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

2021 ◽  
Vol 22 (2) ◽  
pp. 922
Author(s):  
Martin Bartas ◽  
Jiří Červeň ◽  
Simona Guziurová ◽  
Kristyna Slychko ◽  
Petr Pečinka
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Binding Proteins ◽  
Current Knowledge ◽  
Special Focus ◽  
Nucleic Acid Binding ◽  
Nucleic Acid Binding Proteins

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.

scholarly journals ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins

2020 ◽  
Vol 36 (18) ◽  
pp. 4797-4804
Author(s):  
Shu Yang ◽  
Xiaoxi Liu ◽  
Raymond T Ng
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Recommender System ◽  
Binding Proteins ◽  
Rna Binding ◽  
Supplementary Information ◽  
Sequence Information ◽  
Nucleic Acid Binding ◽  
Binding Data ◽  
Nucleic Acid Binding Proteins

Abstract Motivation The interaction between proteins and nucleic acids plays a crucial role in gene regulation and cell function. Determining the binding preferences of nucleic acid-binding proteins (NBPs), namely RNA-binding proteins (RBPs) and transcription factors (TFs), is the key to decipher the protein–nucleic acids interaction code. Today, available NBP binding data from in vivo or in vitro experiments are still limited, which leaves a large portion of NBPs uncovered. Unfortunately, existing computational methods that model the NBP binding preferences are mostly protein specific: they need the experimental data for a specific protein in interest, and thus only focus on experimentally characterized NBPs. The binding preferences of experimentally unexplored NBPs remain largely unknown. Results Here, we introduce ProbeRating, a nucleic acid recommender system that utilizes techniques from deep learning and word embeddings of natural language processing. ProbeRating is developed to predict binding profiles for unexplored or poorly studied NBPs by exploiting their homologs NBPs which currently have available binding data. Requiring only sequence information as input, ProbeRating adapts FastText from Facebook AI Research to extract biological features. It then builds a neural network-based recommender system. We evaluate the performance of ProbeRating on two different tasks: one for RBP and one for TF. As a result, ProbeRating outperforms previous methods on both tasks. The results show that ProbeRating can be a useful tool to study the binding mechanism for the many NBPs that lack direct experimental evidence. and implementation Availability and implementation The source code is freely available at <https://github.com/syang11/ProbeRating>. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Leukocyte Protease Binding to Nucleic Acids Promotes Nuclear Localization and Cleavage of Nucleic Acid Binding Proteins

2014 ◽  
Vol 192 (11) ◽  
pp. 5390-5397 ◽  
Author(s):  
Marshall P. Thomas ◽  
Jennifer Whangbo ◽  
Geoffrey McCrossan ◽  
Aaron J. Deutsch ◽  
Kimberly Martinod ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nuclear Localization ◽  
Binding Proteins ◽  
Nucleic Acid Binding ◽  
Nucleic Acid Binding Proteins

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

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2341 ◽  
Author(s):  
Václav Brázda ◽  
Jiří Červeň ◽  
Martin Bartas ◽  
Nikol Mikysková ◽  
Jan Coufal ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Binding Proteins ◽  
Homo Sapiens ◽  
Specific Protein ◽  
Nucleic Acid Binding ◽  
Dna Structures ◽  
G Quadruplex ◽  
Arginine Residues

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.

scholarly journals Tsetse Salivary Gland Proteins 1 and 2 Are High Affinity Nucleic Acid Binding Proteins with Residual Nuclease Activity

PLoS ONE ◽  
2012 ◽  
Vol 7 (10) ◽  
pp. e47233 ◽  
Author(s):  
Guy Caljon ◽  
Karin De Ridder ◽  
Benoît Stijlemans ◽  
Marc Coosemans ◽  
Stefan Magez ◽  
...  
Keyword(s):  
Salivary Gland ◽  
Nucleic Acid ◽  
Binding Proteins ◽  
Nuclease Activity ◽  
Nucleic Acid Binding ◽  
High Affinity ◽  
Nucleic Acid Binding Proteins

scholarly journals 1P123 DMA binding analyses of bHLH transcription factors by FRET measurements(Nucleic acid-binding proteins,Poster Presentations)

2007 ◽  
Vol 47 (supplement) ◽  
pp. S54
Author(s):  
Koji HASEGAWA ◽  
Tatsushi GOTO ◽  
Daisuke KITANO ◽  
Mari KOTOURA ◽  
Fumio TOKUNAGA ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Nucleic Acid ◽  
Binding Proteins ◽  
Nucleic Acid Binding ◽  
Nucleic Acid Binding Proteins ◽  
Poster Presentations ◽  
Bhlh Transcription Factors

Mouse Cellular Nucleic Acid Binding Proteins: A Highly Conserved Family Identified by Genetic Mapping and Sequencing

Genomics ◽  
1994 ◽  
Vol 24 (1) ◽  
pp. 14-19 ◽  
Author(s):  
Craig H. Warden ◽  
Skaidrite K. Krisans ◽  
Deborah Purcell-Huynh ◽  
Lisa M. Leete ◽  
Aaron Daluiski ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Genetic Mapping ◽  
Binding Proteins ◽  
Nucleic Acid Binding ◽  
Nucleic Acid Binding Proteins
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