Folding and wrapping soluble proteins exploring the molecular basis of cooperativity and aggregation

The repatterning of eukaryotic genomes by random genetic drift

Recent observations on rates of mutation, recombination, and random genetic drift highlight the dramatic ways in which fundamental evolutionary processes vary across the divide between unicellular microbes and multicellular eukaryotes. Moreover, population-genetic theory suggests that the range of variation in these parameters is sufficient to explain the evolutionary diversification of many aspects of genome size and gene structure found among phylogenetic lineages. Most notably, large eukaryotic organisms that experience elevated magnitudes of random genetic drift are susceptible to the passive accumulation of mutationally hazardous DNA that would otherwise be eliminated by efficient selection. Substantial evidence also suggests that variation in the population-genetic environment influences patterns of protein evolution, with the emergence of certain kinds of amino-acid substitutions and protein-protein complexes only being possible in populations with relatively small effective sizes. These observations imply that the ultimate origins of many of the major genomic and proteomic disparities between prokaryotes and eukaryotes and among eukaryotic lineages have been molded as much by intrinsic variation in the genetic and cellular features of species as by external ecological forces.

Quantifying the stabilizing energy of the intraprotein hydrogen bond due to local mutation

MD simulation of the WW domain of PIN based on a dynamically adjusted polarized protein-specific force field from quantum fragment calculations is carried out in both wild and VAL22ALA mutant states. The result shows that the geometry of the Arg14-TYR23 hydrogen bond is conserved upon mutation of VAL22 to ALA. However, the electrostatic energy of this hydrogen bond in the mutant is found to be 0.6 kcal/mol weaker than in the wild state, in close agreement with the experimentally measured upper limit of 1.2 kcal/mol. Analysis shows that the weakened energy of this hydrogen bond in the mutant is due to its dynamically changed polarization resulting from an altered local electrostatic environment near the hydrogen bond which becomes more exposed to the solvent than in the wild.

Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins

The energetic contributions of hydrogen bonding to protein folding are still unclear, despite more than 70 years of study. This is due partly to the difficulty of extracting thermodynamic information about specific interactions from protein mutagenesis data and partly to the context dependence of hydrogen bond strengths. Herein, we test the hypothesis that hydrogen bond strengths depend on the polarity of their microenvironment, with stronger hydrogen bonds forming in nonpolar surroundings. Double-mutant cycle analysis using a combination of amide-to-ester backbone mutagenesis and traditional side chain mutagenesis revealed that hydrogen bonds can be stronger by up to 1.2 kcal mol(-1) when they are sequestered in hydrophobic surroundings than when they are solvent exposed. Such large coupling energies between hydrogen bond strengths and local polarity suggest that the context dependence of hydrogen bond strengths must be accounted for in any comprehensive account of the forces responsible for protein folding.