scholarly journals A Resident State Allows Influenza Polymerase to Smoothly Switch between Transcription and Replication Cycles

2021 ◽  
Author(s):  
Yingfang Liu ◽  
Huanhuan Liang ◽  
Huanhuan Li ◽  
Yixi Wu ◽  
Minke Li
Keyword(s):  
Structural Analysis ◽  
Viral Genome ◽  
Core Region ◽  
Binding Domain ◽  
Structural Basis ◽  
Viral Mrna ◽  
State Structure ◽  
Functional Switching ◽  
Transcription And Replication ◽  
Influenza Polymerase

Influenza polymerase (FluPol) transcripts viral mRNA and switches to replicate viral genome after transcription. However, it remains unknown how FluPol switches between transcription and replication cycles, especially when considering that the structural basis of these two functions is fundamentally different. Here, we proposed a mechanism that FluPol achieves the functional switching between these two cycles through an unreported intermediate conformation, termed as resident state. We obtained a resident state structure of H5N1 FluPol at 3.7 angstroms using cryo-EM, which is characterized by a blocked Cap-binding domain and a contracted core region, distinct from the structures of either transcription or replication states. Structural analysis results suggest that the resident state structure is feasible to smoothly transit into structures of both transcription and replication states. Furthermore, we show that formation of the resident state is required for both transcription and replication activities of FluPol. Together, the transcription and replication cycles of FluPol are connected via a resident state.

Structural basis of the p53 DNA binding domain and PUMA complex

2021 ◽  
Vol 548 ◽  
pp. 39-46
Author(s):  
Chang Woo Han ◽  
Han Na Lee ◽  
Mi Suk Jeong ◽  
So Young Park ◽  
Se Bok Jang
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Structural Basis ◽  
Dna Binding Domain

scholarly journals Heparin Inhibits Cellular Invasion by SARS-CoV-2: Structural Dependence of the Interaction of the Spike S1 Receptor-Binding Domain with Heparin

2020 ◽  
Vol 120 (12) ◽  
pp. 1700-1715
Author(s):  
Courtney J. Mycroft-West ◽  
Dunhao Su ◽  
Isabel Pagani ◽  
Timothy R. Rudd ◽  
Stefano Elli ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Structural Changes ◽  
Rapid Development ◽  
Antiviral Agents ◽  
Vero Cells ◽  
Binding Domain ◽  
Microbial Pathogens ◽  
Minimum Size ◽  
Structural Basis ◽  
Receptor Binding Domain

AbstractThe dependence of development and homeostasis in animals on the interaction of hundreds of extracellular regulatory proteins with the peri- and extracellular glycosaminoglycan heparan sulfate (HS) is exploited by many microbial pathogens as a means of adherence and invasion. Heparin, a widely used anticoagulant drug, is structurally similar to HS and is a common experimental proxy. Exogenous heparin prevents infection by a range of viruses, including S-associated coronavirus isolate HSR1. Here, we show that heparin inhibits severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) invasion of Vero cells by up to 80% at doses achievable through prophylaxis and, particularly relevant, within the range deliverable by nebulisation. Surface plasmon resonance and circular dichroism spectroscopy demonstrate that heparin and enoxaparin, a low-molecular-weight heparin which is a clinical anticoagulant, bind and induce a conformational change in the spike (S1) protein receptor-binding domain (S1 RBD) of SARS-CoV-2. A library of heparin derivatives and size-defined fragments were used to probe the structural basis of this interaction. Binding to the RBD is more strongly dependent on the presence of 2-O or 6-O sulfate groups than on N-sulfation and a hexasaccharide is the minimum size required for secondary structural changes to be induced in the RBD. It is likely that inhibition of viral infection arises from an overlap between the binding sites of heparin/HS on S1 RBD and that of the angiotensin-converting enzyme 2. The results suggest a route for the rapid development of a first-line therapeutic by repurposing heparin and its derivatives as antiviral agents against SARS-CoV-2 and other members of the Coronaviridae.

scholarly journals Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shih-Chi Luo ◽  
Hsin-Yi Yeh ◽  
Wei-Hsuan Lan ◽  
Yi-Min Wu ◽  
Cheng-Han Yang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Structural Analysis ◽  
Md Simulation ◽  
Structural Basis ◽  
High Fidelity ◽  
Dna Dynamics ◽  
Genomic Integrity ◽  
Mismatched Dna ◽  
Dna Backbone ◽  
Loop 2

AbstractBoth high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1. Structural analysis of DMC1 presynaptic and postsynaptic complexes suggested that the lineage-specific Loop 1 Gln244 (Met243 in RAD51) may help stabilize DNA backbone, whereas Loop 2 Pro274 and Gly275 (Val273/Asp274 in RAD51) may provide an open “triplet gate” for mismatch tolerance. In support, DMC1-Q244M displayed marked increase in DNA dynamics, leading to unobservable DNA map. MD simulation showed highly dispersive mismatched DNA ensemble in RAD51 but well-converged DNA in DMC1 and RAD51-V273P/D274G. Replacing Loop 1 or Loop 2 residues in DMC1 with RAD51 counterparts enhanced DMC1 fidelity, while reciprocal mutations in RAD51 attenuated its fidelity. Our results show that three Loop 1/Loop 2 residues jointly enact contrasting fidelities of DNA recombinases.

scholarly journals Gonococcal pili. Primary structure and receptor binding domain.

1984 ◽  
Vol 159 (5) ◽  
pp. 1351-1370 ◽  
Author(s):  
G K Schoolnik ◽  
R Fernandez ◽  
J Y Tai ◽  
J Rothbard ◽  
E C Gotschlich
Keyword(s):  
Amino Acids ◽  
Receptor Binding ◽  
Binding Domain ◽  
Structural Basis ◽  
Receptor Binding Domain ◽  
Variable Regions ◽  
Disulfide Linkage ◽  
Polymeric Structure ◽  
Antigenic Diversity ◽  
Single Polypeptide Chain

The complete amino acid sequence of pilin from gonococcal strain MS11 and the sequence of constant and variable regions from strain R10 pilin have been determined in order to elucidate the structural basis for adherence function, antigenic diversity, and polymeric structure. The MS11 pilin sequence consists of 159 amino acids in a single polypeptide chain with two cysteines in disulfide linkage and serine-bonded phosphate residues. TC-2 (31-111), a soluble monomeric pilus peptide prepared by arginine-specific digestion, bound human endocervical, but not buccal or HeLa cells and therefore is postulated to encompass the receptor binding domain. Variable regions of CNBr-3 appear to confer antigenic diversity and comprise segments in which changes in the position of charged residues occur in hydrophilic, beta-turns. Residues 2-21 and 202-221 of gonococcal pilins and lower eucaryotic actins, respectively, exhibit 50% homology. When these residues are arranged at intervals of 100 degrees of arc on "helical wheels," the identical amino acids comprise a hydrophobic face on one side of the helix. This observation, the hydrophobic character of this region and the tendency for TC-1 (residues 1-30) to aggregate in water, suggest that this stretch interacts with other subunits to stabilize polymeric structure.

scholarly journals Structural analysis of the human SYCE2–TEX12 complex provides molecular insights into synaptonemal complex assembly

Open Biology ◽  
2012 ◽  
Vol 2 (7) ◽  
pp. 120099 ◽  
Author(s):  
Owen R. Davies ◽  
Joseph D. Maman ◽  
Luca Pellegrini
Keyword(s):  
Structural Analysis ◽  
Synaptonemal Complex ◽  
Recurrent Miscarriage ◽  
Central Element ◽  
Biological Data ◽  
Structural Basis ◽  
Structural Framework ◽  
Chromosome Synapsis ◽  
Heterotypic Interactions ◽  
Physical Features

The successful completion of meiosis is essential for all sexually reproducing organisms. The synaptonemal complex (SC) is a large proteinaceous structure that holds together homologous chromosomes during meiosis, providing the structural framework for meiotic recombination and crossover formation. Errors in SC formation are associated with infertility, recurrent miscarriage and aneuploidy. The current lack of molecular information about the dynamic process of SC assembly severely restricts our understanding of its function in meiosis. Here, we provide the first biochemical and structural analysis of an SC protein component and propose a structural basis for its function in SC assembly. We show that human SC proteins SYCE2 and TEX12 form a highly stable, constitutive complex, and define the regions responsible for their homotypic and heterotypic interactions. Biophysical analysis reveals that the SYCE2–TEX12 complex is an equimolar hetero-octamer, formed from the association of an SYCE2 tetramer and two TEX12 dimers. Electron microscopy shows that biochemically reconstituted SYCE2–TEX12 complexes assemble spontaneously into filamentous structures that resemble the known physical features of the SC central element (CE). Our findings can be combined with existing biological data in a model of chromosome synapsis driven by growth of SYCE2–TEX12 higher-order structures within the CE of the SC.

scholarly journals Structural Basis for the Specific Recognition of RET by the Dok1 Phosphotyrosine Binding Domain

2003 ◽  
Vol 279 (6) ◽  
pp. 4962-4969 ◽  
Author(s):  
Ning Shi ◽  
Sheng Ye ◽  
Mark Bartlam ◽  
Maojun Yang ◽  
Jing Wu ◽  
...  
Keyword(s):  
Binding Domain ◽  
Structural Basis ◽  
Specific Recognition ◽  
Phosphotyrosine Binding Domain

scholarly journals Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies

2021 ◽  
Vol 12 ◽  
Author(s):  
Qiaozhen Ye ◽  
Shan Lu ◽  
Kevin D. Corbett
Keyword(s):  
Nucleocapsid Protein ◽  
Rna Binding ◽  
Binding Domain ◽  
Single Domain ◽  
Structural Basis ◽  
Dimerization Domain ◽  
Health Event ◽  
Single Domain Antibodies ◽  
Rna Binding Domain ◽  
Antigen Tests

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, is the most severe public health event of the twenty-first century. While effective vaccines against SARS-CoV-2 have been developed, there remains an urgent need for diagnostics to quickly and accurately detect infections. Antigen tests, particularly those that detect the abundant SARS-CoV-2 Nucleocapsid protein, are a proven method for detecting active SARS-CoV-2 infections. Here we report high-resolution crystal structures of three llama-derived single-domain antibodies that bind the SARS-CoV-2 Nucleocapsid protein with high affinity. Each antibody recognizes a specific folded domain of the protein, with two antibodies recognizing the N-terminal RNA binding domain and one recognizing the C-terminal dimerization domain. The two antibodies that recognize the RNA binding domain affect both RNA binding affinity and RNA-mediated phase separation of the Nucleocapsid protein. All three antibodies recognize highly conserved surfaces on the Nucleocapsid protein, suggesting that they could be used to develop affordable diagnostic tests to detect all circulating SARS-CoV-2 variants.

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