title: Protein-RNA and protein-glycan recognitions in light of amino acid codes.
abstract: BACKGROUND
  RNA-binding proteins, in cooperation with non-coding RNAs, play important roles in post-transcriptional regulation. Non-coding micro-RNAs control information flow from the genome to the glycome by interacting with glycan-synthesis enzymes. Glycan-binding proteins read the cell surface and cytoplasmic glycome and transfer signals back to the nucleus. The profiling of the protein-RNA and protein-glycan interactomes is of significant medicinal importance.
  
  
  METHODS
  This review discusses the state-of-the-art research in the protein-RNA and protein-glycan recognition fields and proposes the application of amino acid codes in profiling and programming the interactomes.
  
  
  CONCLUSIONS
  The deciphered PUF-RNA and PPR-RNA amino acid recognition codes can be explained by the protein-RNA amino acid recognition hypothesis based on the genetic code. The tripartite amino acid code is also involved in protein-glycan interactions. At present, the results indicate that a system of four codons ("gnc", where n=g - guanine, c - cytosine, u - uracil or a - adenine) and four amino acids (G - glycine, A - alanine, V - valine, D - aspartic acid) could be the original genetic code that imprinted "rules" into both recognition processes.
  
  
  CONCLUSIONS
  Amino acid recognition codes have provocative potential in the profiling and programming of the protein-RNA and protein-glycan interactomes. The profiling and even programming of the interactomes will play significant roles in diagnostics and the development of therapeutic procedures against cancer and neurodegenerative, developmental and other diseases.
authors.affiliation: Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic. Electronic address: nahalka@savba.sk.
authors.forename: Jozef
authors.initials: J
authors.lastname: Nahalka
authors.affiliation: Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic.
authors.forename: Eva
authors.initials: E
authors.lastname: Hrabarova
authors.affiliation: Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic.
authors.forename: Klaudia
authors.initials: K
authors.lastname: Talafova
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000235:genetics*; D000818:Animals; D005815:Genetic Code; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011134:Polysaccharides / Q000737:chemistry / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D020539:Sequence Analysis, Protein
chemical_list: D000596:Amino Acids; D011134:Polysaccharides; D011506:Proteins; D012313:RNA
keywords: Amino acid codes; Cell developmental diseases; Computational profiling; Protein engineering; Protein–RNA interactome; Protein–glycan interactome