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107. Structural and mutational analysis of tRNA intron-splicing endonuclease from Thermoplasma acidophilum DSM 1728: catalytic mechanism of tRNA intron-splicing endonucleases

Author

Kim, Young Kwan, Mizutani, Kenji, Rhee, Kyung-Hee, Nam, Ki-Hyun, Lee, Won Ho, Lee, Eun Hye, Kim, Eunice Eunkyeong, Park, Sam-Yong, and Hwang, Kwang Yeon

Subjects
Transfer RNA -- Physiological aspects, Nucleases -- Physiological aspects, Lactobacillus acidophilus -- Genetic aspects, Lactobacillus acidophilus -- Physiological aspects, Introns -- Physiological aspects, Genetic engineering -- Research, Biological sciences
Abstract

In archaea, RNA endonucleases that act specifically on RNA with bulge-helix-bulge motifs play the main role in the recognition and excision of introns, while the eukaryal enzymes use a measuring mechanism to determine the positions of the universally positioned splice sites relative to the conserved domain of pre-tRNA. Two crystallographic structures of tRNA intron-splicing endonuclease from Thermoplasma acidophilum DSM 1728 (End[A.sub.Ta]) have been solved to 2.5-[Angstrom], and 2.7-[Angstrom] resolution by molecular replacement, using the 2.7-[Angstrom] resolution data as the initial model and the single-wavelength anomalous-dispersion phasing method using selenomethionine as anomalous signals, respectively. The models show that End[A.sub.Ta] is a homodimer and that it has overall folding similar to that of other archaeal tRNA endonucleases. From structural and mutational analyses of H236A, Y229F, and K265I in vitro, we have demonstrated that they play critical roles in recognizing the splice site and in cleaving the pre-tRNA substrate.

Published
2007

125. Structural Flexibility of Peripheral Loops and Extended C-Term Domain of Short Length Substrate Binding Protein from Rhodothermus marinus

Author

Bae, Ji-Eun, Kim, In Jung, Xu, Yongbin, and Nam, Ki Hyun

Subjects
life_sciences_other
Abstract

Substrate binding proteins (SBP) bind to specific ligands in the periplasmic region and bind to membrane proteins to participate in transport or signal transduction. Typical SBPs consist of two α/β domains and recognize the substrate by hinge motion between two domains. Conversely, short length Rhodothermus marinus SBP (named as RmSBP) exists around the methyl-accepting chemotaxis protein. We previously determined the crystal structure of RmSBP consisting of a single α/β domain, but the substrate recognition mechanism is still unclear. To better understand the short length RmSBP, we performed comparative structure analysis, computational substrate docking, and X-ray crystallographic study. RmSBP shares a high level of similarity in α/β domain with other SBP proteins, but it has a distinct topology in the C-term region. The substrate binding model suggested that conformational change in the peripheral region of RmSBP was required to recognize the substrate. We determined the crystal structures of RmSBP at pH 5.5, 6.0, and 7.5. RmSBP showed structural flexibility of the β1-α2 loop, β5-β6 loop, and extended C-term domain based on the electron density map and temperature B-factor analysis. These results provide information that will further the understanding of the function of the short length SBP.

Published
2019

126. Sample delivery using capillary and delivery medium for serial crystallography

Author

Cho Yun Je and Nam Ki Hyun

Subjects
Crystallography, Materials science, Capillary action, Sample (graphics), Volumetric flow rate
Abstract

Serial crystallography (SX) is an innovative technology in structural biology that enables the visualization of molecular dynamics of macromolecules at room temperature. SX experiments always require a considerable amount of effort to deliver a crystal sample to the X-ray interaction point continuously and reliably. Here, a sample delivery method using a capillary and a delivery medium is introduced. The crystals embedded in the delivery medium can pass through the capillary tube, which is aligned with the X-ray beam, at very low flow rates without requiring elaborate delivery techniques and drastically reducing sample consumption. This simple but highly efficient sample delivery method can allow researchers to deliver crystals precisely to X-rays in SX experiments.

Published
2019

127. Shortening injection matrix for serial crystallography

Author

Nam, Ki Hyun

Subjects
0301 basic medicine, Materials science, lcsh:Medicine, 02 engineering and technology, Crystal structure, Article, law.invention, Matrix (chemical analysis), 03 medical and health sciences, law, Phase (matter), lcsh:Science, X-ray crystallography, Millisecond, Multidisciplinary, Nanocrystallography, Scattering, lcsh:R, Injector, 021001 nanoscience & nanotechnology, Volumetric flow rate, Crystallography, 030104 developmental biology, Syringe needle, lcsh:Q, 0210 nano-technology
Abstract

Serial crystallography (SX) allows crystal structures to be observed at room temperature through the steady delivery of crystals to the X-ray interaction point. Viscous delivery media are advantageous because they afford efficient sample delivery from an injector or syringe at a low flow rate. Hydrophobic delivery media, such as lipidic cubic phase (LCP) or grease, provide a very stable injection stream and are widely used. The development of new hydrophobic delivery materials can expand opportunities for future SX studies with various samples. Here, I introduce fat-based shortening as a delivery medium for SX experiments. This material is commercially available at low cost and is straightforward to handle because its phase (i.e., solid or liquid) can be controlled by temperature. Shortening was extruded from a syringe needle in a very stable injection stream even below 200 nl/min. X-ray exposed shortening produced several background scattering rings, which have similar or lower intensities than those of LCP and contribute negligibly to data processing. Serial millisecond crystallography was performed using two shortening delivery media, and the room temperature crystal structures of lysozyme and glucose isomerase were successfully determined at resolutions of 1.5–2.0 Å. Therefore, shortening can be used as a sample delivery medium in SX experiments.

Published
2019

128. Apparent power-law behavior of water's isothermal compressibility and correlation length upon supercooling

Author

Spah, Alexander, Pathak, Harshad, Kim, Kyung Hwan, Perakis, Fivos, Mariedahl, Daniel, Amann-Winkel, Katrin, Sellberg, Jonas A., Lee, Jae Hyuk, Kim, Sangsoo, Park, Jaehyun, Nam, Ki Hyun, Katayama, Tetsuo, Nilsson, Anders, Spah, Alexander, Pathak, Harshad, Kim, Kyung Hwan, Perakis, Fivos, Mariedahl, Daniel, Amann-Winkel, Katrin, Sellberg, Jonas A., Lee, Jae Hyuk, Kim, Sangsoo, Park, Jaehyun, Nam, Ki Hyun, Katayama, Tetsuo, and Nilsson, Anders

Abstract

The isothermal compressibility and correlation length of supercooled water obtained from small-angle X-ray scattering (SAXS) were analyzed by fits based on an apparent power-law in the temperature range from 280 K down to the temperature of maximum compressibility at 229 K. Although the increase in thermodynamic response functions is not towards a critical point, it is still possible to obtain an apparent power law all the way to the maximum values with best-fit exponents of gamma = 0.40 +/- 0.01 for the isothermal compressibility and nu = 0.26 +/- 0.03 for the correlation length. The ratio between these exponents is close to a value of approximate to 0.5, as expected for a critical point, indicating the proximity of a potential second critical point. Comparison of gamma obtained from experiment with molecular dynamics simulations on the iAMOEBA water model shows that it would be located at pressures in the neighborhood of 1 kbar. The high value and sharpness of the compressibility maximum observed in the experiment are not reproduced by any of the existing classical water models, thus inviting further development of simulation models of water., QC 20190125

Published
2019
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130. Resistive Switching in Amorphous GeSe-Based Resistive Random Access Memory

Author

Kim Chung‐Hyeok, Cho Won‐Ju, Chung Hong‐Bay, Nam Ki‐Hyun, and Kim Jang‐Han

Subjects
Materials science, business.industry, Resistive switching, Biomedical Engineering, Optoelectronics, General Materials Science, Bioengineering, General Chemistry, Condensed Matter Physics, business, Resistive random-access memory, Amorphous solid
Published
2016

143. Apparent power-law behavior of water's isothermal compressibility and correlation length upon supercooling

Author

Späh, Alexander, primary, Pathak, Harshad, additional, Kim, Kyung Hwan, additional, Perakis, Fivos, additional, Mariedahl, Daniel, additional, Amann-Winkel, Katrin, additional, Sellberg, Jonas A., additional, Lee, Jae Hyuk, additional, Kim, Sangsoo, additional, Park, Jaehyun, additional, Nam, Ki Hyun, additional, Katayama, Tetsuo, additional, and Nilsson, Anders, additional

Published
2019
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144. Response to Comment on 'Maxima in the thermodynamic response and correlation functions of deeply supercooled water'

Author

Kim, Kyung Hwan, Spah, Alexander, Pathak, Harshad, Perakis, Fivos, Mariedahl, Daniel, Amann-Winkel, Katrin, Sellberg, Jonas A., Lee, Jae Hyuk, Kim, Sangsoo, Park, Jaehyun, Nam, Ki Hyun, Katayama, Tetsuo, Nilsson, Anders, Kim, Kyung Hwan, Spah, Alexander, Pathak, Harshad, Perakis, Fivos, Mariedahl, Daniel, Amann-Winkel, Katrin, Sellberg, Jonas A., Lee, Jae Hyuk, Kim, Sangsoo, Park, Jaehyun, Nam, Ki Hyun, Katayama, Tetsuo, and Nilsson, Anders

Abstract

Caupin et al. have raised several issues regarding our recent paper on maxima in thermodynamic response and correlation functions in deeply supercooled water. We show that these issues can be addressed without affecting the conclusion of the paper., QC 201805131

Published
2018
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145. Structural and bioinformatics analysis of single-domain substrate-binding protein from Rhodothermus marinus

Author

Nam, Ki Hyun

Abstract

Substrate-binding proteins (SBPs) are key elements in determining the substrate specificity and high affinity of the ATP-binding cassette uptake system. A typical SBP has two domains that recognize substrates and are responsible for the specific substrate delivery. Conversely, in GenBank, genes for SBPs constituting a single domain SBP are often found in vicinity of a methyl-accepting chemotaxis protein gene. However, the molecular function and mechanism of single domain SBPs are not fully elucidated. To understand their molecular functions, we performed a crystallographic study of single domain SBP from Rhodothermus marinus(RmSBP). RmSBP crystals were soaked in solution containing NaBr or HgCl2and their structures determined at 1.75 and 2.3 Å resolution, respectively. RmSBP soaked in NaBr exhibited disorder of the α2-helix, β5-to β6-strand loop, and C-terminus region, showing the structural dynamic region of RmSBP. RmSBP soaked in HgCl2showed that Hg2+bound to Cys145 located between the α5-and α6-helices. The structural properties of RmSBP were compared with those of single domain SBP homologs. These results will contribute to continued identification of the molecular function and mechanism of single domain SBPs.

Published
2024
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146. Shortening injection matrix for serial crystallography.

Author

Nam, Ki Hyun

Subjects
*CRYSTALLOGRAPHY, *CRYSTAL structure, *HYDROPHOBIC interactions, *INFORMATION storage & retrieval systems, *GLUCOSE isomerase
Abstract

Serial crystallography allows crystal structures to be determined at room temperature through the steady delivery of crystals to the X-ray interaction point. Viscous delivery media are advantageous because they afford efficient sample delivery from an injector or syringe at a low flow rate. Hydrophobic delivery media, such as lipidic cubic phase (LCP) or grease, provide a stable injection stream and are widely used. The development of new hydrophobic delivery materials can expand opportunities for future SX studies with various samples. Here, I introduce fat-based shortening as a delivery medium for SX experiments. This material is commercially available at low cost and is straightforward to handle because its phase (i.e., solid or liquid) can be controlled by temperature. Shortening was extruded from a syringe needle in a stable injection stream even below 200 nl/min. X-ray exposed shortening produced several background scattering rings, which have similar or lower intensities than those of LCP and contribute negligibly to data processing. Serial millisecond crystallography was performed using two shortening delivery media, and the room temperature crystal structures of lysozyme and glucose isomerase were successfully determined at resolutions of 1.5–2.0 Å. Therefore, shortening can be used as a sample delivery medium in SX experiments. [ABSTRACT FROM AUTHOR]

Published
2020
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