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Wilkinson AR, Brewer F, Wright H, Whiteside B, Williams A, Harper L, Wilson AM. A meta-analysis of semiconductor materials fabricated in microgravity. NPJ Microgravity 2024; 10:73. [PMID: 38926402 PMCID: PMC11208414 DOI: 10.1038/s41526-024-00410-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
This meta-analysis of 160 semiconductor crystals that were grown in microgravity on orbital vehicles between 1973 and 2016 is based on publicly available information documented in the literature. This analysis provides comparisons of crystal metrics including size, structure quality, uniformity, and improved performance between crystals grown in microgravity or terrestrially. Improvement in at least one of these metrics was observed for 86% of those materials that included data in their studies.
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Affiliation(s)
- Ashley R Wilkinson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN, USA
| | - Frances Brewer
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN, USA
| | - Hannah Wright
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN, USA
| | - Ben Whiteside
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN, USA
| | - Amari Williams
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN, USA
| | - Lynn Harper
- Ames Research Center, National Aeronautics and Space Administration, Moffett Field, CA, USA
| | - Anne M Wilson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN, USA.
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2
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Medvedeva MV, Kleimenov SY, Samygina VR, Muronetz VI, Schmalhausen EV. S-nitrosylation and S-glutathionylation of GAPDH: Similarities, differences, and relationships. Biochim Biophys Acta Gen Subj 2023; 1867:130418. [PMID: 37355052 DOI: 10.1016/j.bbagen.2023.130418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/24/2023] [Accepted: 06/20/2023] [Indexed: 06/26/2023]
Abstract
The aim of this work was to compare the effect of reversible post-translational modifications, S-nitrosylation and S-glutathionylation, on the properties of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and to reveal the mechanism of the relationship between these modifications. Comparison of S-nitrosylated and S-glutathionylated GAPDH showed that both modifications inactivate the enzyme and change its spatial structure, decreasing the thermal stability of the protein and increasing its sensitivity to trypsin cleavage. Both modifications are reversible in the presence of dithiothreitol, however, in the presence of reduced glutathione and glutaredoxin 1, the reactivation of S-glutathionylated GAPDH is much slower (10% in 2 h) compared to S-nitrosylated GAPDH (60% in 10 min). This suggests that S-glutathionylation is a much less reversible modification compared to S-nitrosylation. Incubation of HEK 293 T cells in the presence of H2O2 or with the NO donor diethylamine NONOate results in accumulation of sulfenated GAPDH (by data of Western blotting) and S-glutathionylated GAPDH (by data of immunoprecipitation with anti-GSH antibodies). Besides GAPDH, a protein of 45 kDa was found to be sulfenated and S-glutathionylated in the cells treated with H2O2 or NO. This protein was identified as beta-actin. The results of this study confirm the previously proposed hypothesis based on in vitro investigations, according to which S-nitrosylation of the catalytic cysteine residue (Cys152) of GAPDH with subsequent formation of cysteine sulfenic acid at Cys152 may promote its S-glutathionylation in the presence of cellular GSH. Presumably, the mechanism may be valid in the case of beta-actin.
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Affiliation(s)
- M V Medvedeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - S Yu Kleimenov
- Bach Institute of Biochemistry, Research Center of Biotechnology of Russian Academy of Sciences, Leninsky prospect 33, bld. 2, Moscow 119071, Russia; Koltzov Institute of Developmental Biology of Russian Academy of Sciences, ul. Vavilova 26, Moscow 119334, Russia
| | - V R Samygina
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre Crystallography and Photonics of Russian Academy of Sciences, Leninsky prospect 59, Moscow 119333, Russia
| | - V I Muronetz
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - E V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia.
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Saha S, Özden C, Samkutty A, Russi S, Cohen A, Stratton MM, Perry SL. Polymer-based microfluidic device for on-chip counter-diffusive crystallization and in situ X-ray crystallography at room temperature. LAB ON A CHIP 2023; 23:2075-2090. [PMID: 36942575 PMCID: PMC10631519 DOI: 10.1039/d2lc01194h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Proteins are long chains of amino acid residues that perform a myriad of functions in living organisms, including enzymatic reactions, signalling, and maintaining structural integrity. Protein function is determined directly by the protein structure. X-ray crystallography is the primary technique for determining the 3D structure of proteins, and facilitates understanding the effects of protein structure on function. The first step towards structure determination is crystallizing the protein of interest. We have developed a centrifugally-actuated microfluidic device that incorporates the fluid handling and metering necessary for protein crystallization. Liquid handling takes advantage of surface forces to control fluid flow and enable metering, without the need for any fluidic or pump connections. Our approach requires only the simple steps of pipetting the crystallization reagents into the device followed by either spinning or shaking to set up counter-diffusive protein crystallization trials. The use of thin, UV-curable polymers with a high level of X-ray transparency allows for in situ X-ray crystallography, eliminating the manual handling of fragile protein crystals and streamlining the process of protein structure analysis. We demonstrate the utility of our device using hen egg white lysozyme as a model system, followed by the crystallization and in situ, room temperature structural analysis of the hub domain of calcium-calmodulin dependent kinase II (CaMKIIβ).
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Affiliation(s)
- Sarthak Saha
- Department of Chemical Engineering, University of Massachusetts Amherst, MA 01003, USA.
| | - Can Özden
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA 01003, USA
| | - Alfred Samkutty
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA 01003, USA
| | - Silvia Russi
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina Cohen
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Margaret M Stratton
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA 01003, USA
| | - Sarah L Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, MA 01003, USA.
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Tran QD, Tran V, Toh LS, Williams PM, Tran NN, Hessel V. Space Medicines for Space Health. ACS Med Chem Lett 2022; 13:1231-1247. [PMID: 35978686 PMCID: PMC9377000 DOI: 10.1021/acsmedchemlett.1c00681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Scientists from around the world are studying the effects of microgravity and cosmic radiation via the "off-Earth" International Space Station (ISS) laboratory platform. The ISS has helped scientists make discoveries that go beyond the basic understanding of Earth. Over 300 medical experiments have been performed to date, with the goal of extending the knowledge gained for the benefit of humanity. This paper gives an overview of these numerous space medical findings, critically identifies challenges and gaps, and puts the achievements into perspective toward long-term space traveling and also adding benefits to our home planet. The medical contents are trifold structured, starting with the well-being of space travelers (astronaut health studies), followed by medical formulation research under space conditions, and then concluding with a blueprint for space pharmaceutical manufacturing. The review covers essential elements of our Earth-based pharmaceutical research such as drug discovery, drug and formulation stability, drug-organ interaction, drug disintegration/bioavailability/pharmacokinetics, pathogen virulence, genome mutation, and body's resistance. The information compiles clinical, medicinal, biological, and chemical research as well as fundamentals and practical applications.
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Affiliation(s)
- Quy Don Tran
- School
of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide 5005, Australia
- Andy
Thomas Centre for Space Resources, University
of Adelaide, Adelaide 5005, Australia
| | - Vienna Tran
- Adelaide
Medical School, University of Adelaide, Adelaide 5005, Australia
| | - Li Shean Toh
- Faculty
of Science, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Philip M. Williams
- Faculty
of Science, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Nam Nghiep Tran
- School
of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide 5005, Australia
- Andy
Thomas Centre for Space Resources, University
of Adelaide, Adelaide 5005, Australia
- Department
of Chemical Engineering, Can Tho University, Can Tho 900000, Vietnam
| | - Volker Hessel
- School
of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide 5005, Australia
- Andy
Thomas Centre for Space Resources, University
of Adelaide, Adelaide 5005, Australia
- School of
Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
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Mechanisms of CP190 Interaction with Architectural Proteins in Drosophila Melanogaster. Int J Mol Sci 2021; 22:ijms222212400. [PMID: 34830280 PMCID: PMC8618245 DOI: 10.3390/ijms222212400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 01/08/2023] Open
Abstract
Most of the known Drosophila architectural proteins interact with an important cofactor, CP190, that contains three domains (BTB, M, and D) that are involved in protein–protein interactions. The highly conserved N-terminal CP190 BTB domain forms a stable homodimer that interacts with unstructured regions in the three best-characterized architectural proteins: dCTCF, Su(Hw), and Pita. Here, we identified two new CP190 partners, CG4730 and CG31365, that interact with the BTB domain. The CP190 BTB resembles the previously characterized human BCL6 BTB domain, which uses its hydrophobic groove to specifically associate with unstructured regions of several transcriptional repressors. Using GST pull-down and yeast two-hybrid assays, we demonstrated that mutations in the hydrophobic groove strongly affect the affinity of CP190 BTB for the architectural proteins. In the yeast two-hybrid assay, we found that architectural proteins use various mechanisms to improve the efficiency of interaction with CP190. Pita and Su(Hw) have two unstructured regions that appear to simultaneously interact with hydrophobic grooves in the BTB dimer. In dCTCF and CG31365, two adjacent regions interact simultaneously with the hydrophobic groove of the BTB and the M domain of CP190. Finally, CG4730 interacts with the BTB, M, and D domains of CP190 simultaneously. These results suggest that architectural proteins use different mechanisms to increase the efficiency of interaction with CP190.
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Eistrikh-Heller PA, Rubinsky SV, Samygina VR, Gabdulkhakov AG, Kovalchuk MV, Mironov AS, Lashkov AA. Crystallization in Microgravity and the Atomic-Resolution Structure of Uridine Phosphorylase from Vibrio cholerae. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Uridine phosphorylases are known as key targets for the development of new anticancer and antiparasitic agents. Crystals of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae were grown in microgravity by the capillary counter-diffusion method on board of the International Space Station. The three-dimensional structure of this enzyme was determined at atomic (1.04 Å) resolution (RCSB PDB ID: 6Z9Z). Alternative conformations of long fragments (β-strands and adjacent loops) of the protein molecule were found for the first time in the three-dimensional structure of uridine phosphorylase in the absence of specific bound ligands. Apparently, these alternative conformations are related to the enzyme function. Conformational analysis with Markov state models demonstrated that conformational rearrangements can occur in the ligand-free state of the enzyme.
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Agapova YK, Altukhov DA, Kamashev DE, Timofeev VI, Smirnova EV, Rakitina TV. Inhibitor Targeting the Interface between Monomers of HU Protein from Spiroplasma melliferum Disrupts Conformational Dynamics and DNA-Binding Properties of the Protein. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520060048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
We present a systematic quality comparison of protein crystals obtained with and without cross-linked protein crystal (CLPC) seeds. Four proteins were used to conduct the experiments, and the results showed that crystals obtained in the presence of CLPC seeds exhibited a better morphology. In addition, the X-ray diffraction data showed that the CLPC seeds method is a powerful tool to obtain high-quality protein crystals. Therefore, we recommend the use of CLPC seeds in preparing high-quality diffracting protein crystals.
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Agapova YK, Talyzina AA, Altukhov DA, Lavrentiev AL, Timofeev VI, Rakitina TV. Virtual Screening Targeting Dimerization Signals of Two Mycoplasma HU Proteins Revealed Different Types of Inhibitors Interacting with Common Binding Determinants. CRYSTALLOGR REP+ 2019. [DOI: 10.1134/s1063774519030027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Dubova KM, Sokolov AV, Gorbunov NP, Samygina VR. Preliminary X-ray Diffraction Study of Macrophage Migration Inhibitory Factor at Near-Atomic Resolution. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518060111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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The Study of the Mechanism of Protein Crystallization in Space by Using Microchannel to Simulate Microgravity Environment. CRYSTALS 2018. [DOI: 10.3390/cryst8110400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Space is expected to be a convection-free, quiescent environment for the production of large-size and high-quality protein crystals. However, the mechanisms by which the diffusion environment in space improves the quality of the protein crystals are not fully understood. The interior of a microfluidic device can be used to simulate a microgravity environment to investigate the protein crystallization mechanism that occurs in space. In the present study, lysozyme crystals were grown in a prototype microchannel device with a height of 50 μm in a glass-polydimethylsiloxane (PDMS)-glass sandwich structure. Comparative experiments were also conducted in a sample pool with a height of 2 mm under the same growth conditions. We compared the crystal morphologies and growth rates of the grown crystals in the two sample pools. The experimental results showed that at very low initial supersaturation, the morphology and growth rates of lysozyme crystals under the simulated microgravity conditions is similar to that on Earth. With increasing initial supersaturation, a convection-free, quiescent environment is better for lysozyme crystal growth. When the initial supersaturation exceeded a threshold, the growth of the lysozyme crystal surface under the simulated microgravity conditions never completely transform from isotropic to anisotropic. The experimental results showed that the convection may have a dual effect on the crystal morphology. Convection can increase the roughness of the crystal surface and promote the transformation of the crystal form from circular to tetragonal during the crystallization process.
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Talyzina AA, Agapova YK, Podshivalov DD, Timofeev VI, Sidorov-Biryukov DD, Rakitina TV. Application of virtual screening and molecular dynamics for the analysis of selectivity of inhibitors of HU proteins targeted to the DNA-recognition site. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s1063774517060244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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