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.

Fig. 1.

The temperature-dependence of the energy of unfolding. Every simulation of unfolding started from the native structure and included 2 × 10⁶ MC steps. The absolute temperature increment is 0.2, and 0.1 in the vicinity of transition temperature. In all plots, curves of the unfolding energy of mesophilic proteins are shown by black, blue, or cyan dots; thermophilic proteins, red dots; hyperthermophilic proteins, orange dots; halophilic protein, green dots. (a) Hydrolases, from E. coli (1INO, black rhombuses) and Thermus thermophilus (2PRD, red squares). (b) Rubredoxins, from D. gigas (1RDG, cyan triangles), Clostridium pasteurianum (5RXN, black rhombuses), D. vulgaris (8RXN, blue rhombuses), and P. furiosus (1CAA, orange squares). (c) 2Fe-2S ferredoxin, from Spirulina platensis (4FXC, cyan triangles), Equisetum arvense (1FRR, black rhombuses), Anabaena PCC7120 (1FRD, blue rhombuses), H. marismortui (1DOI, green rhombuses), and S. elongatus (2CJN, red squares). (d) 4Fe-4S ferredoxin, from C. acidiurici (1FCA, black triangles), Peptostreptococcus asaccharolyticus (1DUR, blue rhombuses), B. thermoproteolyticus (1IQZ, red squares), and T. maritima (1VJW, orange squares). (e) Chemotaxis protein, from E. coli (3CHY, blue rhombuses), Salmonella typhimurium (2CHF, black squares), and T. maritima (1TMY, orange squares).

Fig. 2.

Difference of sequence space entropy S(E) from its maximum value as a function of energy. Sequence space entropy S(E) represents the logarithm of the number of sequences that can fold into a given structure with a given energy E. Red diamonds show S(E) for a more designable structure of high contact trace (or higher compactness in lowest order approximation), and blue circles correspond to a structure of low contact trace. A greater number of low-energy (thermostable) sequences can be “accommodated” by higher trace structures (gray shaded region), and, therefore, such structures can adopt a much larger number of foldable, highly thermostable sequences. The curves presented are for illustrative purposes only; detailed calculations for several specific models are presented in ref. .