Hui-Woog Choe - Profile on Academia.edu (original) (raw)
Papers by Hui-Woog Choe
Crystals, 2022
Crystallization remains a bottleneck for determining the three-dimensional X-ray structure of pro... more Crystallization remains a bottleneck for determining the three-dimensional X-ray structure of proteins. Many parameters influence the complexity of protein crystallization. Therefore, it is not easy to systematically examine all of these parameters individually during crystallization because of a limited quantity of purified protein. We studied several factors that influence crystallization including protein concentration, pH, temperature, age, volume of crystallization, inhibitors, metal ions, seeding, and precipitating agents on RuBisCO samples from Alcaligenes eutrophus which are not only freshly purified, but are also dissolved both individually and in combination from microcrystals and precipitated droplets of recycled RuBisCO. Single-, twin-, and/or microcrystals are dependent upon the concentration of RuBisCO by both RuBisCO samples. The morphology, either orthorhombic- or monoclinic-space group, depends upon pH. Furthermore, ammonium sulfate((NH4)2SO4) concentration at 20 °C...
Crystals, 2022
The three-dimensional structure of protein is determined by analyzing diffraction data collected ... more The three-dimensional structure of protein is determined by analyzing diffraction data collected using X-ray beams. However, X-ray beam can damage protein crystals during data collection, lowering the quality of the crystal data. A way to prevent such damage is by treating protein crystals with cryoprotectants. The cryoprotectant stabilizes the protein crystal and prevents lowering the quality of the diffraction data. Many kinds of cryoprotectants are commercially available, and various treatment methods have also been reported. However, incorrect selection or treatment of such cryoprotectants may lead to deterioration of crystal diffraction data when using X-ray beams.
Structural evidence for visual arrestin priming via complexation of phosphoinositols
Structure, 2021
Visual arrestin (Arr1) terminates rhodopsin signaling by blocking its interaction with transducin... more Visual arrestin (Arr1) terminates rhodopsin signaling by blocking its interaction with transducin. To do this, Arr1 translocates from the inner to the outer segment of photoreceptors upon light stimulation. Mounting evidence indicates that inositol phosphates (InsPs) affect Arr1 activity, but the Arr1-InsP molecular interaction remains poorly defined. We report the structure of bovine Arr1 in a ligand-free state featuring a near-complete model of the previously unresolved C-tail, which plays a crucial role in regulating Arr1 activity. InsPs bind to the N-domain basic patch thus displacing the C-tail, suggesting that they prime Arr1 for interaction with rhodopsin and help direct Arr1 translocation. These structures exhibit intact polar cores, suggesting that C-tail removal by InsP binding is insufficient to activate Arr1. These results show how Arr1 activity can be controlled by endogenous InsPs in molecular detail.
Seibutsu Butsuri, 2013
MHC (Major HistoCompatibility) is a dimer protein which is known as antigen peptide presentation ... more MHC (Major HistoCompatibility) is a dimer protein which is known as antigen peptide presentation in the immune system. However, perspectives on the antigen peptide presentation mechanism have not yet been unified. Therefore, we focused on the single molecule motion and chose six different peptides binding MHC/peptide complex for the comparison. We measured multi-molecule analysis to complement molecular dynamics data from single-molecule measurement. We succeeded in confirming the relationship between single-molecule dynamics from Diffracted X-ray Tracking (DXT) and dimer stability from SDS-PAGE. DXT will be observed the in vivo single molecule stability without separation of dimer proteins.
Crystal structure of the active G-protein-coupled receptor opsin in complex with a C-terminal peptide derived from the Galpha subunit of transducin
Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State
Light‐Induced Conformational Changes of the Chromophore and the Protein in Phytochromes: Bacterial Phytochromes as Model Systems
ChemPhysChem, 2010
Recombinant phytochromes Agp1 and Agp2 from Agrobacterium tumefaciens are used as model phytochro... more Recombinant phytochromes Agp1 and Agp2 from Agrobacterium tumefaciens are used as model phytochromes for biochemical and biophysical studies. In biliverdin binding phytochromes the site for covalent attachment of the chromophore lies in the N‐terminal region of the protein, different from plant phytochromes. The issue which stereochemistry the chromophore adopts in the so‐called Pr and Pfr forms is addressed by using a series of locked chromophores which form spectrally characteristic adducts with Agp1 and Agp2. Studies on light‐induced conformational changes of Agp1 give an insight into how the intrinsic histidine kinase is modulated by light. Comparison of the crystal structure of an Agp1 fragment with other phytochrome crystal structures supports the idea that a light induced rearrangement of subunits within the homodimer modulates the activity of the kinase.
European Journal of Biochemistry
Two mutants of ribonuclease T1 (RNaseTl), [59-tyrosine]ribonuclease T1 (W59Y) and [45tryptophan,5... more Two mutants of ribonuclease T1 (RNaseTl), [59-tyrosine]ribonuclease T1 (W59Y) and [45tryptophan,59-tyrosine]ribonuclease T1 (Y45W/W59Y) possess between 150% and 190% wild-type activity. They have been crystallised as complexes of the inhibitor 2'-guanylic acid and analysed by X-ray diffraction at resolutions of 0.23 nm and 0.24 nm, respectively. The space group for both is monoclinic, P2,, with two molecules/asymmetric unit, W59Y: a = 4.934 nm, b = 4.820 nm, c = 4.025 nm, p = 90.29'. Y45WW59Y: a = 4.915 nm, b = 4.815 nm, c = 4.015 nm, p = 90.35'. Compared to wild-type RNaseTl in complex with 2'-guanylic acid (2'GMP) both mutant inhibitor complexes indicate that the replacement of Trp59 by Tyr leads to a 0.04-nm inward shift of the single a-helix and to significant differences in the active-site geometry, inhibitor conformation and inhibitor binding. Calorimetric studies of a range of mutants [24-tryptophan]ribonuclease T1 (Y24W), [42-tryptophan]ribonuclease T1 (Y42W), [45-tryptophan]ribonuclease T1 (Y45W), [92alanine]ribonuclease T1 (H92A) and [92-threonine]ribonuclease T1 (H92T) with and without the further mutation Trp59-Tyr showed that mutant proteins for which Trp59 is replaced by Tyr exhibit slightly decreased thermal stability.
Scheerer-Hildbrand-PNAS-2009-Appendix-SI-Regular
Scheerer-Hildbrand-PNAS-2009-Appendix-Regular
Scheerer-Hildbrand-PNAS-2009-SI
Crystallization and preliminary X-ray diffraction studies of α-cyclodextrin glucanotransferase isolated from Bacillus macerans
Acta Crystallographica Section D-biological Crystallography, 2003
Choe-Scheerer-Ernst-Nature-2011-SI
Scheerer-Ernst-Nature-2008-SI
Kim-Scheerer-Sommer-Nature-2013-SI
Park-Scheerer-Ernst-Nature-2008-SI
Crystallization and preliminary X-ray diffraction studies of alpha-cyclodextrin glucanotransferase isolated from Bacillus macerans
Acta crystallographica. Section D, Biological crystallography, 2003
Single crystals of alpha-cyclodextrin glucanotransferase isolated from Bacillus macerans have bee... more Single crystals of alpha-cyclodextrin glucanotransferase isolated from Bacillus macerans have been grown with polyethylene glycol 6000 as a precipitating agent by sitting-drop vapour diffusion at room temperature. The crystals were suitable for X-ray analysis and diffracted to at least 2.0 A (space group P2(1)2(1)2(1)), with unit-cell parameters a = 66.79 (2), b = 79.66 (1), c = 141.16 (1) A. Assuming the asymmetric cell to be occupied by a monomer of 74 kDa, the unit cell contains 42.6% solvent with a crystal Volume per protein mass, V(M), of 2.53 A(3) Da(-1).
Cyclodextrin glucanotransferase [CGTase, E.C.2.4.1.19] is an extracellular enzyme, which catalyze... more Cyclodextrin glucanotransferase [CGTase, E.C.2.4.1.19] is an extracellular enzyme, which catalyzes the formation of a-, j3-, ;-CDs from starch. Their proportions of formations depend on enzyme sources and reaction conditions. To understand what determines the product specificity of CGTases, we examined the alteration of product specificity of CGTase from Bacillus macerans by organic solvents and pH. At acidic pH range less than pH 6 where the enzyme was unstable, the ratio of a-//~-CD production was increased 4 times more than that at neutral pH range. As we increased the concentration of 2-butanol, a-//3-CD ratio was proportionally increased but/ratio remained constant. The a-/~-CD ratio of products was increased in the reaction media which yielded low products.
Calcium-dependent assembly of centrin-G-protein complex in photoreceptor cells
Molecular and cellular biology, 2002
Photoexcitation of rhodopsin activates a heterotrimeric G-protein cascade leading to cyclic GMP h... more Photoexcitation of rhodopsin activates a heterotrimeric G-protein cascade leading to cyclic GMP hydrolysis in vertebrate photoreceptors. Light-induced exchanges of the visual G-protein transducin between the outer and inner segment of rod photoreceptors occur through the narrow connecting cilium. Here we demonstrate that transducin colocalizes with the Ca(2+)-binding protein centrin 1 in a specific domain of this cilium. Coimmunoprecipitation, centrifugation, centrin overlay, size exclusion chromatography, and kinetic light-scattering experiments indicate that Ca(2+)-activated centrin 1 binds with high affinity and specificity to transducin. The assembly of centrin-G-protein complex is mediated by the betagamma-complex. The Ca(2+)-dependent assembly of a G protein with centrin is a novel aspect of the supply of signaling proteins in sensory cells and a potential link between molecular translocations and signal transduction in general.
Crystals, 2022
Crystallization remains a bottleneck for determining the three-dimensional X-ray structure of pro... more Crystallization remains a bottleneck for determining the three-dimensional X-ray structure of proteins. Many parameters influence the complexity of protein crystallization. Therefore, it is not easy to systematically examine all of these parameters individually during crystallization because of a limited quantity of purified protein. We studied several factors that influence crystallization including protein concentration, pH, temperature, age, volume of crystallization, inhibitors, metal ions, seeding, and precipitating agents on RuBisCO samples from Alcaligenes eutrophus which are not only freshly purified, but are also dissolved both individually and in combination from microcrystals and precipitated droplets of recycled RuBisCO. Single-, twin-, and/or microcrystals are dependent upon the concentration of RuBisCO by both RuBisCO samples. The morphology, either orthorhombic- or monoclinic-space group, depends upon pH. Furthermore, ammonium sulfate((NH4)2SO4) concentration at 20 °C...
Crystals, 2022
The three-dimensional structure of protein is determined by analyzing diffraction data collected ... more The three-dimensional structure of protein is determined by analyzing diffraction data collected using X-ray beams. However, X-ray beam can damage protein crystals during data collection, lowering the quality of the crystal data. A way to prevent such damage is by treating protein crystals with cryoprotectants. The cryoprotectant stabilizes the protein crystal and prevents lowering the quality of the diffraction data. Many kinds of cryoprotectants are commercially available, and various treatment methods have also been reported. However, incorrect selection or treatment of such cryoprotectants may lead to deterioration of crystal diffraction data when using X-ray beams.
Structural evidence for visual arrestin priming via complexation of phosphoinositols
Structure, 2021
Visual arrestin (Arr1) terminates rhodopsin signaling by blocking its interaction with transducin... more Visual arrestin (Arr1) terminates rhodopsin signaling by blocking its interaction with transducin. To do this, Arr1 translocates from the inner to the outer segment of photoreceptors upon light stimulation. Mounting evidence indicates that inositol phosphates (InsPs) affect Arr1 activity, but the Arr1-InsP molecular interaction remains poorly defined. We report the structure of bovine Arr1 in a ligand-free state featuring a near-complete model of the previously unresolved C-tail, which plays a crucial role in regulating Arr1 activity. InsPs bind to the N-domain basic patch thus displacing the C-tail, suggesting that they prime Arr1 for interaction with rhodopsin and help direct Arr1 translocation. These structures exhibit intact polar cores, suggesting that C-tail removal by InsP binding is insufficient to activate Arr1. These results show how Arr1 activity can be controlled by endogenous InsPs in molecular detail.
Seibutsu Butsuri, 2013
MHC (Major HistoCompatibility) is a dimer protein which is known as antigen peptide presentation ... more MHC (Major HistoCompatibility) is a dimer protein which is known as antigen peptide presentation in the immune system. However, perspectives on the antigen peptide presentation mechanism have not yet been unified. Therefore, we focused on the single molecule motion and chose six different peptides binding MHC/peptide complex for the comparison. We measured multi-molecule analysis to complement molecular dynamics data from single-molecule measurement. We succeeded in confirming the relationship between single-molecule dynamics from Diffracted X-ray Tracking (DXT) and dimer stability from SDS-PAGE. DXT will be observed the in vivo single molecule stability without separation of dimer proteins.
Crystal structure of the active G-protein-coupled receptor opsin in complex with a C-terminal peptide derived from the Galpha subunit of transducin
Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State
Light‐Induced Conformational Changes of the Chromophore and the Protein in Phytochromes: Bacterial Phytochromes as Model Systems
ChemPhysChem, 2010
Recombinant phytochromes Agp1 and Agp2 from Agrobacterium tumefaciens are used as model phytochro... more Recombinant phytochromes Agp1 and Agp2 from Agrobacterium tumefaciens are used as model phytochromes for biochemical and biophysical studies. In biliverdin binding phytochromes the site for covalent attachment of the chromophore lies in the N‐terminal region of the protein, different from plant phytochromes. The issue which stereochemistry the chromophore adopts in the so‐called Pr and Pfr forms is addressed by using a series of locked chromophores which form spectrally characteristic adducts with Agp1 and Agp2. Studies on light‐induced conformational changes of Agp1 give an insight into how the intrinsic histidine kinase is modulated by light. Comparison of the crystal structure of an Agp1 fragment with other phytochrome crystal structures supports the idea that a light induced rearrangement of subunits within the homodimer modulates the activity of the kinase.
European Journal of Biochemistry
Two mutants of ribonuclease T1 (RNaseTl), [59-tyrosine]ribonuclease T1 (W59Y) and [45tryptophan,5... more Two mutants of ribonuclease T1 (RNaseTl), [59-tyrosine]ribonuclease T1 (W59Y) and [45tryptophan,59-tyrosine]ribonuclease T1 (Y45W/W59Y) possess between 150% and 190% wild-type activity. They have been crystallised as complexes of the inhibitor 2'-guanylic acid and analysed by X-ray diffraction at resolutions of 0.23 nm and 0.24 nm, respectively. The space group for both is monoclinic, P2,, with two molecules/asymmetric unit, W59Y: a = 4.934 nm, b = 4.820 nm, c = 4.025 nm, p = 90.29'. Y45WW59Y: a = 4.915 nm, b = 4.815 nm, c = 4.015 nm, p = 90.35'. Compared to wild-type RNaseTl in complex with 2'-guanylic acid (2'GMP) both mutant inhibitor complexes indicate that the replacement of Trp59 by Tyr leads to a 0.04-nm inward shift of the single a-helix and to significant differences in the active-site geometry, inhibitor conformation and inhibitor binding. Calorimetric studies of a range of mutants [24-tryptophan]ribonuclease T1 (Y24W), [42-tryptophan]ribonuclease T1 (Y42W), [45-tryptophan]ribonuclease T1 (Y45W), [92alanine]ribonuclease T1 (H92A) and [92-threonine]ribonuclease T1 (H92T) with and without the further mutation Trp59-Tyr showed that mutant proteins for which Trp59 is replaced by Tyr exhibit slightly decreased thermal stability.
Scheerer-Hildbrand-PNAS-2009-Appendix-SI-Regular
Scheerer-Hildbrand-PNAS-2009-Appendix-Regular
Scheerer-Hildbrand-PNAS-2009-SI
Crystallization and preliminary X-ray diffraction studies of α-cyclodextrin glucanotransferase isolated from Bacillus macerans
Acta Crystallographica Section D-biological Crystallography, 2003
Choe-Scheerer-Ernst-Nature-2011-SI
Scheerer-Ernst-Nature-2008-SI
Kim-Scheerer-Sommer-Nature-2013-SI
Park-Scheerer-Ernst-Nature-2008-SI
Crystallization and preliminary X-ray diffraction studies of alpha-cyclodextrin glucanotransferase isolated from Bacillus macerans
Acta crystallographica. Section D, Biological crystallography, 2003
Single crystals of alpha-cyclodextrin glucanotransferase isolated from Bacillus macerans have bee... more Single crystals of alpha-cyclodextrin glucanotransferase isolated from Bacillus macerans have been grown with polyethylene glycol 6000 as a precipitating agent by sitting-drop vapour diffusion at room temperature. The crystals were suitable for X-ray analysis and diffracted to at least 2.0 A (space group P2(1)2(1)2(1)), with unit-cell parameters a = 66.79 (2), b = 79.66 (1), c = 141.16 (1) A. Assuming the asymmetric cell to be occupied by a monomer of 74 kDa, the unit cell contains 42.6% solvent with a crystal Volume per protein mass, V(M), of 2.53 A(3) Da(-1).
Cyclodextrin glucanotransferase [CGTase, E.C.2.4.1.19] is an extracellular enzyme, which catalyze... more Cyclodextrin glucanotransferase [CGTase, E.C.2.4.1.19] is an extracellular enzyme, which catalyzes the formation of a-, j3-, ;-CDs from starch. Their proportions of formations depend on enzyme sources and reaction conditions. To understand what determines the product specificity of CGTases, we examined the alteration of product specificity of CGTase from Bacillus macerans by organic solvents and pH. At acidic pH range less than pH 6 where the enzyme was unstable, the ratio of a-//~-CD production was increased 4 times more than that at neutral pH range. As we increased the concentration of 2-butanol, a-//3-CD ratio was proportionally increased but/ratio remained constant. The a-/~-CD ratio of products was increased in the reaction media which yielded low products.
Calcium-dependent assembly of centrin-G-protein complex in photoreceptor cells
Molecular and cellular biology, 2002
Photoexcitation of rhodopsin activates a heterotrimeric G-protein cascade leading to cyclic GMP h... more Photoexcitation of rhodopsin activates a heterotrimeric G-protein cascade leading to cyclic GMP hydrolysis in vertebrate photoreceptors. Light-induced exchanges of the visual G-protein transducin between the outer and inner segment of rod photoreceptors occur through the narrow connecting cilium. Here we demonstrate that transducin colocalizes with the Ca(2+)-binding protein centrin 1 in a specific domain of this cilium. Coimmunoprecipitation, centrifugation, centrin overlay, size exclusion chromatography, and kinetic light-scattering experiments indicate that Ca(2+)-activated centrin 1 binds with high affinity and specificity to transducin. The assembly of centrin-G-protein complex is mediated by the betagamma-complex. The Ca(2+)-dependent assembly of a G protein with centrin is a novel aspect of the supply of signaling proteins in sensory cells and a potential link between molecular translocations and signal transduction in general.