Protein structure preference, tRNA copy number, and mRNA stem/loop content.
From statistical analyses of protein sequences for humans and Escherichia coli we found that the messenger RNA segment of m-codons (for m=2 to 6) with average high tRNA copy number (TCN) (larger than approximately 10.5 for humans or approximately 1.95 for E. coli) preferably code for the alpha helix and that with low TCN (smaller than approximately 7.5 for humans or approximately 1.7 for E. coli) preferably code for coil. Between them there is an intermediate region without correlation to structure preference. For the beta strand the preference/ avoidance tendency is not obvious. All strong preference-modes of TCN for protein secondary structures have been deduced. The mutual interaction between two factors--protein secondary structural type and codon TCN--is tested by F distribution. A phenomenological model on the relation between structure preference and translational efficiency or accuracy is proposed. It is pointed out that the structure preference of codons is related to the distribution of mRNA stem/loop content in three TCN regions.
Luo
Liaofu
L
Department of Physics, Inner Mongolia University, Hohhot 010021, China. lfluo@mail.imu.edu.cn
Jia
Mengwen
M
Li
Xiaoqin
X
D001426:Bacterial Proteins / Q000737:chemistry; D003062:Codon; D019992:Databases as Topic; D004926:Escherichia coli / Q000378:metabolism; D006801:Humans; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry*; D012984:Software
D001426:Bacterial Proteins; D003062:Codon; D012333:RNA, Messenger; D012343:RNA, Transfer