Physics and evolution of thermophilic adaptation

Abstract

Analysis of structures and sequences of several hyperthermostable proteins from various sources reveals two major physical mechanisms of their thermostabilization. The first mechanism is ''structure-based,'' whereby some hyperthermostable proteins are significantly more compact than their mesophilic homologues, while no particular interaction type appears to cause stabilization; rather, a sheer number of interactions is responsible for thermostability. Other hyperthermostable proteins employ an alternative, ''sequence-based'' mechanism of their thermal stabilization. They do not show pronounced structural differences from mesophilic homologues. Rather, a small number of apparently strong interactions is responsible for high thermal stability of these proteins. High-throughput comparative analysis of structures and complete genomes of several hyperthermophilic archaea and bacteria revealed that organisms develop diverse strategies of thermophilic adaptation by using, to a varying degree, two fundamental physical mechanisms of thermostability. The choice of a particular strategy depends on the evolutionary history of an organism. Proteins from organisms that originated in an extreme environment, such as hyperthermophilic archaea (Pyrococcus furiosus), are significantly more compact and more hydrophobic than their mesophilic counterparts. Alternatively, organisms that evolved as mesophiles but later recolonized a hot environment (Thermotoga maritima) relied in their evolutionary strategy of thermophilic adaptation on ''sequence-based'' mechanism of thermostability. We propose an evolutionary explanation of these differences based on physical concepts of protein designability.thermostability ͉ structure͞sequence ͉ molecular evolution ͉ molecular packing ͉ genomes͞proteomes T he importance of various factors contributing to protein thermostability remains a subject of intense study (1). The most frequently reported trends include increased van der Waals interactions (2), higher core hydrophobicity (3), additional networks of hydrogen bonds (1), enhanced secondary structure propensity (4), ionic interactions (5), increased packing density (6), and decreased length of surface loops (7). It was shown recently that proteins use various combinations of these mechanisms. However, no general physical mechanism for increased thermostability was found. The diversity of the ''recipes'' for thermostability immediately raises two important questions: (i) What are possible physical mechanisms to increase thermostability of proteins, and (ii) how did evolution use possible physical mechanisms of thermal stabilization to develop strategies of adaptation to high temperature and other possible demands of the environment?In this work, we first analyze in great detail several proteins from various hyperthermophilic organisms and show that some of them draw their thermostability from structural factors such as increased compactness. Furthermore, direct analysis of interactions as well as sequence comparison with mesophilic orthologues i...

Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli

“…Our result is in agreement with the previous findings to define the minimal pharmacophore in moenomycin, in which the EF-ring phosphoglycerate portion together with either the C or the D ring forms critical interactions with proteins (8). Although A. aeolicus (11), like E. coli, was classified as Gram-negative bacterium, the interaction pattern with moenomycin in AaPGT showed differences from our structure and SaPBP2 ( Fig. 2 B and C).…”

Physical Origins of Protein Superfamilies

“…at the earliest (prebiotic) stages of evolution. It seems therefore likely that emergence of wonderfolds dominated the physical selection and design of first thermostable proteins in the course of prebiotic evolution (36).…”

Structural differences between thermophilic and mesophilic membrane proteins

“…[8][9][10][11][12] Although most hydrogen-bonded sidechain interactions that have been experimentally measured in membrane proteins appear to make relatively modest contributions, [21][22][23][24][25][26][27] some have been measured as high as 1.8 kcal/mol and in theory it is possible that they could be made even stronger. 26,28 Thus, it seems reasonable to expect that the number of transmembrane interhelical hydrogen bonds might increase in thermophiles.…”

“…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.…”