DOMIRE: a web server for identifying structural domains and their neighbors in proteins.

SUMMARY: The DOMIRE web server implements a novel, automatic, protein structural domain assignment procedure based on 3D substructures of the query protein which are also found within structures of a non-redundant protein database. These common 3D substructures are transformed into a co-occurrence matrix that offers a global view of the protein domain organization. Three different algorithms are employed to define structural domain boundaries from this co-occurrence matrix. For each query, a list of structural neighbors and their alignments are provided. DOMIRE, by displaying the protein structural domain organization, can be a useful tool for defining protein common cores and for unravelling the evolutionary relationship between different proteins. AVAILABILITY: http://genome.jouy.inra.fr/domire CONTACT: jean.garnier@jouy.inra.fr.

The ability of actinic light to modify the bacteriorhodopsin photocycle revisited: heterogeneity vs photocooperativity.

In 1995, evidence both for photocooperativity and for heterogeneity as possible explanations for the ability of actinic light to modify the kinetics and pathways of the bacteriorhodopsin (BR) photocycle was reviewed ( Shrager, R. I., Hendler, R. W., and Bose, S. (1995) Eur. J. Biochem. 229, 589-595 ). Because both concepts could be successfully modeled to experimental data and there was suggestive published evidence for both, it was concluded that both photocooperativity and heterogeneity may be involved in the adaptation of the BR photocycle to different levels of actinic light. Since that time, more information has become available and it seemed appropriate to revisit the original question. In addition to the traditional models based on all intermediates in strict linear sequences, we have considered both homogeneous and heterogeneous models with branches. It is concluded that an explanation based on heterogeneity is more likely to be the true basis for the variation of the properties of the photocycle caused by changes in actinic light intensity. On the basis of new information presented here, it seems that a heterogeneous branched model is more likely than one with separate linear sequences.

Diffusion delays and unstirred layer effects at monolayer cultures of Chinese hamster ovary cells: radioligand binding, confocal microscopy, and mathematical simulations.

Cells grown in monolayer culture offer a convenient system for binding and other experiments under conditions that preserve the complexity of the living state. Kinetics experiments, however, may be distorted by the time course of drug penetration into even so simple a "tissue" as the monolayer. The impediments include unstirred layers both above and between the cells, the congregation of receptors within the confined space between cells, and nonspecific binding to membrane components. The contributions of these factors were investigated in cultures of Chinese hamster ovary (CHO) cells either nontransfected or stably transfected with mu opioid receptors. The dissociation of [3H]naloxone was four times faster under displacement than under infinite dilution conditions, clearly demonstrating the "retention effect" of receptors confined in space. Even the penetration of this ligand between nontransfected cells showed salient delays with respect to diffusion into a slab, indicating that nonspecific, low-affinity binding to membrane components was arresting its progress. The optical sectioning capabilities of confocal microscopy demonstrated that the kinetics of two fluorescent antagonists depended on the vertical plane, providing direct evidence for slowed diffusion down a single cell depth. Modeling shows that kinetic errors increase with receptor density, forward rate constant, and the thickness of the unstirred layer.