Mussel glue protein has an open conformation

hERG (Human ether-a-go-go-related gene) potassium channel, which plays an essential role in cardiac action potential repolarization, is responsible for inherited and druginduced long QT syndrome. Recently, the Cryo-EM structure capturing the open conformation of hERG channel was determined, thus pushing the study on hERG channel at 3.8 Å resolution. This report focuses primarily on summarizing the design rationale and application of several fluorescent probes that target hERG channels, which enables dynamic and real-time monitoring of potassium pore channel affinity to further advance the understanding of the channels.

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Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation

Communications Biology ◽

10.1038/s42003-021-02132-y ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Komal Soni ◽

Georg Kempf ◽

Karen Manalastas-Cantos ◽

Astrid Hendricks ◽

Dirk Flemming ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Binding Sites ◽

Signal Recognition Particle ◽

Signal Recognition ◽

Closed Conformation ◽

Open Conformation ◽

Structural Database ◽

Alu Rna ◽

Species Specific ◽

Protozoan Species

AbstractThe eukaryotic signal recognition particle (SRP) contains an Alu domain, which docks into the factor binding site of translating ribosomes and confers translation retardation. The canonical Alu domain consists of the SRP9/14 protein heterodimer and a tRNA-like folded Alu RNA that adopts a strictly ‘closed’ conformation involving a loop-loop pseudoknot. Here, we study the structure of the Alu domain from Plasmodium falciparum (PfAlu), a divergent apicomplexan protozoan that causes human malaria. Using NMR, SAXS and cryo-EM analyses, we show that, in contrast to its prokaryotic and eukaryotic counterparts, the PfAlu domain adopts an ‘open’ Y-shaped conformation. We show that cytoplasmic P. falciparum ribosomes are non-discriminative and recognize both the open PfAlu and closed human Alu domains with nanomolar affinity. In contrast, human ribosomes do not provide high affinity binding sites for either of the Alu domains. Our analyses extend the structural database of Alu domains to the protozoan species and reveal species-specific differences in the recognition of SRP Alu domains by ribosomes.

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Crystal structures of an E1–E2–ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification

Nature Communications ◽

10.1038/s41467-021-22598-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Lingmin Yuan ◽

Zongyang Lv ◽

Melanie J. Adams ◽

Shaun K. Olsen

Keyword(s):

Complex Formation ◽

Crystal Structures ◽

Molecular Mechanisms ◽

Conformational State ◽

Biochemical Data ◽

Conformational States ◽

Product Release ◽

Closed Conformation ◽

Open Conformation ◽

Conjugating Enzymes

AbstractE1 enzymes function as gatekeepers of ubiquitin (Ub) signaling by catalyzing activation and transfer of Ub to tens of cognate E2 conjugating enzymes in a process called E1–E2 transthioesterification. The molecular mechanisms of transthioesterification and the overall architecture of the E1–E2–Ub complex during catalysis are unknown. Here, we determine the structure of a covalently trapped E1–E2–ubiquitin thioester mimetic. Two distinct architectures of the complex are observed, one in which the Ub thioester (Ub(t)) contacts E1 in an open conformation and another in which Ub(t) instead contacts E2 in a drastically different, closed conformation. Altogether our structural and biochemical data suggest that these two conformational states represent snapshots of the E1–E2–Ub complex pre- and post-thioester transfer, and are consistent with a model in which catalysis is enhanced by a Ub(t)-mediated affinity switch that drives the reaction forward by promoting productive complex formation or product release depending on the conformational state.

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Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome

Communications Biology ◽

10.1038/s42003-021-01707-z ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Rina Hirano ◽

Yasuhiro Arimura ◽

Tomoya Kujirai ◽

Mikihiro Shibata ◽

Aya Okuda ◽

...

Keyword(s):

Atomic Force Microscopy ◽

Dna Repair ◽

High Speed ◽

Histone Chaperones ◽

Histone H2a ◽

Force Microscopy ◽

Atomic Force ◽

Open Conformation ◽

Replication Sites ◽

Histone Exchange

AbstractH2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes. In cells, H2A.B exchanges rapidly in chromatin, but the mechanism has remained enigmatic. In the present study, we found that the H2A.B-H2B dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from additional factors, such as histone chaperones and nucleosome remodelers. High-speed atomic force microscopy revealed that the H2A.B nucleosome, but not the canonical H2A nucleosome, transiently forms an intermediate “open conformation”, in which two H2A.B-H2B dimers may be detached from the H3-H4 tetramer and bind to the DNA regions near the entry/exit sites. Mutational analyses revealed that the H2A.B C-terminal region is responsible for the adoption of the open conformation and the H2A.B-H2B exchange in the nucleosome. These findings provide mechanistic insights into the histone exchange of the H2A.B nucleosome.

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