OBJECTIVES: To predict the structure of protein, which dictates the function it performs, a newly designed algorithm is developed which blends the concept of self-organization and the genetic algorithm. METHODS: Among many other approaches, genetic algorithm is found to be a promising cooperative computational method to solve protein structure prediction in a reasonable time. To automate the right choice of parameter values the influence of self-organization is adopted to design a new genetic operator to optimize the process of prediction. Torsion angles, the local structural parameters which define the backbone of protein are considered to encode the chromosome that enhances the quality of the confirmation. Newly designed self-configured genetic operators are used to develop self-organizing genetic algorithm to facilitate the accurate structure prediction. RESULTS: Peptides are used to gauge the validity of the proposed algorithm. As a result, the structure predicted shows clear improvements in the root mean square deviation on overlapping the native indicates the overall performance of the algorithm. In addition, the Ramachandran plot results implies that the conformations of phi-psi angles in the predicted structure are better as compared to native and also free from steric hindrances. CONCLUSIONS: The proposed algorithm is promising which contributes to the prediction of a native-like structure by eliminating the time constraint and effort demand. In addition, the energy of the predicted structure is minimized to a greater extent, which proves the stability of protein.
Enkephalin, Methionine ; Islet Amyloid Polypeptide ; Operator Regions, Genetic ; Peptides

Matrix protein 2(M2) is an integral tetrameric membrane protein of influenza A virus, which functions as ion channel. M2 sequence has shown remarkable conservation, so there has been growing interest in it as "universal" vaccine. In order to establish a stable 293 cell line that express M2 protein under the control of the tetracycline operator, M2 gene was obtained by PCR amplification from the plasmid containing the segment 7 of influenza A virus strain A/PR/8/34 firstly. The PCR product was cloned into BamH I/Not I restriction site of pcDNA5/FRT/TO vector, and cotransfected with pOG44 which express Flp recombinase into Flp-In T-REx-293 cell. Integration of pcDNA5/FRT/TO-M2 into the cell genome at the Flp Recombination Target (FRT) site brought the SV40 promoter and the initiation codon in frame with the hygromycin resistance gene. Thus, stable cell lines were selected for hygromycin resistance. The expression of M2 protein from hygromycin-resistant cell was induced by addition of tetracycline into the cell culture media, and then tested by indirect immunofluorescence assay (IFA). 16 strains with high expression of M2 were selected. After subculturing for more than ten passages, the cell lines still stably expressed M2 protein. No M2 protein could be detected without tetracycline induction, suggesting that the expression was strictly controlled by tetracycline operator. The cell lines expressing M2 will be useful for further functional studies of M2 protein, detection of immune response against natural structure M2 protein and development of live attenuated influenza virus vaccine with reverse genetics technique.
Animals ; Cloning, Molecular ; Gene Expression ; Genetic Vectors ; genetics ; HEK293 Cells ; Humans ; Influenza A virus ; genetics ; metabolism ; Influenza Vaccines ; genetics ; Operator Regions, Genetic ; Recombinant Proteins ; biosynthesis ; genetics ; Tetracycline ; pharmacology ; Transfection ; Viral Matrix Proteins ; biosynthesis ; genetics