Protein–RNA and protein–glycan recognitions in light of amino acid codes

Nahálka, Jozef; Hrabárová, Eva; Talafová, Klaudia

doi:10.1016/j.bbagen.2015.06.013

Cited by 4 publications

(5 citation statements)

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“…For example, three nucleobase-amino acid π-interactions have been reported to be important for binding RNA to the U1 small nuclease ribonucleoprotein particle that is involved in pre-mRNA splicing (Shiels et al 2002;Guzman et al 2015). Additionally, a conserved His-nucleobase π-interaction has been implicated in controlling gene expression by the Pumilo and FBF homology family of RNAbinding proteins (Nahalka et al 2015), while the S1 protein involved in translocation initiation primarily uses π-stacking interactions to bind to the ribosome (Byrgazov et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Topology of RNA–protein nucleobase–amino acid π–π interactions and comparison to analogous DNA–protein π–π contacts

Wilson

Holland

Wetmore

2016

RNA

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The present work analyzed 120 high-resolution X-ray crystal structures and identified 335 RNA-protein π-interactions (154 nonredundant) between a nucleobase and aromatic (W, H, F, or Y) or acyclic (R, E, or D) π-containing amino acid. Each contact was critically analyzed (including using a visual inspection protocol) to determine the most prevalent composition, structure, and strength of π-interactions at RNA-protein interfaces. These contacts most commonly involve F and U, with U:F interactions comprising one-fifth of the total number of contacts found. Furthermore, the RNA and protein π-systems adopt many different relative orientations, although there is a preference for more parallel (stacked) arrangements. Due to the variation in structure, the strength of the intermolecular forces between the RNA and protein components (as determined from accurate quantum chemical calculations) exhibits a significant range, with most of the contacts providing significant stability to the associated RNA-protein complex (up to −65 kJ mol −1 ). Comparison to the analogous DNA-protein π-interactions emphasizes differences in RNA-and DNA-protein π-interactions at the molecular level, including the greater abundance of RNA contacts and the involvement of different nucleobase/amino acid residues. Overall, our results provide a clearer picture of the molecular basis of nucleic acid-protein binding and underscore the important role of these contacts in biology, including the significant contribution of π-π interactions to the stability of nucleic acid-protein complexes. Nevertheless, more work is still needed in this area in order to further appreciate the properties and roles of RNA nucleobaseamino acid π-interactions in nature.

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Section: Introductionmentioning

confidence: 99%

Topology of RNA–protein nucleobase–amino acid π–π interactions and comparison to analogous DNA–protein π–π contacts

Wilson

Holland

Wetmore

2016

RNA

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“…The QFS signal increased to 59 in our experiments; in fact, it was previously proposed as a sequon for GlcNAc. The GA/AG and AG/AA frequencies were measured as the maxima for Gal and GlcNAc, respectively [ 12 , 13 ]. This could explain why the QFS glycocodon is among the best glycocodons for Gal recognition in our experiments.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, our previous work gave a number of examples from “modern” proteins in which disordered protein chains recognize/bind the monosaccharide. For example, in the Bacteriocin LLPA–mannose complex (3M7J), a disordered QGDGN175 sequence recognizes and binds mannose [ 12 , 13 ]. The glycocodon theory states that the monosaccharide units of a 3D glycan structure are recognized by the glycocodons, which are short amino acid sequences (sequons) composed of a polar/aromatic amino acid and an amino acid couple specific for the monosaccharide [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

“…In light of this, the first glycocodons were derived from ancient prebiotic conditions when only the G, A, D, and V amino acids were available in building primary proteins. For example, DAA (Asp-Ala-Ala) and DGV (Asp-Gly-Val) were proposed for glucose (Glc), DGG (Asp-Gly-Gly) was proposed for ribose (Rib), (G)DGD (Asp-Gly-Asp) was proposed for mannose (Man), and DAG (Asp-Ala-Gly) was proposed for galactose (Gal) [ 12 , 13 ]. These proposals were based on the measured frequencies of G, A, D, and V amino acid couples in monosaccharide-specific proteins (e.g., 6321 proteins specific for Glc) and were verified on the protein–monosaccharide structures available in the Protein Data Bank (PDB) [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

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Prebiotic Peptides Based on the Glycocodon Theory Analyzed with FRET

Nahálka

Hrabárová

2021

Life

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In modern protein–carbohydrate interactions, carbohydrate–aromatic contact with CH–π interactions are used. Currently, they are considered driving forces of this complexation. In these contacts, tryptophan, tyrosine, and histidine are preferred. In this study, we focus on primary prebiotic chemistry when only glycine, alanine, aspartic acid, and valine are available in polypeptides. In this situation, when the aromatic acids are not available, hydrogen-bonding aspartic acid must be used for monosaccharide complexation. It is shown here that (DAA)n polypeptides play important roles in primary “protein”–glucose recognition, that (DGG)n plays an important role in “protein”–ribose recognition, and that (DGA)n plays an important role in “protein”–galactose recognition. Glucose oxidase from Aspergillus niger, which still has some ancient prebiotic sequences, is chosen here as an example for discussion.

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“…It seems that glycine, alanine, aspartic acid, and valine (G, A, D, and V, respectively), which are coded with GNC codons, were the first amino acids in the first peptides/proteins ( Ikehara, 2009 , 2016 ). Taken together, and after the crystal structures of aminoacyls transfer RNA synthetases, which interact with tRNA, it was stated that the protein–RNA recognition code can be derived from the present genetic code ( Nahalka, 2011 , 2014 ; Nahalka et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Theoretical Analysis of S, M and N Structural Proteins by the Protein–RNA Recognition Code Leads to Genes/proteins that Are Relevant to the SARS-CoV-2 Life Cycle and Pathogenesis

Nahálka

2021

Front. Genet.

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In this conceptual review, based on the protein–RNA recognition code, some theoretical sequences were detected in the spike (S), membrane (M) and capsid (N) proteins that may post-transcriptionally regulate the host genes/proteins in immune homeostasis, pulmonary epithelial tissue homeostasis, and lipid homeostasis. According to the review of literature, the spectrum of identified genes/proteins shows that the virus promotes IL1α/β–IL1R1 signaling (type 1 immunity) and immunity defense against helminths and venoms (type 2 immunity). In the alteration of homeostasis in the pulmonary epithelial tissue, the virus blocks the function of cilia and the molecular programs that are involved in wound healing (EMT and MET). Additionally, the protein–RNA recognition method described here identifies compatible sequences in the S1A-domain for the post-transcriptional promotion of PIKFYVE, which is one of the critical factors for SARS-CoV-2 entry to the host cell, and for the post-transcriptional repression of xylulokinase XYLB. A decrease in XYLB product (Xu5P) in plasma was proposed as one of the potential metabolomics biomarkers of COVID-19. In summary, the protein–RNA recognition code leads to protein genes relevant to the SARS-CoV-2 life cycle and pathogenesis.

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Protein–RNA and protein–glycan recognitions in light of amino acid codes

Cited by 4 publications

References 80 publications

Topology of RNA–protein nucleobase–amino acid π–π interactions and comparison to analogous DNA–protein π–π contacts

Topology of RNA–protein nucleobase–amino acid π–π interactions and comparison to analogous DNA–protein π–π contacts

Prebiotic Peptides Based on the Glycocodon Theory Analyzed with FRET

Theoretical Analysis of S, M and N Structural Proteins by the Protein–RNA Recognition Code Leads to Genes/proteins that Are Relevant to the SARS-CoV-2 Life Cycle and Pathogenesis

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