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.

The design of hazard risk assessment matrices for ranking occupational health risks and their application in mining and minerals processing

Two hazard risk assessment matrices for the ranking of occupational health risks are described. The qualitative matrix uses qualitative measures of probability and consequence to determine risk assessment codes for hazard-disease combinations. A walk-through survey of an underground metalliferous mine and concentrator is used to demonstrate how the qualitative matrix can be applied to determine priorities for the control of occupational health hazards. The semi-quantitative matrix uses attributable risk as a quantitative measure of probability and uses qualitative measures of consequence. A practical application of this matrix is the determination of occupational health priorities using existing epidemiological studies. Calculated attributable risks from epidemiological studies of hazard-disease combinations in mining and minerals processing are used as examples. These historic response data do not reflect the risks associated with current exposures. A method using current exposure data, known exposure-response relationships and the semi-quantitative matrix is proposed for more accurate and current risk rankings.

Verb and context processing in Parkinson's disease

The aim of the present study was to investigate verb and context processing in 10 individuals with Parkinson's disease (PD) and matched controls. A self-paced stop making sense judgment task was employed where participants read a sentence preceded by a context which made the thematic role of the verb plausible or implausible. Participants were required to indicate whether the sentence ceased to make sense at any point by responding yes/no at each word. PD participants were less accurate than the control participants at detecting sentence anomalies based on verb selection restrictions and previously encountered contextual elements. However, further research is required to determine the precise nature of the grammatical processing disturbance associated with PD. (c) 2005 Elsevier Ltd. All rights reserved.

Discovery, structural determination, and putative processing of the precursor protein that produces the cyclic trypsin inhibitor sunflower trypsin inhibitor 1

Backbone-cyclized proteins are becoming increasingly well known, although the mechanism by which they are processed from linear precursors is poorly understood. In this report the sequence and structure of the linear precursor of a cyclic trypsin inhibitor, sunflower trypsin inhibitor 1 (SFTI-1) from sunflower seeds, is described. The structure indicates that the major elements of the reactive site loop of SFTI-1 are present before processing. This may have importance for a protease-mediated cyclizing reaction as the rigidity of SFTI-1 may drive the equilibrium of the reaction catalyzed by proteolytic enzymes toward the formation of a peptide bond rather than the normal cleavage reaction. The occurrence of residues in the SFTI-1 precursor susceptible to cleavage by asparaginyl proteases strengthens theories that involve this enzyme in the processing of SFTI-1 and further implicates it in the processing of another family of plant cyclic proteins, the cyclotides. The precursor reported here also indicates that despite strong active site sequence homology, SFTI-1 has no other similarities with the Bowman-Birk trypsin inhibitors, presenting interesting evolutionary questions.

Eco-efficiency and dairy processing

The dairy industry is a global industry that provides significant nutritional benefit to many cultures. in australia the industry is especially important economically, being a large export earner, as well as a vital domestic sector. in recent years the sector has come under increased competitive pressure and has restructured to cope with the changes. the industry recently undertook an eco-efficiency project to investigate where business and environmental improvements might be found. the project involved collecting and collating previous project data and surveying 38 companies in different dairy operations, from market milk to dried products. after the survey, 10 sites in two states were visited to discuss eco-efficiency issues in detail with key players. From the surveys, visits and data compilation, a comprehensive manual was prepared to help interested companies find relevant eco-efficiency data easily and assist them in the implementation process. ten fact sheets were also produced covering the topics of water management, water recycling and re-use, refrigeration optimisation, boiler optimisation, biogas, the use of treated wastewater, yield optimisation and product recovery, optimisation of ciP systems, chemical use and membranes the project highlighted the large amount of technical and engineering expertise within the sector that could result in eco-efficiency outcomes and also identified the opportunities that exist for changes to occur in some operations to save energy, input raw materials and water.