Hexameric assembly of membrane fusion protein YknX of the sporulation delaying efflux pump from <i>Bacillus amyloliquefaciens</i>

Xu, Yongbin,Jo, Inseong,Wang, Lulu,Chen, Jinli,Fan, Shengdi,Dong, Yuesheng,Quan, Chunshan,Ha, Nam-Chul Elsevier 2017 Biochemical and biophysical research communication Vol.493 No.1

<P><B>Abstract</B></P> <P>Membrane fusion proteins (MFPs) play an essential role in the action of the drug efflux pumps and protein secretion systems in bacteria. The sporulation delaying protein (SDP) efflux pump YknWXYZ has been identified in diverse <I>Bacillus</I> species. The MFP YknX requires the ATP-binding cassette (ABC) transporter YknYZ and the Yip1 family protein YknW to form a functional complex. To date, the crystal structure, molecular function and mechanism of action of YknX remain unknown. In this study, to characterize the structural and biochemical roles of YknX in the functional assembly of YknWXYZ from <I>B. amyloliquefaciens</I>, we successfully obtained crystals of the YknX protein that diffracted X-rays to a resolution of 4.4 Å. We calculated an experimentally phased map using single-wavelength anomalous diffraction (SAD), revealing that YknX forms a hexameric assembly similar to that of MacA from Gram-negative bacteria. The hexameric assembly of YknX exhibited a funnel-like structure with a central channel and a conical mouth. Functional studies <I>in vitro</I> suggest that YknX can bind directly to peptidoglycan. Our study provides an improved understanding of the assembly of the YknWXYZ efflux pump and the role of YknX in the complex.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The functional and structural properties of the YknX from <I>B. amyloliquefaciens.</I> </LI> <LI> The three-dimensional structure of MFP YknX and it has a strong affinity toward peptidoglycan. </LI> <LI> The YknX may forms a hexameric assembly in the crystal packing. </LI> <LI> The YknX displayed a similar upside-down, funnel-shaped orientation as <I>Aa</I> MacA. </LI> </UL> </P>

Spectral and structural analysis of large Stokes shift fluorescent protein dKeima570

Xu, Yongbin,Hwang, Kwang Yeon,Nam, Ki Hyun MICROBIOLOGICAL SOCIETY OF KOREA 2018 JOURNAL OF MICROBIOLOGY -SEOUL- Vol.56 No.11

Assembly and Channel Opening of Outer Membrane Protein in Tripartite Drug Efflux Pumps of Gram-negative Bacteria

Xu, Yongbin,Moeller, Arne,Jun, So-Young,Le, Minho,Yoon, Bo-Young,Kim, Jin-Sik,Lee, Kangseok,Ha, Nam-Chul American Society for Biochemistry and Molecular Bi 2012 The Journal of biological chemistry Vol.287 No.15

<P>Gram-negative bacteria are capable of expelling diverse xenobiotic substances from within the cell by use of three-component efflux pumps in which the energy-activated inner membrane transporter is connected to the outer membrane channel protein via the membrane fusion protein. In this work, we describe the crystal structure of the membrane fusion protein MexA from the <I>Pseudomonas aeruginosa</I> MexAB-OprM pump in the hexameric ring arrangement. Electron microscopy study on the chimeric complex of MexA and the outer membrane protein OprM reveals that MexA makes a tip-to-tip interaction with OprM, which suggests a docking model for MexA and OprM. This docking model agrees well with genetic results and depicts detailed interactions. Opening of the OprM channel is accompanied by the simultaneous exposure of a protein structure resembling a six-bladed cogwheel, which intermeshes with the complementary cogwheel structure in the MexA hexamer. Taken together, we suggest an assembly and channel opening model for the MexAB-OprM pump. This study provides a better understanding of multidrug resistance in Gram-negative bacteria.</P>

Spectral and structural analysis of large Stokes shift fluorescent protein dKeima570

Yongbin Xu,황광연,남기현 한국미생물학회 2018 The journal of microbiology Vol.56 No.11

The Keima family comprises large Stokes shifts fluorescent proteins, which are useful for dual-color fluorescence crosscorrelation spectroscopy and multicolor imaging. dKeima570 belongs to the Keima family. It has a unique chromophore sequence composed of CYG with an emission peak at 570 nm, but its molecular properties are unclear. We report the spectral analysis of dKeima570 and its crystal structure at 2.0 Å resolution. The dKeima570 chromophore is mainly in the protonation state in the entire pH range. The pH-induced non-fluorescence state was observed below pH 4.0. The crystal structure of the dKeima570 chromophore has a cis conformation at pH 6.5. The chromophore is surrounded by a unique hydrogen bonding network containing a water bridge between Glu212 and Arg194. The analysis of the dimeric interface of dKeima570 revealed the key residues that maintain the oligomerization of Keima family. Structural comparisons of dKeima570 and mKeima provided insights into the unique large Stokes shifts characteristics of the Keima family.

Structural and Functional Analyses of Periplasmic 5′-Methylthioadenosine/<i>S</i>-Adenosylhomocysteine Nucleosidase from <i>Aeromonas hydrophila</i>

Xu, Yongbin,Wang, Lulu,Chen, Jinli,Zhao, Jing,Fan, Shengdi,Dong, Yuesheng,Ha, Nam-Chul,Quan, Chunshan American Chemical Society 2017 Biochemistry Vol.56 No.40

<P>The Gram-negative, rod-shaped bacterium Aeromonas hydrophila has two multifunctional 5/-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) enzymes, MtaN-1 and MtaN-2, that differ from those in other bacteria. These proteins are essential for several metabolic pathways, including biological methylation, polyamine biosynthesis, methionine recycling, and bacterial quorum sensing. To gain insight into how these two proteins function, we determined four high-resolution crystal structures of MtaN-1 in its apo form and in complex with the substrates S-adenosyl-L-homocysteine, S'-methylthioadenosine, and 5'-deoxyadenosine. We found that the domain structures were generally similar, although slight differences were evident. The crystal structure demonstrates that AhMtaN-1 has an extension of the binding pocket and revealed that a tryptophan in the active site (Trp199) may playa major role in substrate binding, unlike in other MTAN proteins. Mutation of the Trp199 residue completely abolished the enzyme activity. Trp199 was identified as an active site residue that is essential for catalysis. Furthermore, biochemical characterization of AhMtaN-1 and AhMtaN-2 demonstrated that AhMtaN-1 exhibits inherent trypsin resistance that is higher than that of AhMtaN-2. Additionally, the thermally unfolded AhMtaN-2 protein is capable of refolding into active forms, whereas the thermally unfolded AhMtaN-1 protein does not have this ability. Examining the different biochemical characteristics related to the functional roles of AhMtaN-1 and AhMtaN-2 would be interesting. Indeed, the biochemical characterization of these structural features would provide a structural basis for the design of new antibiotics against A. hydrophila.</P>

Parallel computation for debonding process of externally FRP plated concrete

Xu, Tao,Zhang, Yongbin,Liang, Z.Z.,Tang, Chun-An,Zhao, Jian Techno-Press 2011 Structural Engineering and Mechanics, An Int'l Jou Vol.38 No.6

In this paper, the three dimensional Parallel Realistic Failure Process Analysis ($RFPA^{3D}$-Parallel) code based on micromechanical model is employed to investigate the bonding behavior in FRP sheet bonded to concrete in single shear test. In the model, the heterogeneity of brittle disordered material at a meso-scale was taken into consideration in order to realistically demonstrate the mechanical characteristics of FRP-to-concrete. Modified Mohr-coulomb strength criterion with tension cut-off, where a stressed element can damage in shear or in tension, was adopted and a stiffness degradation approach was used to simulate the initiation, propagation and growth of microcracks in the model. In addition, a Master-Slave parallel operation control technique was adopted to implement the parallel computation of a large numerical model. Parallel computational results of debonding of FRP-concrete visually reproduce the spatial and temporal debonding failure progression of microcracks in FRP sheet bonded to concrete, which agrees well with the existing testing results in laboratory. The numerical approach in this study provides a useful tool for enhancing our understanding of cracking and debonding failure process and mechanism of FRP-concrete and our ability to predict mechanical performance and reliability of these FRP sheet bonded to concrete structures.

Parallel computation for debonding process of externally FRP plated concrete

Tao Xu,Yongbin Zhang,Z.Z. Liang,Chun-an Tang,Jian Zhao 국제구조공학회 2011 Structural Engineering and Mechanics, An Int'l Jou Vol.38 No.6

In this paper, the three dimensional Parallel Realistic Failure Process Analysis (RFPA3D-Parallel) code based on micromechanical model is employed to investigate the bonding behavior in FRP sheet bonded to concrete in single shear test. In the model, the heterogeneity of brittle disordered material at a meso-scale was taken into consideration in order to realistically demonstrate the mechanical characteristics of FRP-to-concrete. Modified Mohr-coulomb strength criterion with tension cut-off, where a stressed element can damage in shear or in tension, was adopted and a stiffness degradation approach was used to simulate the initiation, propagation and growth of microcracks in the model. In addition, a Master-Slave parallel operation control technique was adopted to implement the parallel computation of a large numerical model. Parallel computational results of debonding of FRP-concrete visually reproduce the spatial and temporal debonding failure progression of microcracks in FRP sheet bonded to concrete, which agrees well with the existing testing results in laboratory. The numerical approach in this study provides a useful tool for enhancing our understanding of cracking and debonding failure process and mechanism of FRP-concrete and our ability to predict mechanical performance and reliability of these FRP sheet bonded to concrete structures.

Periplasmic Domain of CusA in an Escherichia coli Cu+/Ag+ Transporter Has Metal Binding Sites

윤보영,Yongbin Xu,Shunfu Piao,Nahee Kim,윤정현,조현수,이강석,하남출 한국미생물학회 2010 The journal of microbiology Vol.48 No.6

The resistance nodulation division (RND)-type efflux systems are utilized in Gram-negative bacteria to export a variety of substrates. The CusCFBA system is the Cu+ and Ag+ efflux system in Escherichia coli,conferring resistance to lethal concentrations of Cu+ and Ag+. The periplasmic component, CusB, which is essential for the assembly of the protein complex, has Cu+ or Ag+ binding sites. The twelve-span membrane protein CusA is a homotrimeric transporter, and has a relatively large periplasmic domain. Here, we constructed the periplasmic domain of CusA by joining two DNA segments and then successfully expressed and purified the protein. Isothermal titration calorimetry experiments revealed Ag+ binding sites with Kds of 10-6-10-5 M. Our findings suggest that the metal binding in the periplasmic domain of CusA might play an important role in the function of the efflux pump.

Inter‑turn short‑circuit fault detection with high‑frequency signal injection for inverter‑fed PMSM systems

Zheng Xu,Jianzhong Zhang,Zakiud Din,Yongbin Wu,Ming Cheng 전력전자학회 2023 JOURNAL OF POWER ELECTRONICS Vol.23 No.6

This paper develops an online inter-turn short-circuit fault (ISF) detection method for inverter-fed permanent magnet synchronous machine (PMSM) systems. A high-frequency (HF) mathematical model of a PMSM with an ISF is established. Based on the presented HF model, the HF responses of the PMSM with various severity of ISF under HF voltage injectionare analyzed in detail, where both the short-circuit ratio and the fault resistance are considered to evaluate the fault severity. In the proposed fault diagnosis method, the amplitude of the HF negative-sequence component is used to determine the fault severity, and the initial phase is used to locate the position of the faulty phase. The simulation and experimental results verify the effectiveness of the proposed method.

Self-nitrogen-doped carbon materials derived from the petioles and blades of apricot leaves as metal-free catalysts for selective oxidation of aromatic alkanes

Sun Yongbin,Hao Junlei,Zhu Xuesai,Zhang Baobin,Yin Hao,Xu Shanguang,Hou Chao,Liu Kun 한국탄소학회 2020 Carbon Letters Vol.30 No.2

Carbon materials with tailorable structures and superior properties have great potential applications in environmental protec�tion, energy conversion, and catalysis. Plant biomass as abundant and green non-toxic raw materials has been considered as good precursors for synthesizing heteroatom-doped carbon materials. However, few studies have been reported on the dif�ferent natures of carbon materials derived from diferent parts of the same plant biomass. In this study, we prepared carbon materials from the petioles and blades of apricot leaves by direct pyrolysis without additives. Detailed characterizations indicate that these two carbon materials are similar in element composition and graphitization degree, but difer greatly in surface area and pore volume. These diferences can be attributed to the diferent contents of inorganic salts, vascular bundles, and proteins in petioles and blades. When used as catalysts for the oxidation of ethylbenzene, the petiole-derived carbon shows better catalytic performance than the blades derived carbon due to its high surface area, large average pore size, and doped nitrogen atoms. Furthermore, the carbon catalysts derived from the petioles and blades of poplar leaves and parasol tree leaves show the same diference in catalytic reaction, implying that the above-mentioned conclusion is rather universal, which can provide reference for the synthesis of carbon materials from leaves.