Nucleic acid chaperons: a theory of an RNA-assisted protein folding.
BACKGROUND
Proteins are assumed to contain all the information necessary for unambiguous folding (Anfinsen's principle). However, ab initio structure prediction is often not successful because the amino acid sequence itself is not sufficient to guide between endless folding possibilities. It seems to be a logical to try to find the "missing" information in nucleic acids, in the redundant codon base.


RESULTS
mRNA energy dot plots and protein residue contact maps were found to be rather similar. The structure of mRNA is also conserved if the protein structure is conserved, even if the sequence similarity is low. These observations led me to suppose that some similarity might exist between nucleic acid and protein folding. I found that amino acid pairs, which are co-located in the protein structure, are preferentially coded by complementary codons. This codon complementarity is not perfect; it is suboptimal where the 1st and 3rd codon residues are complementary to each other in reverse orientation, while the 2nd codon letters may be, but are not necessarily, complementary.


CONCLUSIONS
Partial complementary coding of co-locating amino acids in protein structures suggests that mRNA assists in protein folding and functions not only as a template but even as a chaperon during translation. This function explains the role of wobble bases and answers the mystery of why we have a redundant codon base.
Biro
Jan C
JC
Homulus Foundation, San Francisco, CA 94105, USA. jan.biro@sbcglobal.net
D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D003062:Codon; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D008957:Models, Genetic; D018832:Molecular Chaperones / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D012333:RNA, Messenger / Q000378:metabolism; D012984:Software
D000596:Amino Acids; D003062:Codon; D018832:Molecular Chaperones; D009696:Nucleic Acids; D011506:Proteins; D012333:RNA, Messenger; D012313:RNA