Nonfunctional Missense Mutants in Two Well Characterized Cytosolic Enzymes Reveal Important Information About Protein Structure and Function
- 38 Downloads
The isolation and characterization of 42 unique nonfunctional missense mutants in the bacterial cytosolic β-galactosidase and catechol 2,3-dioxygenase enzymes allowed us to examine some of the basic general trends regarding protein structure and function. A total of 6 out of the 42, or 14.29% of the missense mutants were in α-helices, 17 out of the 42, or 40.48%, of the missense mutants were in β-sheets and 19 out of the 42, or 45.24% of the missense mutants were in unstructured coil, turn or loop regions. While α-helices and β-sheets are undeniably important in protein structure, our results clearly indicate that the unstructured regions are just as important. A total of 21 out of the 42, or 50.00% of the missense mutants caused either amino acids located on the surface of the protein to shift from hydrophilic to hydrophobic or buried amino acids to shift from hydrophobic to hydrophilic and resulted in drastic changes in hydropathy that would not be preferable. There was generally good consensus amongst the widely used algorithms, Chou–Fasman, GOR, Qian–Sejnowski, JPred, PSIPRED, Porter and SPIDER, in their ability to predict the presence of the secondary structures that were affected by the missense mutants and most of the algorithms predicted that the majority of the 42 inactive missense mutants would impact the α-helical and β-sheet secondary structures or the unstructured coil, turn or loop regions that they altered.
KeywordsProtein secondary structure α-Helices β-Sheets Unstructured regions Coils Hydropathy
Compliance with Ethical Standards
Conflict of interest
The authors declare that they have no conflict of interest.
- 29.Pirovano W, Heringa J (2010) Protein secondary structure prediction. In: Carugo O, Eisenhaber F (eds) Data mining techniques for the life sciences, Methods in molecular biology. Humana Press, TotowaGoogle Scholar
- 30.Pavlopoulou A, Michalopoulos I (2011) State-of-the-art bioinformatics protein structure prediction tools (Review). Int J Mol Med 28:295–310Google Scholar
- 33.Conidi A, van den Berghe V, Leslie K, Stryjewska A, Xue H, Chen YG, Seuntjens E, Huylebroeck D (2013) Four amino acids within a tandem QxVx repeat in a predicted extended α helix of the Smad-binding domain of Sip1 are necessary for binding to activated Smad proteins. PLoS ONE 8:10CrossRefGoogle Scholar
- 36.Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
- 38.Bertani G (1951) Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 62:293–300Google Scholar
- 41.Harayama S, Rekik M, Bairoch A, Neidle EL, Ornston LN (1991) Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWWO plasmid xylXYZ, genes encoding benzoate dioxygenases. J Bacteriol 173:7540–7548CrossRefGoogle Scholar
- 51.Greeb J, Atkins JF, Loper JC (1971) Histidinol dehydrogenase (hisD) mutants of Salmonella typhimurium. J Bacteriol 106:421–431Google Scholar
- 52.Truman P, Bergquist PL (1976) Genetic and biochemical characterization of some missense mutations in the lacZ gene of Escherichia coli K-12. J Bacteriol 126:1063–1074Google Scholar
- 56.van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, Kim PM, Kriwacki RW, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright PE, Babu MM (2014) Classification of intrinsically disordered regions and proteins. Chem Rev 114:6589–6631CrossRefGoogle Scholar