Structural Basis forE. coliPenicillin Binding Protein (PBP) 2 Inhibition, a Platform for Drug Design

ACC (amorphous calcium carbonate) plays an important role in biomineralization process for its function as a precursor for calcium carbonate biominerals. However, it is unclear how biomacromolecules regulate the formation of ACC precursor in vivo. In the present study, we used biochemical experiments coupled with bioinformatics approaches to explore the mechanisms of ACC formation controlled by ACCBP (ACC-binding protein). Size-exclusion chromatography, chemical cross-linking experiments and negative staining electron microscopy reveal that ACCBP is a decamer composed of two adjacent pentamers. Sequence analyses and fluorescence quenching results indicate that ACCBP contains two Ca2+-binding sites. The results of in vitro crystallization experiments suggest that one Ca2+-binding site is critical for ACC formation and the other site affects the ACC induction efficiency. Homology modelling demonstrates that the Ca2+-binding sites of pentameric ACCBP are arranged in a 5-fold symmetry, which is the structural basis for ACC formation. To the best of our knowledge, this is the first report on the structural basis for protein-induced ACC formation and it will significantly improve our understanding of the amorphous precursor pathway.

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Structural basis of nucleic acid binding byNicotiana tabacumglycine-rich RNA-binding protein: implications for its RNA chaperone function

Nucleic Acids Research ◽

10.1093/nar/gku468 ◽

2014 ◽

Vol 42 (13) ◽

pp. 8705-8718 ◽

Cited By ~ 12

Author(s):

Fariha Khan ◽

Mark A. Daniëls ◽

Gert E. Folkers ◽

Rolf Boelens ◽

S. M. Saqlan Naqvi ◽

...

Keyword(s):

Nucleic Acid ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Structural Basis ◽

Nucleic Acid Binding ◽

Rna Chaperone ◽

Chaperone Function

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Structural basis of the zinc-induced cytoplasmic aggregation of the RNA-binding protein SFPQ

Nucleic Acids Research ◽

10.1093/nar/gkaa076 ◽

2020 ◽

Vol 48 (6) ◽

pp. 3356-3365 ◽

Cited By ~ 4

Author(s):

Jie Huang ◽

Mitchell Ringuet ◽

Andrew E Whitten ◽

Sofia Caria ◽

Yee Wa Lim ◽

...

Keyword(s):

Crystal Structure ◽

Cortical Neurons ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Zinc Binding ◽

Structural Basis ◽

Rna Biogenesis ◽

Cytoplasmic Accumulation ◽

Nucleocytoplasmic Distribution

Abstract SFPQ is a ubiquitous nuclear RNA-binding protein implicated in many aspects of RNA biogenesis. Importantly, nuclear depletion and cytoplasmic accumulation of SFPQ has been linked to neuropathological conditions such as Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS). Here, we describe a molecular mechanism by which SFPQ is mislocalized to the cytoplasm. We report an unexpected discovery of the infinite polymerization of SFPQ that is induced by zinc binding to the protein. The crystal structure of human SFPQ in complex with zinc at 1.94 Å resolution reveals intermolecular interactions between SFPQ molecules that are mediated by zinc. As anticipated from the crystal structure, the application of zinc to primary cortical neurons induced the cytoplasmic accumulation and aggregation of SFPQ. Mutagenesis of the three zinc-coordinating histidine residues resulted in a significant reduction in the zinc-binding affinity of SFPQ in solution and the zinc-induced cytoplasmic aggregation of SFPQ in cultured neurons. Taken together, we propose that dysregulation of zinc availability and/or localization in neuronal cells may represent a mechanism for the imbalance in the nucleocytoplasmic distribution of SFPQ, which is an emerging hallmark of neurodegenerative diseases including AD and ALS.

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Structural Basis of Glycerophosphodiester Recognition by the Mycobacterium tuberculosis Substrate-Binding Protein UgpB

ACS Chemical Biology ◽

10.1021/acschembio.9b00204 ◽

2019 ◽

Vol 14 (9) ◽

pp. 1879-1887 ◽

Cited By ~ 3

Author(s):

Jonathan S. Fenn ◽

Ridvan Nepravishta ◽

Collette S. Guy ◽

James Harrison ◽

Jesus Angulo ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Binding Protein ◽

Substrate Binding ◽

Structural Basis ◽

Substrate Binding Protein

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Structural Basis for the Activation of Platelet Integrin αIIbβ3 by Calcium- and Integrin-Binding Protein 1

Journal of the American Chemical Society ◽

10.1021/ja2111306 ◽

2012 ◽

Vol 134 (8) ◽

pp. 3864-3872 ◽

Cited By ~ 20

Author(s):

Hao Huang ◽

Hans J. Vogel

Keyword(s):

Binding Protein ◽

Structural Basis ◽

Integrin Αiibβ3

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Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands Bound to the Heteroaryldihydropyrimidine Pocket

Journal of Virology ◽

10.1128/jvi.03058-15 ◽

2016 ◽

Vol 90 (8) ◽

pp. 3994-4004 ◽

Cited By ~ 40

Author(s):

Balasubramanian Venkatakrishnan ◽

Sarah P. Katen ◽

Samson Francis ◽

Srinivas Chirapu ◽

M. G. Finn ◽

...

Keyword(s):

Life Cycle ◽

Hepatitis B Virus ◽

Hepatitis B ◽

Drug Design ◽

Quaternary Structure ◽

Core Protein ◽

Viral Life Cycle ◽

Structural Basis ◽

Allosteric Modulators ◽

B Virus

ABSTRACTThough the hepatitis B virus (HBV) core protein is an important participant in many aspects of the viral life cycle, its best-characterized activity is self-assembly into 240-monomer capsids. Small molecules that target core protein (core protein allosteric modulators [CpAMs]) represent a promising antiviral strategy. To better understand the structural basis of the CpAM mechanism, we determined the crystal structure of the HBV capsid in complex with HAP18. HAP18 accelerates assembly, increases protein-protein association more than 100-fold, and induces assembly of nonicosahedral macrostructures. In a preformed capsid, HAP18 is found at quasiequivalent subunit-subunit interfaces. In a detailed comparison to the two other extant CpAM structures, we find that the HAP18-capsid structure presents a paradox. Whereas the two other structures expanded the capsid diameter by up to 10 Å, HAP18 caused only minor changes in quaternary structure and actually decreased the capsid diameter by ∼3 Å. These results indicate that CpAMs do not have a single allosteric effect on capsid structure. We suggest that HBV capsids present an ensemble of states that can be trapped by CpAMs, indicating a more complex basis for antiviral drug design.IMPORTANCEHepatitis B virus core protein has multiple roles in the viral life cycle—assembly, compartment for reverse transcription, intracellular trafficking, and nuclear functions—making it an attractive antiviral target. Core protein allosteric modulators (CpAMs) are an experimental class of antivirals that bind core protein. The most recognized CpAM activity is that they accelerate core protein assembly and strengthen interactions between subunits. In this study, we observe that the CpAM-binding pocket has multiple conformations. We compare structures of capsids cocrystallized with different CpAMs and find that they also affect quaternary structure in different ways. These results suggest that the capsid “breathes” and is trapped in different states by the drug and crystallization. Understanding that the capsid is a moving target will aid drug design and improve our understanding of HBV interaction with its environment.

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Structural Basis of Lipid Exchange in the Oxysterol-Binding Protein Homologue (OSH) Family

Biophysical Journal ◽

10.1016/j.bpj.2013.11.619 ◽

2014 ◽

Vol 106 (2) ◽

pp. 99a

Author(s):

Stefano Vanni ◽

Joachim Moser von Filseck ◽

Bruno Mesmin ◽

Bruno Antonny ◽

Guillaume Drin

Keyword(s):

Binding Protein ◽

Structural Basis ◽

Oxysterol Binding Protein ◽

Lipid Exchange

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Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS

Quarterly Reviews of Biophysics ◽

10.1017/s0033583515000207 ◽

2015 ◽

Vol 49 ◽

Cited By ~ 21

Author(s):

Marianna Teplova ◽

Thalia A. Farazi ◽

Thomas Tuschl ◽

Dinshaw J. Patel

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Hek293 Cells ◽

Structural Basis ◽

Rna Recognition Motif ◽

Rna Recognition ◽

Binding Studies ◽

Muscle Plasticity ◽

Rrm Domain

AbstractRNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. As anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutations in vivo.

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