Finding the generalized molecular principles of protein thermal stability

Abstract

Are there any generalized molecular principles of thermal adaptation? Here, integrating the concepts of structural bioinformatics, sequence analysis, and classical knot theory, we develop a robust computational framework that seeks for mechanisms of thermal adaptation by comparing orthologous mesophilic‐thermophilic and mesophilic‐hyperthermophilic proteins of remarkable structural and topological similarities, and still leads us to context‐independent results. A comprehensive analysis of 4741 high‐resolution, non‐redundant X‐ray crystallographic structures collected from 11 hyperthermophilic, 32 thermophilic and 53 mesophilic prokaryotes unravels at least five “nearly universal” signatures of thermal adaptation, irrespective of the enormous sequence, structure, and functional diversity of the proteins compared. A careful investigation further extracts a set of amino acid changes that can potentially enhance protein thermal stability, and remarkably, these mutations are overrepresented in protein crystallization experiments, in disorder‐to‐order transitions and in engineered thermostable variants of existing mesophilic proteins. These results could be helpful to find a precise, global picture of thermal adaptation.

Can charge-reversal be considered as a strategy for attaining thermal stability in proteins?

“…Thermophilic proteins feature a higher number of charge-charge interactions than their mesophilic orthologs (6,(27)(28)(29)(30), which may be attributed to the fact that thermophilic sequences are generally more enriched with charged residues (6,31,32…”

“…Condition like extreme temperature demands special designing of proteins in thermophile and hyperthermophiles to function and survive. As proteins in thermophilic and hyperthermophilic organisms are more repellent to proteolysis and denaturation, engineering themostable variants of biocatalysts on the same mechanism that the nature uses (2)(3)(4), is a topic of immense interest for decades (5,6). Among underlying molecular adaptations behind thermostability, number of charged amino acids is one of the few factors those exhibit a consistent incremental tendency from mesophilic to thermophilic and hyperthermophilic organisms (6).…”

Structural Characterization of an ACP from Thermotoga maritima: Insights into Hyperthermal Adaptation

“…Hyperthermophilic proteins are more rigid than their mesophilic counterparts, and this structural rigidity is commonly considered as a prerequisite for high thermostability [51][52][53][54]. Salt bridges have been proposed to play a crucial role in increasing the rigidity and thermostability of hyperthermophilic proteins [29,30]. In addition to ionic interactions, hydrophobic interactions have also been reported to provide additional stabilization to the structures of thermophilic proteins [55,56].…”

“…Proteins must maintain not only the correct structure but also the appropriate dynamic motion to accomplish their functions. Thermophilic proteins often contain extra salt bridges or tightly packed hydrophobic interactions, which help to maintain proper folding at high temperatures [29,30]. It is important to understand the mechanisms through which proteins balance structural stability and functional flexibility in such harsh environments.…”

Biocatalysis at Extreme Temperatures: Enantioselective Synthesis of both Enantiomers of Mandelic Acid by Transesterification Catalyzed by a Thermophilic Lipase in Ionic Liquids at 120 °C

“…However, harsh conditions required for many industrial processes-such as high temperature and/or the use of organic (co)solvents-may impede the use of some enzymes. To address these drawbacks, using thermotolerant biocatalysts obtained from thermophilic organisms is an excellent alternative [20][21][22][23], as these thermozymes can efficiently work at very high temperatures [24,25] and are generally very resistant to organic solvent-promoted denaturation [26,27]. Among all the arsenal of enzymes available for being used in biotransformations, lipases (triacylglycerol hydrolases, EC 3.1.1.3) are one of the most frequently applied, as they are easily available, do not need cofactors and display a wide range of substrate recognition [28][29][30][31].…”