Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation
Interaction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein–DNA complexes, we propose that distortion of the DNA minor groove resulting from interactions...
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| Format: | Article |
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MDPI AG
2020-06-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/11/3986 |
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| author | Kateřina Faltejsková David Jakubec Jiří Vondrášek |
| author_facet | Kateřina Faltejsková David Jakubec Jiří Vondrášek |
| author_sort | Kateřina Faltejsková |
| collection | DOAJ |
| description | Interaction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein–DNA complexes, we propose that distortion of the DNA minor groove resulting from interactions with hydrophobic amino acid residues is a universal element of protein–DNA recognition. We provide evidence to support this by associating each DNA minor groove-binding amino acid residue with the local dimensions of the DNA double helix using a novel algorithm. The widened DNA minor grooves are associated with high GC content. However, some AT-rich sequences contacted by hydrophobic amino acids (e.g., phenylalanine) display extreme values of minor groove width as well. For a number of hydrophobic amino acids, distinct secondary structure preferences could be identified for residues interacting with the widened DNA minor groove. These results hold even after discarding the most populous families of minor groove-binding proteins. |
| first_indexed | 2024-03-10T19:26:04Z |
| format | Article |
| id | doaj.art-9a4b97a2aca7466c9a69a38ebec05280 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T19:26:04Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-9a4b97a2aca7466c9a69a38ebec052802023-11-20T02:34:04ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-06-012111398610.3390/ijms21113986Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure DeformationKateřina Faltejsková0David Jakubec1Jiří Vondrášek2Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech RepublicInstitute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech RepublicInstitute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech RepublicInteraction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein–DNA complexes, we propose that distortion of the DNA minor groove resulting from interactions with hydrophobic amino acid residues is a universal element of protein–DNA recognition. We provide evidence to support this by associating each DNA minor groove-binding amino acid residue with the local dimensions of the DNA double helix using a novel algorithm. The widened DNA minor grooves are associated with high GC content. However, some AT-rich sequences contacted by hydrophobic amino acids (e.g., phenylalanine) display extreme values of minor groove width as well. For a number of hydrophobic amino acids, distinct secondary structure preferences could be identified for residues interacting with the widened DNA minor groove. These results hold even after discarding the most populous families of minor groove-binding proteins.https://www.mdpi.com/1422-0067/21/11/3986protein–DNA interactionDNA shapeminor groovespecific recognitionhydrophobicindirect readout |
| spellingShingle | Kateřina Faltejsková David Jakubec Jiří Vondrášek Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation International Journal of Molecular Sciences protein–DNA interaction DNA shape minor groove specific recognition hydrophobic indirect readout |
| title | Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation |
| title_full | Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation |
| title_fullStr | Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation |
| title_full_unstemmed | Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation |
| title_short | Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation |
| title_sort | hydrophobic amino acids as universal elements of protein induced dna structure deformation |
| topic | protein–DNA interaction DNA shape minor groove specific recognition hydrophobic indirect readout |
| url | https://www.mdpi.com/1422-0067/21/11/3986 |
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