Thermophilic organisms flourish in varied high-temperature environmental niches that are deadly to other organisms. Recently, genomic evidence has implicated a critical role for disulfide bonds in the structural stabilization of intracellular proteins from certain of these organisms, contrary to the conventional view that structural disulfide bonds are exclusively extracellular. Here both compu...

Two computational methods widely used in time series analysis were applied to protein sequences, and their ability to derive structural information not directly accessible through classical sequence comparisons methods was assessed. The primary structures of 19 rubredoxins of both mesophilic and thermophilic bacteria, coded with hydrophobicity values of amino acid residues, were considered as t...

A prerequisite for the survival of (micro)organisms at high temperatures is an adaptation of protein stability to extreme environmental conditions. In contrast to soluble proteins, where many factors have already been identified, the mechanisms by which the thermostability of membrane proteins is enhanced are almost unknown. The hydrophobic membrane environment constrains possible stabilizing f...

We used classical molecular dynamics simulation method to investigate physical factors responsible for the increased thermal stability of proteins from thermophilic and hyperthermophilic organisms. Subject of investigation were two pairs of homologous proteins from the functional classes of: 1) cold shock proteins from Escherichia coli (mesophilic) and Bacillus caldolyticus (thermophilic) and 2...

Identifying determinant(s) of protein thermostability is key for rational and data-driven protein engineering. By analyzing more than 130 pairs of mesophilic/(hyper)thermophilic proteins, we identified the quality (residue-wise energy) of hydrophobic interactions as a key factor for protein thermostability. This distinguishes our study from previous ones that investigated predominantly structur...

Thermophilic bacteria have recently attracted great attention because of their potential application in improving different biochemical processes such as anaerobic digestion of various substrates, wastewater treatment or hydrogen production. In this study we report on the design of a specific 16S rRNA-targeted oligonucleotide probe for detecting members of Coprothermobacter genus characterized ...

Thermophilic proteins have great potential to be utilized as biocatalysts in biotechnology. Machine learning algorithms are gaining increasing use identifying such enzymes, reducing or even eliminating the need for experimental studies. While most previously used machine methods were based on manually designed features, we developed BertThermo, a model using Bidirectional Encoder Representation...

Analysis of the structural basis for thermostability in proteins has come mainly from pairwise comparisons of mesophilic and thermophilic structures and has often yielded conflicting results. Interpretation of these results would be enhanced by knowing the normal range of features found for mesophilic proteins. In order to provide the average and distribution values of structural features among...

Ribonucleases H from the thermophilic bacterium Thermus thermophilus and the mesophile Escherichia coli demonstrate a dramatic and surprising difference in their change in heat capacity upon unfolding (DeltaCp degrees ). The lower DeltaCp degrees of the thermophilic protein directly contributes to its higher thermal denaturation temperature (Tm). We propose that this DeltaCp degrees difference ...

The laborious, and cost-inefficient biochemical methods for identifying thermophilic proteins necessarily require a rapid accurate method proteins. Recently, machine learning has become more effective specific classes of extremophiles. There is still need low-cost proteins, despite the fact that studies employing yielded superior results to conventional methods. Here, we avoid problem manually ...