Non-polar nuclei in fungal microbial RNases

An application of a previously proposed method for the analysis of the non-polar structure of proteins is presented. A detailed analysis of the composition and properties of non-polar nuclei and microclusters of fungal microbial ribonucleases has been performed on the basis of the 3-D structures of RNase T1 and related proteins. Three hydrophobic nuclei were found in these structures. It has been shown that all residues in non-polar nuclei have high homology (approximately 89%). Residues in the nuclei are practically fully buried in the interior of a molecule. Detailed analysis of non-polar nuclei properties shows that these nuclei determine the hydrophobic core of a protein and the location and role of each residue in the non-polar interior of proteins. In addition it was found that there are variable residues not only on the surface of a protein but on the surface of the nuclei inside the protein and between the nuclei and that there is a consistent region in all proteins, the hydrophobic gamma-nuclei. An evaluation of the stability of non-polar nuclei, the conservation of their compositions and their positions in the protein globule, allows one to assume that these three nuclei play an important functional role in the stability and folding of molecules of RNases and possibly can be considered as independent structural elements of 3-D structures of these proteins.