Adaptive amino acid replacements accompanied by domain fusion in reverse transcriptase

Detection of subunit interfacial modifications by tracing the evolution of clamp–loader complex

The archaeal and eukaryal clamp-loader and clamp proteins were investigated with the evolutionary trace method. The molecular phylogeny of the proteins suggested that the hetero-pentameric complex of the archaeal clamp-loader with two subunits (RFCL and RFCS) was not a preserved ancestral type, but a degenerated version of the eukaryal complex of five subunits (RFC1-5). The evolutionary trace of amino acid replacements during the course of subunit differentiation revealed that the replacements had accumulated preferentially at the subunit interface regions. Some of the interfacial modifications that might be responsible for the specific interaction between the subunits were conserved in the current complex.

Design, construction, crystallization, and preliminary X-ray studies of a fine-tuning mutant (F133V) of module-substituted chimera hemoglobin

A chimera betaalpha-subunit of human hemoglobin was crystallized into a carbonmonoxy form. The protein was assembled by substituting the structural portion of a beta-subunit of hemoglobin (M4 module of the subunit) for its counterpart in the alpha-subunit. In order to overcome the inherent instability in the crystallization of the chimera subunit, a site-directed mutagenesis (F133V) technique was employed based on a computer model. The crystal was used for an X-ray diffraction study yielding a data set with a resolution of 2.5 A. The crystal belongs to the monoclinic space group P21, with cell dimensions of a = 62.9, b = 81.3, c = 55.1 A, and beta = 91.0 degrees . These dimensions are similar to the crystallographic parameters of the native beta-subunit tetramers in three different ligand states, one of which is a cyanide form that was also crystallized in this study.

Favorable domain size in proteins

BACKGROUND

It has been observed that single-domain proteins and domains in multidomain proteins favor a chain length in the range 100-150 amino acids. To understand the origin of the favored size, we construct an empirical function for the free energy of unfolding versus the chain length. The parameters in the function are derived by fitting to the energy of hydration, entropy and enthalpy of unfolding of nine proteins. Our energy function cannot be used to calculate the energetics accurately for individual proteins because the energetics also depend on other factors, such as the composition and the conformation of the protein. Nevertheless, the energy function statistically characterizes the general relationship between the free energy of unfolding and the size of the protein.

RESULTS

The predicted optimal number of residues, which corresponds to the maximum free energy of unfolding, is 100. This is in agreement with a statistical analysis of protein domains derived from their experimental structures. When a chain is too short, our energy function indicates that the change in enthalpy of internal interactions is not favorable enough for folding because of the limited number of inter-residue contacts. A long chain is also unfavorable for a single domain because the cost of configurational entropy increases quadratically as a function of the chain length, whereas the favorable change in enthalpy of internal interactions increases linearly.

CONCLUSIONS

Our study shows that the energetic balance is the dominant factor governing protein sizes and it forces a large protein to break into several domains during folding.