Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins

被引:23
作者
Bartas, Martin [1 ]
Cerven, Jiri [1 ]
Guziurova, Simona [1 ]
Slychko, Kristyna [1 ]
Pecinka, Petr [1 ]
机构
[1] Univ Ostrava, Dept Biol & Ecol, Inst Environm Technol, Fac Sci, Ostrava 71000, Czech Republic
关键词
DNA; RNA; protein binding; G-quadruplex; triplex; i-motif; Z-DNA; Z-RNA; cruciform; amino acid composition; G-QUADRUPLEX STRUCTURES; ZINC-FINGER PROTEINS; DNA-BINDING; RNA-BINDING; DOMAIN; SEQUENCE; ROLES; IDENTIFICATION; RECOGNITION; ANNOTATION;
D O I
10.3390/ijms22020922
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.
引用
收藏
页码:1 / 12
页数:11
相关论文
共 113 条
[1]   Type IA topoisomerases can be "magicians" for both DNA and RNA in all domains of life [J].
Ahmad, Muzammil ;
Xu, Dongyi ;
Wang, Weidong .
RNA BIOLOGY, 2017, 14 (07) :854-864
[2]  
[Anonymous], 2005, Protein identification and analysis tools on the ExPASy server, DOI [10.1385/1-59259-584-7:531, 10.1385/1-59259-890-0:571]
[3]   The many faces of the helix-turn-helix domain: Transcription regulation and beyond [J].
Aravind, L ;
Anantharaman, V ;
Balaji, S ;
Babu, MM ;
Iyer, LM .
FEMS MICROBIOLOGY REVIEWS, 2005, 29 (02) :231-262
[4]   A natural classification of the basic helix-loop-helix class of transcription factors [J].
Atchley, WR ;
Fitch, WM .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (10) :5172-5176
[5]   AN ARGININE TO LYSINE SUBSTITUTION IN THE BZIP DOMAIN OF AN OPAQUE-2 MUTANT IN MAIZE ABOLISHES SPECIFIC DNA-BINDING [J].
AUKERMAN, MJ ;
SCHMIDT, RJ ;
BURR, B ;
BURR, FA .
GENES & DEVELOPMENT, 1991, 5 (02) :310-320
[6]  
Bacolla A., 2018, ELS, P1
[7]   Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences [J].
Bacolla, Albino ;
Tainer, John A. ;
Vasquez, Karen M. ;
Cooper, David N. .
NUCLEIC ACIDS RESEARCH, 2016, 44 (12) :5673-5688
[8]   Identification of Distinct Amino Acid Composition of Human Cruciform Binding Proteins [J].
Bartas, M. ;
Bazantova, P. ;
Brazda, V. ;
Liao, J. C. ;
Cerven, J. ;
Pecinka, P. .
MOLECULAR BIOLOGY, 2019, 53 (01) :97-106
[9]   In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles [J].
Bartas, Martin ;
Brazda, Vaclav ;
Bohalova, Natalia ;
Cantara, Alessio ;
Volna, Adriana ;
Stachurova, Tereza ;
Malachova, Katerina ;
Jagelska, Eva B. ;
Porubiakova, Otilia ;
Cerven, Jiri ;
Pecinka, Petr .
FRONTIERS IN MICROBIOLOGY, 2020, 11
[10]   Genome-Wide Analysis of RNA Secondary Structure [J].
Bevilacqua, Philip C. ;
Ritchey, Laura E. ;
Su, Zhao ;
Assmann, Sarah M. .
ANNUAL REVIEW OF GENETICS, VOL 50, 2016, 50 :235-266