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

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Václav BrázdaPetr Pečinka

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 potent...Continue Reading

References

Jan 1, 1991·Critical Reviews in Biochemistry and Molecular Biology·E Palecek
Jan 1, 1994·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·K van Holde, J Zlatanova
Dec 10, 1998·Nature Medicine·J L Mergny, C Hélène
Jul 5, 2001·Proceedings of the National Academy of Sciences of the United States of America·C SchaffitzelA Plückthun
Jun 7, 2002·Nature·Gary N ParkinsonStephen Neidle
Jul 18, 2002·Nature Reviews. Drug Discovery·Stephen Neidle, Gary Parkinson
Jan 10, 2003·Nucleic Acids Research·Christian von MeringBerend Snel
Dec 15, 1962·Proceedings of the National Academy of Sciences of the United States of America·M GELLERTD R DAVIES
Apr 7, 2005·Neuroreport·Xianfeng LiHajime Arai
May 26, 2005·Nucleic Acids Research·Alan K ToddStephen Neidle
May 26, 2005·Nucleic Acids Research·Julian L Huppert, Shankar Balasubramanian
Oct 4, 2005·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Sergey ChasovskikhAnatoly Dritschilo
Apr 6, 2006·Bioinformatics·Ryota Suzuki, Hidetoshi Shimodaira
Jul 18, 2006·Nucleic Acids Research·Oleg KikinParamjeet S Bagga
Dec 16, 2006·Nucleic Acids Research·Julian L Huppert, Shankar Balasubramanian
Feb 27, 2007·Nature Chemical Biology·Sunita KumariShankar Balasubramanian
May 12, 2007·Trends in Biochemical Sciences·Robert D Wells
Apr 9, 2008·Biochimie·Stephen Neidle, Gary N Parkinson
Apr 26, 2008·PLoS Computational Biology·Martin C FrithTimothy L Bailey
May 22, 2009·Nucleic Acids Research·Timothy L BaileyWilliam S Noble
Aug 20, 2009·Journal of the American Chemical Society·Zoë A E WallerShankar Balasubramanian
Dec 23, 2009·Biochemical and Biophysical Research Communications·Eva B JagelskáVáclav Brázda
Sep 22, 2010·PloS One·Juliette MartinNarayanaswamy Srinivasan
Feb 19, 2011·Bioinformatics·Charles E GrantWilliam Stafford Noble
Apr 2, 2011·Nature Reviews. Drug Discovery·Shankar BalasubramanianStephen Neidle
Aug 6, 2011·BMC Molecular Biology·Václav BrázdaCheryl Arrowsmith
Sep 9, 2011·Chemical Society Reviews·Jungkweon Choi, Tetsuro Majima
Oct 25, 2011·Nucleic Acids Research·Peter SarkiesJulian E Sale
Nov 16, 2011·Database : the Journal of Biological Databases and Curation·Arek Kasprzyk
Mar 1, 2012·Bioinformatics·Konstantin OkonechnikovUNKNOWN UGENE team
Oct 4, 2012·Nature Reviews. Genetics·Matthew L BochmanVirginia A Zakian
Apr 4, 2013·BMC Molecular Biology·Nicholas W AshtonDerek J Richard
Jun 12, 2013·Molecular Cell·Palaniraja ThandapaniStéphane Richard
Jun 12, 2013·PloS One·Wataru YoshidaKazunori Ikebukuro
Jun 19, 2013·Nucleic Acids Research·Sebastian L B KönigAmanda C Evans
Oct 19, 2013·Biochemical and Biophysical Research Communications·Jan CoufalVáclav Brázda
Oct 24, 2013·Nucleic Acids Research·Mikhail Yu LobanovOxana V Galzitskaya
Dec 4, 2013·Journal of the American Chemical Society·Dengguo WeiStephen Neidle
Sep 7, 2014·The EMBO Journal·Pau Castillo BoschPuck Knipscheer
Oct 1, 2014·International Journal of Molecular Sciences·Václav BrázdaMiroslav Fojta

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Citations

Feb 10, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Antara SenguptaShantanu Chowdhury
Feb 6, 2019·Bioinformatics·Václav BrázdaJean-Louis Mergny
Sep 25, 2020·Biomolecules·Václav BrázdaJean-Louis Mergny
Jun 21, 2019·Nucleic Acids Research·Aldana P DavidPablo Armas
May 6, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Martin BartasPetr Pečinka
Dec 3, 2020·Nucleic Acids Research·Prakash KharelPavel Ivanov
Dec 20, 2020·Cellular Microbiology·Pratima GurungJose-Juan Lopez-Rubio
Dec 18, 2020·Frontiers in Cell and Developmental Biology·Alexandra A KuznetsovaNikita A Kuznetsov
Jan 23, 2021·International Journal of Molecular Sciences·Martin BartasPetr Pečinka
Mar 28, 2021·Nucleic Acids Research·Kaixin LyuChun Kit Kwok
Apr 4, 2021·International Journal of Molecular Sciences·Natália BohálováVáclav Brázda
Jan 4, 2019·Chemical Reviews·Jean-Louis Mergny, Dipankar Sen
Dec 6, 2018·Journal of the American Chemical Society·Zhou-Li HuangZhi-Shu Huang
Sep 3, 2021·Biochimica Et Biophysica Acta. General Subjects·Pablo ArmasNora B Calcaterra
Feb 16, 2021·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Steven J DupasSean A McKenna
Nov 19, 2021·Nucleic Acids Research·Satyajit PatraJérome Wenger
Nov 28, 2021·International Journal of Molecular Sciences·Rebecca LinkeKatrin Paeschke

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Methods Mentioned

BETA
Profiler
CLAP

Software Mentioned

GLAM2
Excel
Composition Profiler
protParam
GLAM
UGENE
MEME Suite
R package “ pvclust ”
R package pvclust
FIMO

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