Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation

0531026 - ÚOCHB 2021 RIV CH eng J - Journal Article
Faltejsková, Kateřina - Jakubec, Dávid - Vondrášek, Jiří
Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation.
International Journal of Molecular Sciences. Roč. 21, č. 11 (2020), č. článku 3986. E-ISSN 1422-0067
R&D Projects: GA MŠMT(CZ) EF16_019/0000729
Institutional support: RVO:61388963
Keywords : protein-DNA interaction * DNA shape * minor groove * specific recognition * hydrophobic * indirect readout
OECD category: Biochemistry and molecular biology
Impact factor: 5.924, year: 2020
Method of publishing: Open access
https://www.mdpi.com/1422-0067/21/11/3986

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.
Permanent Link: http://hdl.handle.net/11104/0309790