Evolutionary analysis of actinins(ACTN) gene family for positive selective sites by finding the dn/ds (ω) value

Abstract

Identifying positively selected amino acid sites is an important approach for making a conclusion about the function of proteins; an amino acid site that is undergoing positive selection is likely to play a key role in the function of the protein. Here, we used codon-based substitution models and maximum-likelihood (ML) methods to identify positively selected sites that are likely to influence the cohesiveness and mechanics of the cytoskeleton by cross-linking actinins filaments and other cytoskeleton components to create a scaffold that imparts stability and forms a bridge between the cytoskeleton and signaling pathways. We use MEGA 7 and PAML for polygenetic Analysis and positive selective Sites. Alpha-actinins from skeletal muscle as a protein factor promoting the super precipitation of actomyosin and inducing the gelation of F-actin solutions. The protein is located in Z-bands of sarcomeres in skeletal and cardiac muscles as well as near the fascia adherents of intercalated discs in cardiac muscle. In smooth muscle, it exists in cytoplasmic dense bodies and membrane-associated dense plaques. We used PAMLX to find out specific sites in these DNA sequences.  These results show the location and identification of positively selected sites in the ACTININS gene family. ACTN1, ACTN2, ACTN3 and ACTN4 had (248G,250L), (234I,236N ,238P, 239K, 252F, 260E, 261Q, 314Q, 590N, 607L, 869S), (NO) and (248G, 250L) positive selective sites respectively. The aims of our work are the prediction of these sites to find the specific location of these sites in 3D structure and to replace it with suitable amino acids for the cure of obesity, muscles, cancer, and other chronic diseases