Proteins from thermophilic and mesophilic organisms essentially do not differ in packing

The role of the packing density in the elevation of thermal stability of proteins from thermophilic organisms is widely discussed in the literature. In the present study, this issue was reconsidered in the scale of an unbiased set of protein structures. Partial specific volumes, void and cavity volumes were calculated for a set of 80 non-homologous proteins and for 24 proteins from thermophilic organisms and analysed in the context of their possible role in thermal stabilization. The results showed that there is no significant difference between the two sets in respect to the partial specific volume and cavity volume. The proteins from thermophilic organisms showed a slight tendency of increasing void volume, i.e. reducing the packing density. However this observation was not confirmed by the comparison of this parameter for proteins within different structural families. The results suggested that neither the reduction of the packing density nor the reduction of the packing defects can be considered as a common mechanism for increasing the thermal stability of the proteins from thermophilic organisms. Combining the result from this and our previous study we concluded that the electrostatic interactions seem to be a common factor regulating the thermal tolerance of proteins from thermostable organisms.