Structural insights into the binding of uranyl with human serum protein apotransferrin structure and spectra of protein-uranyl interactions.

Ab initio quantum mechanical computational studies for the structure and IR spectra of the uranyl complex with human serum apotransferrin (TF) protein are carried out to model uranyl intake into the human cell through endocytosis and formation of a coordination complex with the protein binding sites. The computed IR spectra and structure of the uranyl-protein complex facilitate interpretation of the observed spectra and confirm the primary binding sites of the transferrin protein with the uranyl ion. Our computed equilibrium geometry and the IR spectra of the uranyl-TF complex reveal that uranyl ion is bound to two tyrosines, one aspartate group, and one carbonate ion. Our IR spectra indicate that histidine is not involved in binding to uranyl with transferrin protein. Our computations reveal a short, strong hydrogen bond, which could play an important role in the stabilization and formation of the uranyl-TF complex. Computed Laplacian charge plots indicate high chemical reactivity on this complex as both an electrophile and a nucleophile, facilitating binding to different receptors and thus entry into a number of target organs and the blood-brain barrier. The Mulliken charge density plots and the three-dimensional charge density plots suggest a donor-acceptor mechanism in the complex formation.

Loop entropy and cytochrome c stability.

The loop entropy model proposes that loop closure in a protein becomes entropically more costly as the length of the loop increases. A model protein, cytochrome c, is composed of four loops connecting five helices surrounding a heme-containing core. To test the loop entropy model a series of mutant proteins are constructed with (Gly)n or (Thr)n segments (n = 4-20) inserted between Gly23 and Gly24 of omega loop A of a pseudo wild-type reference protein. Scanning calorimetry shows that protein stability decreases as n increases in the (Gly)n or (Thr)n segment. The dependence of stability on loop length is analyzed with the loop entropy model. Fitting to the model gives a quantitative description of stability differences for the mutant proteins, but with a smaller power-dependence of the probability of loop closure (c-value) than expected from polymer theory. A possible explanation for the discrepancy is that thermodynamically unfavorable loop entropy is partially offset by interactions between the inserted homopolymer and flanking heteropolymer portions of the unfolded protein. The interactions may involve molecular crowding that favors coalescence of the heteropolymer at the insert site and thus closure of the homopolymer loops, possibly as an aspect of the folding code. This may allow use of loop insert mutants to assess the strength of the heteropolymer-encoded folding signals that facilitate loop closure at the insert site.