The Genomics of Disulfide Bonding and Protein Stabilization in Thermophiles

Abstract

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 computational and structural data are presented to explore the occurrence of disulfide bonds as a protein-stabilization method across many thermophilic prokaryotes. Based on computational studies, disulfide-bond richness is found to be widespread, with thermophiles containing the highest levels. Interestingly, only a distinct subset of thermophiles exhibit this property. A computational search for proteins matching this target phylogenetic profile singles out a specific protein, known as protein disulfide oxidoreductase, as a potential key player in thermophilic intracellular disulfide-bond formation. Finally, biochemical support in the form of a new crystal structure of a thermophilic protein with three disulfide bonds is presented together with a survey of known structures from the literature. Together, the results provide insight into biochemical specialization and the diversity of methods employed by organisms to stabilize their proteins in exotic environments. The findings also motivate continued efforts to sequence genomes from divergent organisms.

Prevalence of myocilin gene mutations in a novel UK cohort of POAG patients

“…They play important roles in a variety of functions, including metal binding and formation of disulphide bonds that alter protein structure. 18 For these reasons, mutations causing the appearance or loss of this residue are often pathogenic. Furthermore, the 296 location within the myocilin gene shows significant evolutionary conservation (UniProt database http://www.uniprot.org/) through to the Zebrafish species Danio rerio (data not presented).…”

Redox Biology: Computational Approaches to the Investigation of Functional Cysteine Residues

“…A modification of this approach has been reported (4,59): by analyzing Cys a-carbons located within a distance of 8 Å from each other (C-C distance in Fig. 3), the majority (up to 80%) of disulfide bonds could be detected.…”

Structural differences between thermophilic and mesophilic membrane proteins

“…As a result, the stabilizing mechanisms have been extensively explored for water-soluble proteins. The mechanisms observed include an increase in secondary structure propensity; 1,2 changes that decrease unfolded state entropy such as the introduction of Pro residues, reduction of Gly residues, 3 smaller loops, 4 and the addition of disulfide bonds; [5][6][7] an increase of hydrogen bonds and salt bridges; [8][9][10][11][12] and better optimized hydrophobicity. 13 Szilagyi and Zavodszky 3 made an extensive study of many protein families and found that few of these mechanisms were general, except an increase in salt bridges.…”