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.

Target similarity effects: Support for the parallel distributed processing assumptions

Recent research has begun to provide support for the assumptions that memories are stored as a composite and are accessed in parallel (Tehan & Humphreys, 1998). New predictions derived from these assumptions and from the Chappell and Humphreys (1994) implementation of these assumptions were tested. In three experiments, subjects studied relatively short lists of words. Some of the Lists contained two similar targets (thief and theft) or two dissimilar targets (thief and steal) associated with the same cue (ROBBERY). AS predicted, target similarity affected performance in cued recall but not free association. Contrary to predictions, two spaced presentations of a target did not improve performance in free association. Two additional experiments confirmed and extended this finding. Several alternative explanations for the target similarity effect, which incorporate assumptions about separate representations and sequential search, are rejected. The importance of the finding that, in at least one implicit memory paradigm, repetition does not improve performance is also discussed.

A twin study of psychometric intelligence and efficiency of information processing

Intelligence (IQ) can be seen as the efficiency of mental processes or cognition, as can basic information processing (IP) tasks like those used in our ongoing Memory, Attention and Problem Solving (MAPS) study. Measures of IQ and IP are correlated and both have a genetic component, so we are studying how the genetic variance in IQ is related to the genetic variance in IP. We measured intelligence with five subscales of the Multidimensional Aptitude Battery (MAB). The IP tasks included four variants of choice reaction time (CRT) and a visual inspection time (IT). The influence of genetic factors on the variances in each of the IQ, IP, and IT tasks was investigated in 250 identical and nonidentical twin pairs aged 16 years. For a subset of 50 pairs we have test–retest data that allow us to estimate the stability of the measures. MX was used for a multivariate genetic analysis that addresses whether the variance in IQ and IP measures is possibly mediated by common genetic factors. Analyses that show the modeled genetic and environmental influences on these measures of cognitive efficiency will be presented and their relevance to ideas on intelligence will be discussed.

Parallel processing and image analysis in the eyes of mantis shrimps

The compound eyes of mantis shrimps, a group of tropical marine crustaceans, incorporate principles of serial and parallel processing of visual information that may be applicable to artificial imaging systems. Their eyes include numerous specializations for analysis of the spectral and polarizational properties of light, and include more photoreceptor classes for analysis of ultraviolet light, color, and polarization than occur in any other known visual system. This is possible because receptors in different regions of the eye are anatomically diverse and incorporate unusual structural features, such as spectral filters, not seen in other compound eyes. Unlike eyes of most other animals, eyes of mantis shrimps must move to acquire some types of visual information and to integrate color and polarization with spatial vision. Information leaving the retina appears to be processed into numerous parallel data streams leading into the central nervous system, greatly reducing the analytical requirements at higher levels. Many of these unusual features of mantis shrimp vision may inspire new sensor designs for machine vision

Identifying rate-limiting nodes in large-scale cortical networks for visuospatial processing: an illustration using fMRI

With the advent of functional neuroimaging techniques, in particular functional magnetic resonance imaging (fMRI), we have gained greater insight into the neural correlates of visuospatial function. However, it may not always be easy to identify the cerebral regions most specifically associated with performance on a given task. One approach is to examine the quantitative relationships between regional activation and behavioral performance measures. In the present study, we investigated the functional neuroanatomy of two different visuospatial processing tasks, judgement of line orientation and mental rotation. Twenty-four normal participants were scanned with fMRI using blocked periodic designs for experimental task presentation. Accuracy and reaction time (RT) to each trial of both activation and baseline conditions in each experiment was recorded. Both experiments activated dorsal and ventral visual cortical areas as well as dorsolateral prefrontal cortex. More regionally specific associations with task performance were identified by estimating the association between (sinusoidal) power of functional response and mean RT to the activation condition; a permutation test based on spatial statistics was used for inference. There was significant behavioral-physiological association in right ventral extrastriate cortex for the line orientation task and in bilateral (predominantly right) superior parietal lobule for the mental rotation task. Comparable associations were not found between power of response and RT to the baseline conditions of the tasks. These data suggest that one region in a neurocognitive network may be most strongly associated with behavioral performance and this may be regarded as the computationally least efficient or rate-limiting node of the network.

Processing of urinary pheromones in Antechinus stuartii (Marsupialia: Dasyuridae): Functional magnetic resonance imaging of the brain

Little is known of the neural mechanisms of marsupial olfaction. However, functional magnetic resonance imaging (fMRI) has made it possible to visualize dynamic brain function in mammals without invasion. In this study, central processing of urinary pheromones was investigated in the brown antechinus, Antechinus stuartii, using fMRI. Images were obtained from 18 subjects (11 males, 7 females) in response to conspecific urinary olfactory stimuli. Significant indiscriminate activation occurred in the accessory olfactory bulb, entorhinal, frontal, and parietal cortices in response to both male and female urine. The paraventricular nucleus of hypothalamus, ventrolateral thalamic nucleus, and medial preoptic area were only activated in response to male urine. Results of this MRI study indicate that projections of accessory olfactory system are activated by chemo-sensory cues. Furthermore, it appears that, based on these experiments, urinary pheromones may act on the hypothalamo-pituitary-adrenocortical axis via the paraventricular nucleus of the hypothalamus and may play an important role in the unique life history pattern of A. stuartii. Finally, this study has demonstrated that fMRI may be a powerful tool for investigations of olfactory processes in mammals.

Dormancy release in Lolium rigidum seeds is a function of thermal after-ripening time and seed water content

Dormancy release in seeds of Lolium rigidum Gaud. (annual ryegrass) was investigated in relation to temperature and seed water content. Freshly matured seeds were collected from cropping fields at Wongan Hills and Merredin, Western Australia. Seeds from Wongan Hills were equilibrated to water contents between 6 and 18% dry weight and after-ripened at constant temperatures between 9 and 50degreesC for up to 23 weeks. Wongan Hills and Merredin seeds at water contents between 7 and 17% were also after-ripened in full sun or shade conditions. Dormancy was tested at regular intervals during after-ripening by germinating seeds on agar at 12-h alternating 15degreesC (dark) and 25degreesC (light) periods. Rate of dormancy release for Wongan Hills seeds was a positive linear function of after-ripening temperature above a base temperature (T-b) of 5.4degreesC. A thermal after-ripening time model for dormancy loss accounting for seed moisture in the range 6-18% was developed using germination data for Wongan Hills seeds after-ripened at constant temperatures. The model accurately predicted dormancy release for Wongan Hills seeds after-ripened under naturally fluctuating temperatures. Seeds from Merredin responded similarly but had lower dormancy at collection and a faster rate of dormancy release in seeds below 9% water content.

Local-global processing in early-onset schizophrenia: Evidence for an impairment in shifting the spatial scale of attention

In this study we report the results of two experiments on visual attention conducted with patients with early-onset schizophrenia. These experiments investigated the effect of irrelevant spatial-scale information upon the processing of relevant spatial-scale information, and the ability to shift the spatial scale of attention, across consecutive trials, between different levels of the hierarchical stimulus. Twelve patients with early-onset schizophrenia and matched controls performed local-global tasks under: (1) directed attention conditions with a consistency manipulation and (2) divided-attention conditions. In the directed-attention paradigm, the early-onset patients exhibited the normal patterns of global advantage and interference, and were not unduly affected by the consistency manipulation. Under divided-attention conditions, however, the early-onset patients exhibited a local-processing deficit. The source of this local processing deficit lay in the prolonged reaction time to local targets, when these had been preceded by a global target, but not when preceded by a local target. These findings suggest an impaired ability to shift the spatial scale of attention from a global to a local spatial scale in early-onset schizophrenia. (C) 2003 Elsevier Science (USA). All rights reserved.

Combined in-fermenter extraction and cross-flow microfiltration for improved inclusion body processing

In this study we demonstrate a new in-fermenter chemical extraction procedure that degrades the cell wall of Escherichia coli and releases inclusion bodies (IBs) into the fermentation medium. We then prove that cross-flow microfiltration can be used to remove 91% of soluble contaminants from the released IBs. The extraction protocol, based on a combination of Triton X-100, EDTA, and intracellular T7 lysozyme, effectively released most of the intracellular soluble content without solubilising the IBs. Cross-flow microfiltration using a 0.2 mum ceramic membrane successfully recovered the granulocyte macrophagecolony stimulating factor (GM-CSF) IBs with removal of 91% of the soluble contaminants and virtually no loss of IBs to the permeate. The filtration efficiency, in terms of both flux and transmission, was significantly enhanced by infermenter Benzonase(R) digestion of nucleic acids following chemical extraction. Both the extraction and filtration methods exerted their efficacy directly on a crude fermentation broth, eliminating the need for cell recovery and re-suspension in buffer. The processes demonstrated here can all be performed using just a fermenter and a single cross-flow filtration unit, demonstrating a high level of process intensification. Furthermore, there is considerable scope to also use the microfiltration system to subsequently solubilise the IBs, to separate the denatured protein from cell debris, and to refold the protein using diafiltration. In this way refolded protein can potentially be obtained, in a relatively pure state, using only two unit operations. (C) 2004 Wiley Periodicals Inc.

Females of the weevil Zabrotes subfasciatus manipulate the size and number of eggs according to the host seed availability

In some insects, the finding of oviposition substrate triggers the uptake into oocytes of yolk proteins that are stored in the fat body during post-embryonic development. The main host of the bean weevil Zabrotes subfasciatus (Coleoptera; Chrysomelidae; Bruchinae; Amblycerini), in which larval resources are the sole source for future egg maturation, is Phaseolus vulgaris. Despite not feeding as adults, females of this species are able to lay eggs after encountering host seeds but it is not known how females react to changes in the availability of bean seeds. In the present study, the behaviour of Z. subfasciatus facing two very different environments for oviposition is investigated, as well as how this influences offspring fitness. The results obtained show that females of Z. subfasciatus react to variations in the availability of seeds belonging to the same host species by adjusting egg size and number. Females on low bean seed density lay larger and fewer eggs than those on high bean seed density, demonstrating a trade-off between these reproductive traits. Moreover, females can adjust egg size to changing levels of host availability during the first 4 days of their oviposition period. Although no difference in offspring weight is found, those from small eggs (low competition environment) result in larger adults. No response to selection on these traits after rearing beetles on the same host for 40 generations is observed. This unresponsiveness may indicate that beetle populations behave according to their reaction norm that already allows rapid adaptation to a varying amount of host-seed availability and better exploitation of the environments of this widespread stored-seed pest.

Salinity tolerance in Schinopsis quebracho colorado: Seed germination, growth, ion relations and metabolic responses

Soil salinity is a major abiotic stress influencing plant productivity worldwide. Schinopsis quebracho colorado is one of the most important woody species in the Gran Chaco, an and and salt-prone subtropical biome of South America. To gain a better understanding of the physiological mechanisms that allow plant establishment under salt conditions, germination and seedling growth of S. quebracho colorado were examined under treatment with a range of NaCl solutions (germination: 0-300 mmol l(-1) NaCl; seedling growth: 0-200 mmol l(-1) NaCl). The aim was to test the hypothesis that S. quebracho colorado is a glycophite that shows different salt tolerance responses with development stage. Proline content, total soluble carbohydrates and Na+, K+ and Cl- concentrations in leaves and roots of seedlings, and the chlorophyll concentration and relative water content of leaves were measured. Germination was not affected by 100 mmol l(-1) NaCl, but decreased at a concentration of 200 mmol l(-1). At 300 mmol l(-1) NaCl, germination did not occur. Seedling growth decreased drastically with increasing salinity. An increase in NaCl from 0 to 100 mmol l(-1) also significantly reduced the leaf relative water content by 22% and increased the proline concentration by 60% in roots. In contrast, total soluble carbohydrates were not significantly affected by salinity. Seedlings showed a sodium exclusion capacity, and there was an inverse correlation between Cl- concentration and the total chlorophyll concentration. S. quebracho colorado was more tolerant to salinity during germination than in the seedling phase. The results suggest that this increased tolerance during germination might, in part, be the result of lower sensitivity to high tissue Na+ concentrations. The significant increment of proline in the roots suggests the positive role of this amino acid as a compatible solute in balancing the accumulation of Na+ and Cl- as a result of salinity. These results help clarify the physiological mechanisms that allow establishment of S. quebracho colorado on salt-affected soils in arid and semi-arid Gran Chaco. (c) 2008 Elsevier Ltd. All rights reserved.

Maturation temperature and rainfall influence seed dormancy characteristics of annual ryegrass (Lolium rigidum)

The role of temperature and rainfall during seed development in modulating subsequent seed dormancy status was studied for Lolium rigidum Gaud. (annual ryegrass). Climatic parameters relating to geographic origin were compared with annual ryegrass seed dormancy characteristics for seeds collected from 12 sites across the southern Western Australian cropping region. Seed germination was tested soon after collection and periodically during subsequent after-ripening. Temperature in the year of seed development and long-term rainfall patterns showed correlations with aspects of seed dormancy, particularly the proportion of seeds remaining dormant following 5 months of after-ripening. Consequently, for one population the temperature (warm/cool) and water supply (adequate/reduced) during seed development were manipulated to investigate the role of maternal environment in the quantity and dormancy characteristics of seeds produced. Seeds from plants grown at warm temperatures were fewer in number, weighed less, and were less dormant than those from plants grown at cool temperature. Seeds that developed under both cool temperature and reduced moisture conditions lost dormancy faster than seeds from well-watered plants. Seed maturation environment, particularly temperature, can have a significant effect on annual ryegrass seed numbers and seed dormancy characteristics.

Virtual models of the HLA class I antigen processing pathway

Antigen recognition by cytotoxic CD8 T cells is dependent upon a number of critical steps in MHC class I antigen processing including proteosomal cleavage, TAP transport into the endoplasmic reticulum, and MHC class 1 binding. Based on extensive experimental data relating to each of these steps there is now the capacity to model individual antigen processing steps with a high degree of accuracy. This paper demonstrates the potential to bring together models of individual antigen processing steps, for example proteosome cleavage, TAP transport, and MHC binding, to build highly informative models of functional pathways. In particular, we demonstrate how an artificial neural network model of TAP transport was used to mine a HLA-binding database so as to identify H LA-binding peptides transported by TAP. This integrated model of antigen processing provided the unique insight that HLA class I alleles apparently constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3, and -A24) and those that are TAP-inefficient (HLA-A2, -B7, and -B8). Hence, using this integrated model we were able to generate novel hypotheses regarding antigen processing, and these hypotheses are now capable of being tested experimentally. This model confirms the feasibility of constructing a virtual immune system, whereby each additional step in antigen processing is incorporated into a single modular model. Accurate models of antigen processing have implications for the study of basic immunology as well as for the design of peptide-based vaccines and other immunotherapies. (C) 2004 Elsevier Inc. All rights reserved.