Protein: structure and functionJ-17-26Solution structure of the Zβdomain of human DNA-dependent activatorof IFN-regulatory factors and its binding modes to B- and Z-DNAsKyungmin Kim 1, 2 , Bulat I. Khayrutdinov 2, 3 , Chung-Kyung Lee 2 , Hae-Kap Cheong 2 ,Sung Wook Kang 1 , Hyejin Park 1 , Sangho Lee 4 , Yang-Gyun Kim 5 , JunGoo Gee 6 ,Alexander Rich 7 , Kyeong Kyu Kim a and Young Ho Jeon 2, 81Department of Molecular Cell Biology Samsung Biomedical Research Institute, SungkyunkwanUniversity School of Medicine, Suwon 440-746, Korea, 2 Magnetic Resonance Team, Korea BasicScience Institute (KBSI), Ochang, Chungbuk 363-883, Korea, 3 Department of General Physics,Kazan State University, Kazan, 42<strong>00</strong>08, Republic of Tatarstan, Russian Federation, 4 Departmentsof Biological Science and 5 Chemistry, Sungkyunkwan University, Suwon 440-746, Korea, 6 Centerfor Priority Areas, Tokyo Metropolitan University, Tokyo 192-0397, Japan, 7 Department ofBiology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America,and 8 College of Pharmacy, Korea University, Jochiwon, Chungnam 339-7<strong>00</strong>, KoreaThe DNA-dependent activator of IFN-regulatory factors (DAI), also known as DLM1/ZBP1, initiates an innateimmune response by binding to foreign DNAs in the cytosol. For full activation of the immune response, threeDNA binding domains at the N-terminus are required: two Z-DNA binding domains (ZBDs), Zαand Zβ, and anadjacent putative B-DNA binding domain. The crystal structure of the Zβdomain of human DAI (hZβDAI) incomplex with Z-DNA revealed structural features distinct from other known Z-DNA binding proteins. To gainstructural insights into the DNA-binding mechanism of hZβDAI, the free hZβDAI stucture was solved and itsbindings to B- and Z-DNAs were analyzed by NMR spectroscopy. Compared to the Z-DNA-bound structure, theconformation of free hZβDAI has notable alterations in the α3 recognition helix, the wing and Y145, which arecritical in Z-DNA recognition. Unlike other Zαdomains, hZβDAI appears to have conformational flexibility andstructural adaptation is required for Z-DNA binding. Chemical shift perturbation experiments (CSPs) revealed thathZβDAI also binds weakly to B-DNA via a different binding mode. During the innate immune response, hZβDAI islikely to play an active role in binding to DNAs in both B and Z conformations in the recognition of foreign DNAs.J-17-27Antimicrobial and LPS-neutralizing activities of bovine myeloidantimicrobial peptide-18 (BMAP-18) analogsYong Hai Nan, Eun Kyu Lee and Song Yub ShinDepartment of Bio-Materials, Graduate School and Department Cellular & Molecular Medicine,School of Medicine, Chosun University, KoreaIn this study, we synthesized bovine myeloid antimicrobial peptide-18 (BMAP-18) and itsanalogs. These peptides displayed much higher cell selectivity as compared to BMAP-27.BMAP-27 caused near-complete dye leakage from bacterial-membrane-mimickingvesicles even at very low concentration of 0.5 µM, whereas BMAP-18 and its analogsinduced very little dye leakage at 16 µM. These peptides induced near-completemembrane depolarization of Staphylococcus aureus cells under their MIC. These resultssuggests that BMAP-18 and its analogs exhibit lethality toward microbes due to theirability to form small channels that permit the transit of ions or protons, but not moleculesas large as calcein. BMAP-18 and its analogs significantly inhibited NO production orTNF-αrelease in LPS-stimulated mouse macrophage RAW264.7 cells at <strong>10</strong> µM. Inparticular, there was a significant linear correlation between the increase in thehydrophobicity of peptides and LPS-neutralizing activity. Although BMAP-18-W has lowerhydrophobicity than BMAP-18-L, it showed higher LPS-neutralizing activity as comparedto BMAP-18-L. This result suggests other important parameters of AMPs may beinvolved in their LPS-neutralizing activity, as well as positive charge and hydrophobicity.J-17-29Crystallization and preliminary structural study of human PTPRQKeum Ran Yu , , Suk-Kyeong Jung , In Seok Hong , Young Jun Kim*, ByoungChul Park , Kwang Hee Bae , Sang Chul Lee and Seung Jun Kim Department of Medical Proteomics Research Center, Korea Research Institute of Bioscience andBiotechnology, <strong>11</strong>1 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea Department of Chemistry,College of Natural Science, Kongju National University, 182 Shin Gwan-Dong, Kongju 314-701,Korea *Department of Radiology, College of Medical, Kun Kuk University, 1 Hwayang-dong,Gwangjin-gu, Seoul 143-701, KoreaThe PTPRQ belongs to a receptor-type classical protein tyrosine phosphatase (PTP)family with one catalytic domain in the cytoplasmic region. Unlike other classical PTPs,PTPRQ has de-phosphorylating activities toward phosphatidyl-inositol (PIP) substrates.We successfully cloned, over-expressed and purified the catalytic domain of PTPRQ.Subsequently PTPRQ was crystallized in two forms. The first crystal form, whichdiffracted X-ray to 3.0 Å, belonged to cubic space group I4132, with cell dimensions of a= b = c = 165 Å, α= β= γ= 90. The second form, which behaves better than the firstone, belonged to hexagonal space group, P64 with cell dimensions of a = b = 78 Å, c =84 Å, α= β= 90, γ= <strong>12</strong>0. From the hexagonal crystal form, we collected diffraction dataset to 1.6 Å resolution. Structural solution was obtained by molecular replacementmethod using PTPRO structure as a search model and model refinement is in progress.J-17-30Crystal structure of Rnase H from xenotrophic Murine leukemia virusrelatedvirus (XMRV)Ju Hee Kim , , Seong Hyun Kang , Suk-Kyeong Jung , Joon Sig Choi , ByungChul Park and Seung Jun Kim Department of Medical Proteomics Research Center, Korea Research Institute of Bioscience andBiotechnology ,<strong>11</strong>1 Gwahangno,Yu-seong-gu, Deajeon 305-806, Korea, Department ofBiochemistry, College of Natural Sciences, Chungnam National University, Daejeon 305-764,KoreaThe infection of xenotropic murine leukemia virus-related virus (XMRV) is associated withprostate cancer and is also arguably responsible for pathogenesis of chronic fatiguesyndrome. However, very little are known about XMRV proteins biochemically andstructurally so far. Although RNASE H structure of moloney murine leukemia virus (Mo-MLV), the most closely related to XMRV RNASE H at the primary structure level, havebeen determined, no structural information about C-helix and other loop that areresponsible for RNA/DNA binding and catalytic specificity. Here we present 2.8 Åresolution structure of RNASE H from XMRV, which was reliably defined for virtually allresidues of RNASE H. Structure of RNASE H would not only facilitate the process fordeveloping specific inhibitors that could be used as drugs for clinic, but broaden theunderstanding the physiological function of XMRV.J-17-28Identification and characterization of a novel SGNH-family esterasefrom Sinorhizobium melilotiSong Yi Bae, Heejin Hwang, Seul-gi Kim and T. Doohun KimDepartment of Molecular Science and Technology Graduate School of Interdisciplinary Program,Ajou University, Suwon 443-749, KoreaBacterial esterases were known to have important roles in the synthesis and processingof optically pure compounds such as drugs, fine chemicals, and food ingredients. SGNHhydorlase,subgroup of GDSL family esterase, has various functional properties such asbroad substrate specificity and regiospecificity. A novel oligomeric SGNH-arylesterasesfrom Sinorhizobium mellioti, SM24A, was identified and characterized using biochemicaland biophysical methods. A sequences comparison of SM24A with other SGNH-familyesterases confirmed the presence of a canonical catalytic triad (Ser13, Asp187, andHis190). SM24A was overexpressed and purified as a his-tagged protein. Structural andfunctional properties of SM24A were investigated using circular dichroism (CD),fluorescence, dynamic light scattering (DLS), electron microscopy (EM), and time of flight(TOF) mass spectrometry. It was able to hydrolyze p-nitrophenyl acetate, α-, and β-naphthyl acetate. Site-directed mutagenesis and crystallographic analysis is currentlyunder progress for its industrial applications.J-17-31Molecular mimicry-based repositioning of Nutlin-3 to anti-apoptoticBcl-2 family proteinsJi-Hyang Ha , Eun-Young Won , Jae-Sun Shin , Mi Jang , Kyoung-Seok Ryu ,Kwang-Hee Bae Sung Goo Park , Byoung Chul Park , Ho Sup Yoon* , § and Seung-Wook Chi* ,Medical Proteomics Research Center, KRIBB, Daejeon 305-806, Korea, Division of MagneticResonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup,Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883, Korea, § Division of Structural andComputational Biology, School of Biological Sciences, Nanyang Technological University, 60Nanyang Drive, Singapore 6375<strong>11</strong>, SingaporeThe identification of off-target binding of drugs is a key to repositioning drugs to newtherapeutic categories. Here we show the universal interactions of the p53 transactivationdomain (p53TAD) with various antiapoptotic Bcl-2 family proteins via a mouse doubleminute 2(MDM2) binding motif, which play an important role in transcription-independentapoptotic pathways of p53. Interestingly, our structural studies reveal that the antiapoptoticBcl-2 family proteins and MDM2 share a similar mode of interaction with thep53TAD. On the basis of this close molecular mimicry, our NMR results demonstrate thatthe potent MDM2 antagonists Nutlin-3 and PMI bind to the anti-apoptotic Bcl-2 familyproteins in a manner analogous to that with the p53TAD.266 Korean Society for Biochemistry and Molecular Biology
Protein: structure and function
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