Communications in Information and Systems

Volume 18 (2018)

Number 4

Natural distinct inter-preference between genetic codon and protein secondary structure combinations

Pages: 331 – 347

DOI: http://dx.doi.org/10.4310/CIS.2018.v18.n4.a6

Authors

Zhuomaji Gong (Institute for Mathematical Sciences, Renmin University of China, Beijing, China)

Xinqi Gong (Institute for Mathematical Sciences, Renmin University of China, Beijing, China)

Abstract

The central dogma of molecular biology describes the process of genetic information transferred to protein. Many studies have found that genetic codon not only influences the protein amino acid sequence, but also affects protein 3D structure, such as local protein 3D structure may be affected by synonymous codon preferred usage. Here, in addition to the effect of single codons, we furtherly considering the preferences of short codon sequences for protein secondary structures. Also, we studied the preferences of short protein secondary structures for codon sequences. We studied in six cases that how codon combinations with length of $N$ ($N$-codons) affect protein secondary structure element combinations with the same length ($N$-secondary structures), where $N=1 , \dotsc , 6$. A few distinct codon combination sequences and their corresponding structure sequences were found by calculating Relative Codon Usage (RCU) and Relative Structure Usage (RSU). The preferences of many codon combinations vary for secondary structure combinations when N is different; similar preference patterns were found for protein secondary structure preference for genetic codons. This work is based on the CSandS database. In order to further confirm our conclusion, we selected seven proteins of human that are not in the CSandS to predict its secondary structures from nucleotide sequences using the statistical results. Prediction accuracy can reach 75.72%. It is sufficient to show the imprint of codons on protein structure, and it also indicates that codon usage probably is related to species.

Keywords

codon, short codon sequence, protein secondary structure, short structure sequence, distinct codon combination, predicting secondary structure

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Published 26 November 2018