STEAROTHERMOPHILUS RIBOSOMAL PROTEIN L11 & 23S RNA FRAGMENT THERMODYNAMICS

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The understanding of the driving forces mediating protein-nucleic acid interaction requires knowledge of the thermodynamic parameters contributed by each species. In the case where two "rigid bodies" associate, the heat capacity of complex formation is related to the amount of nonpolar surface area from solvation upon binding. However, when such an interaction causes local conformational changes to the protein, additional nonpolar surfaces may also be buried thereby affecting the Cp (association). Spolar and Record (Science 1994 263:777) have established a thermodynamic model to describe the interaction between protein-deoxyribonucleic acid complexes. While complexes between protein and RNA have been well documented, an exhaustive thermodynamic analyses of the thermodynamic parameters of such an interaction have not been applies to these systems. The interaction between the prokaryotic ribosomal protein L11 and a 58 nt. region of 23S rRNA is an excellent model system for the application of this thermodynamic model. The unfolding thermodynamics show that the rRNA fragment in stabile within the physiological temperature range. The L11 solution structure of its binding domain shows remarkable structural homology with the helix-turn-helix superfamily of DNA binding proteins. Isothermal Titration Calorimetry experiments will be conducted to determine the Cp (association) of the interaction. These experiments along with the NMR structure information of the bound and unbound protein will provide information to improve our understanding of the energetics of protein-RNA interaction.