 45
Figure 2 EndoV overall fold, surface characteristics and protein-DNA complex structure…….Page 46
Figure 3 Protein-DNA contacts…….Page 47
Figure 5 Active-site architecture of the EndoV-DNA complex…….Page 48
Table 1 X-ray data collection and refinement statistics……Page 49
References……Page 50
miRNA-mediated repression is abolished in extended ORFs……Page 51
Figure 1 miRNA-mediated repression is abolished in extended ORFs…….Page 52
Figure 2 miRNA-mediated repression studies were concordant in mouse liver in vivo…….Page 53
Figure 4 Insertion of rare codons increases the accessibility of downstream sequences to RNase H-mediated cleavage…….Page 54
Cell culture and transfections……Page 55
References……Page 56
Assembly of dinucleosomes with defined separation……Page 58
Figure 1 Chromatin assembly on defined dinucleosomal templates…….Page 59
Figure 3 AFM imaging of dinucleosomes…….Page 60
Figure 4 Helical phasing is required for the condensation of overlapping dinucleosomes…….Page 61
Figure 5 Formation of overlapping nucleosomes as a result of repositioning…….Page 62
References……Page 64
SRS2 and SGS1 prevent chromosomal breaks and stabilize triplet repeats by restraining recombination……Page 66
Figure 2 Effect of the trinucleotide repeat tract orientation on stability…….Page 67
Table 2 Instability of CTG and CAG triplets on the YAC in srs2Delta and sgs1Delta mutants……Page 68
Figure 3 Analysis of replication intermediates at the ARG2 locus by two-dimensional gel electrophoresis…….Page 69
Figure 4 Analysis of replication intermediates at ARG2 by two-dimensional gel electrophoresis in wild-type (WT) and mutant strains…….Page 70
Figure 5 A model showing different pathways to repair replication fork damage due to structure-forming sequences…….Page 71
Two-dimensional gel analyses……Page 72
References……Page 73
Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation……Page 75
Figure 1 Structural changes involving the conserved Cys110-Cys187 disulfide link on activation of rhodopsin…….Page 76
Figure 3 A view of the extracellular side of rhodopsin from the crystal structure6…….Page 77
Figure 5 Two-dimensional DARR NMR of Tyr(Czeta)-Met(Cepsiv) contacts in rhodopsin and the M288L rhodopsin mutant…….Page 78
Figure 6 Crystal structure of rhodopsin20 highlighting EL2 and H5…….Page 79
Synthesis of 13C-labeled retinals and regeneration into rhodopsin……Page 80
References……Page 81
Some 5prime ss do not base-pair to U1 by the canonical register……Page 83
Figure 1 Shifted base-pairing between atypical 5prime ss and the 5prime end of U1 snRNA…….Page 84
Figure 3 Compensatory U1 mutations that restore shifted but not canonical base-pairing rescue splicing at atypical 5prime ss…….Page 85
Figure 4 U1 but not U1A7 snRNA decoys reduce splicing via the atypical 5prime ss…….Page 86
Table 2 Counts for the atypical 5prime ss in five species and for the conserved 5prime ss between human and mouse……Page 87
References……Page 88
Distinct small RNAs encoded by miRNA loci……Page 90
Figure 2 Coincident expression of 5prime and 3prime moR sequences from the C…….Page 91
Figure 3 Direct detection of the 5prime-moR-133 species…….Page 92
Figure 4 Ectopic expression of Drosophila pri-miRNAs can induce moR production in C…….Page 93
Figure 5 A speculative model for the biogenesis of moRs…….Page 94
References……Page 95
Conformational flexibility of metazoan fatty acid synthase enables catalysis……Page 97
Figure 2 Structural and functional organization of the metazoan FAS…….Page 98
Figure 3 Conformational variability of Delta22-FAS in the absence of substrates…….Page 99
Figure 4 Distribution of FAS conformations is altered in the presence of substrates…….Page 100
Figure 5 Changes in domain position bring catalytic domains into proximity of the ACP to facilitate catalytic interactions…….Page 101
Processing of single-particle images……Page 102
References……Page 103
MIA40 is an oxidoreductase that catalyzes oxidative protein folding in mitochondria……Page 105
Figure 1 MIA40 is functionally active in binding substrates…….Page 106
Figure 2 The redox and structural properties of the CPC intramolecular disulfide bonds of human MIA40…….Page 107
Figure 5 The solution structure of MIA402S-S…….Page 108
Figure 6 Interaction of MIA40 with substrates…….Page 109
Figure 7 The second cysteine, Cys55, of the active-site CPC is essential in vivo and in vitro…….Page 110
Figure 8 Model for the interaction of MIA40 with its substrates…….Page 111
Table 1 NMR and refinement statistics for MIA402S-S……Page 112
DDH motif mutants are only partially RNAi deficient……Page 114
Figure 1 Mismatched siRNA duplexes bypass mutations in the RDE-1 DDH motif…….Page 115
Figure 2 In RDE-1 DDH mutants, the passenger strand accumulates and remains associated with the guide strand and RDE-1…….Page 116
References……Page 117
A general acid in nucleic acid polymerase catalysis……Page 119
Figure 1 Extending the two-metal-ion mechanism of nucleotidyl transfer to include general acid catalysis…….Page 120
Figure 2 Interactions of NTP in the active sites of various polymerase families…….Page 121
Table 1 Kinetic analysis of PV RdRp, HIV-1 RT, RB69 DdDp and T7 DdRp supports general acid catalysis in nucleotidyl transfer……Page 122
Figure 4 Altering nucleotidyl transfer kinetics by changing the amino acid that acts as the general acid…….Page 123
References……Page 124
Polyubiquitin substrates allosterically activate their own degradation by the 26S proteasome……Page 126
Figure 1 MUC1-derived model substrates for 26S proteasomes…….Page 127
Figure 2 PolyUb proteins stimulate the activity of the 26S proteasome…….Page 128
Figure 5 PolyUb-mediated stimulation requires ATP hydrolysis…….Page 129
Figure 6 Conformational changes of the proteasome caused by Ub5-MUC4…….Page 130
SDS-PAGE and immunoblotting……Page 131
References……Page 132
Figure 1 Replication fork stalling at CGG repeats in mammalian cells…….Page 133
Figure 3 Model of chromosomal fragility at expanded CGG repeats…….Page 134
References……Page 135