Protein Conformation Changes in 3D Protein Models as a Result of Mutations in Genes Associated with Maize Gynogenesis and Embryogenesis

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The article presents an analysis of the secondary, tertiary structures and conformation changes in 3D protein models as a result of spontaneous mutations in genes associated with maize (Zea mays L.) gynogenesis and embryogenesis. In particular, it was found that the of four-nucleotides insertion into the Zm_Mtl/Nld/Pla1 gene sequence leads to substitution of two α-helices with an unstructured section and a change in the amino acid composition of one of the β-folds in haploid-inducing (Stock 6, ZMS-8, ZMS-P) maize lines. The SNP at 131 position from the Zm_Dmp7 gene starting codon change the α-helix position in the haploid-inducing line CAU5 change, unlike the ZMS-8 line, which has a similar SNP and two additional amino acid substitutions. On the other hand, the SNP in the Zm_Bbm1 gene from parthenogenetic line AT-4 and Zm_CenH3 gene of haploid-inducing (ZMS-8, ZMS-P), and control (KM) maize lines do not lead to the amino acid substitutions in the corresponding proteins.

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作者简介

V. Fadeev

Institute of Biochemistry and Physiology of Plants and Microorganisms of the Saratov Scientific Center of the Russian Academy of Sciences

Email: chumakov_m@ibppm.ru
俄罗斯联邦, Saratov, 410049

Yu. Fadeeva

Institute of Biochemistry and Physiology of Plants and Microorganisms of the Saratov Scientific Center of the Russian Academy of Sciences

Email: chumakov_m@ibppm.ru
俄罗斯联邦, Saratov, 410049

E. Moiseeva

Institute of Biochemistry and Physiology of Plants and Microorganisms of the Saratov Scientific Center of the Russian Academy of Sciences

Email: chumakov_m@ibppm.ru
俄罗斯联邦, Saratov, 410049

M. Chumakov

Institute of Biochemistry and Physiology of Plants and Microorganisms of the Saratov Scientific Center of the Russian Academy of Sciences

编辑信件的主要联系方式.
Email: chumakov_m@ibppm.ru
俄罗斯联邦, Saratov, 410049

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2. Fig. 1. Multiple alignment of the amino acid sequence fragment of the Zm_MTL/NLD/PLA1 protein sequence of Stock 6/ZMS-8/ZMS-P haploinducing lines. The site of the amino acid sequence change is marked with a box. Dots in the figure indicate amino acid matches, and dashes indicate the absence of amino acids.

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3. Fig. 2. Three-dimensional model of the Zm_PLA1 protein of the B73 (a) and Stock 6/ZMS-8/ZMS-P (b) lines (AlphaFold3). The β-fold and two α-helices of line B73, highlighted in green, are replaced by an unstructured region and an amino acid composition-altered β-fold, highlighted in red, as a result of a four-nucleotide insertion.

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4. Fig. 3. Multiple amino acid sequence alignment of DMP8/DUF679 proteins of the B73, CAU5, ZMS-P, and ZMS-8 lines. Amino acid substitutions are shown in bold.

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5. Fig. 4. AlphaFold3-predicted three-dimensional structures of the DMP8/DUF679 protein encoded by the Zm_Dmp7/Duf679 gene of maize lines B73 (a), CAU5 (b), ZMS-P (c), and ZMS-8 (d). The locations of amino acid substitutions are marked in red colour.

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6. Fig. 5. Nucleotide alignment fragments of the Zm_Bbm1 gene of maize lines B73 and AT-4 containing single-nucleotide substitutions. Dots indicate nucleotide matches; bold letters indicate single-nucleotide substitutions.

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