Publications by authors named "Zhiliang Gong"

5 Publications

  • Page 1 of 1

Gene Diversity of Quinoprotein Glucose Dehydrogenase in the Sediment of Sancha Lake and Its Response to the Environment.

Int J Environ Res Public Health 2018 12 20;16(1). Epub 2018 Dec 20.

State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu 610059, China.

Quinoprotein glucose dehydrogenase (GDH) is the most important enzyme of inorganic phosphorus-dissolving metabolism, catalyzing the oxidation of glucose to gluconic acid. The insoluble phosphate in the sediment is converted into soluble phosphate, facilitating mass reproduction of algae. Therefore, studying the diversity of genes which encode GDH is beneficial to reveal the microbial group that has a significant influence on the eutrophication of water. Taking the eutrophic Sancha Lake sediments as the research object, we acquired samples from six sites in the spring and autumn. A total of 219,778 high-quality sequences were obtained by DNA extraction of microbial groups in sediments, PCR amplification of the gene, and high-throughput sequencing. Six phyla, nine classes, 15 orders, 29 families, 46 genera, and 610 operational taxonomic units (OTUs) were determined, suggesting the high genetic diversity of . genes came mainly from the genera of (1.63⁻77.99%), (0.13⁻56.95%), (0.32⁻25.49%), and (0.16⁻11.88%) in the phylum of Proteobacteria (25.10⁻98.85%). The abundance of these dominant -harboring bacteria was higher in the spring than in autumn, suggesting that they have an important effect on the eutrophication of the Sancha Lake. The alpha and beta diversity of genes presented spatial and temporal differences due to different sampling site types and sampling seasons. Pearson correlation analysis and canonical correlation analysis (CCA) showed that the diversity and abundance of genes were significantly correlated with environmental factors such as dissolved oxygen (DO), phosphorus hydrochloride (HCl⁻P), and dissolved total phosphorus (DTP). OTU composition was significantly correlated with DO, total organic carbon (TOC), and DTP. GDH encoded by genes transformed insoluble phosphate into dissolved phosphate, resulting in the eutrophication of Sancha Lake. The results suggest that genes encoding GDH may play an important role in lake eutrophication.
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http://dx.doi.org/10.3390/ijerph16010001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339069PMC
December 2018

Sensitivity of peripheral membrane proteins to the membrane context: A case study of phosphatidylserine and the TIM proteins.

Biochim Biophys Acta Biomembr 2018 10 18;1860(10):2126-2133. Epub 2018 Jun 18.

Program in Biophysical Sciences, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, United States of America; Department of Chemistry, The University of Chicago, Chicago, IL, United States of America; James Franck Institute, The University of Chicago, Chicago, IL, United States of America. Electronic address:

There is a diverse class of peripheral membrane-binding proteins that specifically bind phosphatidylserine (PS), a lipid that signals apoptosis or cell fusion depending on the membrane context of its presentation. PS-receptors are specialized for particular PS-presenting pathways, indicating that they might be sensitive to the membrane context. In this review, we describe a combination of thermodynamic, structural, and computational techniques that can be used to investigate the mechanisms underlying this sensitivity. As an example, we focus on three PS-receptors of the T-cell Immunoglobulin and Mucin containing (TIM) protein family, which we have previously shown to differ in their sensitivity to PS surface density.
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http://dx.doi.org/10.1016/j.bbamem.2018.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6290684PMC
October 2018

Coupling X-Ray Reflectivity and In Silico Binding to Yield Dynamics of Membrane Recognition by Tim1.

Biophys J 2017 Oct;113(7):1505-1519

Program in Biophysical Sciences, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois; Department of Chemistry, The University of Chicago, Chicago, Illinois; James Franck Institute, The University of Chicago, Chicago, Illinois. Electronic address:

The dynamic nature of lipid membranes presents significant challenges with respect to understanding the molecular basis of protein/membrane interactions. Consequently, there is relatively little known about the structural mechanisms by which membrane-binding proteins might distinguish subtle variations in lipid membrane composition and/or structure. We have previously developed a multidisciplinary approach that combines molecular dynamics simulation with interfacial x-ray scattering experiments to produce an atomistic model for phosphatidylserine recognition by the immune receptor Tim4. However, this approach requires a previously determined protein crystal structure in a membrane-bound conformation. Tim1, a Tim4 homolog with distinct differences in both immunological function and sensitivity to membrane composition, was crystalized in a closed-loop conformation that is unlikely to support membrane binding. Here we have used a previously described highly mobile membrane mimetic membrane in combination with a conventional lipid bilayer model to generate a membrane-bound configuration of Tim1 in silico. This refined structure provided a significantly improved fit of experimental x-ray reflectivity data. Moreover, the coupling of the x-ray reflectivity analysis with both highly mobile membrane mimetic membranes and conventional lipid bilayer molecular dynamics simulations yielded a dynamic model of phosphatidylserine membrane recognition by Tim1 with atomic-level detail. In addition to providing, to our knowledge, new insights into the molecular mechanisms that distinguish the various Tim receptors, these results demonstrate that in silico membrane-binding simulations can remove the requirement that the existing crystal structure be in the membrane-bound conformation for effective x-ray reflectivity analysis. Consequently, this refined methodology has the potential for much broader applicability with respect to defining the atomistic details of membrane-binding proteins.
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http://dx.doi.org/10.1016/j.bpj.2017.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627149PMC
October 2017

Quantitative analysis of total reflection X-ray fluorescence from finely layered structures using XeRay.

Rev Sci Instrum 2017 Mar;88(3):033112

James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.

Total reflection x-ray fluorescence (TXRF) is a widely applicable experimental technique for studying chemical element distributions across finely layered structures at extremely high sensitivity. To promote and facilitate scientific discovery using TXRF, we developed a MATLAB-based software package with a graphical user interface, named XeRay, for quick, accurate, and intuitive data analysis. XeRay lets the user model any layered system, each layer with its independent chemical composition and thickness, and enables fine-tuned data fitting. The accuracy of XeRay has been tested in the analysis of TXRF data from both air/liquid interface and liquid/liquid interfacial studies and has been compared to literature results. In an air/liquid interface study, Ca sequestration was measured at a Langmuir monolayer of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidic acid (SOPA) on a buffer solution of 1 mM CaCl at pH 7.5. Data analysis with XeRay reveals that each 1 nm of interfacial area contains 2.38 ± 0.06 Ca ions, which corresponds to a 1:1 ratio between SOPA headgroups and Ca ions, consistent with several earlier reports. For the liquid/liquid interface study of Sr enrichment at the dodecane/surfactant/water interface, analysis using XeRay gives a surface enrichment of Sr at 68 Å per ion, consistent with the result published for the same dataset.
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http://dx.doi.org/10.1063/1.4978654DOI Listing
March 2017

Molecular mechanism for differential recognition of membrane phosphatidylserine by the immune regulatory receptor Tim4.

Proc Natl Acad Sci U S A 2014 Apr 31;111(15):E1463-72. Epub 2014 Mar 31.

Program in Biophysical Sciences, Institute for Biophysical Dynamics, Department of Chemistry, and James Franck Institute, The University of Chicago, Chicago, IL 60637.

Recognition of phosphatidylserine (PS) lipids exposed on the extracellular leaflet of plasma membranes is implicated in both apoptotic cell removal and immune regulation. The PS receptor T cell immunoglobulin and mucin-domain-containing molecule 4 (Tim4) regulates T-cell immunity via phagocytosis of both apoptotic (high PS exposure) and nonapoptotic (intermediate PS exposure) activated T cells. The latter population must be removed at lower efficiency to sensitively control immune tolerance and memory cell population size, but the molecular basis for how Tim4 achieves this sensitivity is unknown. Using a combination of interfacial X-ray scattering, molecular dynamics simulations, and membrane binding assays, we demonstrate how Tim4 recognizes PS in the context of a lipid bilayer. Our data reveal that in addition to the known Ca(2+)-coordinated, single-PS binding pocket, Tim4 has four weaker sites of potential ionic interactions with PS lipids. This organization makes Tim4 sensitive to PS surface concentration in a manner capable of supporting differential recognition on the basis of PS exposure level. The structurally homologous, but functionally distinct, Tim1 and Tim3 are significantly less sensitive to PS surface density, likely reflecting the differences in immunological function between the Tim proteins. These results establish the potential for lipid membrane parameters, such as PS surface density, to play a critical role in facilitating selective recognition of PS-exposing cells. Furthermore, our multidisciplinary approach overcomes the difficulties associated with characterizing dynamic protein/membrane systems to reveal the molecular mechanisms underlying Tim4's recognition properties, and thereby provides an approach capable of providing atomic-level detail to uncover the nuances of protein/membrane interactions.
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http://dx.doi.org/10.1073/pnas.1320174111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992656PMC
April 2014