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

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Abstract

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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V. 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
Russian Federation, Saratov, 410049

Yu. V. 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
Russian Federation, Saratov, 410049

E. M. 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
Russian Federation, Saratov, 410049

M. I. Chumakov

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

Author for correspondence.
Email: chumakov_m@ibppm.ru
Russian Federation, 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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