Cation–π interactions: computational analyses of the aromatic box motif and the fluorination strategy for experimental evaluation

Cation–π interactions are common in biological systems, and many structural studies have revealed the aromatic box as a common motif. With the aim of understanding the nature of the aromatic box, several computational methods were evaluated for their ability to reproduce experimental cation–π binding energies. We find the DFT method M06 with the 6-31G(d,p) basis set performs best of several methods tested. The binding of benzene to a number of different cations (sodium, potassium, ammonium, tetramethylammonium, and guanidinium) was studied. In addition, the binding of the organic cations NH_4+ and NMe_4+ to ab initio generated aromatic boxes as well as examples of aromatic boxes from protein crystal structures were investigated. These data, along with a study of the distance dependence of the cation–π interaction, indicate that multiple aromatic residues can meaningfully contribute to cation binding, even with displacements of more than an angstrom from the optimal cation–π interaction. Progressive fluorination of benzene and indole was studied as well, and binding energies obtained were used to reaffirm the validity of the “fluorination strategy” to study cation–π interactions in vivo

Land of the Jewish Indians: How the Hebrew Bible made race and territory in the early United States

This project traces the rise and fall from 1790-1850 of the idea, once popular in the United States, that Native Americans were descended from Ancient Israelites. White evangelicals, Native Americans, American Jews, and early Mormons all told “Israelite Indian stories” to intervene in the contest over land in North America. Their stories staked divinely-backed claims on “promised lands” in North America. In the process, they re-drew or disrupted racial boundaries by suggesting unlikely bonds of kinship among Native Americans, white Protestants, and Jews. In aggregate, these stories show that a broad swath of Americans, not just white proponents of the nation’s “manifest destiny” to rule the continent, used Christian motifs to understand and debate the future of this expansive empire. This project, therefore, clarifies the links between religion and empire in the early United States. In contrast to studies focusing on the religious and political theories of white elites alone, it demonstrates that a broad range of Americans of multiple races, classes, and confessions used religious narratives and Christian theology understand life in a colonial society. For those who told them, Israelite Indian narratives forged new political alliances and dramatized the crises brought about by white Americans’ appropriation of American Indian land.Doctor of Philosoph

Who Chooses? A Preliminary Analysis of Hartford Public Schools

In this preliminary analysis of Hartford Public School district choice applications from Spring 2010, the authors examine which Hartford students were more likely to voluntarily apply to another district school operated by the city. Among the 6,591 potential voluntary choosers in grades 3-7, only 227 (3%) submitted voluntary district choice applications, and among these, the highest percentage (43%) were willing to travel farther for a higher-scoring school. But when excluding about one-third of these students who listed the city\u27s high-scoring district school (Achievement First) as their first choice, a large percentage (35%) were willing to travel farther for a lower-scoring school

Electron Cryomicroscopy of Biological Machines at Subnanometer Resolution

Advances in electron cryomicroscopy (cryo-EM) have made possible the structural determination of large biological machines in the resolution range of 6–9 Å. Rice dwarf virus and the acrosomal bundle represent two distinct types of machines amenable to cryo-EM investigations at subnanometer resolutions. However, calculating the density map is only the first step, and much analysis remains to extract structural insights and the mechanism of action in these machines. This paper will review the computational and visualization methodologies necessary for analysis (structure mining) of the computed cryo-EM maps of these machines. These steps include component segmentation, averaging based on local symmetry among components, density connectivity trace, incorporation of bioinformatics analysis, and fitting of high-resolution component data, if available. The consequences of these analyses can not only identify accurately some of the secondary structure elements of the molecular components in machines but also suggest structural mechanisms related to their biological functions

Structural Requirements in the Transmembrane Domain of GLIC Revealed by Incorporation of Noncanonical Histidine Analogs

The cyanobacterial pentameric ligand-gated ion channel GLIC, a homolog of the Cys-loop receptor superfamily, has provided useful structural and functional information about its eukaryotic counterparts. X-ray diffraction data and site-directed mutagenesis have previously implicated a transmembrane histidine residue (His234) as essential for channel function. Here, we investigated the role of His234 via synthesis and incorporation of histidine analogs and α-hydroxy acids using in vivo nonsense suppression. Receptors were expressed heterologously in Xenopus laevis oocytes, and whole-cell voltage-clamp electrophysiology was used to monitor channel activity. We show that an interhelix hydrogen bond involving His234 is important for stabilization of the open state, and that the shape and basicity of its side chain are highly sensitive to perturbations. In contrast, our data show that two other His residues are not involved in the acid-sensing mechanism

One hundred twenty-five concomitant endovascular and open procedures for lower extremity arterial disease

AbstractObjective: Although the results of staged endovascular and open surgical reconstructions have been well documented, the safety and efficacy of concomitant procedures in the operating room are less well defined. Suboptimal performance of endovascular procedures in an operative setting, or inappropriate reliance on endovascular techniques, might theoretically compromise graft patency. We questioned whether late graft thrombosis is frequently attributable to failure at the endovascularly treated site in this setting. Materials and Methods: Between May 1, 1993, and June 30, 2001, we performed 125 concomitant endovascular and open arterial reconstructions (73 primary reconstructions, 52 graft revisions) in 106 patients. Endovascular techniques were used to treat inflow lesions in 72 cases, outflow lesions in 14 cases, both in four cases, and the graft itself in 35 cases. Fifty-five iliac, 18 femoral, 13 popliteal, six tibial, and 35 graft lesions were treated. For primary bypasses, 33 were to the popliteal level (21 prosthetic, 12 autogenous), 19 were to the tibial or pedal arteries (16 autogenous, three prosthetic or composite), and 12 were to the femoral arteries (one autogenous, 11 prosthetic). Nine patch angioplasties (eight femoral, one popliteal) were performed. For graft revisions, endovascular intervention was for inflow in 13 cases, outflow in three cases, both in one case, and of the graft itself in 35 cases. Surgical revisions involved segmental grafts in 33 cases, patch angioplasty in 18 cases, and both in one case. Results: In the primary group, the initial technical success rate of the endovascular procedure was 93% (68/73), with five patients needing open conversion. The 30-day mortality rate was 1.4%, and the morbidity rate was 11.0%. Of the 19 grafts in the primary group that occluded during the follow-up period (mean, 11.9 months), five thromboses could possibly be attributed to failure at the endovascular site. In the revision group, the initial technical success rate of the endovascular procedure was 88% (46/52), with six patients undergoing conversion to open procedure. The 30-day mortality rate was 0%, and the morbidity rate was 15.4%. Of 22 late graft occlusions in the revision group, only three were attributed to failure at the endovascular site. Conclusion: This largest report to date of concomitant lower extremity endovascular and open revascularization procedures shows the approach to be safe. Few late graft occlusions were attributable to failure at the endovascularly treated site. The concomitant approach offers the efficiency and convenience of single stage therapy and allows immediate treatment for inadequate endovascular results or their complications and potential cost savings. (J Vasc Surg 2003;37:316-22.

Perturbation of Critical Prolines in Gloeobacter violaceus Ligand-gated Ion Channel (GLIC) Supports Conserved Gating Motions among Cys-loop Receptors.

Gloeobacter violaceus ligand-gated ion channel (GLIC) has served as a valuable structural and functional model for the eukaryotic Cys-loop receptor superfamily. In Cys-loop and other receptors, we have previously demonstrated the crucial roles played by several conserved prolines. Here we explore the role of prolines in the gating transitions of GLIC. As conventional substitutions at some positions resulted in nonfunctional proteins, we used in vivo non-canonical amino acid mutagenesis to determine the specific structural requirements at these sites. Receptors were expressed heterologously in Xenopus laevis oocytes, and whole-cell electrophysiology was used to monitor channel activity. Pro-119 in the Cys-loop, Pro-198 and Pro-203 in the M1 helix, and Pro-299 in the M4 helix were sensitive to substitution, and distinct roles in receptor activity were revealed for each. In the context of the available structural data for GLIC, the behaviors of Pro-119, Pro-203, and Pro-299 mutants are consistent with earlier proline mutagenesis work. However, the Pro-198 site displays a unique phenotype that gives evidence of the importance of the region surrounding this residue for the correct functioning of GLIC.This work was supported by grants from the NIH (NS 34407 to DAD) and the Wellcome Trust (WT 81925 to SCRL), and an NIH/NRSA training grant (GM07616 to MR).This is the final version of the article. It first appeared from American Society for Biochemistry and Molecular Biology via http://dx.doi.org/10.1074/jbc.M115.69437