  In this work we employ various methods of analysis (unfolding simulations and
comparative analysis of structures and sequences of proteomes of thermophilic
organisms) to show that organisms can follow two major strategies of
thermophilic adaptation: (i) General, non-specific, structure-based, when
proteomes of certain thermophilic organisms show significant structural bias
toward proteins of higher compactness. In this case thermostability is achieved
by greater overall number of stabilizing contacts, none of which may be
especially strong, and (ii) Specific, sequence-based, whereby sequence
variations aimed at strengthening specific types of interactions (e.g.
electrostatics) are applied without significantly changing structures of
proteins. The choice of a certain strategy is a direct consequence of
evolutionary history and environmental conditions of particular (hyper)
thermophilic species: ancient hyperthermophilic organisms that directly evolved
in hot environment, pursued mostly structure-based strategy, while later
evolved organisms whose thermophilic adaptation was a consequence of their
recolonization of hot environment, pursued specific, sequence-based strategy of
thermophilic adaptation.
