Genetic affinities of inbred mouse strains of uncertain origin

Phylogenetic analyses of genetic data arising from 144 gene loci are used to describe the interrelationships among 24 widely used inbred strains of mice. An unordered-parsimony analysis gives a cladogram that is virtually identical to the known genealogy of the mouse strains. A loss-parsimony analysis is used to evaluate the hypothesis that the observed patterns of genetic divergence among these 24 strains can be explained by the segregation of residual heterozygosity arising from a small population of highly heterozygous mice. The loss-parsimony cladogram is very similar to both the unordered-parsimony cladogram and the known genealogy of the mice. The phylogenetic analyses of these 144 loci are integrated with data on the type and origin of the Y chromosome. Inclusion of the Y-chromosome data provides additional insights into the genetic composition of several of the original stocks used to produce the current inbred strains of mice. Ten strains of uncertain origin are contained in these analyses, including AKR, BUB, CE, I, NZB, P, RF, SJL, ST, and SWR. SJL is hypothesized to have been derived from the same Swiss albino stock previously used to produce SWR. The BUB strain appears to have had a complex origin and shows closest genetic similarity to SWR and ST. AKR and RF are shown to be closely related, while the I strain shows greatest genetic similarity to DBA/2 for the 144 loci. However, I and DBA possess different types of Y chromosome. The NZB strain shows genetic similarity to several stocks of both U.S. and European origins. The power of the genetic data used in these analyses reiterates that inbred strains of mice can be a valuable paradigm for studies in evolutionary biology.      

The nonidentity of invariable positions in the cytochromes c of different species

This study answers the question: Are the variable and invariable codons of cytochrome c largely the same in all species? A method is presented for estimating the number of invariable (as opposed to unvaried) codons common to two taxa. The two taxa in this study were comprised of four fungi and four metazoans. Given the number of mutations fixed in each taxon, one calculates the number of codons that would be expected to have fixed mutations in both taxa, in one taxon only, in the other taxon only, and in neither taxon. This expectation depends upon the number of invariable codons that are assumed to be common to both taxa. In the present example, the assumption of 41 invariable codons in common leads to estimates that deviate by less than 2% from the values actually observed. This leads to the conclusion that there are 46 positions that are variable in one taxon but invariable in the other, thereby demonstrating that the invariable codons are not largely the same between the fungi and the metazoans.     

High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp

The dielectric properties of proteins are poorly understood and difficult to describe quantitatively. This limits the accuracy of methods for structure-based calculation of electrostatic energies and pK(a) values. The pK(a) values of many internal groups report apparent protein dielectric constants of 10 or higher. These values are substantially higher than the dielectric constants of 2-4 measured experimentally with dry proteins. The structural origins of these high apparent dielectric constants are not well understood. Here we report on structural and equilibrium thermodynamic studies of the effects of pH on the V66D variant of staphylococcal nuclease. In a crystal structure of this protein the neutral side chain of Asp-66 is buried in the hydrophobic core of the protein and hydrated by internal water molecules. Asp-66 titrates with a pK(a) value near 9. A decrease in the far UV-CD signal was observed, concomitant with ionization of this aspartic acid, and consistent with the loss of 1.5 turns of alpha-helix. These data suggest that the protein dielectric constant needed to reproduce the pK(a) value of Asp-66 with continuum electrostatics calculations is high because the dielectric constant has to capture, implicitly, the energetic consequences of the structural reorganization that are not treated explicitly in continuum calculations with static structures.     

Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins

Molecular dynamics simulations of Staphylococcal nuclease and of 10 variants with internal polar or ionizable groups were performed to investigate systematically the molecular determinants of hydration of internal cavities and pockets in proteins. In contrast to apolar cavities in rigid carbon structures, such as nanotubes or buckeyballs, internal cavities in proteins that are large enough to house a few water molecules will most likely be dehydrated unless they contain a source of polarity. The water content in the protein interior can be modulated by the flexibility of protein elements that interact with water, which can impart positional disorder to water molecules, or bias the pattern of internal hydration that is stabilized. This might explain differences in the patterns of hydration observed in crystal structures obtained at cryogenic and room temperature conditions. The ability of molecular dynamics simulations to determine the most likely sites of water binding in internal pockets and cavities depends on its efficiency in sampling the hydration of internal sites and alternative protein and water conformations. This can be enhanced significantly by performing multiple molecular dynamics simulations as well as simulations started from different initial hydration states.     

Developmental regulation of hepatic ceruloplasmin mRNA and serum activity by exogenous thyroxine and dexamethasone.

Ceruloplasmin (Cp) is a copper-dependent oxidase with roles that include the regulation of iron metabolism, participation in the acute-phase response to inflammation, and antioxidant systems. Although developmental increases in hepatic Cp gene expression and serum activity have been described, the molecular mechanisms that are responsible for this regulation are not fully understood. The studies described here explored the possible role of glucocorticoids and thyroxine (T4) in the early neonatal development of Cp by the administration of these hormones on postnatal Day 1 (24 hr after birth), and the measurement of both hepatic Cp mRNA and serum activity through postnatal Day 10. Administration of the synthetic glucocorticoid hormone, dexamethasone (2 micrograms/g body wt), resulted in an increase in Cp mRNA on Days 3-7 that was accompanied by an increase in serum Cp activity that reached statistical significance at Day 10. Exogenous T4 (2 micrograms/g body wt) significantly increased Cp mRNA 24 hr after administration. Serum Cp activity was also significantly elevated by the early neonatal administration of T4. Furthermore, gestational hypothyroidism resulted in a significant decrease in Cp activity after postnatal Day 3. These data suggest a role for thyroid hormone and possibly glucocorticoids in the normal developmental regulation of Cp.