Statistical correlation between protein secondary structure and messenger RNA stem-loop structure.
A new integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect.
Jia
Mengwen
M
Department of Physics, Inner Mongolia University, Hohhot 010021, China.
Luo
Liaofu
L
Liu
Ciquan
C
D019992:Databases as Topic; D004926:Escherichia coli / Q000378:metabolism; D006801:Humans; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D013269:Stochastic Processes
D011506:Proteins; D012333:RNA, Messenger