Next Article in Journal
Anti-Inflammatory and Skin-Moisturizing Effects of a Flavonoid Glycoside Extracted from the Aquatic Plant Nymphoides indica in Human Keratinocytes
Next Article in Special Issue
Zinc Finger Readers of Methylated DNA
Previous Article in Journal
Optimization of Antioxidant and Skin-Whitening Compounds Extraction Condition from Tenebrio molitor Larvae (Mealworm)
Previous Article in Special Issue
Mechanisms of Protein Search for Targets on DNA: Theoretical Insights
Article Menu
Issue 9 (September) cover image

Export Article

Open AccessFeature PaperArticle
Molecules 2018, 23(9), 2341; https://doi.org/10.3390/molecules23092341

The Amino Acid Composition of Quadruplex Binding Proteins Reveals a Shared Motif and Predicts New Potential Quadruplex Interactors

1
Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
2
Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 27 August 2018 / Revised: 9 September 2018 / Accepted: 12 September 2018 / Published: 13 September 2018
(This article belongs to the Special Issue Protein-DNA Interactions: From Biophysics to Genomics)
Full-Text   |   PDF [2499 KB, uploaded 13 September 2018]   |  

Abstract

The importance of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes are perhaps the most well-characterized to date, and their presence has been demonstrated in many genomes, including that of humans. G-quadruplexes are selectively bound by many regulatory proteins. In this paper, we have analyzed the amino acid composition of all seventy-seven described G-quadruplex binding proteins of Homo sapiens. Our comparison with amino acid frequencies in all human proteins and specific protein subsets (e.g., all nucleic acid binding) revealed unique features of quadruplex binding proteins, with prominent enrichment for glycine (G) and arginine (R). Cluster analysis with bootstrap resampling shows similarities and differences in amino acid composition of particular quadruplex binding proteins. Interestingly, we found that all characterized G-quadruplex binding proteins share a 20 amino acid long motif/domain (RGRGR GRGGG SGGSG GRGRG) which is similar to the previously described RG-rich domain (RRGDG RRRGG GGRGQ GGRGR GGGFKG) of the FRM1 G-quadruplex binding protein. Based on this protein fingerprint, we have predicted a new set of potential G-quadruplex binding proteins sharing this interesting domain rich in glycine and arginine residues. View Full-Text
Keywords: quadruplex binding proteins; protein-DNA interactions; RG-rich domain; amino acid composition quadruplex binding proteins; protein-DNA interactions; RG-rich domain; amino acid composition
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material

SciFeed

Share & Cite This Article

MDPI and ACS Style

Brázda, V.; Červeň, J.; Bartas, M.; Mikysková, N.; Coufal, J.; Pečinka, P. The Amino Acid Composition of Quadruplex Binding Proteins Reveals a Shared Motif and Predicts New Potential Quadruplex Interactors. Molecules 2018, 23, 2341.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top