title: Polarity and hydrophobicity interactions in protein synthesis process.
abstract: About 30 years ago, experiments found that there are polarity and hydrophobicity (P and H) correlations and affinity between amino acids and their anticodons. Although it is shown that these experimental findings are important for explaining the origins of the genetic code, the great potential of P and H interactions in investigating other bio-functions have not been fully explored. Here, through raising, discussing and answering seven relevant questions hidden in tRNA aminoacylation, the formation of peptide bonds, and the ending of translations, etc., we show our theoretical findings that the P and H correlations and affinity take vital roles in the protein synthesis process. We found the relationship between the 3' end ACCN sequences of tRNA molecules and the activated amino acids and its biological significance, the rRNAs' consensus sequences 5'NCC...TGG3' or 5'TGG...NCC3' which may perform as functional segments of rRNAs to help triggering the reaction of peptide formation, and common nature of releasing factors that the first amino acid residue of releasing factors ERF, RF1 and RF2 are all Methionine, except a few Alanine, which may be necessary for releasing the translated polypeptide and stopping the translating process. In the terms of P and H correlations and affinity, we provide explanations of why only using the poly (G) as mRNA template cannot get the poly (Gly) in experiments deciphering the genetic code, why Gly often appears in beta turns and why translational bypassing might occur when translating 5'GGAUGA on mRNA. Since amino acids and nucleotides are the subunits, respectively, for composing proteins and nucleic acids, these findings will help in further understanding interactions among the bio-macromolecules. These findings are also helpful for investigating rRNAs, further understanding the protein synthesis process and analysing similar bio-problems, and should be proved useful for experimental biologists.
authors.affiliation: Department of Biomedical Engineering, Kunming University of Science and Technology, Kunming 650051, PR China.
authors.forename: Xu-Qing
authors.initials: XQ
authors.lastname: Li
authors.forename: Ping
authors.initials: P
authors.lastname: Fan
authors.forename: Jinghong
authors.initials: J
authors.lastname: Fan
mesh_terms: D000818:Animals; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D001483:Base Sequence; D005057:Eukaryotic Cells / Q000166:cytology; D057927:Hydrophobic and Hydrophilic Interactions; D008969:Molecular Sequence Data; D014176:Protein Biosynthesis / Q000235:genetics*; D017433:Protein Structure, Secondary; D012329:RNA, Bacterial / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000235:genetics; D012341:RNA, Ribosomal, 5S / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics
chemical_list: D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; D012341:RNA, Ribosomal, 5S; D012343:RNA, Transfer