Argonaute Protein Domain Annotation And Its Three Dimensianal Structure Modeling

Argonaute proteins(Ago)are ubiquitous in almost all organisms.Ago proteins can be divided into two major groups according to their source organisms,namely the eukaryotic Ago protein and the prokaryotic Ago protein.In eukaryotes,it is a key protein in the RNAi pathway and functions as a regulatory system for gene expression.The Ago proteins have been designed for gene silencing and genome editing and play an important role in biological studies.With more and more genomes and proteomes of various microbes becoming available,computational tools are urgently needed to study Ago proteins.Here,we introduce two Ago protein research tools,AGONOTES(argonaute notes)and AGO3D(argonaute three-dimensional).AGONOTES is a web service specially designed for identifying and annotating Ago.It uses BLASTP similarity search algorithm to categorize all submitted proteins into three groups: prokaryotic argonaute protein(pAgo),eukaryotic argonaute protein(eAgo),and not argonaute protein(not Ago).Argonaute proteins can then be aligned to the corresponding standard set of Ago sequences using the multiple sequence alignment program MUSCLE.All functional domains of Ago can furtherly be curated from the alignment results and visualized friendly through Bio::Graphic modules in the BioPerl bundle.Compared with existing tools such as CD-Search and databases such as UniProt,AGONOTES showed a much better performance on domain annotations,which is fundamental in studying new Ago.AGONOTES can be freely accessed at http://i.uestc.edu.cn/agonotes/.AGO3D is an online service that recognizes the Ago proteins and builds their three-dimensional structures.Like AGONOTES,it uses the BLASTP similarity search algorithm to identify Ago proteins.The construction of the three-dimensional structure of the Ago protein can then be automated using the protein homology three-dimensional structure modeling algorithm MODELLER.The three-dimensional structure of Ago protein can be visualized by JSmol software.Compared with existing tools such as Swiss-Model,Phyre2 and ModWeb,AGO3 D has advantages in the running time and the quality in constructing the three-dimensional structure of the Ago protein.And it has a more user-friendly interface.Therefore,AGO3 D is important for studying the potential Ago proteins.The free website of AGO3 D is http://i.uestc.edu.cn/ago3d/.We developed AGONOTES and AGO3 D specifically for Ago protein research.They can identify Ago proteins from the primary sequence of proteins,and then annotate the Ago protein domains and finally construct the tertiary structure of Ago proteins.Our work will facilitate the primary study of Ago protein for researchers in the field.