Binding to the open conformation of HIV‐1 protease

A recent crystal structure of HIV‐1 protease (HIVp) was the first to experimentally observe a ligand targeting an open‐flap conformation. Researchers studying a symmetric pyrrolidine inhibitor found that two ligands cocrystallized with the protease, forcing an unusual configuration and unique crystallographic contacts. One molecule is centered in the traditional binding site (α pose) and the other binds between the flaps (β pose). The ligands stack against each other in a region termed the “eye” site. Ligands bound to the eye site should prevent flap closure, but it is unclear if the pyrrolidine inhibitors or the crystal packing are causing the open state. Molecular dynamics simulations were used to examine the solution‐state behavior of three possible binding modes: the ternary complex of HIVp+αβ and the binary complexes, HIVp+α and HIVp+β. We show that HIVp+α is the most stable of the three states. During conformational sampling, α takes an asymmetric binding pose, with one naphthyl ring occupying the eye site and the other reoriented down to occupy positions seen with traditional inhibitors. This finding supports previous studies that reveal a requirement for asymmetric binding at the eye site. In fact, if the α pose is modified to splay both naphthyl rings across the binding site like traditional inhibitors, one ring consistently flips to occupy the eye site. Our simulations reveal that interactions to the eye site encourage a conformationally restrained state, and understanding those contacts may aid the design of ligands to specifically target alternate conformations of the protease. Proteins 2011; © 2011 Wiley‐Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87021/1/23054_ftp.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/87021/2/PROT_23054_sm_suppinfo.pd

DEVELOPMENT OF AN INSTRUMENT TO MEASURE K-12 TEACHER DEMORALIZATION IN A TEST-BASED ACCOUNTABILITY CONTEXT

The purpose of this study was to develop an instrument to measure K-12 teacher demoralization. An increasing body of literature has labeled modern education policies as having a demoralizing effect on teachers (Darling-Hammond & Rustique-Forrester, 2002; Noddings, 2004; Ryan & Brown, 2005; Nichols & Berliner, 2007; Santoro, 2011; Hargreaves, Braun, & Gebhardt, 2013). Teacher demoralization has been defined as a teacher’s “inability to access the moral rewards of teaching” (Santoro, 2011, p. 3). Data was collected from a population of K-12 educators through cognitive interviews (n=6) and a large scale data collection analyzed with a principal component analysis (n=430) in an effort to determine which constructs should be included in the measurement of teacher demoralization. Feedback on the survey instrument was incorporated in an iterative process at each stage of data collection. Results revealed that the theory of teacher demoralization should include two factors: teacher dispositions and feelings of demoralization. The current study failed to find strong evidence of convergent validity with teacher burnout and self-determination need thwarting; however, results suggest that emotional exhaustion and autonomy need thwarting are moderately related to teacher demoralization. Evidence of discriminant validity in relation to teacher self-efficacy was found; however, other discriminant validity evidence was inconclusive. This study extends the literature by providing the first attempt to measure the phenomenon of teacher demoralization. Future studies should continue to refine the instrument of teacher demoralization, and can use this instrument as one way to examine the impact of policy on teachers

Beginning to track 1000 datasets from public repositories into the published literature

Data sharing provides many potential benefits, although the amount of actual data reused is unknown. Here we track the reuse of data from three data repositories (NCBI\u27s Gene Expression Omnibus, PANGAEA, and TreeBASE) by searching for dataset accession number or unique identifier in Google Scholar and using ISI Web of Science to find articles that cited the data collection article. We found that data reuse and data attribution patterns vary across repositories. Data reuse appears to correlate with the number of citations to the data collection article. This preliminary investigation has demonstrated the feasibility of this method for tracking data reuse

Computational studies and peptidomimetic design for the human p53–MDM2 complex

The interaction between human p53 and MDM2 is a key event in controlling cell growth. Many studies have suggested that a p53 mimic would be sufficient to inhibit MDM2 to reduce cell growth in cancerous tissue. In order to design a potent p53 mimic, molecular dynamics (MD) simulations were used to examine the binding interface and the effect of mutating key residues in the human p53–MDM2 complex. The Generalized Born surface area (GBSA) method was used to estimate free energies of binding, and a computational alanine-scanning approach was used to calculate the relative effects in the free energy of binding for key mutations. Our calculations determine the free energy of binding for a model p53–MDM2 complex to be −7.4 kcal/mol, which is in very good agreement with the experimentally determined values (−6.6–−8.8 kcal/mol). The alanine-scanning results are in good agreement with experimental data and calculations by other groups. We have used the information from our studies of human p53–MDM2 to design a Β-peptide mimic of p53. MD simulations of the mimic bound to MDM2 estimate a free energy of binding of −8.8 kcal/mol. We have also applied alanine scanning to the mimic–MDM2 complex and reveal which mutations are most likely to alter the binding affinity, possibly giving rise to escape mutants. The mimic was compared to nutlins, a new class of inhibitors that block the formation of the p53–MDM2 complex. There are interesting similarities between the nutlins and our mimic, and the differences point to ways that both inhibitors may be improved. Finally, an additional hydrophobic pocket is noted in the interior of MDM2. It may be possible to design new inhibitors to take advantage of that pocket. Proteins 2005. © 2004 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34979/1/20275_ftp.pd

What Motivates Men\u27s Involvement in Gender-Based Violence Prevention? Latent Class Profiles and Correlates in an International Sample of Men

Data from an international sample of 392 men who had attended gender-based violence (GBV) prevention events were used to examine motivations for involvement in GBV prevention work. Participants responded to an online survey (available in English, French, and Spanish). The most commonly reported reasons for involvement included concern for related social justice issues (87 percent), exposure to the issue of violence through work (70 percent), hearing a moving story about domestic or sexual violence (59 percent), and disclosure of abuse from someone close to the participant (55 percent). Using a latent class analysis, we identified four profiles of men\u27s motivations: low personal connection (22 percent), empathetic connection (26 percent), violence exposed connection (23 percent), and high personal and empathetic connection (29 percent). Participants classified into these profiles did not differ in length of movement involvement but some differences on key ally variables and by global region did emerge. Implications for engagement strategies and future research are discussed

Cattail Invasion of Sedge/Grass Meadows in Lake Ontario: Photointerpretation Analysis of Sixteen Wetlands over Five Decades

Photointerpretation studies were conducted to evaluate vegetation changes in wetlands of Lake Ontario and the upper St. Lawrence River associated with regulation of water levels since about 1960. The studies used photographs from 16 sites (four each from drowned river mouth, barrier beach, open embayment, and protected embayment wetlands) and spanned a period from the 1950s to 2001 at roughly decadal intervals. Meadow marsh was the most prominent vegetation type in most wetlands in the late 1950s when water levels had declined following high lake levels in the early 1950s. Meadow marsh increased at some sites in the mid-1960s in response to low lake levels and decreased at all sites in the late 1970s following a period of high lake levels. Typha increased at nearly all sites, except waveexposed open embayments, in the 1970s. Meadow marsh continued to decrease and Typha to increase at most sites during sustained higher lake levels through the 1980s, 1990s, and into 2001. Most vegetation changes could be correlated with lake-level changes and with life-history strategies and physiological tolerances to water depth of prominent taxa. Analyses of GIS coverages demonstrated that much of the Typha invasion was landward into meadow marsh, largely by Typha × glauca. Lesser expansion toward open water included both T. × glauca and T. angustifolia. Although many models focus on the seed bank as a key component of vegetative change in wetlands, our results suggest that canopy-dominating, moisture- requiring Typha was able to invade meadow marsh at higher elevations because sustained higher lake levels allowed it to survive and overtake sedges and grasses that can tolerate periods of drier soil conditions

A poke in the eye: Inhibiting HIV-1 protease through its flap-recognition pocket

A novel mechanism of inhibiting HIV-1 protease (HIVp) is presented. Using computational solvent mapping to identify complementary interactions and the Multiple Protein Structure method to incorporate protein flexibility, we generated a receptor-based pharmacophore model of the flexible flap region of the semiopen, apo state of HIVp. Complementary interactions were consistently observed at the base of the flap, only within a cleft with a specific structural role. In the closed, bound state of HIVp, each flap tip docks against the opposite monomer, occupying this cleft. This flap-recognition site is filled by the protein and cannot be identified using traditional approaches based on bound, closed structures. Virtual screening and dynamics simulations show how small molecules can be identified to complement this cleft. Subsequent experimental testing confirms inhibitory activity of this new class of inhibitor. This may be the first new inhibitor class for HIVp since dimerization inhibitors were introduced 17 years ago. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 643–652, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [email protected] Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58588/1/20993_ftp.pd

Temporal and spatial perspectives on the fate of anthropogenic carbon : a carbon cycle slide deck for broad audiences

This slide deck was developed to inform broader scientific, as well as general audiences about the role of the ocean in the global carbon cycle, including key sinks and sources of anthropogenic carbon and how they have evolved through time and space