Imperial College London

DrBingLiu

Faculty of Natural SciencesDepartment of Life Sciences

Visiting Researcher
 
 
 
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Contact

 

+44 (0)20 7594 5464b.liu05

 
 
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Location

 

Sir Ernst Chain BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

43 results found

Li L, Zhong Q, Zhao Y, Bao J, Liu B, Zhong Z, Wang J, Yang L, Zhang T, Cheng M, Wu N, Zhu T, Le Set al., 2023, First-in-human application of double-stranded RNA bacteriophage in the treatment of pulmonary Pseudomonas aeruginosa infection, MICROBIAL BIOTECHNOLOGY, ISSN: 1751-7915

Journal article

Li Y, Zhu F, Li Y, Pan S, Wang H, Yang Z, Wang Z, Hu Z, Yu J, Barritt JD, Li T, Liu X, Wang Y, Ma X, Liu Bet al., 2022, Bacteriophages allow selective depletion of gut bacteria to produce a targeted-bacterium-depleted mouse model, CELL REPORTS METHODS, Vol: 2, ISSN: 2667-2375

Journal article

Guo R, Gao J, Hui L, Li Y, Liu J, Fu Y, Shi L, Wang Y, Liu Bet al., 2022, An Improved Method for Quick Quantification of Unsaturated Transferrin, BIOSENSORS-BASEL, Vol: 12

Journal article

Zhang K, Li S, Wang Y, Wang Z, Mulvenna N, Yang H, Zhang P, Chen H, Li Y, Wang H, Gao Y, Wigneshweraraj S, Matthews S, Zhang K, Liu Bet al., 2022, Bacteriophage protein PEIP is a potent Bacillus subtilis enolase inhibitor, CELL REPORTS, Vol: 40, ISSN: 2211-1247

Journal article

Yang H, Yuan H, Zhao X, Xun M, Guo S, Wang N, Liu B, Wang Het al., 2022, Cytoplasmic domain and enzymatic activity of ACE2 are not required for PI4KB dependent endocytosis entry of SARS-CoV-2 into host cells, VIROLOGICA SINICA, Vol: 37, Pages: 380-389, ISSN: 1674-0769

Journal article

Zhang P, Zhao X, Wang Y, Du K, Wang Z, Yu J, Chang G, Matthews S, Wang H, Liu Bet al., 2022, Bacteriophage protein Gp46 is a cross-species inhibitor of nucleoid-associated HU proteins., Proc Natl Acad Sci U S A, Vol: 119

The architectural protein histone-like protein from Escherichia coli strain U93 (HU) is the most abundant bacterial DNA binding protein and highly conserved among bacteria and Apicomplexan parasites. It not only binds to double-stranded DNA (dsDNA) to maintain DNA stability but also, interacts with RNAs to regulate transcription and translation. Importantly, HU is essential to cell viability for many bacteria; hence, it is an important antibiotic target. Here, we report that Gp46 from bacteriophage SPO1 of Bacillus subtilis is an HU inhibitor whose expression prevents nucleoid segregation and causes filamentous morphology and growth defects in bacteria. We determined the solution structure of Gp46 and revealed a striking negatively charged surface. An NMR-derived structural model for the Gp46-HU complex shows that Gp46 occupies the DNA binding motif of the HU and therefore, occludes DNA binding, revealing a distinct strategy for HU inhibition. We identified the key residues responsible for the interaction that are conserved among HUs of bacteria and Apicomplexans, including clinically significant Mycobacterium tuberculosis, Acinetobacter baumannii, and Plasmodium falciparum, and confirm that Gp46 can also interact with these HUs. Our findings provide detailed insight into a mode of HU inhibition that provides a useful foundation for the development of antibacteria and antimalaria drugs.

Journal article

Liu B, Li S, Liu Y, Chen H, Hu Z, Wang Z, Zhao Y, Zhang L, Ma B, Wang H, Matthews S, Wang Y, Zhang Ket al., 2021, Bacteriophage Twort protein Gp168 is a beta-clamp inhibitor by occupying the DNA sliding channel, NUCLEIC ACIDS RESEARCH, Vol: 49, Pages: 11367-11378, ISSN: 0305-1048

Journal article

Zhao K, Ke Z, Hu H, Liu Y, Li A, Hua R, Guo F, Xiao J, Zhang Y, Duan L, Yan X-F, Gao Y-G, Liu B, Xia Y, Li Yet al., 2021, Erratum for Zhao et al., "Structural Basis and Function of the N Terminus of SARS-CoV-2 Nonstructural Protein 1"., Microbiol Spectr, Vol: 9

Journal article

Zhao K, Ke Z, Hu H, Liu Y, Li A, Hua R, Guo F, Xiao J, Zhang Y, Duan L, Yan X-F, Gao Y-G, Liu B, Xia Y, Li Yet al., 2021, Structural Basis and Function of the N Terminus of SARS-CoV-2 Nonstructural Protein 1, MICROBIOLOGY SPECTRUM, Vol: 9, ISSN: 2165-0497

Journal article

Wang Z, Wang H, Mulvenna N, Sanz-Hernandez M, Zhang P, Li Y, Ma J, Wang Y, Matthews S, Wigneshweraraj S, Liu Bet al., 2021, A Bacteriophage DNA Mimic Protein Employs a Non-specific Strategy to Inhibit the Bacterial RNA Polymerase, FRONTIERS IN MICROBIOLOGY, Vol: 12, ISSN: 1664-302X

Journal article

Zhang K, Li X, Wang Z, Li G, Ma B, Chen H, Li N, Yang H, Wang Y, Liu Bet al., 2021, Systemic Expression, Purification, and Initial Structural Characterization of Bacteriophage T4 Proteins Without Known Structure Homologs, FRONTIERS IN MICROBIOLOGY, Vol: 12, ISSN: 1664-302X

Journal article

Wang Z, Zhao S, Li Y, Zhang K, Mo F, Zhang J, Hou Y, He L, Liu Z, Wang Y, Xu Y, Wang H, Buck M, Matthews SJ, Liu Bet al., 2021, RssB-mediated sigma(S) Activation is Regulated by a Two-Tier Mechanism via Phosphorylation and Adaptor Protein - IraD, JOURNAL OF MOLECULAR BIOLOGY, Vol: 433, ISSN: 0022-2836

Journal article

Li Y, Li G, Wang Z, Chen W, Wang H, Wang Y, Liu Bet al., 2021, Resonance assignments of the cytoplasmic domain of ECF sigma factor W pathway protein YsdB from Bacillus subtilis, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 15, Pages: 103-106, ISSN: 1874-2718

Journal article

Xu C, Ke Z, Liu C, Wang Z, Liu D, Zhang L, Wang J, He W, Xu Z, Li Y, Yang Y, Huang Z, Lv P, Wang X, Han D, Li Y, Qiao N, Liu Bet al., 2020, Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server, JOURNAL OF CHEMICAL INFORMATION AND MODELING, Vol: 60, Pages: 5735-5745, ISSN: 1549-9596

Journal article

Zhu F, Guo R, Wang W, Ju Y, Wang Q, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Liu B, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H, Ma Xet al., 2020, Transplantation of microbiota from drug-free patients with schizophrenia causes schizophrenia-like abnormal behaviors and dysregulated kynurenine metabolism in mice, MOLECULAR PSYCHIATRY, Vol: 25, Pages: 2905-2918, ISSN: 1359-4184

Journal article

Krishna A, Liu B, Peacock SJ, Wigneshweraraj Set al., 2020, The prevalence and implications of single-nucleotide polymorphisms in genes encoding 3 the RNA polymerase of clinical isolates of Staphylococcus aureus, MicrobiologyOpen, Vol: 9, Pages: 1-8, ISSN: 2045-8827

Central to the regulation of bacterial gene expression is the multisubunit enzyme RNA polymerase (RNAP), which is responsible for catalyzing transcription. As all adaptive processes are underpinned by changes in gene expression, the RNAP can be considered the major mediator of any adaptive response in the bacterial cell. In bacterial pathogens, theoretically, single nucleotide polymorphisms (SNPs) in genes that encode subunits of the RNAP and associated factors could mediate adaptation and confer a selective advantage to cope with biotic and abiotic stresses. We investigated this possibility by undertaking a systematic survey of SNPs in genes encoding the RNAP and associated factors in a collection of 1,429 methicillin‐resistant Staphylococcus aureus (MRSA) clinical isolates. We present evidence for the existence of several, hitherto unreported, nonsynonymous SNPs in genes encoding the RNAP and associated factors of MRSA ST22 clinical isolates and propose that the acquisition of amino acid substitutions in the RNAP could represent an adaptive strategy that contributes to the pathogenic success of MRSA.

Journal article

Yang Y, Ke Z, Wang Z, Li Y, Li Y, Wang Y, Liu Bet al., 2020, H-1, C-13 and (15) N NMR assignments of solubility tag protein Msyb of Escherichia coli, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 14, Pages: 251-254, ISSN: 1874-2718

Journal article

Wang Z, Liang Y, Liu H, Wang Y, Wang H, Liu Bet al., 2020, Resonance assignments of bacteriophage SPO1 Gp49 protein, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 14, Pages: 111-114, ISSN: 1874-2718

Journal article

Zhang K, Wang Z, Chang G, Wang H, Wang Y, Liu Bet al., 2019, Resonance assignments of bacteriophage T4 Y04L protein, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 14, Pages: 51-54, ISSN: 1874-2718

Journal article

Wang Z, Zhao S, Jiang S, Wang Y, Buck M, Matthews S, Liu Bet al., 2019, Resonance assignments of N-terminal receiver domain of sigma factor S regulator RssB from Escherichia coli, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 13, Pages: 333-337, ISSN: 1874-2718

Journal article

Zhao S, Zhang K, Jiang S, Liu Z, Wang Z, Wang Y, Liu Bet al., 2019, Resonance assignments of sigma factor S binding protein Crl from Escherichia coli, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 13, Pages: 223-226, ISSN: 1874-2718

Journal article

Zhang P, Wang Z, Zhao S, Wang Y, Matthews S, Liu Bet al., 2019, H-1, C-13 and N-15 NMR assignments of Bacillus subtilis bacteriophage SPO1 protein Gp46, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 13, Pages: 245-247, ISSN: 1874-2718

Journal article

Darvill N, Blake T, Rouse S, Hammoudi P-M, Benjamin S, Liu B, Soldati-Favre D, Matthews Set al., 2018, Structural basis of phosphatidic acid sensing by APH in apicomplexan parasites, Structure, Vol: 26, Pages: 1059-1071.e6, ISSN: 0969-2126

Plasmodium falciparum and Toxoplasma gondii are obligate intracellular parasites that belong to the phylum of Apicomplexa and cause major human diseases. Their access to an intracellular lifestyle is reliant on the coordinated release of proteins from the specialized apical organelles called micronemes and rhoptries. A specific phosphatidic acid effector, the acylated pleckstrin homology domain-containing protein (APH) plays a central role in microneme exocytosis and thus is essential for motility, cell entry, and egress. TgAPH is acylated on the surface of the micronemes and recruited to phosphatidic acid (PA)-enriched membranes. Here, we dissect the atomic details of APH PA-sensing hub and its functional interaction with phospholipid membranes. We unravel the key determinant of PA recognition for the first time and show that APH inserts into and clusters multiple phosphate head-groups at the bilayer binding surface.

Journal article

Liu B, Wang Z, Lan L, Yang Q, Zhang P, Shi L, Lang Y, Tabib-Salazar A, Wigneshweraraj S, Zhang J, Wang Y, Tang Y, Matthews S, Zhang Xet al., 2018, A rapid colorimetric method to visualize protein interactions, Chemistry - A European Journal, Vol: 24, Pages: 6727-6731, ISSN: 0947-6539

As key molecules in most biological pathways, proteins physically contact one or more biomolecules in a highly specific manner. Several driving forces (i.e., electrostatic and hydrophobic) facilitate such interactions and a variety of methods have been developed to monitor these processes both in vivo and in vitro. In this work, a new method is reported for the detection of protein interactions by visualizing a color change of a cyanine compound, a supramolecule complex of 3,3-di-(3-sulfopropyl)-4,5,4',5'-dibenzo-9-methyl-thiacarbocyanine triethylammonium salt (MTC). Nuclear magnetic resonance (NMR) studies suggest that the hydrophobic nature of the protein surfaces drives MTC into different types of aggregates with distinct colors. When proteins interact with other biomolecules, the hydrophobic surface of the complex differs, resulting in a shift in the form of MTC aggregation, which results in a color change. As a result, this in vitro method has the potential to become a rapid tool for the confirmation of protein-biomolecule interactions, without the requirements for sophisticated instrumentation or approaches.

Journal article

Tabib-Salazar A, Liu B, Declan B, Burchell L, Qimron U, Matthews S, Wigneshweraraj Set al., 2018, T7 phage factor required for managing RpoS in Escherichia coli, Proceedings of the National Academy of Sciences, Vol: 115, Pages: E5353-E5362, ISSN: 0027-8424

T7 development in Escherichia coli requires the inhibition of the housekeepingform of the bacterial RNA polymerase (RNAP), Eσ70, by two T7 proteins: Gp2and Gp5.7. While the biological role of Gp2 is well understood, that of Gp5.7remains to be fully deciphered. Here, we present results from functional andstructural analyses to reveal that Gp5.7 primarily serves to inhibit EσS, thepredominant form of the RNAP in the stationary phase of growth, whichaccumulates in exponentially growing E. coli as a consequence of buildup ofguanosine pentaphosphate ((p)ppGpp) during T7 development. We furtherdemonstrate a requirement of Gp5.7 for T7 development in E. coli cells in thestationary phase of growth. Our finding represents a paradigm for how somelytic phages have evolved distinct mechanisms to inhibit the bacterialtranscription machinery to facilitate phage development in bacteria in theexponential and stationary phases of growth.

Journal article

Zhang P, Yang X, He Y, Chen Z, Liu B, Emesto CS, Yang G, Wang W, Zhang J, Lin Ret al., 2017, Preparation, characterization and toxicity evaluation of amphotericin B loaded MPEG-PCL micelles and its application for buccal tablets, APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, Vol: 101, Pages: 7357-7370, ISSN: 0175-7598

Journal article

Tabib-Salazar A, Liu B, Shadrin A, Burchell L, Wang Z, Wang Z, Goren MG, Yosef I, Qimron U, Severinov K, Matthews SJ, Wigneshweraraj Set al., 2017, Full shut-off of Escherichia coli RNA-polymerase by T7 phage requires a small phage-encoded DNA-binding protein, Nucleic Acids Research, Vol: 45, Pages: 7697-7707, ISSN: 1362-4962

Infection of Escherichia coli by the T7 phage leads to rapid and selective inhibition of the bacterial RNA polymerase (RNAP) by the 7 kDa T7 protein Gp2. We describe the identification and functional and structural characterisation of a novel 7 kDa T7 protein, Gp5.7, which adopts a winged helix-turn-helix-like structure and specifically represses transcription initiation from host RNAP-dependent promoters on the phage genome via a mechanism that involves interaction with DNA and the bacterial RNAP. Whereas Gp2 is indispensable for T7 growth in E. coli, we show that Gp5.7 is required for optimal infection outcome. Our findings provide novel insights into how phages fine-tune the activity of the host transcription machinery to ensure both successful and efficient phage progeny development.

Journal article

Jønsson R, Liu B, Struve C, Yang Y, Jenssen H, Krogfelt K, Matthews SJet al., 2016, Structural and functional studies of Escherichia coli Aggregative Adherence Fimbriae (AAF/V) reveal a deficiency in extracellular matrix binding, BBA Protein and Proteomics, Vol: 1865, Pages: 304-311, ISSN: 1570-9639

Enteroaggregative Escherichia coli (EAEC) is an emerging cause of acute and persistent diarrhea worldwide. The pathogenesis of different EAEC stains is complicated, however, the early essential step begins with attachment of EAEC to intestinal mucosa via aggregative adherence fimbriae (AAFs). Currently, five different variants have been identified, which all share a degree of similarity in the gene organization of their operons and sequences. Here, we report the solution structure of Agg5A from the AAF/V variant. While preserving the major structural features shared by all AAF members, only Agg5A possesses an inserted helix at the beginning of the donor strand, which together with altered surface electrostatics, renders the protein unable to interact with fibronectin. Hence, here we characterize the first AAF variant with a binding mode that varies from previously described AAFs

Journal article

Liang X, Liu B, Zhu F, Scannapieco FA, Haase EM, Matthews S, Wu Het al., 2016, A distinct sortase SrtB anchors and processes a streptococcal adhesin AbpA with a novel structural property., Scientific Reports, Vol: 6, ISSN: 2045-2322

Surface display of proteins by sortases in Gram-positive bacteria is crucial for bacterial fitness and virulence. We found a unique gene locus encoding an amylase-binding adhesin AbpA and a sortase B in oral streptococci. AbpA possesses a new distinct C-terminal cell wall sorting signal. We demonstrated that this C-terminal motif is required for anchoring AbpA to cell wall. In vitro and in vivo studies revealed that SrtB has dual functions, anchoring AbpA to the cell wall and processing AbpA into a ladder profile. Solution structure of AbpA determined by NMR reveals a novel structure comprising a small globular α/β domain and an extended coiled-coil heliacal domain. Structural and biochemical studies identified key residues that are crucial for amylase binding. Taken together, our studies document a unique sortase/adhesion substrate system in streptococci adapted to the oral environment rich in salivary amylase.

Journal article

Liu B, Zhu F, Wu H, Matthews Set al., 2015, NMR assignment of the amylase-binding protein A from Streptococcus parasanguinis, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 9, Pages: 173-175, ISSN: 1874-2718

Journal article

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