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O'Malley A, Sankaran S, Carriuolo A, Khatri K, Kowal K, Chruszcz M. Structural homology of mite profilins to plant profilins is not indicative of allergic cross-reactivity. Biol Chem 2024; 405:367-381. [PMID: 38662449 DOI: 10.1515/hsz-2023-0366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/03/2024] [Indexed: 06/02/2024]
Abstract
Structural and allergenic characterization of mite profilins has not been previously pursued to a similar extent as plant profilins. Here, we describe structures of profilins originating from Tyrophagus putrescentiae (registered allergen Tyr p 36.0101) and Dermatophagoides pteronyssinus (here termed Der p profilin), which are the first structures of profilins from Arachnida. Additionally, the thermal stabilities of mite and plant profilins are compared, suggesting that the high number of cysteine residues in mite profilins may play a role in their increased stability. We also examine the cross-reactivity of plant and mite profilins as well as investigate the relevance of these profilins in mite inhalant allergy. Despite their high structural similarity to other profilins, mite profilins have low sequence identity with plant and human profilins. Subsequently, these mite profilins most likely do not display cross-reactivity with plant profilins. At the same time the profilins have highly conserved poly(l-proline) and actin binding sites.
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Affiliation(s)
- Andrea O'Malley
- Department of Biochemistry and Molecular Biology, 3078 Michigan State University , 603 Wilson Road, East Lansing, MI 48824, USA
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Sahana Sankaran
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Avery Carriuolo
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Kriti Khatri
- Department of Biochemistry and Molecular Biology, 3078 Michigan State University , 603 Wilson Road, East Lansing, MI 48824, USA
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Krzysztof Kowal
- Department of Experimental Allergology and Immunology, Medical University of Bialystok, Sklodowskiej-Curie 24, 15-276, Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Biochemistry and Molecular Biology, 3078 Michigan State University , 603 Wilson Road, East Lansing, MI 48824, USA
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
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Shang G, Yang M, Li M, Ma L, Liu Y, Ma J, Chen Y, Wang X, Fan S, Xie M, Wu W, Dai S, Chen Z. Structural Basis of Nucleic Acid Recognition and 6mA Demethylation by Caenorhabditis elegans NMAD-1A. Int J Mol Sci 2024; 25:686. [PMID: 38255759 PMCID: PMC10815869 DOI: 10.3390/ijms25020686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/24/2024] Open
Abstract
N6-methyladenine (6mA) of DNA is an emerging epigenetic mark in the genomes of Chlamydomonas, Caenorhabditis elegans, and mammals recently. Levels of 6mA undergo drastic fluctuation and thus affect fertility during meiosis and early embryogenesis. Here, we showed three complex structures of 6mA demethylase C. elegans NMAD-1A, a canonical isoform of NMAD-1 (F09F7.7). Biochemical results revealed that NMAD-1A prefers 6mA Bubble or Bulge DNAs. Structural studies of NMAD-1A revealed an unexpected "stretch-out" conformation of its Flip2 region, a conserved element that is usually bent over the catalytic center to facilitate substrate base flipping in other DNA demethylases. Moreover, the wide channel between the Flip1 and Flip2 of the NMAD-1A explained the observed preference of NMAD-1A for unpairing substrates, of which the flipped 6mA was primed for catalysis. Structural analysis and mutagenesis studies confirmed that key elements such as carboxy-terminal domain (CTD) and hypothetical zinc finger domain (ZFD) critically contributed to structural integrity, catalytic activity, and nucleosome binding. Collectively, our biochemical and structural studies suggest that NMAD-1A prefers to regulate 6mA in the unpairing regions and is thus possibly associated with dynamic chromosome regulation and meiosis regulation.
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Affiliation(s)
- Guohui Shang
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Meiting Yang
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Min Li
- National Protein Science Facility, Tsinghua University, Beijing 100084, China
| | - Lulu Ma
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yunlong Liu
- School of Life Sciences, Tiangong University, Tianjin 300387, China
| | - Jun Ma
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiyun Chen
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Xue Wang
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shilong Fan
- National Protein Science Facility, Tsinghua University, Beijing 100084, China
| | - Mengjia Xie
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wei Wu
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zhongzhou Chen
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Bijak V, Gucwa M, Lenkiewicz J, Murzyn K, Cooper DR, Minor W. Continuous Validation Across Macromolecular Structure Determination Process. NIHON KESSHO GAKKAI SHI 2023; 65:10-16. [PMID: 37416056 PMCID: PMC10321142 DOI: 10.5940/jcrsj.65.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The overall quality of the experimentally determined structures contained in the PDB is exceptionally high, mainly due to the continuous improvement of model building and structural validation programs. Improving reproducibility on a large scale requires expanding the concept of validation in structural biology and all other disciplines to include a broader framework that encompasses the entire project. A successful approach to science requires diligent attention to detail and a focus on the future. An earnest commitment to data availability and reuse is essential for scientific progress, be that by human minds or artificial intelligence.
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Affiliation(s)
- Vanessa Bijak
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia
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Song G, Li X, Wang Z, Dong C, Xie X, Yan X. Structure of AcrVIA2 and its binding mechanism to CRISPR-Cas13a. Biochem Biophys Res Commun 2022; 612:84-90. [PMID: 35512461 DOI: 10.1016/j.bbrc.2022.04.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 11/26/2022]
Abstract
Phages and non-phage derived bacteria have evolved many anti-CRISPR proteins (Acrs) to escape the adaptive immune system of prokaryotes. Thus Acrs can be applied as a regulatory tool for gene edition by CRISPR system. Recently, a non-phage derived AcrVIA2 has been identified as an inhibitor that blocks the editing activity of Cas13a in vitro by binding to Cas13a. Here, we solved the crystal structure of AcrVIA2 at a resolution of 2.59 Å and confirmed that AcrVIA2 can bind to Helical-I domain in LshCas13a. Structural analysis show that the V-shaped acidic groove formed by β3-β3 hairpin of AcrVIA2 dimer is the key region that mediates the interaction between AcrVIA2 and Helical-I domain. In addition, we also reveal that Asp37 of AcrVIA2 plays an essential role in the functioning of the V-shaped acidic groove, and the functional dimer conformation of AcrVIA2 is stabilized by hydrogen bonds formed between Tyr41 of one monomer with Glu35 and Asp37 of the other monomer. These data expand the current understanding of the diverse interaction mechanisms between Acrs and Cas proteins, and also provide new ideas for the development of CRISPR-Cas13a regulatory tool.
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Affiliation(s)
- Guangyong Song
- Department of Biochemistry and Molecular Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xuzichao Li
- Department of Biochemistry and Molecular Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Zhangzhao Wang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, 300134, China
| | - Cheng Dong
- Department of Biochemistry and Molecular Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xiangyang Xie
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, 300134, China.
| | - Xiaojie Yan
- Department of Biochemistry and Molecular Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
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Yang W, Sun L, Dong P, Chen Y, Zhang H, Huang X, Wu L, Chen L, Jing D, Wu Y. Structure-guided rational design of the Geobacillus thermoglucosidasius feruloyl esterase GthFAE to improve its thermostability. Biochem Biophys Res Commun 2022; 600:117-122. [DOI: 10.1016/j.bbrc.2022.02.074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 02/18/2022] [Indexed: 12/27/2022]
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