New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface

Abstract

Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

Cloning, Expression, and Structural Elucidation of a Biotechnologically Potential Alkaline Serine Protease From a Newly Isolated Haloalkaliphilic Bacillus lehensis JO-26

“…Therefore, the coil regions in APrBL provide a flexible conformation enhancing its activity and stability under the saline and alkaline conditions. On the contrary, non-halophilic enzymes contain more α-helix and β-strand-forming regions (Zorgani et al, 2014). A similar trend was observed in an alkaline protease from B. pumilus (Baweja et al, 2016).…”

“…The SOPMA tool revealed that the APrBL contained 31.75% α-helices, 22.55% β-strands, and 45.70% coils, suggesting the dominance of the coils. The halophilic and alkaliphilic enzymes need to maintain a balance between enough rigidity to prevent the unfolding and flexibility to allow the motions necessary for the catalysis (Zorgani et al, 2014). Therefore, the coil regions in APrBL provide a flexible conformation enhancing its activity and stability under the saline and alkaline conditions.…”

Analysis on evolutionary relationship of amylases from archaea, bacteria and eukaryota

“…Another property is that haloarchaeal amylases have lower propensity for helix formation but higher propensity for coil formation, which keeps amylases being active in high salt concentration through highly negative charged surface with over representation of acidic residues (Liu et al 2011 ; Zorgani et al 2014 ). This haloadaptation in hypersaline environments can be tracked in Fig.…”

Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments

“…a-amylases form H. marismortui (Zorgani et al 2014), xylanase from Planococcus sp. SL4 (Huang et al 2015b) and protease from Halobacterium sp.…”