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Principles of chemical geometry underlying chiral selectivity in RNA minihelix aminoacylation
- Source :
- Nucleic Acids Research
- Publication Year :
- 2018
-
Abstract
- The origin of homochirality in L-amino acid in proteins is one of the mysteries of the evolution of life. Experimental studies show that a non-enzymatic aminoacylation reaction of an RNA minihelix has a preference for L-amino acid over D-amino acid. The reaction initiates by approaching of a 3′-oxygen of the RNA minihelix to the carbonyl carbon of an aminoacyl phosphate oligonucleotide. Here, employing molecular dynamics simulations, we examined the possible mechanisms that determine this chiral selectivity. The simulation system adopted a geometry required for the chemical reaction to occur more frequently with L-alanine than that with D-alanine. For L-alanine, the structure with this geometry was formed by a combination of stable dihedral angles along alanyl phosphate backbone with a canonical RNA structure, where the methyl group of alanine was placed on the opposite side of the approaching 3′-hydroxyl group with respect to the carbonyl plane. For D-alanine, the methyl group and the 3′-hydroxyl group were placed on the same side with respect to the carbonyl plane, which significantly decreased its ability to approach 3′-oxygen close to the carbonyl carbon compared to L-alanine. The mechanism suggested herein can explain experimentally observed chiral preferences.
- Subjects :
- 0301 basic medicine
Static Electricity
Glycine
Aminoacylation
Geometry
Biology
Dihedral angle
Molecular Dynamics Simulation
01 natural sciences
Chemical reaction
Phosphates
03 medical and health sciences
chemistry.chemical_compound
Chemical Biology and Nucleic Acid Chemistry
0103 physical sciences
Genetics
Amino Acids
Alanine
010304 chemical physics
Oligonucleotide
RNA
Stereoisomerism
Oxygen
030104 developmental biology
chemistry
Nucleic Acid Conformation
Homochirality
Methyl group
Subjects
Details
- ISSN :
- 13624962
- Volume :
- 46
- Issue :
- 21
- Database :
- OpenAIRE
- Journal :
- Nucleic acids research
- Accession number :
- edsair.doi.dedup.....fc302ca4ba2ffca3e5b8333a6ace00fe