Aim To determine whether the proapoptotic effect of proprotein-convertase cubtilisin/kexin 9(PCSK9)is related to its effect on Caspase-3 activation by bioinformatics analysis.Methods HUVEC-12 were incubated with 80 mg/L oxidized low density lipoprotein(ox-LDL)for 24 h,and groups of blank control,transfection reagent control,negative control,and 80 nmol/L PCSK9 siRNA+80 mg/L ox-LDL were established.Apoptosis rate was measured by flow cytometry.Western blotting and ELISA were used to measure Caspase-3 protein expression and activity,respectively.Bioinformatics methods were used to compare PCSK9,Caspase-8 and Caspase-9,in order to find the similarity of sequence and whether a common conservative motif existed.Results An inhibitory effect of PCSK9 siRNA on both expression and activity of Caspase-3 was observed.The sequence similarity of PCSK9,Caspase-8 and Caspase-9 was 22.14%,there was a similar second structure in C-terminal of the three proteins,the content of helix,strand,turn and coil was nearly the same in PCSK9 and Caspase-9,the profile of PCSK9 and Caspase-9 was similar,and there was common cleft in their abdomen,this cleft may be related to their similar enzyme activity.Conclusion There are similar motif in PCSK9 and Caspase-9.The proapoptotic capacity of PCSK9 is related to its effect on Caspase-3 activation.