Exploring the energy landscape of the genetic code

New insights into the arrangement of the genetic code table, based on the analysis of the physico-chemical properties of its molecular constituents, are reported in this paper. It will be demonstrated that the code has a twofold symmetry that is not apparent from the conventional code table, but bec...

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Bibliographic Details
Published in:Archives of biochemistry and biophysics 2006-09, Vol.453 (1), p.87-92
Main Author: Klump, H.H.
Format: Article
Language:English
Subjects:
Biological Evolution
Chromosome Mapping - methods
Codon - genetics
Computer Simulation
Conserved Sequence
Energy Transfer - genetics
Engery landscape
Evolution, Molecular
Free energy
Genetic Code
Models, Genetic
Mutation
Sequence Analysis, DNA - methods
Sequence Homology, Nucleic Acid
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Summary:New insights into the arrangement of the genetic code table, based on the analysis of the physico-chemical properties of its molecular constituents, are reported in this paper. It will be demonstrated that the code has a twofold symmetry that is not apparent from the conventional code table, but becomes apparent when the codon–anticodon energies are listed for each triplet. The evolutionary development of the current code based on single base replacement mutations (transitions) from an ‘iso-energetic’ degenerated subset of 16 of the 64 codons is discussed. The energy landscape of all 64 codons is presented. A detailed analysis of the energy changes due to mutations in the 3rd, 1st or 2nd position of a codon reveals that the modern genetic code is highly robust. Changes come in small discrete steps that can be quantified in relation to the thermal noise of the system. The relation of the individual codon to its neighbours in the rearranged codon table can be completely understood based on thermodynamic considerations.
ISSN:0003-9861
1096-0384
DOI:10.1016/j.abb.2006.01.018