Maximum-entropy calculation of free energy distributions in tRNAs

Abstract

We have previously shown that the distribution function describing the probability that a biological macromolecule picked at random has a particular enthalpy value can be calculated from the temperature dependence of the heat capacity of the macromolecule. The free energy as a function of enthalpy (free energy distribution) can then be determined from the enthalpy probability distribution. In addition, the free energy distribution at an arbitrary temperature can be calculated from the free energy distribution at a reference temperature. Here we apply this approach to a family of similar macromolecules, namely a set of transfer RNAs, specifically tRNA Phe, tRNA Val, tRNA Met, tRNA Ser, tRNA Asp and tRNA Ile. Using published heat-capacity data, we calculate the enthalpy probability distribution functions for all of these molecules at five different temperatures covering the range from 30 to 80 °C. We then use these distributions to give a reference free-energy distribution, from which the thermodynamics at any temperature can be calculated for each species. We compare the reference free-energy distribution for the five tRNAs and find that, while the overall form of the distributions is similar, the local behavior of the functions varies considerably between the species.