Application of principal component analysis to determine the key structural features contributing to iron superoxide dismutase thermostability

Abstract

Iron superoxide dismutase (Fe-SOD) is predominantly found in bacteria and mitochondria. The thermal stability of Fe-SOD from different sources can vary dramatically. We have studied the influence of structural parameters on Fe-SOD thermostability by principal component analysis (PCA). The results show that an increased α-helical and turn content, an increased α-helix and loop length, an increase in the number of main-main chains and charged-uncharged hydrogen bonds, a decrease in the 3(10) -helix content, and a decreased β-strand and loop length are all important factors for Fe-SOD thermostability. Interestingly, the use of charged residues to form salt bridges is tendentious in thermophilic Fe-SOD. Negatively charged Arg and positively charged Glu are efficiently used to form salt bridges. The cooperative action of the exposed area, the hydrogen bonds, and the secondary structure plays a crucial role in resisting high temperatures, which demonstrates that the increased stability of thermophilic Fe-SOD is provided by several structural factors acting together.

Improving the thermostability and stress tolerance of an archaeon hyperthermophilic superoxide dismutase by fusion with a unique N-terminal domain

“…However, its applications are limited by SOD leakage and desorption. The subunits that constitute Fe- and Mn-SOD dimers or tetramers share a wide range of sequence similarities (which can be as low as 25.4 %) but possess virtually identical protein folds and active-site geometries (Jackson and Brunold 2004 ; Wintjens et al 2004 ; Ding et al 2012 ). SODA NG2215 and SODA Ss share highly similar backbones, conserved metal-binding residues and nearly identical tetrameric structures (Additional file 1 : Fig S1).…”

A novel mechanism of protein thermostability: a unique N-terminal domain confers heat resistance to Fe/Mn-SODs

“…It was believed that α-helical content, α-helix length, and even the salt bridges formed by the charged residues, such as Arg and Glu, are important factors for Fe-SOD thermostability. In contrast, the β-strand is negatively correlated via a principal component analysis of five thermophilic SODs and six mesophilic counterparts 25 . Superimposing this model with SOD structures (1MA1, 3AK1, 3EVK, 1B06, and 1WB8) revealed that these tertiary structures are well conserved, especially the regions around the ion binding site.…”

“…Recent efforts to improve the thermal resistance of SODs through chemical modification, gene recombination, and simulated SOD compounds have achieved considerable success 23 24 . Bioinformatic methods have also been used to guide the bioengineering process 25 . Nevertheless, the generality of these methods is limited because the determinants of protein thermostability are numerous.…”

“…Nevertheless, the generality of these methods is limited because the determinants of protein thermostability are numerous. Previous studies indicated that SOD thermostability was affected by many factors, such as ion pairs, hydrogen bonds, hydrophobicity, polar interactions, molecular weight and secondary structures 25 26 27 28 29 . Optimising the thermostability of a SOD using more than one strategy could offer significant progress but also faces great challenges 29 .…”

Rigidity versus flexibility: the dilemma of understanding protein thermal stability

“…It can be considered as a rule that natural thermostable and especially hyperthermostable proteins are characterized by a larger number of charged (titratable) amino acids. This feature has been reported for a large number of individual cases and summarized in comparative studies . Although the physical principles of the stabilizing effect of electrostatic interactions at high temperature are known, the picture will be incomplete without considering the internal motion (flexibility) inherent to the protein molecule.…”