Zhixia Liu

@scripps.edu

Chemistry
The Scripps Research Institute

Zhixia Liu


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https://researchid.co/zhixialiu

RESEARCH INTERESTS

Protein folding, Protein engineering, Aptamer discovery, Drug delivery
16

Scopus Publications

Scopus Publications

  • Selection of Aptamers with Large Hydrophobic 2′-Substituents
    Qian Shao, Tingjian Chen, Kai Sheng, Zhixia Liu, Zhuochen Zhang, Floyd E. Romesberg
    Journal of the American Chemical Society, 2020
    Previously, we evolved a DNA polymerase, SFM4-3, for the recognition of substrates modified at their 2' positions with a fluoro, O-methyl, or azido substituent. Here we use SFM4-3 to synthesize 2'-azido-modified DNA; we then use the azido group to attach different, large hydrophobic groups via click chemistry. We show that SFM4-3 recognizes the modified templates under standard conditions, producing natural DNA and thereby allowing amplification. To demonstrate the utility of this remarkable property, we use SFM4-3 to select aptamers with large hydrophobic 2' substituents that bind human neutrophil elastase or the blood coagulation protein factor IXa. The results indicate that SFM4-3 should facilitate the discovery of aptamers that adopt novel and perhaps more protein-like folds with hydrophobic cores that in turn allow them to access novel activities.
  • Selection of 2′-Fluoro-Modified Aptamers with Optimized Properties
    Deepak Thirunavukarasu, Tingjian Chen, Zhixia Liu, Narupat Hongdilokkul, Floyd E. Romesberg
    Journal of the American Chemical Society, 2017
    RNA or single-stranded DNA aptamers with 2'-F pyrimidines have been pursued to increase resistance to nucleases, and while it seems likely that these and other modifications, including the modification of purines, could be used to optimize additional properties, this has been much less explored because such aptamers are challenging to discover. Using a thermostable DNA polymerase, SFM4-3, which was previously evolved to accept nucleotides with 2'-modifications, we now report the selection of 2'-F purine aptamers that bind human neutrophil elastase (HNE). Two aptamers were identified, 2fHNE-1 and 2fHNE-2, that bind HNE with reasonable affinity. Interestingly, the 2'-F substituents facilitate the selection of specific interactions with HNE and overcome nonspecific electrostatic interactions that can otherwise dominate. The data demonstrate that inclusion of only a few 2'-F substituents can optimize properties far beyond simple nuclease resistance and that SFM4-3 should prove valuable for the further exploration and production of aptamers with properties optimized for various applications.
  • Evolved polymerases facilitate selection of fully 2′-OMe-modified aptamers
    Zhixia Liu, Tingjian Chen, Floyd E. Romesberg
    Chemical Science, 2017
    Evolved DNA polymerases are used in selections with fully 2′-OMe modified libraries to identify aptamers with high affinity for HNE.
  • The expanding world of DNA and RNA
    Tingjian Chen, Narupat Hongdilokkul, Zhixia Liu, Deepak Thirunavukarasu, Floyd E Romesberg
    Current Opinion in Chemical Biology, 2016
    DNA and RNA are remarkable because they can both encode information and possess desired properties, including the ability to bind specific targets or catalyze specific reactions. Nucleotide modifications that do not interfere with enzymatic synthesis are now being used to bestow DNA or RNA with properties that further increase their utility, including phosphate and sugar modifications that increase nuclease resistance, nucleobase modifications that increase the range of activities possible, and even whole nucleobase replacement that results in selective pairing and the creation of unnatural base pairs that increase the information content. These modifications are increasingly being applied both in vitro and in vivo, including in efforts to create semi-synthetic organisms with altered or expanded genetic alphabets.
  • Evolution of thermophilic DNA polymerases for the recognition and amplification of C2'-modified DNA
    Tingjian Chen, Narupat Hongdilokkul, Zhixia Liu, Ramkrishna Adhikary, Shujian S. Tsuen, Floyd E. Romesberg
    Nature Chemistry, 2016
    The PCR amplification of oligonucleotides enables the evolution of sequences called aptamers that bind specific targets with antibody-like affinity. However, the use of these aptamers is limited in many applications by nuclease-mediated degradation. In contrast, oligonucleotides that are modified at their sugar C2' positions with methoxy or fluorine substituents are stable to nucleases but cannot be synthesized by natural polymerases. Here, we report the development of a polymerase evolution system and its use to evolve thermostable polymerases that efficiently interconvert C2'-OMe modified oligonucleotides and their DNA counterparts via “transcription” and “reverse transcription,” or more importantly, PCR amplify partially C2'-OMe or C2'-F modified oligonucleotides. A mechanistic analysis demonstrates that the ability to amplify the modified oligonucleotides was evolved by optimizing interdomain interactions that stabilize the catalytically competent closed conformation of the polymerase. The evolved polymerases should find practical applications and the developed evolution system should be a powerful tool for the tailoring of polymerases to have other types of novel function.
  • Capture and enumeration of mRNA transcripts from single cells using a microfluidic device
    Matthew T. Walsh, Alexander P. Hsiao, Ho Suk Lee, Zhixia Liu, Xiaohua Huang
    Lab on A Chip, 2015
    We report an integrated microfluidic device for direct capture and digital counting of polyadenylated mRNA molecules from single cells.
  • Strengthening the stability of a tunnel-shaped homotetramer protein with nanogels
    Zhixia Liu, Diannan Lu, Ling Yin, Jianmin Li, Yuanchen Cui, Wei Chen, Zheng Liu
    Journal of Physical Chemistry B, 2011
    Urate oxidase (UOX, EC 1.7.3.3) is effective for the treatment of gout and hyperuricaemia associated with tumor lysis syndrome. The inherent poor stability of UOX to temperature, proteolysis, and acidic environments is known to limit its efficacy. Herein, we encapsulated UOX into spherical and porous nanogels with diameters of 20-40 nm via a two-step in situ polymerization in the presence of oxonic acid potassium salt, an inhibitor of UOX. The UOX nanogel retained 70% of the initial activity but showed an expanded pH spectrum from pH 6-10 to 3-10 and an extended half-life at 37 °C from 5 min to 3 h. The enhanced pH stability, thermal stability, and enzyme resistance of the UOX nanogels were also confirmed by using fluorescence spectroscopy and enzymatic digestion. A molecular dynamics simulation was performed as a way to probe the mechanism underlying the formation of UOX nanogels as well as the strengthened stability against harsh conditions. It was shown that the encapsulation into the polyacrylamide network reinforced the intersubunit hydrogen bonding, shielded the hydrolytic reaction site, and thus protected the tertiary and quaternary structure of UOX. The UOX nanogel with enhanced stability provided a stable enzyme model that enables the exploration of UOX in the diagnosis and therapy of disorders associated with altered purine metabolism.
  • Recent advances in nanostructured biocatalysts
    Jun Ge, Diannan Lu, Zhixia Liu, Zheng Liu
    Biochemical Engineering Journal, 2009
    Recent years have witnessed a renaissance in the field of chemically re-engineering of enzymes to obtain highly selective and efficient biocatalysts for catalyzing processes under various conditions. The incorporation of enzyme into nanostructured materials is particularly noteworthy from a structural perspective since there are unprecedented opportunities in such systems to establish suitable microenvironments for chosen enzymes. This review summarizes recent developments in the nanostructured biocatalyst with emphasis on those formed with polymers. Based on the synthetic procedures employed, the established methods are grouped into three major categories—“grafting onto”, “grafting from”, and “self-assembly”. The merits of the methods in enhancing enzyme stability at adverse conditions and their potential for large-scale preparation and the use of the nanostructured biocatalysts are discussed. The molecular fundamentals underlying each method are highlighted, and the use of molecular simulation as a tool for the design and application of nanostructured biocatalysts, although at a nascent stage, is presented. Finally, the problems encountered with nanostructured biocatalysts are discussed together with the future prospects of such systems.
  • Strengthening intersubunit hydrogen bonds for enhanced stability of recombinant urate oxidase from Aspergillus flavus: Molecular simulations and experimental validation
    Zhixia Liu, Diannan Lu, Jianmin Li, Wei Chen, Zheng Liu
    Physical Chemistry Chemical Physics, 2009
    The aim of this study was to obtain molecular insight into the deactivation of recombinant urate oxidase (uricase, UOX, EC 1.7.3.3) (rUOX) from Aspergillus flavus. The enzyme is a tunnel-shaped homotetramer and has important clinical applications. By means of molecular dynamics simulations, multidimensional structural characterization and enzyme activity assays, we concluded that the thermal deactivation of UOX at neutral pH was associated with the loss of intersubunit hydrogen (H) bonds. This mechanism could also explain the deactivation of dilute aqueous UOX. Thermal deactivation of aqueous UOX due to dissociation of its subunits was ruled out. Displacement of H(2)O from the surface of UOX by less polar solvents such as methanol and dimethyl sulfoxide (DMSO) was proposed as an approach for strengthening intersubunit H bonds and consequently UOX stability. The effectiveness of this method was validated by both in silico and in vitro experiments. The results mentioned above provide insights for improving the stability of UOX and extending its applications. They may also be helpful for understanding the properties of other multimeric proteins.
  • Role of intersubunit hydrogen bond to urate oxidase stability: Molecular simulation and experimental validation
    Aiche Annual Meeting Conference Proceedings, 2008
  • Robust biocatalytic single enzyme nanogels by versatile strategies
    2007 Aiche Annual Meeting, 2007
  • Fabrication of single carbonic anhydrase nanogel against denaturation and aggregation at high temperature
    Ming Yan, Zhixia Liu, Diannan Lu, Zheng Liu
    Biomacromolecules, 2007
  • Dextran-grafted-PNIPAAm as an artificial chaperone for protein refolding
    Diannan Lu, Zhixia Liu, Minlian Zhang, Xiaogong Wang, Zheng Liu
    Biochemical Engineering Journal, 2006
  • Surfactant assisted protein refolding in vitro: Molecular simulation
    Huagong Xuebao Journal of Chemical Industry and Engineering China, 2005
  • The mechanism of PNIPAAm-assisted refolding of lysozyme denatured by urea
    Diannan Lu, Zhixia Liu, Minlian Zhang, Zheng Liu, Haimeng Zhou
    Biochemical Engineering Journal, 2005
  • Molecular simulation of surfactant-assisted protein refolding
    Diannan Lu, Zheng Liu, Zhixia Liu, Minlian Zhang, Pingkai Ouyang
    Journal of Chemical Physics, 2005

Publications

Liu Z, Chen T, Romesberg FE, Evolved polymerases facilitate selection of fully 2’-OMe-modified aptamers, Chemical Science, 2017, 8: 8179
Thirunavukarasu D, Chen T, Liu Z, Hongdilokkul N, Romesberg FE, Selection of 2’-Fluoro-Modified Aptamers with Optimized Properties, Journal of the American Chemical Society, 2017, 139: 2892
Chen T, Hongdilokkul N, Liu Z, Thirunavukarasu D, Romesberg FE, The expanding world of DNA and RNA, Current Opinion in Chemical Biology, 2016, 34: 80
Chen T, Hongdilokkul N, Liu Z, Adhikary R, Tsuen SS, Romesberg FE, Evolution of thermophilic DNA polymerases for the recognition and amplification of C2ʹ-modified DNA, Nature Chemistry, 2016, 8: 556
Walsh M, Hsiao A, Lee HS, Liu Z, Huang X, Capture and enumeration of mRNA transcripts from single cells using a microfluidic device, Lab on a Chip, 2015, 15: 2968
Liu Z, Lu D, Yin L, Li J, Cui Y, Chen W, Liu Z, Strengthening the stability of a tunnel-shaped homotetramer protein with nanogels, The Journal of Physical Chemistry B, 2011, 115: 8875
Liu Z, Lu D, Li J, Chen W, Liu Z, Strengthening intersubunit hydrogen bonds for enhanced stability of recombinant urate oxidase from Aspergillus flavus: Molecular simulations and experimental validation, Physical Chemistry Chemical Physics, 2009, 11: 333
Ge J, Lu D, Liu Z, Liu Z, Recent advances in nanostructured biocatalysts, Biochemical Engineering Journal, 2009, 44: 53
Yan M, Liu Z, Lu D, Liu Z, Fabrication of single carbonic anhydrase nanogel against denaturation and aggregation at high temperature, Biomacromolecules, 2007, 8: 560
Lu D, Liu Z, Zhang M, Wang X, Liu Z, Dextran-grafted-PNIPAAm as an artificial chaperone for protein refolding, Biochemical Engineering Journal, 2006, 27: 336
Lu D, Liu Z, Zhang M, Liu Z, Zhou H, The mechanism of PNIPAAm-assisted refolding of lysozyme denatured by urea, Biochemical Engineering Journal, 2005, 24: 55
Lu D, Liu Z, Liu Z, Zhang M, Ouyang P, Molecular simulation of surfactant-assisted protein refolding, The Journal of Chemical Physics, 2005, 122: Art
Lu D, Wang J, Liu Z, Zhang M, Liu Z, Surfactant assisted protein refolding in vitro: molecular simulation, Journal of Chemical Industry and Engineering-China, 2005, 56: 1063
Ge J, Yan M, Lu D, Liu Z, Liu Z, Preparation and Characterization of Single-Enzyme Nanogels, In: Wang P. (eds) Nanoscale Biocatalysis. Methods in Molecular Biology (Methods and Protocols), vol 743. Humana Press, 2011

RESEARCH OUTPUTS (PATENTS, SOFTWARE, PUBLICATIONS, PRODUCTS)

Yan M, Liu Z, Ge J, Liu Z, Zhang M, Ouyang P, Method for manufacturing nanoscale macromolecular biocatalytic particles containing horseradish peroxidase, Patent No. CN1904042; CN 100469873