Energy Landscape and Global Optimization for a Frustrated Model Protein

The three-color (BLN) 69-residue model protein was designed to exhibit frustrated folding. We investigate the energy landscape of this protein using disconnectivity graphs and compare it to a Go model, which is designed to reduce the frustration by removing all non-native attractive interactions. Finding the global minimum on a frustrated energy landscape is a good test of global optimization techniques, and we present calculations evaluating the performance of basin-hopping and genetic algorithms for this system.Comparisons are made with the widely studied 46-residue BLN protein.We show that the energy landscape of the 69-residue BLN protein contains several deep funnels, each of which corresponds to a different β-barrel structure

Early Evolution of Ionotropic GABA Receptors and Selective Regimes Acting on the Mammalian-Specific Theta and Epsilon Subunits

BACKGROUND: The amino acid neurotransmitter GABA is abundant in the central nervous system (CNS) of both invertebrates and vertebrates. Receptors of this neurotransmitter play a key role in important processes such as learning and memory. Yet, little is known about the mode and tempo of evolution of the receptors of this neurotransmitter. Here, we investigate the phylogenetic relationships of GABA receptor subunits across the chordates and detail their mode of evolution among mammals. PRINCIPAL FINDINGS: Our analyses support two major monophyletic clades: one clade containing GABA(A) receptor alpha, gamma, and epsilon subunits, and another one containing GABA(A) receptor rho, beta, delta, theta, and pi subunits. The presence of GABA receptor subunits from each of the major clades in the Ciona intestinalis genome suggests that these ancestral duplication events occurred before the divergence of urochordates. However, while gene divergence proceeded at similar rates on most receptor subunits, we show that the mammalian-specific subunits theta and epsilon experienced an episode of positive selection and of relaxed constraints, respectively, after the duplication event. Sites putatively under positive selection are placed on a three-dimensional model obtained by homology-modeling. CONCLUSIONS: Our results suggest an early divergence of the GABA receptor subunits, before the split from urochordates. We show that functional changes occurred in the lineages leading to the mammalian-specific subunit theta, and we identify the amino acid sites putatively responsible for the functional divergence. We discuss potential consequences for the evolution of mammals and of their CNS

The power of civilizational nationalism in Russian foreign policy making

The article draws upon theories of identity to understand Russian foreign policy towards Ukraine since 2000. The article argues that contemporary Russian foreign policy can be best understood as an articulation of ‘civilizational nationalism’ which relies on the myth of cultural superiority. The focus is on not only treating Russia as an imperial power, but on the cultural claims that this relies upon and its configuration within changing historical ideas of ‘Russianness’. Since the Orange Revolution, Russian presidents have accused Ukraine of following anti-Russian policies. This has been aided by a discourse of ‘civilizational nationalism’ where Ukraine is described as being part of a ‘Greater Russia’, rather than as a sovereign territory. This article analyses how imagined civilization and greatness of Russian culture is driving foreign policy making towards the Ukraine. Rather than an external territory, Ukraine is constructed as a ‘little brother’ which renders interventions legitimate

Using Shifts in Amino Acid Frequency and Substitution Rate to Identify Latent Structural Characters in Base-Excision Repair Enzymes

Protein evolution includes the birth and death of structural motifs. For example, a zinc finger or a salt bridge may be present in some, but not all, members of a protein family. We propose that such transitions are manifest in sequence phylogenies as concerted shifts in substitution rates of amino acids that are neighbors in a representative structure. First, we identified rate shifts in a quartet from the Fpg/Nei family of base excision repair enzymes using a method developed by Xun Gu and coworkers. We found the shifts to be spatially correlated, more precisely, associated with a flexible loop involved in bacterial Fpg substrate specificity. Consistent with our result, sequences and structures provide convincing evidence that this loop plays a very different role in other family members. Second, then, we developed a method for identifying latent protein structural characters (LSC) given a set of homologous sequences based on Gu's method and proximity in a high-resolution structure. Third, we identified LSC and assigned states of LSC to clades within the Fpg/Nei family of base excision repair enzymes. We describe seven LSC; an accompanying Proteopedia page (http://proteopedia.org/wiki/index.php/Fpg_Nei_Protein_Family) describes these in greater detail and facilitates 3D viewing. The LSC we found provided a surprisingly complete picture of the interaction of the protein with the DNA capturing familiar examples, such as a Zn finger, as well as more subtle interactions. Their preponderance is consistent with an important role as phylogenetic characters. Phylogenetic inference based on LSC provided convincing evidence of independent losses of Zn fingers. Structural motifs may serve as important phylogenetic characters and modeling transitions involving structural motifs may provide a much deeper understanding of protein evolution

African-American health: the role of the social environment

Cooper and colleagues have noted that the forces affecting the health of minority populations are the same forces, on a less intensive scale, that affect the health of the overall population. 90 That is, we can view the health of the African-American population as the visible tip of an iceberg. This tip of the iceberg is a function of the average health of the entire population. Thus, an effective strategy must address not only the tip, but also should attack the entire iceberg and reduce the risk that it is creating throughout the population. Similarly, Wallace and Wallace have shown how the mechanisms of hierarchical diffusion, spatial contagion, and network diffusion lead to the spread of health and social problems initially confined in inner cities to suburban areas and smaller cities. 91 That is, because of the economic links typing various communities together, there are mechanisms that will ensure the diffusion of disease and disorder from one area to another. If unaddressed, the problems of stigmatized and marginalized urban populations will have adverse impacts on the health, well-being, and quality of life of the more affluent. Thus, investments that will improve the social conditions of a marginalized population can have long-term positive health and social consequences for the entire society.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45781/1/11524_2006_Article_BF02345099.pd

Palliative care: End-of-life symptoms

Gregory B. Crawford, Katherine A. Hauser, and Wendy I. Janse