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Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA
Kim, Doyoun,Reddy, Sanjith,Kim, Dong Young,Rich, Alexander,Lee, Sangho,Kim, Kyeong Kyu,Kim, Yang-Gyun Oxford University Press 2009 Nucleic acids research Vol.37 No.13
<P>Base extrusion is a major structural feature at the junction between B- and Z-DNA (the B–Z junction) where a base pair is broken, and the two bases are extruded from the double helix. Despite the demonstration of base extrusion at the B–Z junction, it is not clear whether a similar base extrusion occurs at other types of junctions involving the left-handed Z conformation. Here, we investigate structural changes of bases at three Z-form junctions: DNA B–Z and Z–Z and RNA A–Z junctions. By monitoring fluorescently labeled duplex nucleic acids using 2-aminopurines at various positions relative to the junction point, we show that base extrusion occurs not only at the DNA B–Z junction, but also at the RNA A–Z and DNA Z–Z junctions. Our data suggest that base extrusion is a general feature of Z-form nucleic-acid junctions.</P>
Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ)
Kim, Doyoun,Hur, Jeonghwan,Park, Kwangsoo,Bae, Sangsu,Shin, Donghyuk,Ha, Sung Chul,Hwang, Hye-Yeon,Hohng, Sungchul,Lee, Joon-Hwa,Lee, Sangho,Kim, Yang-Gyun,Kim, Kyeong Kyu Oxford University Press 2014 Nucleic acids research Vol.42 No.9
<P>Double-stranded ribonucleic acid-activated protein kinase (PKR) downregulates translation as a defense mechanism against viral infection. In fish species, PKZ, a PKR-like protein kinase containing left-handed deoxyribonucleic acid (Z-DNA) binding domains, performs a similar role in the antiviral response. To understand the role of PKZ in Z-DNA recognition and innate immune response, we performed structural and functional studies of the Z-DNA binding domain (Zα) of PKZ from <I>Carassius auratus</I> (caZα<SUB>PKZ</SUB>). The 1.7-Å resolution crystal structure of caZα<SUB>PKZ</SUB>:Z-DNA revealed that caZα<SUB>PKZ</SUB> shares the overall fold with other Zα, but has discrete structural features that differentiate its DNA binding mode from others. Functional analyses of caZα<SUB>PKZ</SUB> and its mutants revealed that caZα<SUB>PKZ</SUB> mediates the fastest B-to-Z transition of DNA among Zα, and the minimal interaction for Z-DNA recognition is mediated by three backbone phosphates and six residues of caZα<SUB>PKZ</SUB>. Structure-based mutagenesis and B-to-Z transition assays confirmed that Lys56 located in the β-wing contributes to its fast B-to-Z transition kinetics. Investigation of the DNA binding kinetics of caZα<SUB>PKZ</SUB> further revealed that the B-to-Z transition rate is positively correlated with the association rate constant. Taking these results together, we conclude that the positive charge in the β-wing largely affects fast B-to-Z transition activity by enhancing the DNA binding rate.</P>
Structural and functional study of ChuY from <i>Escherichia coli</i> strain CFT073
Kim, Hun,Chaurasia, Akhilesh Kumar,Kim, Truc,Choi, Jongkeun,Ha, Sung Chul,Kim, Doyoun,Kim, Kyeong Kyu Elsevier 2017 Biochemical and biophysical research communication Vol.482 No.4
<P><B>Abstract</B></P> <P>The uropathogenic <I>Escherichia coli</I> strain CFT073 contains multiple iron and heme transport systems, which facilitate infection of the host urinary tract. To elucidate the molecular and cellular function of ChuY, a hypothetical gene in the heme degradation/utilization pathway, we solved the crystal structure of ChuY at 2.4 Å resolution. ChuY has high structural homology with human biliverdin and flavin reductase. We confirmed that ChuY has flavin mononucleotide (FMN) reductase activity, using NAD(P)H as a cofactor, and shows porphyrin ring binding affinity. A <I>chuY</I> deletion-insertion strain showed reduced survival potential compared to wild-type and complemented strains in mammalian cells. Current results suggest ChuY acts as a reductase in heme homeostasis to maintain the virulence potential of <I>E</I>. <I>coli</I> CFT073.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Crystal structure of ChuY of uropathogenic <I>E</I>. <I>coli</I> was determined at 2.4 Å resolution. </LI> <LI> ChuY has high structural homology with human biliverdin and flavin reductase. </LI> <LI> ChuY has flavin mononucleotide (FMN) reductase activity using NADPH as a cofactor. </LI> <LI> A <I>chuY</I> knockout strain showed reduced survival potential in mammalian cells. </LI> <LI> ChuY plays a role in heme homeostasis and the virulence potential of <I>E</I>. <I>coli</I> CFT073. </LI> </UL> </P>
Kim, Jung A,Kim, Doyoun,Won, Seoung Youn,Han, Kyung Ah,Park, Dongseok,Cho, Eunju,Yun, Nayoung,An, Hyun Joo,Um, Ji Won,Kim, Eunjoon,Lee, Jie-Oh,Ko, Jaewon,Kim, Ho Min Elsevier 2017 Neuron Vol.94 No.6
<P><B>Summary</B></P> <P>Membrane-associated mucin domain-containing glycosylphosphatidylinositol anchor proteins (MDGAs) bind directly to neuroligin-1 (NL1) and neuroligin-2 (NL2), thereby respectively regulating excitatory and inhibitory synapse development. However, the mechanisms by which MDGAs modulate NL activity to specify development of the two synapse types remain unclear. Here, we determined the crystal structures of human NL2/MDGA1 Ig1-3 complex, revealing their stable 2:2 arrangement with three interaction interfaces. Cell-based assays using structure-guided, site-directed MDGA1 mutants showed that all three contact patches were required for the MDGA’s negative regulation of NL2-mediated synaptogenic activity. Furthermore, MDGA1 competed with neurexins for NL2 via its Ig1 domain. The binding affinities of both MDGA1 and MDGA2 for NL1 and NL2 were similar, consistent with the structural prediction of similar binding interfaces. However, MDGA1 selectively associated with NL2, but not NL1, in vivo. These findings collectively provide structural insights into the mechanism by which MDGAs negatively modulate synapse development governed by NLs/neurexins.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Crystal structure of neuroligin-2 (NL2) in complex with MDGA1 Ig1-Ig3 domains </LI> <LI> MDGA1 Ig1-Ig2 domains interact with NL2 dimer with 2:2 stoichiometry </LI> <LI> MDGA1 competes with Nrx1β for NL2 binding via their overlapping binding site on NL2 </LI> <LI> MDGA1 selectively forms complexes with NL2, but not NL1, in vivo </LI> </UL> </P>
김도윤(Kim DoYoun),김광희(Kim KwangHoi),김용진(Kim YongJin),김기연(Kim GiYeon) 인하대학교 스포츠과학연구소 2007 스포츠과학논문집 Vol.19 No.-
본 연구는 여자 핸드볼 선수와 배구선수를 대상으로 유연성이 등척성 및 등속성 근력과 어떠한 관계가 있는지를 알아보기 위하여 두 요인간의 상관분석을 실시하였으며 다음과 같은 결과를 얻었다. 1. 배구선수가 핸드볼 선수보다 유연성이 좋았지만 등척성 최대 근력은 낮았다. 2. 유연성이 좋은 배구선수는 핸드볼 선수와의 부하속도 60˚/sec 등속성 근력요인 비교에 있어 최대토크, 체중대비 발현근력이 낮았으며 굴근 발현각도는 핸드볼 선수보다 배구선수가 유의하게 높았다. 3. 부하속도 180˚/sec의 근파워 비교에 있어 유연성이 낮은 핸드볼선수가 배구선수보다 평균 근파워, 체중대비 근파워가 낮았으며 180˚/sec의 최대토크 발현각도는 배구선수보다 유의하게 높았다. 4. 종목별 요인간 상관관계에 있어서는 배구선수의 왼쪽 각굴력과 유연성간 유의한 부적 상관관계가 있었다. 그러므로 종목별 요구되는 근력의 종류에 따라 다양한 유연성 훈련 프로그램이 필요할 것으로 생각되며 특히, 근파워를 요하는 종목에서는 보다 심도있는 유연성 프로그램이 필요할 것으로 판단된다. This study was to investigate the relationship between flexibility and muscular factors including isometric and isokinetic strength. For the purpose, 11 females volleyball and 15 handball players participated this study. we measured the sit and reach for flexibility and isometric strength of knee flexion, in addition, isokinetic strength and power by isokinetic equipment. After then, we analyzed the correlation between flexibility and strength. The results were followed as: 1. flexibility of volleyball players was higher but isometric strength was lower. 2. handball players' isokinetic strength was higher in peak torque, %BW. 3. On the peak power, volley ball players' power was higher than handball with higher flexibility. 4. flexibility had positive correlation with peak power, the other side had negative correlation with peak strength. Therefore we concluded that according to the kind of strength demanded various flexibility program should be prepared for the improvement, especially for the peak power improvement.
Li, Yan,Kim, Ryunhee,Cho, Yi Sul,Song, Woo Seok,Kim, Doyoun,Kim, Kyungdeok,Roh, Junyeop Daniel,Chung, Changuk,Park, Hanwool,Yang, Esther,Kim, Soo-Jeong,Ko, Jaewon,Kim, Hyun,Kim, Myoung-Hwan,Bae, Yong- Society for Neuroscience 2018 The Journal of neuroscience Vol.38 No.26
<P>SALM1 (SALM (synaptic adhesion-like molecule), also known as LRFN2 (leucine rich repeat and fibronectin type III domain containing), is a postsynaptic density (PSD)-95-interacting synaptic adhesion molecule implicated in the regulation of NMDA receptor (NMDAR) clustering largely based on in vitro data, although its in vivo functions remain unclear. Here, we found that mice lacking SALM1/LRFN2 (Lrfn2(-/-) mice) show a normal density of excitatory synapses but altered excitatory synaptic function, including enhanced NMDAR-dependent synaptic transmission but suppressed NMDAR-dependent synaptic plasticity in the hippocampal CA1 region. Unexpectedly, SALM1expression was detected in both glutamatergic and GABAergic neurons and Lrfn2(-/-) CA1 pyramidal neurons showed decreases in the density of inhibitory synapses and the frequency of spontaneous inhibitory synaptic transmission. Behaviorally, ultrasonic vocalization was suppressed in Lrfn2(-/-) pups separated from their mothers and acoustic startle was enhanced, but locomotion, anxiety-like behavior, social interaction, repetitive behaviors, and learning and memory were largely normal in adult male Lrfn2(-/-) mice. These results suggest that SALM1/LRFN2 regulates excitatory synapse function, inhibitory synapse development, and social communication and startle behaviors in mice.</P>
Sequence preference and structural heterogeneity of BZ junctions
Kim, Doyoun,Hur, Jeonghwan,Han, Ji ,Hoon,Ha, Sung ,Chul,Shin, Donghyuk,Lee, Sangho,Park, Soyoung,Sugiyama, Hiroshi,Kim, Kyeong ,Kyu Oxford University Press 2018 Nucleic acids research Vol.46 No.19
<P><B>Abstract</B></P><P>BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We determined three crystal structures of BZ junctions with diverse sequences followed by spectroscopic validation of DNA conformation. The structural features of the BZ junctions were well conserved regardless of sequences via the continuous base stacking through B-to-Z DNA with A-T base extrusion. However, the sequence-dependent structural heterogeneity of the junctions was also observed in base step parameters that are correlated with steric constraints imposed during Z-DNA formation. Further, circular dichroism and fluorescence-based analysis of BZ junctions revealed that a base extrusion was only found at the A-T base pair present next to a stable dinucleotide Z-DNA unit. Our findings suggest that Z-DNA formation in the genome is influenced by the sequence preference for BZ junctions.</P>