Different potential energy functions have predominated in protein dynamics simulations, protein design calculations, and protein structure prediction. Clearly, the same physics applies in all three cases. The differences in potential energy functions reflect differences in how the calculations are performed. With improvements in computer power and algorithms, the same potential energy function should be applicable to all three problems. In this review, we examine energy functions currently used for protein design, and look to the molecular mechanics field for advances that could be used in the next generation of design algorithms. In particular, we focus on improved models of the hydrophobic effect, polarization and hydrogen bonding.9. Bass JL, Bhatia A, Boas FE, Sansary J, Rauch D. (2006) "Validation of a body mass index nomogram for children as an obesity screening tool in young children." Clinical pediatrics. 45(8): 718-24. More »
Translation of an mRNA is generally divided into three stages: initiation, elongation and termination. The relative rates of these steps determine both the number and position of ribosomes along the mRNA, but traditional velocity sedimentation assays for the translational status of mRNA determine only the number of bound ribosomes. We developed a procedure, termed Ribosome Density Mapping (RDM), that uses site-specific cleavage of polysomal mRNA followed by separation on a sucrose gradient and northern analysis, to determine the number of ribosomes associated with specified portions of a particular mRNA. This procedure allows us to test models for translation and its control, and to examine properties of individual steps of translation in vivo. We tested specific predictions from the current model for translational control of GCN4 expression in yeast and found that ribosomes were differentially associated with the uORFs elements and coding region under different growth conditions, consistent with this model. We also mapped ribosome density along the ORF of several mRNAs, to probe basic kinetic properties of translational steps in yeast. We found no detectable decline in ribosome density between the 5' and 3' ends of the ORFs, suggesting that the average processivity of elongation is very high. Conversely, there was no queue of ribosomes at the termination site, suggesting that termination is not very slow relative to elongation and initiation. Finally, the RDM results suggest that less frequent initiation of translation on mRNAs with longer ORFs is responsible for the inverse correlation between ORF length and ribosomal density that we observed in a global analysis of translation. These results provide new insights into eukaryotic translation in vivo.7. Boas FE. (2000) "Linkage to Gaucher Mutations in the Ashkenazi Population: Effect of Drift on Decay of Linkage Disequilibrium and Evidence for Heterozygote Selection." Blood Cells, Molecules, and Diseases. 26(4): 348-59. More »
The two most common Gaucher disease mutations in the Ashkenazi population, 1226A→G and 84G→GG in the glucocerebrosidase gene, are tightly linked to a marker in the nearby pyruvate kinase gene. This paper develops a simulation of the Ashkenazi population that considers the effects of selection and drift on the mutant allele frequency and the recombinant haplotype frequency over time. Although the fraction of mutants that are linked to the original marker decays exponentially on average, this expected value is not very likely to occur. Instead, due to random loss of the recombinant haplotype, a mutation has a significant probability of retaining complete linkage disequilibrium long after its origin, so there may be large errors in estimating the age of a mutation based on linkage data. The simulations show that the 1226G mutation probably originated between 40 and 1000 generations ago (1000 to 25,000 years ago), and the 84GG mutation probably originated between 50 and 4800 generations ago (1300 to 120,000 years ago). The recent origin of the 1226G mutation and its high current allele frequency provide strong evidence for heterozygote selection. New techniques and results developed in this paper have general applicability towards analyzing linkage disequilibrium near other mutations. For example, they potentially explain the unexpected pattern of linkage disequilibrium seen around the ΔF508 mutation of the cystic fibrosis transmembrane conductance regulator gene.6. Boas FE. (1999) "Polyvalent Inhibitors of Pseudomonas aeruginosa Adhesion." Senior honors thesis, Harvard University. More »
Key words: Gaucher disease, linkage disequilibrium, heterozygote advantage, genetic drift, Ashkenazi, computer simulation
We synthesized polymers displaying multiple copies of a peptide from the cystic fibrosis transmembrane conductance regulator (residues 108-117). This peptide is the minimal sequence needed for binding of Pseudomonas aeruginosa. Using an in vitro bacterial internalization assay, our preliminary results indicate that such a polyvalent ligand can prevent P. aeruginosa from attaching to (and being internalized by) epithelial cells. The most effective polymer we synthesized was a polyacrylamide with CFTR peptide covalently attached to 0.5% of its acrylamide subunits. This polymer has an IC50 value of 700 pM, 40,000 times lower than monovalent CFTR peptide. Polyacrylamide at the same concentration does not inhibit internalization.5. Demina A, Boas E, and Beutler E. (1998) "Structure and Linkage Relationships of the Region Containing the Human L-type Pyruvate Kinase (PKLR) and Glucocerebrosidase (GBA) Genes." Hematopathol. Mol. Hematol. 11(2): 63-71.
We also developed a simulation to qualitatively describe how a polyvalent ligand binds to a surface. This simulation demonstrates that the polymer binds to the surface cooperatively. Binding can be enhanced by a larger degree of polymerization, a larger fraction of polymer subunits that can attach to the surface, and greater diffusibility of binding sites on the surface.
Both the L-type pyruvate kinase gene (PKLR) and glucocerebrosidase (GBA) gene are on band q21 of chromosome 1 in humans. Two overlapping P1 bacteriophage clones containing PKLR and GBA were identified and mapped, defining the locations of these two genes as well as those of the GBA pseudogene (ΨGBA), metaxin (MTX), the MTX pseudogene (ΨMTX), and thrombospondin 3 (THBS3). The distance between 5' ends of GBA and PKLR was determined to be 71 kb. The direction of transcription of the PKLR gene was convergent to that of the GBA gene. All 195 Gaucher disease patients homozygous for the 1226G mutation, representing 390 chromosomes with the 1226G mutation, had a PvuII −/− GBA haplotype and a C/C at nt 1705 of the PKLR gene (−/− haplotype). All 56 Gaucher disease patients who were 1226G/84GG compound heterozygotes manifested a −/+ GBA haplotype and 55 of 56 patients were −/+ at PKLR nt 1705. Only 1 patient with 1226G/84GG genotype showed a crossover with the PKLR polymorphism, with a −/− haplotype at nt 1705. Similarly, 9 patients deficient in pyruvate kinase with the PKLR 1529A/1529A genotype were all found to have the same −/− GBA haplotype.4. Boas FE, Forman L, and Beutler E. (1998) "Phosphatidylserine Exposure and Red Cell Viability in Red Cell Aging and in Hemolytic Anemia." Proc. Natl. Acad. Sci., USA. 95: 3077-3081. More »
Key words: Gaucher disease, anemia, hemolytic, mapping, polymorphism, linkage.
Phosphatidylserine (PS) normally localizes to the inner leaflet of cell membranes but becomes exposed in abnormal or apoptotic cells, signaling macrophages to ingest them. Along similar lines, it seemed possible that the removal of red cells from circulation because of normal aging or in hemolytic anemias might be triggered by PS exposure. To investigate the role of PS exposure in normal red cell aging, we used N-hydroxysuccinimide-biotin to tag rabbit red cells in vivo, then used phycoerythrin-streptavidin to label the biotinylated cells, and annexin V-fluorescein isothiocyanate (FITC) to detect the exposed PS. Flow cytometric analysis of these cells drawn at 10-day intervals up to 70 days after biotinylation indicated that older, biotinylated cells expose more PS. Furthermore, our data match a simple model of red cell senescence that assumes both an age-dependent destruction of senescent red cells preceded by several hours of PS exposure and a random destruction of red cells without PS exposure. By using this model, we demonstrated that the exposure of PS parallels the rate at which biotinylated red cells are removed from circulation. On the other hand, using an annexin V-FITC label and f low cytometry demonstrates that exposed PS does not cause the reduced red cell life span of patients with hemolytic anemia, with the possible exception of those with unstable hemoglobins or sickle cell anemia. Thus, in some cases PS exposure on the cell surface may signal the removal of red cells from circulation, but in other cases some other signal must trigger the sequestration of cells.3. Boas FE, Forman L, and Beutler E. (1997) "Phosphatidylserine Exposure and Red Cell Viability in Red Cell Ageing, Storage, and in Hemolytic Anemia." Blood. 90.10 (Supplement 1, Part 1): 272a.
(We investigate the hunting and fleeing strategies of a fast predator and its agile prey in a chase of finite time.)
Last updated: 2007-06-12