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Ford BA, Sullivan GJ, Moore L, Varkey D, Zhu H, Ostrowski M, Mabbutt BC, Paulsen IT, Shah BS. Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria. Biochem Soc Trans 2021; 49:2465-2481. [PMID: 34882230 PMCID: PMC8786288 DOI: 10.1042/bst20200244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/03/2021] [Accepted: 11/16/2021] [Indexed: 12/05/2022]
Abstract
Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.
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Affiliation(s)
- Benjamin A. Ford
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | | | - Lisa Moore
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Deepa Varkey
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Hannah Zhu
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Martin Ostrowski
- Climate Change Cluster (C3), University of Technology Sydney, Sydney, Australia
| | - Bridget C. Mabbutt
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Bhumika S. Shah
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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2
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Gangwar SP, Green MN, Michard E, Simon AA, Feijó JA, Sobolevsky AI. Structure of the Arabidopsis Glutamate Receptor-like Channel GLR3.2 Ligand-Binding Domain. Structure 2020; 29:161-169.e4. [PMID: 33027636 DOI: 10.1016/j.str.2020.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/21/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022]
Abstract
Glutamate receptor-like channels (GLRs) play important roles in numerous plant physiological processes. GLRs are homologous to ionotropic glutamate receptors (iGluRs) that mediate neurotransmission in vertebrates. Here we determine crystal structures of Arabidopsis thaliana GLR3.2 ligand-binding domain (LBD) in complex with glycine and methionine to 1.58- and 1.75-Å resolution, respectively. Our structures show a fold similar to that of iGluRs, but with several secondary structure elements either missing or different. The closed clamshell conformation of GLR3.2 LBD suggests that both glycine and methionine act as agonists. The mutation R133A strongly increases the constitutive activity of the channel, suggesting that the LBD mutated at the residue critical for agonist binding produces a more stable closed clamshell conformation. Furthermore, our structures explain the promiscuity of GLR activation by different amino acids, confirm evolutionary conservation of structure between GLRs and iGluRs, and predict common molecular principles of their gating mechanisms driven by bilobed clamshell-like LBDs.
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Affiliation(s)
- Shanti Pal Gangwar
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Marriah N Green
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA; Training Program in Nutritional and Metabolic Biology, Institute of Human Nutrition, Columbia University Irving Medical Center, 630 West 168(th) Street, New York, NY 10032, USA
| | - Erwan Michard
- Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Bldg, College Park, MD 20742-5815, USA
| | - Alexander A Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Bldg, College Park, MD 20742-5815, USA
| | - José A Feijó
- Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Bldg, College Park, MD 20742-5815, USA.
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA.
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Stroebel D, Paoletti P. Architecture and function of NMDA receptors: an evolutionary perspective. J Physiol 2020; 599:2615-2638. [PMID: 32786006 DOI: 10.1113/jp279028] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022] Open
Abstract
Ionotropic glutamate receptors (iGluRs) are a major class of ligand-gated ion channels that are widespread in the living kingdom. Their critical role in excitatory neurotransmission and brain function of arthropods and vertebrates has made them a compelling subject of interest for neurophysiologists and pharmacologists. This is particularly true for NMDA receptor (NMDARs), a subclass of iGluRs that act as central drivers of synaptic plasticity in the CNS. How and when the unique properties of NMDARs arose during evolution, and how they relate to the evolution of the nervous system, remain open questions. Recent years have witnessed a boom in both genomic and structural data, such that it is now possible to analyse the evolution of iGluR genes on an unprecedented scale and within a solid molecular framework. In this review, combining insights from phylogeny, atomic structure and physiological and mechanistic data, we discuss how evolution of NMDAR motifs and sequences shaped their architecture and functionalities. We trace differences and commonalities between NMDARs and other iGluRs, emphasizing a few distinctive properties of the former regarding ligand binding and gating, permeation, allosteric modulation and intracellular signalling. Finally, we speculate on how specific molecular properties of iGuRs arose to supply new functions to the evolving structure of the nervous system, from early metazoan to present mammals.
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Affiliation(s)
- David Stroebel
- Ecole Normale Supérieure, CNRS, INSERM, Institute de Biologie de l'Ecole Normale Supérieure (IBENS), Université PSL, Paris, France
| | - Pierre Paoletti
- Ecole Normale Supérieure, CNRS, INSERM, Institute de Biologie de l'Ecole Normale Supérieure (IBENS), Université PSL, Paris, France
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The structural bases for agonist diversity in an Arabidopsis thaliana glutamate receptor-like channel. Proc Natl Acad Sci U S A 2019; 117:752-760. [PMID: 31871183 DOI: 10.1073/pnas.1905142117] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Arabidopsis thaliana glutamate receptor-like (GLR) channels are amino acid-gated ion channels involved in physiological processes including wound signaling, stomatal regulation, and pollen tube growth. Here, fluorescence microscopy and genetics were used to confirm the central role of GLR3.3 in the amino acid-elicited cytosolic Ca2+ increase in Arabidopsis seedling roots. To elucidate the binding properties of the receptor, we biochemically reconstituted the GLR3.3 ligand-binding domain (LBD) and analyzed its selectivity profile; our binding experiments revealed the LBD preference for l-Glu but also for sulfur-containing amino acids. Furthermore, we solved the crystal structures of the GLR3.3 LBD in complex with 4 different amino acid ligands, providing a rationale for how the LBD binding site evolved to accommodate diverse amino acids, thus laying the grounds for rational mutagenesis. Last, we inspected the structures of LBDs from nonplant species and generated homology models for other GLR isoforms. Our results establish that GLR3.3 is a receptor endowed with a unique amino acid ligand profile and provide a structural framework for engineering this and other GLR isoforms to investigate their physiology.
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De Bortoli S, Teardo E, Szabò I, Morosinotto T, Alboresi A. Evolutionary insight into the ionotropic glutamate receptor superfamily of photosynthetic organisms. Biophys Chem 2016; 218:14-26. [PMID: 27586818 DOI: 10.1016/j.bpc.2016.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 07/20/2016] [Accepted: 07/20/2016] [Indexed: 01/14/2023]
Abstract
Photosynthetic eukaryotes have a complex evolutionary history shaped by multiple endosymbiosis events that required a tight coordination between the organelles and the rest of the cell. Plant ionotropic glutamate receptors (iGLRs) form a large superfamily of proteins with a predicted or proven non-selective cation channel activity regulated by a broad range of amino acids. They are involved in different physiological processes such as C/N sensing, resistance against fungal infection, root and pollen tube growth and response to wounding and pathogens. Most of the present knowledge is limited to iGLRs located in plasma membranes. However, recent studies localized different iGLR isoforms to mitochondria and/or chloroplasts, suggesting the possibility that they play a specific role in bioenergetic processes. In this work, we performed a comparative analysis of GLR sequences from bacteria and various photosynthetic eukaryotes. In particular, novel types of selectivity filters of bacteria are reported adding new examples of the great diversity of the GLR superfamily. The highest variability in GLR sequences was found among the algal sequences (cryptophytes, diatoms, brown and green algae). GLRs of land plants are not closely related to the GLRs of green algae analyzed in this work. The GLR family underwent a great expansion in vascular plants. Among plant GLRs, Clade III includes sequences from Physcomitrella patens, Marchantia polymorpha and gymnosperms and can be considered the most ancient, while other clades likely emerged later. In silico analysis allowed the identification of sequences with a putative target to organelles. Sequences with a predicted localization to mitochondria and chloroplasts are randomly distributed among different type of GLRs, suggesting that no compartment-related specific function has been maintained across the species.
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Affiliation(s)
| | - Enrico Teardo
- Department of Biology, University of Padova, Italy; CNR Institute of Neuroscience, Padova, Italy
| | - Ildikò Szabò
- Department of Biology, University of Padova, Italy; CNR Institute of Neuroscience, Padova, Italy
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Alberstein R, Grey R, Zimmet A, Simmons DK, Mayer ML. Glycine activated ion channel subunits encoded by ctenophore glutamate receptor genes. Proc Natl Acad Sci U S A 2015; 112:E6048-57. [PMID: 26460032 PMCID: PMC4640758 DOI: 10.1073/pnas.1513771112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent genome projects for ctenophores have revealed the presence of numerous ionotropic glutamate receptors (iGluRs) in Mnemiopsis leidyi and Pleurobrachia bachei, among our earliest metazoan ancestors. Sequence alignments and phylogenetic analysis show that these form a distinct clade from the well-characterized AMPA, kainate, and NMDA iGluR subtypes found in vertebrates. Although annotated as glutamate and kainate receptors, crystal structures of the ML032222a and PbiGluR3 ligand-binding domains (LBDs) reveal endogenous glycine in the binding pocket, whereas ligand-binding assays show that glycine binds with nanomolar affinity; biochemical assays and structural analysis establish that glutamate is occluded from the binding cavity. Further analysis reveals ctenophore-specific features, such as an interdomain Arg-Glu salt bridge, present only in subunits that bind glycine, but also a conserved disulfide in loop 1 of the LBD that is found in all vertebrate NMDA but not AMPA or kainate receptors. We hypothesize that ctenophore iGluRs are related to an early ancestor of NMDA receptors, suggesting a common evolutionary path for ctenophores and bilaterian species, and suggest that future work should consider both glycine and glutamate as candidate neurotransmitters in ctenophore species.
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Affiliation(s)
- Robert Alberstein
- Laboratory of Cellular and Molecular Neurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Richard Grey
- Laboratory of Cellular and Molecular Neurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Austin Zimmet
- Laboratory of Cellular and Molecular Neurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - David K Simmons
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080
| | - Mark L Mayer
- Laboratory of Cellular and Molecular Neurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892;
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Lomash S, Chittori S, Brown P, Mayer ML. Anions mediate ligand binding in Adineta vaga glutamate receptor ion channels. Structure 2013; 21:414-25. [PMID: 23434404 DOI: 10.1016/j.str.2013.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 01/10/2023]
Abstract
AvGluR1, a glutamate receptor ion channel from the primitive eukaryote Adineta vaga, is activated by alanine, cysteine, methionine, and phenylalanine, which produce lectin-sensitive desensitizing responses like those to glutamate, aspartate, and serine. AvGluR1 LBD crystal structures reveal an unusual scheme for binding dissimilar ligands that may be utilized by distantly related odorant/chemosensory receptors. Arginine residues in domain 2 coordinate the γ-carboxyl group of glutamate, whereas in the alanine, methionine, and serine complexes a chloride ion acts as a surrogate ligand, replacing the γ-carboxyl group. Removal of Cl(-) lowers affinity for these ligands but not for glutamate or aspartate nor for phenylalanine, which occludes the anion binding site and binds with low affinity. AvGluR1 LBD crystal structures and sedimentation analysis also provide insights into the evolutionary link between prokaryotic and eukaryotic iGluRs and reveal features unique to both classes, emphasizing the need for additional structure-based studies on iGluR-ligand interactions.
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Affiliation(s)
- Suvendu Lomash
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development/NIH/DHHS, Bethesda, MD 20892, USA
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Abstract
X-ray crystal structures for the soluble amino-terminal and ligand-binding domains of glutamate receptor ion channels, combined with a 3.6-Å-resolution structure of the full-length AMPA receptor GluA2 homotetramer, provide unique insights into the mechanisms of the assembly and function of glutamate receptor ion channels. Increasingly sophisticated biochemical, computational, and electrophysiological experiments are beginning to reveal the mechanism of action of partial agonists and suggest new models for the mechanism of action of allosteric modulators. Newly identified NMDA receptor ligands acting at novel sites offer hope for the development of subtype-selective modulators. The many unresolved issues include the role of the amino-terminal domain in AMPA receptor signaling and the mechanisms by which auxiliary proteins regulate receptor activity. The structural basis for ion permeation and ion channel block also remain areas of uncertainty, and despite substantial progress, molecular dynamics simulations have yet to reveal how glutamate binding opens the ion channel pore.
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Affiliation(s)
- Janesh Kumar
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, NICHD, NIH, DHHS, Bethesda, Maryland 20892, USA
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9
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Kim M, Rho Y, Jin KS, Ahn B, Jung S, Kim H, Ree M. pH-dependent structures of ferritin and apoferritin in solution: disassembly and reassembly. Biomacromolecules 2011; 12:1629-40. [PMID: 21446722 DOI: 10.1021/bm200026v] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The pH-dependent structures of the ferritin shell (apoferritin, 24-mer) and the ferrihydrite core, under physiological conditions that permit enzymatic activity, were investigated by synchrotron small-angle X-ray scattering (SAXS). The solution structure of apoferritin was found to be nearly identical to the crystal structure. The shell thickness and hollow core volumes were estimated. The intact hollow spherical apoferritin was stable over a wide pH range, 3.40-10.0, and the ferrihydrite core was stable over the pH range 2.10-10.0. The apoferritin subunits underwent aggregation below pH 0.80, whereas the ferrihydrite cores aggregated below pH 2.10 as a result of the disassembly of the ferritin shell under the strongly acidic conditions. As the pH decreased from 3.40 to 0.80, apoferritin underwent stepwise disassembly by first forming a hollow sphere with two holes, then a headset-shaped structure, and, finally, rodlike oligomers. As the pH was increased from pH 1.96, the disassembled rodlike oligomers recovered only to the headset-shaped structure, and the disassembled headset-shaped intermediates recovered only to the hollow spherical structure with two hole defects. The apoferritin hole defects that formed during the disassembly process did not heal as the pH was increased to neutral or slightly basic conditions. The pH-induced apoferritin disassembly and reassembly processes were not fully reversible, although they were pseudoreversible over a limited pH range, between 10.0 and 2.66.
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Affiliation(s)
- Mihee Kim
- Department of Chemistry, Division of Advanced Material Science, BK School of Molecular Science, Pohang University of Science and Technology, Pohang, Republic of Korea
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Jin KS, Shin SR, Ahn B, Jin S, Rho Y, Kim H, Kim SJ, Ree M. Effect of C(60) fullerene on the duplex formation of i-motif DNA with complementary DNA in solution. J Phys Chem B 2010; 114:4783-8. [PMID: 20218585 DOI: 10.1021/jp9122453] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural effects of fullerene on i-motif DNA were investigated by characterizing the structures of fullerene-free and fullerene-bound i-motif DNA, in the presence of cDNA and in solutions of varying pH, using circular dichroism and synchrotron small-angle X-ray scattering. To facilitate a direct structural comparison between the i-motif and duplex structures in response to pH stimulus, we developed atomic scale structural models for the duplex and i-motif DNA structures, and for the C(60)/i-motif DNA hybrid associated with the cDNA strand, assuming that the DNA strands are present in an ideal right-handed helical conformation. We found that fullerene shifted the pH-induced conformational transition between the i-motif and the duplex structure, possibly due to the hydrophobic interactions between the terminal fullerenes and between the terminal fullerenes and an internal TAA loop in the DNA strand. The hybrid structure showed a dramatic reduction in cyclic hysteresis.
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Affiliation(s)
- Kyeong Sik Jin
- Pohang Accelerator Laboratory, Department of Chemistry, National Research Lab for Polymer Synthesis and Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, Division of Advanced Materials Science, Polymer Research Institute, and BK School of Molecular Science, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Republic of Korea
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A light-gated, potassium-selective glutamate receptor for the optical inhibition of neuronal firing. Nat Neurosci 2010; 13:1027-32. [PMID: 20581843 PMCID: PMC2915903 DOI: 10.1038/nn.2589] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 05/26/2010] [Indexed: 12/12/2022]
Abstract
Genetically targeted light-activated ion channels and pumps make it possible to determine the role of specific neurons in neuronal circuits, information processing and behavior. Here, we describe the development of a K+-selective ionotropic glutamate receptor that reversibly inhibits neuronal activity in response to light in dissociated neurons and brain slice and reversibly suppresses behavior in zebrafish. The receptor is a chimera of the pore region of a K+-selective bacterial glutamate receptor and the ligand binding domain of the light-gated mammalian kainate receptor (iGluR6/GluK2). This hyperpolarizing light-gated channel, HyLighter, is turned on by a brief light pulse at one wavelength and turned off by a pulse at a second wavelength. The control is obtained at moderate intensity. After optical activation, the photo-current and optical silencing of activity persist in the dark for extended periods. The low light requirement and bi-stability of HyLighter represent advantages for the dissection of neural circuitry.
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Jin S, Higashihara T, Jin KS, Yoon J, Rho Y, Ahn B, Kim J, Hirao A, Ree M. Synchrotron X-ray Scattering Characterization of the Molecular Structures of Star Polystyrenes with Varying Numbers of Arms. J Phys Chem B 2010; 114:6247-57. [DOI: 10.1021/jp911928b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sangwoo Jin
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Tomoya Higashihara
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Kyeong Sik Jin
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Jinhwan Yoon
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Yecheol Rho
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Byungcheol Ahn
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Jehan Kim
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Akira Hirao
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
| | - Moonhor Ree
- Department of Chemistry, National Research Lab for Polymer Synthesis & Physics, Center for Electro-Photo Behaviors in Advanced Molecular Systems, BK School of Molecular Science, Division of Advanced Materials Science, and Polymer Research Institute, Pohang University of Science & Technology (POSTECH), Pohang 790-784, Republic of Korea, Polymeric and Organic Materials Department, Graduate School of Science and Engineering, Tokyo Institute of Technology, H-127, 2-12-1, Ohokayama, Meguro-ku, Tokyo 152-8552,
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Jin KS, Shin SR, Ahn B, Rho Y, Kim SJ, Ree M. pH-dependent structures of an i-motif DNA in solution. J Phys Chem B 2009; 113:1852-6. [PMID: 19173566 DOI: 10.1021/jp808186z] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated for the first time the structure of i-motif DNA in solution at various pH conditions by using synchrotron small-angle X-ray scattering technique. To facilitate direct structural comparison between solution structures of i-motif DNA at various pH values, we created atomic coordinates of i-motif DNA from a fully folded to unfolded atomic model. Under mild acidic conditions, the conformations for i-motif DNA appeared to be similar to that of the partially unfolded i-motif atomic model in overall shape, rather than the fully folded i-motif atomic model. Collectively, our observations indicate that i-motif DNA molecule is structurally dynamic over a wide pH range, adopting multiple conformations ranging from the folded i-motif structure to a random coil conformation. As the i-motif structure has been used as an important component in nanomachines, we can therefore believe that the structural evidence presented herein will promote the development of future DNA-based molecular-actuator devices.
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Affiliation(s)
- Kyeong Sik Jin
- Department of Chemistry, National Research Laboratory for Polymer Synthesis and Physics, Pohang Accelerator Laboratory, Center for Electro-Photo Behaviors in Advanced Molecular Systems, Polymer Research Institute, Republic of Korea.
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15
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Jin KS, Rho Y, Kim J, Kim H, Kim IJ, Ree M. Synchrotron Small-Angle X-ray Scattering Studies of the Structure of Porcine Pepsin under Various pH Conditions. J Phys Chem B 2008; 112:15821-7. [DOI: 10.1021/jp805940d] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyeong Sik Jin
- Department of Chemistry, National Research Laboratory for Polymer Synthesis and Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, Polymer Research Institute, and BK School of Molecular Science, Pohang University of Science and Technology (Postech), Pohang 790-784, Republic of Korea, and Department of Microbiology, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju 780-714, Republic of Korea
| | - Yecheol Rho
- Department of Chemistry, National Research Laboratory for Polymer Synthesis and Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, Polymer Research Institute, and BK School of Molecular Science, Pohang University of Science and Technology (Postech), Pohang 790-784, Republic of Korea, and Department of Microbiology, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju 780-714, Republic of Korea
| | - Jehan Kim
- Department of Chemistry, National Research Laboratory for Polymer Synthesis and Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, Polymer Research Institute, and BK School of Molecular Science, Pohang University of Science and Technology (Postech), Pohang 790-784, Republic of Korea, and Department of Microbiology, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju 780-714, Republic of Korea
| | - Heesoo Kim
- Department of Chemistry, National Research Laboratory for Polymer Synthesis and Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, Polymer Research Institute, and BK School of Molecular Science, Pohang University of Science and Technology (Postech), Pohang 790-784, Republic of Korea, and Department of Microbiology, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju 780-714, Republic of Korea
| | - Ik Jung Kim
- Department of Chemistry, National Research Laboratory for Polymer Synthesis and Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, Polymer Research Institute, and BK School of Molecular Science, Pohang University of Science and Technology (Postech), Pohang 790-784, Republic of Korea, and Department of Microbiology, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju 780-714, Republic of Korea
| | - Moonhor Ree
- Department of Chemistry, National Research Laboratory for Polymer Synthesis and Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, Polymer Research Institute, and BK School of Molecular Science, Pohang University of Science and Technology (Postech), Pohang 790-784, Republic of Korea, and Department of Microbiology, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju 780-714, Republic of Korea
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16
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Yoon J, Jin S, Ahn B, Rho Y, Hirai T, Maeda R, Hayakawa T, Kim J, Kim KW, Ree M. Phase Transitions in Thin Films of a Diblock Copolymer Composed of a Linear Polymer Block and a Brush Polymer Block with Mesogenic Oligothiophenyl Bristles. Macromolecules 2008. [DOI: 10.1021/ma801727r] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jinhwan Yoon
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, and Department of Organic & Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S8-26, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Sangwoo Jin
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, and Department of Organic & Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S8-26, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Byungcheol Ahn
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, and Department of Organic & Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S8-26, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Yecheol Rho
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, and Department of Organic & Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S8-26, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Tomoyasu Hirai
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, and Department of Organic & Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S8-26, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Rina Maeda
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, and Department of Organic & Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S8-26, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Teruaki Hayakawa
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, and Department of Organic & Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S8-26, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Jehan Kim
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, and Department of Organic & Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S8-26, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Kwang-Woo Kim
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, and Department of Organic & Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S8-26, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Moonhor Ree
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, and Department of Organic & Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S8-26, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
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17
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Yoon J, Kim KW, Kim J, Heo K, Jin KS, Jin S, Shin TJ, Lee B, Rho Y, Ahn B, Ree M. Small-angle x-ray scattering station 4C2 BL of pohang accelerator laboratory for advance in Korean polymer science. Macromol Res 2008. [DOI: 10.1007/bf03218563] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Yoon J, Jung SY, Ahn B, Heo K, Jin S, Iyoda T, Yoshida H, Ree M. Order−Order and Order−Disorder Transitions in Thin Films of an Amphiphilic Liquid Crystalline Diblock Copolymer. J Phys Chem B 2008; 112:8486-95. [DOI: 10.1021/jp803664h] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jinhwan Yoon
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK school of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, Graduate School of Environmental Science, Tokyo Metropolitan University, 1-1- Minami-Osawa, Hachiouji, Tokyo 192-0397, Japan, CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan, and Chemical Resources Laboratory,
| | - Sun Young Jung
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK school of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, Graduate School of Environmental Science, Tokyo Metropolitan University, 1-1- Minami-Osawa, Hachiouji, Tokyo 192-0397, Japan, CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan, and Chemical Resources Laboratory,
| | - Byungcheol Ahn
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK school of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, Graduate School of Environmental Science, Tokyo Metropolitan University, 1-1- Minami-Osawa, Hachiouji, Tokyo 192-0397, Japan, CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan, and Chemical Resources Laboratory,
| | - Kyuyoung Heo
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK school of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, Graduate School of Environmental Science, Tokyo Metropolitan University, 1-1- Minami-Osawa, Hachiouji, Tokyo 192-0397, Japan, CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan, and Chemical Resources Laboratory,
| | - Sangwoo Jin
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK school of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, Graduate School of Environmental Science, Tokyo Metropolitan University, 1-1- Minami-Osawa, Hachiouji, Tokyo 192-0397, Japan, CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan, and Chemical Resources Laboratory,
| | - Tomokazu Iyoda
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK school of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, Graduate School of Environmental Science, Tokyo Metropolitan University, 1-1- Minami-Osawa, Hachiouji, Tokyo 192-0397, Japan, CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan, and Chemical Resources Laboratory,
| | - Hirohisa Yoshida
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK school of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, Graduate School of Environmental Science, Tokyo Metropolitan University, 1-1- Minami-Osawa, Hachiouji, Tokyo 192-0397, Japan, CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan, and Chemical Resources Laboratory,
| | - Moonhor Ree
- Department of Chemistry, National Research Laboratory for Polymer Synthesis & Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, and BK school of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea, Graduate School of Environmental Science, Tokyo Metropolitan University, 1-1- Minami-Osawa, Hachiouji, Tokyo 192-0397, Japan, CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan, and Chemical Resources Laboratory,
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