Conformational selection of inhibitors and substrates by proteolytic enzymes: Implications for drug design and polypeptide processing

Inhibitors of proteolytic enzymes (proteases) are emerging as prospective treatments for diseases such as AIDS and viral infections, cancers, inflammatory disorders, and Alzheimer's disease. Generic approaches to the design of protease inhibitors are limited by the unpredictability of interactions between, and structural changes to, inhibitor and protease during binding. A computer analysis of superimposed crystal structures for 266 small molecule inhibitors bound to 48 proteases (16 aspartic, 17 serine, 8 cysteine, and 7 metallo) provides the first conclusive proof that inhibitors, including substrate analogues, commonly bind in an extended beta-strand conformation at the active sites of all these proteases. Representative superimposed structures are shown for (a) multiple inhibitors bound to a protease of each class, (b) single inhibitors each bound to multiple proteases, and (c) conformationally constrained inhibitors bound to proteases. Thus inhibitor/substrate conformation, rather than sequence/composition alone, influences protease recognition, and this has profound implications for inhibitor design. This conclusion is supported by NMR, CD, and binding studies for HIV-1 protease inhibitors/ substrates which, when preorganized in an extended conformation, have significantly higher protease affinity. Recognition is dependent upon conformational equilibria since helical and turn peptide conformations are not processed by proteases. Conformational selection explains the resistance of folded/structured regions of proteins to proteolytic degradation, the susceptibility of denatured proteins to processing, and the higher affinity of conformationally constrained 'extended' inhibitors/substrates for proteases. Other approaches to extended inhibitor conformations should similarly lead to high-affinity binding to a protease.

Patterns of variation within self-incompatibility loci

Diverse self-incompatibility (SI) mechanisms permit flowering plants to inhibit fertilization by pollen that express specificities in common with the pistil. Characteristic of at least two model systems is greatly reduced recombination across large genomic tracts surrounding the S-locus, which regulates SI. In three angiosperm families, including the Solanaceae, the gene that controls the expression of gametophytic SI in the pistil encodes a ribonuclease (S-RNase). The gene that controls pollen SI expression is currently unknown, although several candidates have recently been proposed. Although each candidate shows a high level of polymorphism and complete allelic disequilibrium with the S-RNase gene, such properties may merely reflect tight linkage to the S-locus, irrespective of any functional role in SI. We analyzed the magnitude and nature of nucleotide variation, with the objective of distinguishing likely candidates for regulators of SI from other genes embedded in the S-locus region. We studied the S-RNase gene of the Solanaceae and 48A, a candidate for the pollen gene in this system, and we also conducted a parallel analysis of the regulators of sporophytic SI in Brassica, a system in which both the pistil and pollen genes are known. Although the pattern of variation shown by the pollen gene of the Brassica system is consistent with its role as a determinant of pollen specificity, that of 48A departs from expectation. Our analysis further suggests that recombination between 48A and S-RNase may have occurred during the interval spanned by the gene genealogy, another indication that 48A may not regulate SI expression in pollen.

Governing society today: Editors' introduction

The notion of governing society has for a long time seemed self-evident. Society was conceived as a totality coincident with a certain space, a territory, and occupied by a population. Governing was undertaken by a unified agency that acted upon the society of which it was also a specialized part--the government, or, more broadly, "the state." The notion of "governing society" thus referred unproblematically to the binary of state and society. The articles in this special issue of Alternatives, however, each in its own and different way, address the question of "governing society today."

Modern Society and Culture in Brazil The Sociology of Florestan Fernandes

The establishment of modern sociology in Brazil was part of a thoroughgoing modernization of the country that began in the 1930s and the years immediately following World War II. The founding of the University of Sao Paulo made possible the systematic training of scientists devoted to teaching and research and broadened the way learning was understood. Florestan Fernandes was the outstanding personality among the first social scientists that the university produced, and the picture of the Brazilian sociologist today is largely inspired by his career. Enthusiasm and scientific rigor were the hallmarks of his approach. His early work reflects intellectuals` shared belief in the power of ideas to regenerate the nation, freeing it from a past that they condemned. The mature reflection of his later works retreats from this optimistic view, recognizing the emergence of modern society in Brazil as a complex process with mixed results.

Destiny and will, religion and politics: Jesus Society and Enlightenment in the posthumous Malabar Rites controversy

The first presentation of Antoine-Marin Le Mierre`s tragedy Malabar Widow, or the Empire of Customs, took place in 1770. It was based on the famous controversy over the Malabar (south west India) Rites. The object of the controversy was the Jesuit project in India, which started in the beginning of XVII century and was stopped by the Pope Benedict XIV, with the Apostolic Constitution Omnium Sollicitudinum. The papal condemnation of the rites closed a long process which shows the progressive loss of power of the Jesuit Company in the Age of Enlightenment, which will be definitive in 1773, with the suppression of the Company. In Le Mierre`s tragedy, we find the judgment of Malabar rites according to the rationalist ideas of the Enlightenment, with some typical topoi of the philosophes`s cultural perspective. At the same time, the enlightened disputation reproduces the Jesuit internal debate about India itself. Starting from a religious universal perspective of the different strategies of Christianization in India, or in the entire East, the missionary controversy had been about the religious or political interpretation of local signs. Briefly, this polemic would turn into the controversy on the rites. The criticism to the Jesuitical strategy of mission, in XVII and XVIII centuries, would start from here. The enormous number of documents on this issue became a powerful instrument in the battle against the Jesuits, in the XVIII century. On the base of the missionary disputation, the Enlightenment constructs the proposal of a new political and humanistic universal perspective. According to this, eventuality, the religion becomes just a privileged instrument to realize this operation.

Waves of Change Within Civil Society in Latin America: Mexico City and Sao Paulo

For the past half a century, Latin American scholars have been pointing toward the emergence of new social actors as agents of social and political democratization. The first wave of actors was characterized by the emergence of novel agents-mainly, new popular movements-of social transformation. At first, the second wave, epitomized by nongovernmental organizations (NGOs), was celebrated as the upsurge of a new civil society, but later on, it was the target of harsh criticism. The literature often portrays this development in Latin American civil society as a displacement trend of actors of the first wave by the second wave-""NGOization""-""and even denounces new civil society as rootless, depoliticized, and functional to retrenchment. Thus, supposedly, NGOization encumbers social change. The authors argue that NGOization diagnosis is a flawed depiction of change within civil society. Rather than NGOization related to the depoliticization and neoliberalization of civil society, in Mexico City and Sao Paulo, there has been modernization of organizational ecologies, changes in the functional status of civil society, and interestingly, specialization aimed at shaping public agenda. The authors argue that such specialization, instead of encumbering social change, brings about different repertoires of strategies and skills purposively developed for influencing policy and politics. Their argument relies on comparative systematic evidence. Through network analysis, they examine the organizational ecology of civil society in Mexico City and Sao Paulo.