Publications by authors named "Jinxin Xu"

23 Publications

  • Page 1 of 1

Correspondence between DOM molecules and microbial community in a subtropical coastal estuary on a spatiotemporal scale.

Environ Int 2021 Apr 23;154:106558. Epub 2021 Apr 23.

State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China. Electronic address:

Dissolved organic matter (DOM) changes in quantity and quality over time and space, especially in highly dynamic coastal estuaries. Bacterioplankton usually display seasonal and spatial variations in abundance and composition in the coastal regions, and influence the DOM pool via assimilation, transformation and release of organic molecules. The change in DOM can also affect the composition of bacterial community. However, little is known on the correspondence between DOM molecules and bacterial composition, particularly through a systematic field survey. In this study, the spatiotemporal signatures of microbial communities and DOM composition in the subtropical coastal estuary of Xiamen are investigated over one and half years. The co-occurrence analysis between bacteria and DOM suggested microorganisms likely transformed the DOM from a relatively high (>400 Da) to a low (<400 Da) molecular weight, corresponding to an apparent increase in overall aromaticity. This might be the reason why microbial transformation renders "dark" organic matter visible in mass spectrometry due to more efficient ionization of microbial metabolites, as well as photodegradation processes. K- and r-strategists exhibited different correlations with two-size categories of DOM molecules owing to their different lifestyles and responses to environmental nutrient conditions. A comparison of the environmental variables and DOM composition with the microbial communities showed that the environmental/DOM variations played a more important role in shaping the microbial communities than vice versa. This study sheds light on the interactions between microbial populations and DOM molecules at the spatiotemporal scale, improving our understanding of microbial roles in marine biogeochemical cycles.
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http://dx.doi.org/10.1016/j.envint.2021.106558DOI Listing
April 2021

Structural studies reveal flexible roof of active site responsible for ω-transaminase CrmG overcoming by-product inhibition.

Commun Biol 2020 Aug 19;3(1):455. Epub 2020 Aug 19.

State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China.

Amine compounds biosynthesis using ω-transaminases has received considerable attention in the pharmaceutical industry. However, the application of ω-transaminases was hampered by the fundamental challenge of severe by-product inhibition. Here, we report that ω-transaminase CrmG from Actinoalloteichus cyanogriseus WH1-2216-6 is insensitive to inhibition from by-product α-ketoglutarate or pyruvate. Combined with structural and QM/MM studies, we establish the detailed catalytic mechanism for CrmG. Our structural and biochemical studies reveal that the roof of the active site in PMP-bound CrmG is flexible, which will facilitate the PMP or by-product to dissociate from PMP-bound CrmG. Our results also show that amino acceptor caerulomycin M (CRM M), but not α-ketoglutarate or pyruvate, can form strong interactions with the roof of the active site in PMP-bound CrmG. Based on our results, we propose that the flexible roof of the active site in PMP-bound CrmG may facilitate CrmG to overcome inhibition from the by-product.
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http://dx.doi.org/10.1038/s42003-020-01184-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7438487PMC
August 2020

Residue Asn21 acts as a switch for calcium binding to modulate the enzymatic activity of human phospholipase A2 group IIE.

Biochimie 2020 Sep 10;176:117-121. Epub 2020 Jul 10.

State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. Electronic address:

Secreted phospholipases A2 (sPLA2) group IIE (GIIE) is involved in several biological events, such as lipid metabolism and possibly inflammation that may mainly depend on its catalytic reaction. We previously showed that Asn21 is a critical residue that contributes to the enzymatic activity of hGIIE, but the underlying mechanism is still not clear. Here, combined with crystal structures and mutagenesis studies of the Asn21Gly mutant, we demonstrate that Asn21 acts as a switch responsible for the calcium binding and the catalytic efficiency. Our results of the atypical feature of calcium binding in hGIIE not only provide clues to understand the molecular basis of its enzymatic activity and physiological function, but also confer improved specificity for potential inhibitor design of sPLA2.
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http://dx.doi.org/10.1016/j.biochi.2020.07.003DOI Listing
September 2020

Molecular Basis for PI(3,5)P Recognition by SNX11, a Protein Involved in Lysosomal Degradation and Endosome Homeostasis Regulation.

J Mol Biol 2020 07 16;432(16):4750-4761. Epub 2020 Jun 16.

State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China. Electronic address:

Phosphatidylinositol 3,5-bisphosphate (PI(3,5)P) is an essential phosphoinositide required for endosome homeostasis and sorting for lysosomal degradation; however, the underlying mechanisms, especially in mammals, remain elusive or unexplored. Here we determined a structure of PI(3,5)P bound to Sorting Nexin 11 (SNX11) with an opened PPII-C loop. We also obtained an SNX11 structure with its PPII-C in "closed" form that serves as a potential PI3P-binding model. In addition, our results reveal that SNX11 can interact with the V1D subunit of vacuolar H-ATPase (V-ATPase), which provides a link between PI(3,5)P and human V-ATPase and further evidence for their roles in the endosome homeostasis regulation. Lastly, a new apo-form structure of SNX11, combined with molecular dynamics (MD) studies, indicates that the α5 helix can unfold from the PX domain of SNX11 when targeting the membrane or interacting with its partner. Taken together, these findings identify a novel PI(3,5)P effector, which will shed light on the PIs recognizing mechanism and the understanding of the downstream sorting events triggered by different PI binding.
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http://dx.doi.org/10.1016/j.jmb.2020.06.010DOI Listing
July 2020

The clinical significance of the intraoperative pathological examination of bilateral recurrent laryngeal nerve lymph nodes using frozen sections in cervical field lymph node dissection of thoracic esophageal squamous cell carcinoma.

J Thorac Dis 2019 Aug;11(8):3525-3533

Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou 350001, China.

Background: The aim of this study was to evaluate intraoperative pathological examination of the left and right recurrent laryngeal nerve lymph nodes (LNs) using frozen section as a predictor of cervical LN metastasis.

Methods: Retrospectively collected data from 69 patients with esophageal squamous cell carcinoma who had undergone intraoperative pathological examination of the left and right recurrent laryngeal nerve LNs using frozen sections and three-field LN dissection in the Fujian Medical University Union Hospital from December 2015 to April 2018, was used to explore the relationship between recurrent laryngeal nerve LN metastasis and cervical LN metastasis and to determine whether cervical-field LN dissection should be performed in patients with thoracic esophageal cancer.

Results: In the entire cohort, 15.9% (11/69) of patients had metastasis in the cervical LNs. We detected 1,195 cervical LN, with an average of 17.3 LN dissections per patient; 28 (2.3%) cases had LN metastasis. Patients with recurrent laryngeal nerve LN metastasis tended to have a high incidence of cervical LN metastasis (P=0.017). Multivariate analysis showed that left recurrent laryngeal nerve LN metastasis was the only independent risk factor for cervical LN metastasis (P=0.02). The incidence of postoperative pulmonary infection was 18.8% (13/69), chylothorax was 2.9% (2/69), anastomotic leakage was 2.9% (2/69), and hoarseness was 8.7% (6/69) for the entire cohort. There was no significant increase in complications compared with patients with 2-field LN dissection in our hospital during the same period. Additional studies are necessary to establish postoperative locoregional recurrence rates and long-term survival.

Conclusions: Intraoperative pathological examination of left recurrent laryngeal nerve LN using frozen sections has some prognostic value in predicting cervical LN metastasis and it can be an indicator for the selection of cervical-field dissection in thoracic esophageal carcinoma.
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http://dx.doi.org/10.21037/jtd.2019.07.59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753458PMC
August 2019

Effects of preoperative sarcopenia on postoperative complications of minimally invasive oesophagectomy for oesophageal squamous cell carcinoma.

J Thorac Dis 2019 Jun;11(6):2535-2545

Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou 350001, China.

Background: Sarcopenia is closely associated with surgical complications in patients with certain cancers. In this study we assessed the relationship between sarcopenia and postoperative complications in patients with oesophageal squamous cell carcinoma.

Methods: We retrospectively analysed of patients who underwent thoracoscopic combined with laparoscopic radical resection of oesophageal cancer. Preoperative computed tomography to evaluate skeletal muscle mass to diagnose sarcopenia and to evaluate associations with age, body mass index (BMI), lung function and postoperative complications.

Results: Among 141 patients, 73 presented with sarcopenia (sarcopenia group) and 68 did not (non-sarcopenia group). The mean skeletal muscle index in all patients was 49.5±9.0 cm/m; median, 49.3 cm/m. The sarcopenia group included a higher proportion of men (P=0.039) and had a lower BMI than the non-sarcopenia group (P=0.001). There were no significant differences in any other clinical and pathological features. The incidences of postoperative complications in the sarcopenia and non-sarcopenia groups were 63.0% and 36.8%, respectively (P=0.002). The incidences of pulmonary infections and postoperative pleural effusions were 28.8% 11.8% (P=0.011) and 38.4% 20.6% (P=0.020) in the sarcopenia and non-sarcopenia groups, respectively. The incidences of other complications were not significantly different between the two groups. Univariate and multivariate analyses of pulmonary infection-related clinical factors revealed that sarcopenia and forced expiratory volume in the first second as a percent of forced vital capacity (FEV1.0%) were independent risk factors for pulmonary infection after minimally invasive surgery.

Conclusions: Preoperative sarcopenia is an independent risk factor for pulmonary infection after minimally invasive oesophagectomy (MIE). Evaluation of preoperative sarcopenia will thus help to prevent postoperative complications.
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http://dx.doi.org/10.21037/jtd.2019.05.55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6626787PMC
June 2019

Discovery and Characterization of XY101, a Potent, Selective, and Orally Bioavailable RORγ Inverse Agonist for Treatment of Castration-Resistant Prostate Cancer.

J Med Chem 2019 05 22;62(9):4716-4730. Epub 2019 Apr 22.

Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences , Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences ; Guangzhou Medical University, Guangzhou 510530 , China.

We report the design, optimization, and biological evaluation of nuclear receptor RORγ inverse agonists as therapeutic agents for prostate cancer treatment. The most potent compound 27 (designated as XY101) exhibited cellular activity with an IC value of 30 nM in a cell-based reporter gene assay with good selectivity against other nuclear receptor subtypes. The cocrystal structure of 27 in complex with the RORγ ligand binding domain provided a solid structural basis for its antagonistic mechanism. 27 potently inhibited cell growth, colony formation, and the expression of AR, AR-V7, and PSA. 27 also exhibited good metabolic stability and a pharmacokinetic profile with oral bioavailability of 59% and a half-life of 7.3 h. Notably, 27 demonstrated promising therapeutic effects with significant tumor growth inhibition in a prostate cancer xenograft model in mice. The potent, selective, metabolically stable, and orally available RORγ inverse agonists represent a new class of compounds as potential therapeutics against prostate cancer.
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http://dx.doi.org/10.1021/acs.jmedchem.9b00327DOI Listing
May 2019

Ligand binding and heterodimerization with retinoid X receptor α (RXRα) induce farnesoid X receptor (FXR) conformational changes affecting coactivator binding.

J Biol Chem 2018 11 1;293(47):18180-18191. Epub 2018 Oct 1.

the State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China, and. Electronic address:

Nuclear receptor farnesoid X receptor (FXR) functions as the major bile acid sensor coordinating cholesterol metabolism, lipid homeostasis, and absorption of dietary fats and vitamins. Because of its central role in metabolism, FXR represents an important drug target to manage metabolic and other diseases, such as primary biliary cirrhosis and nonalcoholic steatohepatitis. FXR and nuclear receptor retinoid X receptor α (RXRα) form a heterodimer that controls the expression of numerous downstream genes. To date, the structural basis and functional consequences of the FXR/RXR heterodimer interaction have remained unclear. Herein, we present the crystal structures of the heterodimeric complex formed between the ligand-binding domains of human FXR and RXRα. We show that both FXR and RXR bind to the transcriptional coregulator steroid receptor coactivator 1 with higher affinity when they are part of the heterodimer complex than when they are in their respective monomeric states. Furthermore, structural comparisons of the FXR/RXRα heterodimers and the FXR monomers bound with different ligands indicated that both heterodimerization and ligand binding induce conformational changes in the C terminus of helix 11 in FXR that affect the stability of the coactivator binding surface and the coactivator binding in FXR. In summary, our findings shed light on the allosteric signal transduction in the FXR/RXR heterodimer, which may be utilized for future drug development targeting FXR.
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http://dx.doi.org/10.1074/jbc.RA118.004652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6254343PMC
November 2018

DDX24 Mutations Associated With Malformations of Major Vessels to the Viscera.

Hepatology 2019 02 6;69(2):803-816. Epub 2019 Jan 6.

Department of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University.

Vascular malformations present diagnostic and treatment challenges. In particular, malformations of vessels to the viscera are often diagnosed late or incorrectly due to the insidious onset and deep location of the disease. Therefore, a better knowledge of the genetic mutations underlying such diseases is needed. Here, we evaluated a four-generation family carrying vascular malformations of major vessels that affect multiple organs, which we named "multiorgan venous and lymphatic defect" (MOVLD) syndrome. Genetic analyses identified an association between a mutation in DEAD-box helicase 24 (DDX24), a gene for which the function is largely unknown, and MOVLD. Next, we screened 161 patients with sporadic vascular malformations of similar phenotype to our MOVLD family and found the same mutation or one of the two additional DDX24 mutations in 26 cases. Structural modeling revealed that two of the mutations are located within the adenosine triphosphate-binding domain of DDX24. Knockdown of DDX24 expression in endothelial cells resulted in elevated migration and tube formation. Transcriptomic analysis linked DDX24 to vascular system-related functions. Conclusion: Our results provide a link between DDX24 and vascular malformation and indicate a crucial role for DDX24 in endothelial cell functions; these findings create an opportunity for genetic diagnosis and therapeutic targeting of malformations of vessels to the viscera.
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http://dx.doi.org/10.1002/hep.30200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6590330PMC
February 2019

Structural basis for functional selectivity and ligand recognition revealed by crystal structures of human secreted phospholipase A group IIE.

Sci Rep 2017 09 7;7(1):10815. Epub 2017 Sep 7.

State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.

Secreted phospholipases As (sPLAs) are involved in various pathological conditions such as rheumatoid arthritis and cardiovascular disease. Many inhibitors were developed and studied in clinical trials, but none have reached the market yet. This failure may be attributed to the lack of subtype selectivity for these inhibitors. Therefore, more structural information for subtype sPLA is needed to guide the selective inhibitor development. In this study, the crystal structure of human sPLA Group IIE (hGIIE), coupled with mutagenesis experiments, proved that the flexible second calcium binding site and residue Asn21 in hGIIE are essential to its enzymatic activity. Five inhibitor bound hGIIE complex structures revealed the key residues (Asn21 and Gly6) of hGIIE that are responsible for interacting with inhibitors, and illustrated the difference in the inhibitor binding pocket with other sPLAs. This will facilitate the structure-based design of sPLA's selective inhibitors.
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http://dx.doi.org/10.1038/s41598-017-11219-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5589937PMC
September 2017

SNX16 Regulates the Recycling of E-Cadherin through a Unique Mechanism of Coordinated Membrane and Cargo Binding.

Structure 2017 08 14;25(8):1251-1263.e5. Epub 2017 Jul 14.

State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China. Electronic address:

E-Cadherin is a major component of adherens junctions on cell surfaces. SNX16 is a unique member of sorting nexins that contains a coiled-coil (CC) domain downstream of the PX domain. We report here that SNX16 regulates the recycling trafficking of E-cadherin. We solved the crystal structure of PX-CC unit of SNX16 and revealed a unique shear shaped homodimer. We identified a novel PI3P binding pocket in SNX16 that consists of both the PX and the CC domains. Surprisingly, we showed that the PPII/α2 loop, which is generally regarded as a membrane insertion loop in PX family proteins, is involved in the E-cadherin binding with SNX16. We then proposed a multivalent membrane binding model for SNX16. Our study postulates a new mechanism for coordinated membrane binding and cargo binding for SNX family proteins in general, and provide novel insights into recycling trafficking of E-cadherin.
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http://dx.doi.org/10.1016/j.str.2017.06.015DOI Listing
August 2017

Structure of the PX domain of SNX25 reveals a novel phospholipid recognition model by dimerization in the PX domain.

FEBS Lett 2017 07 11;591(13):2011-2018. Epub 2017 Jun 11.

State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, China.

SNX25, a regulator of GPCR signaling-phox-homology (PX) domain containing sorting nexin (SNX) member, has been proposed to be involved in the lysosomal degradation of the transforming growth factor β receptor and the development of temporal lobe epilepsy. Targeting to the endosomal membranes by the specific binding of phosphorylated phosphatidylinositols (PIPs) through the PX domain is critical for the function of SNXs. However, the mechanism for SNX25-PX targeting to the endosomes remains unclear. Here, we demonstrate that the PX domain of zebrafish SNX25 (zSNX25-PX) is capable of binding to PI3P only in its dimeric form. We also present the crystal structure of zSNX25-PX. Combined with biochemical experiments, we further identify a potential PI3P-binding region and propose a novel PI-binding model based on dimerization in the PX domain of SNXs.
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http://dx.doi.org/10.1002/1873-3468.12688DOI Listing
July 2017

Malassezia globosa MgMDL2 lipase: Crystal structure and rational modification of substrate specificity.

Biochem Biophys Res Commun 2017 06 20;488(2):259-265. Epub 2017 Apr 20.

School of Food Science and Engineering, South China University of Technology, Guangzhou, PR China. Electronic address:

Lipases play an important role in physiological metabolism and diseases, and also have multiple industrial applications. Rational modification of lipase specificity may increase the commercial utility of this group of enzymes, but is hindered by insufficient mechanistic understanding. Here, we report the 2.0 Å resolution crystal structure of a mono- and di-acylglycerols lipase from Malassezia globosa (MgMDL2). Interestingly, residues Phe278 and Glu282 were found to involve in substrate recognition because mutation on each residue led to convert MgMDL2 to a triacylglycerol (TAG) lipase. The Phe278Ala and Glu282Ala mutants also acquired ability to synthesize TAGs by esterification of glycerol and fatty acids. By in silicon analysis, steric hindrance of these residues seemed to be key factors for the altered substrate specificity. Our work may shed light on understanding the unique substrate selectivity mechanism of mono- and di-acylglycerols lipases, and provide a new insight for engineering biocatalysts with desired catalytic behaviors for biotechnological application.
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http://dx.doi.org/10.1016/j.bbrc.2017.04.103DOI Listing
June 2017

Structural insights into the binding mechanism of IDO1 with hydroxylamidine based inhibitor INCB14943.

Biochem Biophys Res Commun 2017 05 13;487(2):339-343. Epub 2017 Apr 13.

State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China. Electronic address:

IDO1 (indoleamine 2, 3-dioxygenase 1), a well characterized immunosuppressive enzyme, has attracted growing attention as a potential target for cancer immunotherapy. Hydroxylamidine compounds INCB024360 and INCB14943 (INCB024360 analogue) are highly effective IDO1 inhibitors. INCB024360 is undergoing clinical trials for treatment of various types of human cancer. Here, we determined the co-crystal structure of IDO1 and INCB14943, and elucidate the detailed binding mode. INCB14943 binds to heme iron in IDO1 protein through the oxime nitrogen. Further analysis also reveals that a halogen bonding interaction between the chlorine atom (3-Cl) of INCB14943 and the sulphur atom of C129 significantly improves the inhibition activity against IDO1. Comparing with the other reported inhibitors, the oxime nitrogen and halogen bond interaction are identified as the unique features of INCB14943 among the IDO1 inhibitors. Thus, our study provides novel insights into the interaction between a small molecule inhibitor INCB14943 and IDO1 protein. The structural information will facilitate future IDO1 inhibitor design.
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http://dx.doi.org/10.1016/j.bbrc.2017.04.061DOI Listing
May 2017

Bionic Vision-Based Intelligent Power Line Inspection System.

Comput Math Methods Med 2017 19;2017:4964287. Epub 2017 Jan 19.

Key Laboratory of Sensor Networks and Environmental Sensing, Hohai University, Changzhou 213022, China.

Detecting the threats of the external obstacles to the power lines can ensure the stability of the power system. Inspired by the attention mechanism and binocular vision of human visual system, an intelligent power line inspection system is presented in this paper. Human visual attention mechanism in this intelligent inspection system is used to detect and track power lines in image sequences according to the shape information of power lines, and the binocular visual model is used to calculate the 3D coordinate information of obstacles and power lines. In order to improve the real time and accuracy of the system, we propose a new matching strategy based on the traditional SURF algorithm. The experimental results show that the system is able to accurately locate the position of the obstacles around power lines automatically, and the designed power line inspection system is effective in complex backgrounds, and there are no missing detection instances under different conditions.
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http://dx.doi.org/10.1155/2017/4964287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288559PMC
April 2017

Absolute Position Sensing Based on a Robust Differential Capacitive Sensor with a Grounded Shield Window.

Sensors (Basel) 2016 05 11;16(5). Epub 2016 May 11.

School of Electrical Engineering and Automation, Harbin Institute of Technology, Harbin 150080, China.

A simple differential capacitive sensor is provided in this paper to measure the absolute positions of length measuring systems. By utilizing a shield window inside the differential capacitor, the measurement range and linearity range of the sensor can reach several millimeters. What is more interesting is that this differential capacitive sensor is only sensitive to one translational degree of freedom (DOF) movement, and immune to the vibration along the other two translational DOFs. In the experiment, we used a novel circuit based on an AC capacitance bridge to directly measure the differential capacitance value. The experimental result shows that this differential capacitive sensor has a sensitivity of 2 × 10(-4) pF/μm with 0.08 μm resolution. The measurement range of this differential capacitive sensor is 6 mm, and the linearity error are less than 0.01% over the whole absolute position measurement range.
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http://dx.doi.org/10.3390/s16050680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883371PMC
May 2016

Biochemical and Structural Insights into the Aminotransferase CrmG in Caerulomycin Biosynthesis.

ACS Chem Biol 2016 Apr 12;11(4):943-52. Epub 2016 Jan 12.

CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China.

Caerulomycin A (CRM A 1) belongs to a family of natural products containing a 2,2'-bipyridyl ring core structure and is currently under development as a potent novel immunosuppressive agent. Herein, we report the functional characterization, kinetic analysis, substrate specificity, and structure insights of an aminotransferase CrmG in 1 biosynthesis. The aminotransferase CrmG was confirmed to catalyze a key transamination reaction to convert an aldehyde group to an amino group in the 1 biosynthetic pathway, preferring l-glutamate and l-glutamine as the amino donor substrates. The crystal structures of CrmG in complex with the cofactor 5'-pyridoxal phosphate (PLP) or 5'-pyridoxamine phosphate (PMP) or the acceptor substrate were determined to adopt a canonical fold-type I of PLP-dependent enzymes with a unique small additional domain. The structure guided site-directed mutagenesis identified key amino acid residues for substrate binding and catalytic activities, thus providing insights into the transamination mechanism of CrmG.
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http://dx.doi.org/10.1021/acschembio.5b00984DOI Listing
April 2016

Structure of product-bound SMG1 lipase: active site gating implications.

FEBS J 2015 Dec 1;282(23):4538-47. Epub 2015 Oct 1.

School of Light Industry and Food Science, South China University of Technology, Guangzhou, China.

Monoacylglycerol and diacylglycerol lipases are industrially interesting enzymes, due to the health benefits that arise from the consumption of diglycerides compared to the traditional triglyceride oils. Most lipases possess an α-helix (lid) directly over the catalytic pocket which regulates the activity of the enzyme. Generally, lipases exist in active and inactive conformations, depending on the positioning of this lid subdomain. However, lipase SMG1, a monoacylglycerol and diacylglycerol specific lipase, has an atypical activation mechanism. In the present study we were able to prove by crystallography, in silico analysis and activity tests that only two positions, residues 102 and 278, are responsible for a gating mechanism that regulates the active and inactive states of the lipase, and that no significant structural changes take place during activation except for oxyanion hole formation. The elucidation of the gating effect provided data enabling the rational design of improved lipases with 6-fold increase in the hydrolytic activity toward diacylglycerols, just by providing additional substrate stabilization with a single mutation (F278N or F278T). Due to the conservation of F278 among the monoacylglycerol and diacylglycerol lipases in the Rhizomucor miehei lipase-like family, the gating mechanism described herein might represent a general mechanism applicable to other monoacylglycerol and diacylglycerol lipases as well. Database: Structural data are available in the Protein Data Bank under the accession numbers 4ZRE (F278D mutant) and 4ZRD (F278N mutant).
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http://dx.doi.org/10.1111/febs.13513DOI Listing
December 2015

Residue Asn277 affects the stability and substrate specificity of the SMG1 lipase from Malassezia globosa.

Int J Mol Sci 2015 Mar 31;16(4):7273-88. Epub 2015 Mar 31.

College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China.

Thermostability and substrate specificity are important characteristics of enzymes for industrial application, which can be improved by protein engineering. SMG1 lipase from Malassezia globosa is a mono- and diacylglycerol lipase (MDL) that shows activity toward mono- and diacylglycerols, but no activity toward triacylglycerols. SMG1 lipase is considered a potential biocatalyst applied in oil/fat modification and its crystal structure revealed that an interesting residue-Asn277 may contribute to stabilize loop 273-278 and the 3104 helix which are important to enzyme characterization. In this study, to explore its role in affecting the stability and catalytic activity, mutagenesis of N277 with Asp (D), Val (V), Leu (L) and Phe (F) was conducted. Circular dichroism (CD) spectral analysis and half-life measurement showed that the N277D mutant has better thermostability. The melting temperature and half-life of the N277D mutant were 56.6 °C and 187 min, respectively, while that was 54.6 °C and 121 min for SMG1 wild type (WT). Biochemical characterization of SMG1 mutants were carried out to test whether catalytic properties were affected by mutagenesis. N277D had similar enzymatic properties as SMG1 WT, but N277F showed a different substrate selectivity profile as compared to other SMG1 mutants. Analysis of the SMG1 3D model suggested that N277D formed a salt bridge via its negative charged carboxyl group with a positively charged guanidino group of R227, which might contribute to confer N277D higher temperature stability. These findings not only provide some clues to understand the molecular basis of the lipase structure/function relationship but also lay the framework for engineering suitable MDL lipases for industrial applications.
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http://dx.doi.org/10.3390/ijms16047273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425016PMC
March 2015

[Expression, purification and phosphoinositide binding specifity of recombinant human SNX7 expressed in Escherichia coli].

Sheng Wu Gong Cheng Xue Bao 2014 Sep;30(9):1436-45

Sorting nexins (SNXs) are a large group of proteins that contain Phox (PX) domain and involve in regulating endocytosis and endosome sorting. SNX7, a member of SNXs family, contains a PX domain and a BAR domain. In zebrafish, SNX7 is a liver-enriched anti-apoptotic protein and indispensible for the liver development. A fragment of SNX7 cDNA ((px-bar)snx7), encoding the PX domain and the BAR domain, was inserted into the expressing vector p28a, transformed into E. coli Rosseta 2 (DE3), and then induced by isopropyl β-D-1-Thiogalactopyranoside (IPTG). After affinity, ion exchange and gel filtration purification, the purity of (PX-BAR)SNX7 reached over 95%. Dynamic light scattering (DLS) experiment indicated that (PX-BAR)SNX7 was homogeneous in solution. Lipid overlay assay showed that (PX-BAR)SNX7 can bind to PtdIns(5)P, PtdIns(4,5)P2 and PtdIns(3,4,5)P3.
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September 2014

Structure of human SNX10 reveals insights into its role in human autosomal recessive osteopetrosis.

Proteins 2014 Dec 1;82(12):3483-9. Epub 2014 Oct 1.

State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.

Sorting nexin 10 (SNX10), the unique member of the SNX family having vacuolation activity in cells, was shown to be involved in the development of autosomal recessive osteopetrosis (ARO) in recent genetic studies. However, the molecular mechanism of the disease-related mutations affecting the biological function of SNX10 is unclear. Here, we report the crystal structure of human SNX10 to 2.6 Å resolution. The structure reveals that SNX10 contains the extended phox-homology domain we previously proposed. Our study provides the structural details of those disease-related mutations. Combined with the vacuolation study of those mutations, we found that Tyr32 and Arg51 are important for the protein stability and both play a critical role in vacuolation activity, while Arg16Leu may affect the function of SNX10 in osteoclast through protein-protein interactions.
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http://dx.doi.org/10.1002/prot.24689DOI Listing
December 2014

Structure of sorting nexin 11 (SNX11) reveals a novel extended phox homology (PX) domain critical for inhibition of SNX10-induced vacuolation.

J Biol Chem 2013 Jun 24;288(23):16598-16605. Epub 2013 Apr 24.

State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530; School of Life Sciences, University of Science and Technology of China, Hefei 230026. Electronic address:

Sorting nexins are phox homology (PX) domain-containing proteins involved in diverse intracellular endosomal trafficking pathways. The PX domain binds to certain phosphatidylinositols and is recruited to vesicles rich in these lipids. The structure of the PX domain is highly conserved, containing a three-stranded β-sheet, followed by three α-helices. Here, we report the crystal structures of truncated human SNX11 (sorting nexin 11). The structures reveal that SNX11 contains a novel PX domain, hereby named the extended PX (PXe) domain, with two additional α-helices at the C terminus. We demonstrate that these α-helices are indispensible for the in vitro functions of SNX11. We propose that this PXe domain is present in SNX10 and is responsible for the vacuolation activity of SNX10. Thus, this novel PXe domain constitutes a structurally and functionally important PX domain subfamily.
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http://dx.doi.org/10.1074/jbc.M112.449306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675595PMC
June 2013

Crystal structure of a mono- and diacylglycerol lipase from Malassezia globosa reveals a novel lid conformation and insights into the substrate specificity.

J Struct Biol 2012 Jun 29;178(3):363-9. Epub 2012 Mar 29.

School of Life Sciences, University of Science and Technology of China, Hefei 230026, People's Republic of China.

Most lipases contain a lid domain to shield the hydrophobic binding site from the water environment. The lid, mostly in helical form, can undergo a conformational change to expose the active cleft during the interfacial activation. Here we report the crystal structures of Malassezia globosa LIP1 (SMG1) at 1.45 and 2.60 Å resolution in two crystal forms. The structures present SMG1 in its closed form, with a novel lid in loop conformation. SMG1 is one of the few members in the fungal lipase family that has been found to be strictly specific for mono- and diacylglycerol. To date, the mechanism for this substrate specificity remains largely unknown. To investigate the substrate binding properties, we built a model of SMG1 in open conformation. Based on this model, we found that the two bulky hydrophobic residues adjacent to the catalytic site and the N-terminal hinge region of the lid both may act as steric hindrances for triacylglycerols binding. These unique structural features of SMG1 will provide a better understanding on the substrate specificity of mono- and diacylglycerol lipases and a platform for further functional study of this enzyme.
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http://dx.doi.org/10.1016/j.jsb.2012.03.006DOI Listing
June 2012