A little less than a decade ago a study suggested that there are two major physical mechanisms for protein thermal stabilization depending on the evolutionary history of the source organism, a ''structure-based" and a ''sequence-based" one [Berezovsky and Shakhnovich, 2005]. Proteins from organisms that originated in hot environments (therein archaea) have a much more compact structure and hydrophobic core. On the other hand, proteins from organisms that started as mesophiles and later recolonized a hotter environment (therein bacteria) remain structurally similar to mesophilic homologues but present some sequence substitutions that result in a few key interactions in the final fold.
However, this strict assignment of evolutionary history to these two domains of life, archaea and bacteria, has no solid ground. In fact, more recent studies showed that the ancestors of bacteria were also thermophiles [Boussau et al., 2008; Akanuma et al. 2013]. Yet, the same study had also another dark point. The structure of the hyperthermophilic protein rubredoxin from archaeon Pyrococcus furiosus was found to be more tightly packed (number of contacts per residue) as compared to the rubredoxins from another 3 mesophilic bacteria. This result seems to contradict an earlier H/D experiment suggesting that the flexibility of this protein is typical to that of mesophiles [Hernandez et al., 2000] but the authors dedicate no comment to that. One certain aspect is that structural studies, although they put things in a first informative perspective, they neglect dynamics and are based on X-ray structures resolved at low temperatures. Notably, the effect of temperature on the structure and the magnitude of fluctuations of the exact same protein has been pointed out by short timescale MD simulations [Ergenekan et al., 2005]. Although the dynamics of rubredoxin from Pyrococcus furiosus was quite recently studied in detail using incoherent quasi-elastic neutron scattering in combination with MD [Borreguero et al., 2011], further comparative MD studies between mesophilic and thermophilic rubredoxins might shed light to contradictions such as the above.
However, this strict assignment of evolutionary history to these two domains of life, archaea and bacteria, has no solid ground. In fact, more recent studies showed that the ancestors of bacteria were also thermophiles [Boussau et al., 2008; Akanuma et al. 2013]. Yet, the same study had also another dark point. The structure of the hyperthermophilic protein rubredoxin from archaeon Pyrococcus furiosus was found to be more tightly packed (number of contacts per residue) as compared to the rubredoxins from another 3 mesophilic bacteria. This result seems to contradict an earlier H/D experiment suggesting that the flexibility of this protein is typical to that of mesophiles [Hernandez et al., 2000] but the authors dedicate no comment to that. One certain aspect is that structural studies, although they put things in a first informative perspective, they neglect dynamics and are based on X-ray structures resolved at low temperatures. Notably, the effect of temperature on the structure and the magnitude of fluctuations of the exact same protein has been pointed out by short timescale MD simulations [Ergenekan et al., 2005]. Although the dynamics of rubredoxin from Pyrococcus furiosus was quite recently studied in detail using incoherent quasi-elastic neutron scattering in combination with MD [Borreguero et al., 2011], further comparative MD studies between mesophilic and thermophilic rubredoxins might shed light to contradictions such as the above.
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