Aminoglycoside-RNA interactions

The structural and physico-chemical parameters promoting the binding of aminoglycosides to RNAs are becoming clear. The strength of the interaction is dominated by electrostatics, with the positively charged aminoglycosides displacing metal ions. Although aminoglycosides inhibit most known ribozymes, aminoglycosides or polyamines are able to catalyze specific RNA cleavage in the absence of metal ions.     

Annexin-actin interactions

The actin cytoskeleton is a malleable framework of polymerised actin monomers that may be rapidly restructured to enable diverse cellular activities such as motility, endocytosis and cytokinesis. The regulation of actin dynamics involves the coordinated activity of numerous proteins, among which members of the annexin family of Ca2+- and phospholipid-binding proteins play an important role. Although the roles of annexins in actin dynamics are not understood at a mechanistic level, annexins have the requisite properties to integrate Ca2+-signaling with actin dynamics at membrane contact sites. In this review we discuss the current state of knowledge on this topic, and consider how and where annexins may fit into the complex molecular machinery that regulates the actin cytoskeleton.     

Clathrin-protein interactions

There is a complex network of protein–protein and protein–lipid interactions that underlie clathrin-mediated vesicular traffic in all compartmentalized cells from yeast to man. Major progress has been made in the determination of the three-dimensional structures of many of the components. Recently, there has been an explosion in the identification and characterization of clathrin binding partners. This review integrates the structural and biochemical information that is currently available to present a unified view of how many clathrin binding partners interact with clathrin.     

Plant-nematode interactions

Root-knot nematodes and cyst nematodes are obligate, biotrophic pathogens of numerous plant species. These organisms cause dramatic changes in the morphology and physiology of their hosts. The molecular characterization of induced plant genes has provided insight into the plant processes that are usurped by nematodes as they establish their specialized feeding cells. Recently, several gene products have been identified that are secreted by the nematode during parasitism. The corresponding genes have strong similarity to microbial genes or to genes that are found in nematodes that parasitize animals. New information on host resistance genes and nematode virulence genes provides additional insight into this complex interaction.     

Bacterial interactions

The review deals with specific features of interactions in microbial biocenoses. The subdivision of the mechanisms of microbial interactions in associations into direct and indirect ones is proposed. The formation of intercellular contacts and matrix belongs to one group of mechanisms, the second group includes the products of metabolism (changes in the physical and chemical composition of the medium, specific growth regulators) and secreted factors (antibacterial substances, pheromones and signal molecules, vitamins, specific mediators). The applied aspects of the knowledge of microbial interactions in the human body are presented.     

Leukocyte-epithelial interactions

As a 'double-edged sword', neutrophil (polymorphonuclear leukocyte) migration across epithelial-lined organs is an important component of host defense, but it also results in epithelial pathophysiology and disease symptoms. There have been significant advances in better understanding the mechanisms of how leukocytes cross the vascular endothelium to exit the bloodstream; however, many of the mechanisms that govern polymorphonuclear leukocyte transepithelial migration are different and we are only just beginning to understand them. Recent findings include new junctional adhesion molecules and carbohydrate moieties as receptors for migrating neutrophils. In addition, new insights into leukocyte-epithelial signaling events have emerged that are beginning to shed light on the role of SIRP-CD47 interactions in regulating the rate of neutrophil transepithelial migration and how neutrophils modulate epithelial barrier function.     

Thalamocortical interactions

Glutamatergic pathways dominate information processing in the brain, but these are not homogeneous. They include two distinct types: Class 1, which carries the main information for processing, and Class 2, which serves a modulatory role. Identifying the Class 1 inputs in a circuit can lead to a better understanding of its function. Also, identifying Class 1 inputs to a thalamic nucleus tells us its main function (e.g. the lateral geniculate nucleus, or LGN, is the relay of retinal Class 1 input), and such identification leads to a division of thalamic relays into first and higher order: the former receives Class 1 inputs from subcortical sources; the latter, from layer 5 of cortex, which it then relays to another cortical area. When a cortical area directly connects with another, it often has a parallel, transthalamic connection through these higher order relays. This leads to a novel appreciation of cortical functioning and raises many new questions.     

Lipid-protein interactions

Intrinsic membrane proteins are solvated by a shell of lipid molecules interacting with the membrane-penetrating surface of the protein; these lipid molecules are referred to as annular lipids. Lipid molecules are also found bound between transmembrane α-helices; these are referred to as non-annular lipids. Annular lipid binding constants depend on fatty acyl chain length, but the dependence is less than expected from models based on distortion of the lipid bilayer alone. This suggests that hydrophobic matching between a membrane protein and the surrounding lipid bilayer involves some distortion of the transmembrane α-helical bundle found in most membrane proteins, explaining the importance of bilayer thickness for membrane protein function. Annular lipid binding constants also depend on the structure of the polar headgroup region of the lipid, and hotspots for binding anionic lipids have been detected on some membrane proteins; binding of anionic lipid molecules to these hotspots can be functionally important. Binding of anionic lipids to non-annular sites on membrane proteins such as the potassium channel KcsA can also be important for function. It is argued that the packing preferences of the membrane-spanning α-helices in a membrane protein result in a structure that matches nicely with that of the surrounding lipid bilayer, so that lipid and protein can meet without either having to change very much.     

Environmental interactions

Abstract

The circaseptan rhythm seems to be an important prognostic factor in oncology. The function F=d[Na]/ d[K], where d[Na], d[K] are natrium and potassium respectively urine concentration changes within 24 hours were used for its analysis. The decreasing oscillations of the F function could probably be used for the supportive high dose corticosteroid and cyclosporine therapy timing.     

Serpin-ligand interactions

One of the more common features of serpins is the ability to bind various ligands. Ligand binding can occur so that the inhibitory properties of the serpin are regulated, so that the serpin can be localized, or to produce or modulate some other biological function of the serpin. Ligands known to affect serpin biologic activity include glycosaminoglycans such as heparin, heparan sulfate and dermatan sulfate, DNA, extracellular matrix proteins such as vitronectin and collagen, and small organic molecule hormones. Many different biochemical and biophysical techniques in conjunction with molecular biology and cell biology approaches have been used to study the binding of various ligands to serpins and to assess the influence of this binding on activity and structure. We summarize here the different approaches that have been used to identify serpin ligands and the many methods that have been used to characterize the interactions of these ligands with their cognate serpins.     

Lectin-parasite interactions

Lectins are proteins that bind specifically to carbohydrate residues and are widely distributed in Nature. All parasites have such residues which vary in their configurations. Here, Jake Jacobson and Ron Doyle review the application of lectins in defining the developmental stages of parasites and the characterization, localization and structural composition of parasite glycoconjugates. The lectins of some parasites and lectin-mediated host-parasite interaction are also discussed.