Xuemei Li

Chinese Academy of Sciences, Peping, Beijing, China

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Publications (83)377.21 Total impact

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    ABSTRACT: Aimsa study was conducted to compare the intestinal microbial compositions of two fish species with similar feeding strategy; paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond.Methods and Resultsage-0 paddlefish and bighead carp with mean average body lengths of 43.39±2.78 cm and 19.33± 3.68 cm, respectively were reared with natural prey items in the same pond (20 m2). After 30-days of rearing the intestinal microbiota of the two fish species were assessed by pyrosequencing of 16S rRNA genes. Interestingly, deviations were observed in the microbial communities of the two fish species according to the alpha- and beta-diversity measurements and detrended correspondence analysis (DCA). Shannon diversity (P=0.015) and Pielou.evenness (P=0.035) revealed significant lower diversity of the intestinal microbiota of paddlefish. Moreover, different core intestinal microbiota was noticed in the two fish species. Proteobacteria (57.3%), Firmicutes (11.9%), Fusobacteria (8.9%), Planctomycetes (7.3%), Actinobacteria (6.0%) and Verrucomicrobia (3.2%) were detected in bighead carp, while the dominant phyla in paddlefish intestines were Bacteroidetes (37.0%), Fusobacteria (35.1%), Firmicutes (14.8%) and Proteobacteria (12.6%).Conclusionsour results revealed that the intestinal microbiota differed between paddlefish and bighead carp reared in the same pond when fed similar nature food. The potential host factors, such as the genetic background, gut histology and physiology are assumed to be involved in the intestinal bacterial compositions.Significance and Impact of the Studyconsidering the similar feeding strategy of paddlefish and bighead carp, the present study presents basic knowledge for evaluation of the importance of host factors (genetic background and gut anatomy) on intestinal microbial composition.This article is protected by copyright. All rights reserved.
    Journal of Applied Microbiology 08/2014; · 2.20 Impact Factor
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    ABSTRACT: Unlike the well-established picture for the entry of enveloped viruses, the mechanism of cellular entry of non-enveloped eukaryotic viruses remains largely mysterious. Picornaviruses are representative models for such viruses, and initiate this entry process by their functional receptors. Here we present the structural and functional studies of SCARB2, a functional receptor of the important human enterovirus 71 (EV71). SCARB2 is responsible for attachment as well as uncoating of EV71. Differences in the structures of SCARB2 under neutral and acidic conditions reveal that SCARB2 undergoes a pivotal pH-dependent conformational change which opens a lipid-transfer tunnel to mediate the expulsion of a hydrophobic pocket factor from the virion, a pre-requisite for uncoating. We have also identified the key residues essential for attachment to SCARB2, identifying the canyon region of EV71 as mediating the receptor interaction. Together these results provide a clear understanding of cellular attachment and initiation of uncoating for enteroviruses.
    Protein & Cell 07/2014; · 3.22 Impact Factor
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    ABSTRACT: The prokaryotic 5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) catalyzes the irreversible cleavage of the glycosidic bond in 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH), a process that plays a key role in several metabolic pathways. Its absence in all mammalian species has implicated this enzyme as a promising target for antimicrobial drug design. Here, we report the crystal structure of BmMTAN in complex with its product adenine at a resolution of 2.6 Å determined by single-wavelength anomalous dispersion method. 11 key residues were mutated for kinetic characterization. Mutations of Tyr134 and Met144 resulted in the largest overall increase in Km, whereas mutagenesis of residues Glu18, Glu145 and Asp168 completely abolished activity. Glu145 and Asp168 were identified as active site residues essential for catalysis. The catalytic mechanism and implications of this structure for broad-based antibiotic design are discussed.
    Biochemical and Biophysical Research Communications 03/2014; · 2.41 Impact Factor
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    ABSTRACT: Enterovirus 71 (HEV71) epidemics in children and infants result mainly in mild symptoms; however, especially in the Asia-Pacific region, infection can be fatal. At present, no therapies are available. We have used structural analysis of the complete virus to guide the design of HEV71 inhibitors. Analysis of complexes with four 3-(4-pyridyl)-2-imidazolidinone derivatives with varying anti-HEV71 activities pinpointed key structure-activity correlates. We then identified additional potentially beneficial substitutions, developed methods to reliably triage compounds by quantum mechanics-enhanced ligand docking and synthesized two candidates. Structural analysis and in vitro assays confirmed the predicted binding modes and their ability to block viral infection. One ligand (with IC50 of 25 pM) is an order of magnitude more potent than the best previously reported inhibitor and is also more soluble. Our approach may be useful in the design of effective drugs for enterovirus infections.
    Nature Structural & Molecular Biology 02/2014; · 11.90 Impact Factor
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    ABSTRACT: GPCR proteins represent the largest family of signaling membrane proteins in eukaryotic cells. Their importance to basic cell biology, human diseases, and pharmaceutical interventions is well established. Many crystal structures of GPCR proteins have been reported in both active and inactive conformations. These data indicate that agonist binding alone is not sufficient to trigger the conformational change of GPCRs necessary for binding of downstream G-proteins, yet other essential factors remain elusive. Based on analysis of available GPCR crystal structures, we identified a potential conformational switch around the conserved Asp2.50, which consistently shows distinct conformations between inactive and active states. Combining the structural information with the current literature, we propose an energy-coupling mechanism, in which the interaction between a charge change of the GPCR protein and the membrane potential of the living cell plays a key role for GPCR activation.
    Protein & Cell 09/2013; · 3.22 Impact Factor
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    ABSTRACT: Coxsackievirus A16 belongs to the family Picornaviridae, and is a major agent of hand-foot-and-mouth disease that infects mostly children, and to date no vaccines or antiviral therapies are available. 2A protease of enterovirus is a nonstructural protein and possesses both self-cleavage activity and the ability to cleave the eukaryotic translation initiation factor 4G. Here we present the crystal structure of coxsackievirus A16 2A protease, which interestingly forms hexamers in crystal as well as in solution. This structure shows an open conformation, with its active site accessible, ready for substrate binding and cleavage activity. In conjunction with a previously reported "closed" state structure of human rhinovirus 2, we were able to develop a detailed hypothesis for the conformational conversion triggered by two "switcher" residues Glu88 and Tyr89 located within the bll2-cII loop. Substrate recognition assays revealed that amino acid residues P1', P2 and P4 are essential for substrate specificity, which was verified by our substrate binding model. In addition, we compared the in vitro cleavage efficiency of 2A proteases from coxsackievirus A16 and enterovirus 71 upon the same substrates by fluorescence resonance energy transfer (FRET), and observed higher protease activity of enterovirus 71 compared to that of coxsackievirus A16. In conclusion, our study shows an open conformation of coxsackievirus A16 2A protease and the underlying mechanisms for conformational conversion and substrate specificity. These new insights should facilitate the future rational design of efficient 2A protease inhibitors.
    Protein & Cell 09/2013; · 3.22 Impact Factor
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    ABSTRACT: Disulfide bond-forming (Dsb) protein is a bacterial periplasmic protein that is essential for the correct folding and disulfide bond formation of secreted or cell wallassociated proteins. DsbA introduces disulfide bonds into folding proteins, and is re-oxidized through interaction with its redox partner DsbB. Mycobacterium tuberculosis, a Gram-positive bacterium, expresses a DsbA-like protein ( Rv2969c), an extracellular protein that has its Nterminus anchored in the cell membrane. Since Rv2969c is an essential gene, crucial for disulfide bond formation, research of DsbA may provide a target of a new class of anti-bacterial drugs for treatment of M.tuberculosis infection. In the present work, the crystal structures of the extracellular region of Rv2969c (Mtb DsbA) were determined in both its reduced and oxidized states. The overall structure of Mtb DsbA can be divided into two domains: a classical thioredoxin-like domain with a typical CXXC active site, and an α-helical domain. It largely resembles its Escherichia coli homologue EcDsbA, however, it possesses a truncated binding groove; in addition, its active site is surrounded by an acidic, rather than hydrophobic surface. In our oxidoreductase activity assay, Mtb DsbA exhibited a different substrate specificity when compared to EcDsbA. Moreover, structural analysis revealed a second disulfide bond in Mtb DsbA, which is rare in the previously reported DsbA structures, and is assumed to contribute to the overall stability of Mtb DsbA. To investigate the disulphide formation pathway in M.tuberculosis, we modeled Mtb Vitamin K epoxide reductase (Mtb VKOR), a binding partner of Mtb DsbA, to Mtb DsbA.
    Protein & Cell 07/2013; · 3.22 Impact Factor
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    ABSTRACT: It remains largely mysterious how the genomes of non-enveloped eukaryotic viruses are transferred across a membrane into the host cell. Picornaviruses are simple models for such viruses, and initiate this uncoating process through particle expansion, which reveals channels through which internal capsid proteins and the viral genome presumably exit the particle, although this has not been clearly seen until now. Here we present the atomic structure of an uncoating intermediate for the major human picornavirus pathogen CAV16, which reveals VP1 partly extruded from the capsid, poised to embed in the host membrane. Together with previous low-resolution results, we are able to propose a detailed hypothesis for the ordered egress of the internal proteins, using two distinct sets of channels through the capsid, and suggest a structural link to the condensed RNA within the particle, which may be involved in triggering RNA release.
    Nature Communications 06/2013; 4:1929. · 10.02 Impact Factor
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    ABSTRACT: Gut microbiota has shown tight and coordinated connection with various functions of its host such as metabolism, immunity, energy utilization, and health maintenance. To gain insight into whether gut microbes affect the metabolism of fish, we employed fast-growing transgenic common carp (Cyprinus carpio L.) to study the connections between its large body feature and gut microbes. Metagenome-based fingerprinting and high-throughput sequencing on bacterial 16S rRNA genes indicated that fish gut was dominated by Proteobacteria, Fusobacteria, Bacteroidetes and Firmicutes, which displayed significant differences between transgenic fish and wild-type controls. Analyses to study the association of gut microbes with the fish metabolism discovered three major phyla having significant relationships with the host metabolic factors. Biochemical and histological analyses indicated transgenic fish had increased carbohydrate but decreased lipid metabolisms. Additionally, transgenic fish has a significantly lower Bacteroidetes:Firmicutes ratio than that of wild-type controls, which is similar to mammals between obese and lean individuals. These findings suggest that gut microbiotas are associated with the growth of fast growing transgenic fish, and the relative abundance of Firmicutes over Bacteroidetes could be one of the factors contributing to its fast growth. Since the large body size of transgenic fish displays a proportional body growth, which is unlike obesity in human, the results together with the findings from others also suggest that the link between obesity and gut microbiota is likely more complex than a simple Bacteroidetes:Firmicutes ratio change.
    PLoS ONE 01/2013; 8(5):e64577. · 3.73 Impact Factor
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    ABSTRACT: One group of Bcl-2 protein family, which shares only the BH3 domain (BH3-only), is critically involved in the regulation of programmed cell death. Herein we demonstrated a novel human BH3-only protein (designated as Bop) which could induce apoptosis in a BH3 domain-dependent manner. Further analysis indicated that Bop mainly localized to mitochondria and used its BH3 domain to contact the loop regions of voltage dependent anion channel 1 (VDAC1) in the outer mitochondrial membrane. In addition, purified Bop protein induced the loss of mitochondrial transmembrane potential (Δψm) and the release of cytochrome c. Furthermore, Bop used its BH3 domain to contact pro-survival Bcl-2 family members (Bcl-2, Bcl-X(L), Mcl-1, A1 and Bcl-w), which could inhibit Bop-induced apoptosis. Bop would be constrained by pro-survival Bcl-2 proteins in resting cells, because Bop became released from phosphorylated Bcl-2 induced by microtubule-interfering agent like vincristine (VCR). Indeed, knockdown experiments indicated that Bop was partially required for VCR induced cell death. Finally, Bop might need to function through Bak and Bax, likely by releasing Bak from Bcl-X(L) sequestration. In conclusion, Bop may be a novel BH3-only factor that can engage with the regulatory network of Bcl-2 family members to process intrinsic apoptotic signaling.
    Protein & Cell 10/2012; 3(10):790-801. · 3.22 Impact Factor
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    ABSTRACT: MCP-1-induced protein 1 (MCPIP1) plays an important role in the downregulation of the LPS-induced immune response by acting as an RNase targeting IL-6 and IL-12b mRNAs. A conserved domain located in the N-terminal part of MCPIP1 is thought to be responsible for its RNase activity, but its catalytic mechanism is not well understood due to the lack of an atomic resolution structure. We determined the 3D crystal structure of this MCPIP1 N-terminal conserved RNase domain at a resolution of 2.0 Å. The overall structure of MCPIP1 N-terminal conserved domain shares high structural homology with PilT N-terminal domain. We show that the RNase catalytic center is composed of several acidic residues, verifying their importance by site-specific mutagenesis. A positively charged arm close to the catalytic center may act as an RNA substrate-binding site, since exchange of critical positively charged residues on this arm with alanine partially abolish the RNase activity of MCPIP1 in vivo. Our structure of the MCPIP1 N-terminal conserved domain reveals the details of the catalytic center and provides a greater understanding of the RNA degradation mechanism.
    Nucleic Acids Research 05/2012; 40(14):6957-65. · 8.28 Impact Factor
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    Protein & Cell 03/2012; 3(3):239. · 3.22 Impact Factor
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    ABSTRACT: We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized using rank-abundance plots fitted with linear regression models. Results showed that the intestinal bacterial evenness was significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal eukaryotic microorganisms were almost identical.
    The Journal of Microbiology 02/2012; 50(1):29-37. · 1.28 Impact Factor
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    ABSTRACT: The human Gadd45 protein family plays critical roles in DNA repair, negative growth control, genomic stability, cell cycle checkpoints and apoptosis. Here we report the crystal structure of human Gadd45γ [corrected], revealing a unique dimer formed via a bundle of four parallel helices, involving the most conserved residues among the Gadd45 isoforms. Mutational analysis of human Gadd45γ [corrected] identified a conserved, highly acidic patch in the central region of the dimer for interaction with the proliferating cell nuclear antigen (PCNA), p21 and cdc2, suggesting that the parallel dimer is the active form for the interaction. Cellular assays indicate that: (1) dimerization of Gadd45γ [corrected] is necessary for apoptosis as well as growth inhibition, and that cell growth inhibition is caused by both cell cycle arrest and apoptosis; (2) a conserved and highly acidic patch on the dimer surface, including the important residues Glu87 and Asp89, is a putative interface for binding proteins related to the cell cycle, DNA repair and apoptosis. These results reveal the mechanism of self-association by Gadd45 proteins and the importance of this self-association for their biological function.
    Protein & Cell 10/2011; 2(10):814-26. · 3.22 Impact Factor
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    ABSTRACT: The aspartate kinase (AK) from Mycobacterium tuberculosis (Mtb) catalyzes the biosynthesis of aspartate family amino acids, including lysine, threonine, isoleucine and methionine. We determined the crystal structures of the regulatory subunit of aspartate kinase from Mtb alone (referred to as MtbAKβ) and in complex with threonine (referred to as MtbAKβ-Thr) at resolutions of 2.6 Å and 2.0 Å, respectively. MtbAKβ is composed of two perpendicular non-equivalent ACT domains [aspartate kinase, chorismate mutase, and TyrA (prephenate dehydrogenase)] per monomer. Each ACT domain contains two α helices and four antiparallel β strands. The structure of MtbAKβ shares high similarity with the regulatory subunit of the aspartate kinase from Corynebacterium glutamicum (referred to as CgAKβ), suggesting similar regulatory mechanisms. Biochemical assays in our study showed that MtbAK is inhibited by threonine. Based on crystal structure analysis, we discuss the regulatory mechanism of MtbAK.
    Protein & Cell 09/2011; 2(9):745-54. · 3.22 Impact Factor
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    ABSTRACT: To evaluate the detection of IgM and IgG antibodies to Orientia tsutsugamushi (O. tsutsugamushi) by rapid diagnostic test (RDT) and microimmunofluorescence assay (mIFA). RDT using a mixture of recombinant 56-kDa proteins of O. tsutsugamushi and mIFA assay were performed on 20 patients from Fujian and 13 patients from Yunnan Province, and 82 sera samples from healthy farmers in Anhui Province and Beijing City in 2009. Comparison of the RDT and mIFA assay was performed by using X(2) test and the P level of <0.05 was considered to be significance. Among these 82 normal sera samples, the specificity of RDT was 100% for both IgM and IgG tests. In 33 samples from patients with scrub typhus, 5 cases were positively detected earlier by RDT than by mIFA in IgM test, and 2 cases were positive in IgG test. Sensitivities of RDT were 93.9% and 90.9% for IgM and IgG, respectively. The sensitivity of combination test of IgM and IgG was 100%. Geometric mean titer diluted sera from confirmed cases by IFA and RDT assay were 1:37 vs. 1:113 (P<0.001) in IgM test and 1:99 vs. 1:279 (P<0.05) in IgG test. RDT is more sensitivite than mIFA in the early diagnosis of scrub typhus and it is particularly applicable in rural areas.
    Asian Pacific Journal of Tropical Medicine 08/2011; 4(8):666-8. · 0.50 Impact Factor
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    ABSTRACT: A 16S rDNA-based polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method was applied to detect intestinal bacterial communities of juvenile allogynogenetic crucian carp, Carassius auratus gibelio, fed with chitosan-containing diet. This is the first time to use the molecular method to analyze the bacterial communities in the allogynogenetic crucian carp intestine. The DGGE profile with universal bacterial primers revealed simple communities in all treatment groups. Sequencing and phylogenetic analysis of excised DGGE bands showed that the dominant bacteria belonged to class γ-Proteobacteria and Fusobacteria. The relative abundance and diversity of detected bacteria suggested that 0.5 and 0.75% of chitosan in diet were optimum for juvenile allogynogenetic crucian carp. As in these concentrations, some detected pathogen bacteria either disappeared or decreased. However, the DGGE profile with Aeromonas-specific primers showed a similar composition among all treatment groups, which suggested that Aeromonas was one of relative stable bacteria components in the intestine of juvenile allogynogenetic crucian carp.
    Journal of the World Aquaculture Society 08/2011; 42(4). · 0.75 Impact Factor
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    ABSTRACT: SARS coronavirus (SARS-CoV) is the aetiological agent of the highly infectious severe acute respiratory syndrome (SARS). To gain a better understanding of SARS-CoV replication and transcription proteins, a preliminary X-ray crystallographic study of the C-terminal domain of SARS-CoV nonstructural protein 2 (nsp2) is reported here. The C-terminal domain of SARS-CoV nsp2 was cloned, overexpressed, purified and crystallized using polyethylene glycol 5000 monomethyl ether as the precipitant; the crystals diffracted to 2.5 Å resolution. The crystals belonged to space group P6(5), with unit-cell parameters a=b=112.8, c=91.1 Å, α=β=90, γ=120°. One molecule is assumed to be present per asymmetric unit, which gives a Matthews coefficient of 2.89 Å3 Da(-1) and a solvent content of 56.2%.
    Acta Crystallographica Section F Structural Biology and Crystallization Communications 07/2011; 67(Pt 7):790-3. · 0.55 Impact Factor
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    ABSTRACT: Noroviruses, an important cause of acute gastroenteritis in humans, recognize the histo-blood group antigens (HBGAs) as host susceptible factors in a strain-specific manner. The crystal structures of the HBGA-binding interfaces of two A/B/H-binding noroviruses, the prototype Norwalk virus (GI.1) and a predominant GII.4 strain (VA387), have been elucidated. In this study we determined the crystal structures of the P domain protein of the first Lewis-binding norovirus (VA207, GII.9) that has a distinct binding property from those of Norwalk virus and VA387. Co-crystallization of the VA207 P dimer with Le(y) or sialyl Le(x) tetrasaccharides showed that VA207 interacts with these antigens through a common site found on the VA387 P protein which is highly conserved among most GII noroviruses. However, the HBGA-binding site of VA207 targeted at the Lewis antigens through the α-1, 3 fucose (the Lewis epitope) as major and the β-N-acetyl glucosamine of the precursor as minor interacting sites. This completely differs from the binding mode of VA387 and Norwalk virus that target at the secretor epitopes. Binding pocket of VA207 is formed by seven amino acids, of which five residues build up the core structure that is essential for the basic binding function, while the other two are involved in strain-specificity. Our results elucidate for the first time the genetic and structural basis of strain-specificity by a direct comparison of two genetically related noroviruses in their interaction with different HBGAs. The results provide insight into the complex interaction between the diverse noroviruses and the polymorphic HBGAs and highlight the role of human HBGA as a critical factor in norovirus evolution.
    PLoS Pathogens 07/2011; 7(7):e1002152. · 8.14 Impact Factor
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    ABSTRACT: The guanine-nucleotide exchange factor (GEF) RalGPS1a activates small GTPase Ral proteins such as RalA and RalB by stimulating the exchange of Ral bound GDP to GTP, thus regulating various downstream cellular processes. RalGPS1a is composed of an Nterminal Cdc25-like catalytic domain, followed by a PXXP motif and a C-terminal pleckstrin homology (PH) domain. The Cdc25 domain of RalGPS1a, which shares about 30% sequence identity with other Cdc25-domain proteins, is thought to be directly engaged in binding and activating the substrate Ral protein. Here we report the crystal structure of the Cdc25 domain of RalGPS1a. The bowl shaped structure is homologous to the Cdc25 domains of SOS and RasGRF1. The most remarkable difference between these three Cdc25 domains lies in their active sites, referred to as the helical hairpin region. Consistent with previous enzymological studies, the helical hairpin of RalGPS1a adopts a conformation favorable for substrate binding. A modeled RalGPS1a-RalA complex structure reveals an extensive binding surface similar to that of the SOS-Ras complex. However, analysis of the electrostatic surface potential suggests an interaction mode between the RalGPS1a active site helical hairpin and the switch 1 region of substrate RalA distinct from that of the SOS-Ras complex.
    Protein & Cell 04/2011; 2(4):308-19. · 3.22 Impact Factor

Publication Stats

1k Citations
377.21 Total Impact Points

Institutions

  • 2003–2014
    • Chinese Academy of Sciences
      • • Institute of Biophysics
      • • Institute of Hydrobiology
      • • State Key Laboratory of Reproductive Biology
      • • Institute of Zoology
      Peping, Beijing, China
  • 2013
    • Chinese Academy of Fishery Sciences
      北江, Zhejiang Sheng, China
  • 2003–2013
    • Northeast Institute of Geography and Agroecology
      • • Institute of Biophysics
      • • Institute of Hydrobiology
      • • Institute of Zoology
      Beijing, Beijing Shi, China
  • 2010–2011
    • Yunnan Academy of Agricultural Sciences
      Yün-nan, Yunnan, China
    • Nankai University
      • College of Life Sciences
      T’ien-ching-shih, Tianjin Shi, China
  • 2008–2011
    • Yunnan University
      • The Key Laboratory for Microbial Resources of the Ministry of Education
      Yün-nan, Yunnan, China
    • Jiangnan University
      Wu-hsi, Jiangsu Sheng, China
    • Kunming Medical College
      Yün-nan, Yunnan, China
  • 2004–2010
    • Tsinghua University
      • • Laboratory of Structural Biology
      • • School of Life Sciences
      Beijing, Beijing Shi, China
  • 2007
    • Oklahoma Medical Research Foundation
      Oklahoma City, Oklahoma, United States