Ceramide modulates the lipid membrane organization at molecular and supramolecular levels

The role of lipids in membranes has changed rapidly from static to dynamic and emphasized their involvement in information transduction, linking temporal and topological structuring through compositionally driven effects. Ceramide has been described as an important modulator of different membrane functions. In mixtures with ganglioside GM1, the condensation induced by ceramide increases intermolecular interactions, leading to an increase of the phase transition temperature and size of the self-assembled structure. In mixtures with phosphatidylcholines, ceramide segregates laterally in the gel state, forming domains whose thickness depend on global concentration and chain asymmetry of the sphingolipid.     

Lectin-carbohydrate interactions: different folds, common recognition principles

Lectins can be found in many organisms and are involved in a multitude of cellular processes that depend on specific recognition of complex carbohydrates. The stereochemical principles underlying the recognition process have been the subject of extensive biochemical and structural studies. When examined from the viewpoint on the bound sugar, the structural information accumulated so far on lectins and other proteins that are specific to galactose and glucose (or mannose), provides suggestive evidence for distinct ligand-dependent distribution of hydrogen-bond partners in the combining site.     

Protein-protein interactions: structural motifs and molecular recognition.

The past year has brought new insights into common structural motifs used for protein-protein interactions by DNA-binding proteins. In addition, there have been significant advances in our understanding of antibody-protein complexes.     

The N-end rule pathway: emerging functions and molecular principles of substrate recognition

The N-end rule defines the protein-destabilizing activity of a given amino-terminal residue and its post-translational modification. Since its discovery 25 years ago, the pathway involved in the N-end rule has been thought to target only a limited set of specific substrates of the ubiquitin-proteasome system. Recent studies have provided insights into the components, substrates, functions and structural basis of substrate recognition. The N-end rule pathway is now emerging as a major cellular proteolytic system, in which the majority of proteins are born with or acquire specific N-terminal degradation determinants through protein-specific or global post-translational modifications.     

The use of the electrostatic potential at the molecular surface in recognition interactions: Dibenzo-p-dioxinsand related systems

An ab initio self-consistent-field molecular orbital approach was used to compute the electrostatic potentials of dibenzo-p-dioxin, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), two analogues of the latter, and two isomeric benzoflavones on a three-dimensional molecular surface corresponding to the contour of constant electronic density equal to 0.002 electrons/bohr³. The results are discussed in relation to the biological activities of the respective molecules. It is shown that the electrostatic potential graphically depicted on the molecular surface is well suited for the study of recognition interactions, such as are believed to be involved in the initial receptor-mediated step leading to toxicity in the dibenzo-p-dioxins. The surface potential has the advantage of clearly showing steric features that may play a role in understanding the recognition process being investigated.     

Emerging trends in molecular recognition: utility of weak aromatic interactions

Aromatic interactions play a vital role in chemistry and biology. As about 20% are aromatic in nature, so the role of aromatic interactions become prominent in drug receptor interactions. Not only in drug receptor interactions but also in crystal engineering, protein folding, stacking interactions in DNA/RNA the role of the interactions is of utmost importance. With the emergence of supramolecular chemistry dendrimers, tweezers, rotaxanes, catenanes, and several supramolecular aggregates are associated with aromatic interactions. The mechanism of such interactions is still unknown by the replacement of a small substituent from the aromatic molecule may lead or destroy the interactions. In the present review several models are being discussed with arene interactions under selected heads.     

DNA recognition and nucleosome organization

The affinity of a DNA sequence for the histone octamer in a core nucleosome depends on the intrinsic flexibility of the DNA. This parameter can be affected both by the sequence-dependent conformational preferences of individual base steps and by the nature and location of the exocyclic groups of the DNA bases. By adopting highly preferred conformations particular types of base step can influence the rotational positioning of the DNA on the surface of the histone octamer. The asymmetry of the next higher order of chromatin structure is determined in part by the asymmetric binding of the globular domain of histone H5 to the core nucleosome. © 1998 John Wiley & Sons, Inc. Biopoly 44: 423–433 1997     

A general criterion for molecular recognition: implications for chiral interactions

A general criterion is formulated for molecular recognition. The criterion for recognition is the inequality of the distance matrices of complexes of different compounds with a resolving agent under ambient experimental conditions. It is shown how this criterion provides for an objective, well-defined, and simple explanation for recognition of chiral compounds. This approach may be used to explain models (e.g., three-point of attachment) and relationships for chiral recognition. It is also shown how one-, two-, or three-point mechanisms are equivalent in this formalism and could result in chiral recognition. Examples are used to illustrate how the so called one- or two-point mechanisms may be operative in many experimental findings. Symmetry requirements of resolving agents may also be derived from considerations of distance matrices. Finally, the reciprocal relationship of chiral resolving agents is easily derived from the present method of analysis.     

Dna organization in histone-free nuclei at various stages of rat spermatogenesis

Electron microscopy analysis of DNA organization in histone-depleted nuclei of rat spermatogonial cells was performed. It was shown that the rosette-like structures are one of the forms of the loop organization of the meiotic cell nuclear DNA. Ions of bivalent metal play an important role in stabilizing the rosette-like structures of meiotic cells. A scheme for the restructuring of the mitotic organization of nuclear DNA into the meiotic one is suggested.     

Analysis ligand-receptor interactions from the molecular to the organism levels

A system of quantitative analysis is proposed for evaluation of ligand-receptor interaction on models of different levels of complexity. For two discrete receptor pools, binding of radio-labelled ligands to specific receptors and the magnitude of physiological response for an effector system with two discrete pools of receptors with different affinities are described with the aid of developed respective equations. The equations' parameters characterise properties of the effector system under study: the number of receptor pools differing in their affinity to a ligand; the number of active receptors of the maximum response magnitude; and the number of ligand's molecules bound to the receptor. The derived parameter's efficiency provides a general characteristic of affinity for the effector system under study. The described method of analysis of the ligand-receptor interactions is applicable to studies of any biological responses yielding quantitative results.     

Directionality of evolution at molecular and organismic levels.

The molecular evolution theories of Eigen and Kimura are compared and their difference is explained. In terms of Eigen's theory for the evolution of macromolecules, the selection of genotypes occurs directly. The physical meaning of the neutral theory is the degeneracy of the correlation between a phenotype and a genotype at the molecular level. A model theory of evolution on a fitness landscape is proposed. The theory shows that the constraints of selection determined by the structure and dynamics of previous evolution stages increases its rate strongly.     

Geomorphic principles of terrain organization and vegetation gradients

Abstract. Moisture and nutrient gradients consistently explain much of the variation in plant species composition and abundance, but these gradients are not spatially explicit and only reveal species responses to resource levels. This study links these abstract gradients to quantitative, spatial models of hill‐slope assembly. A gradient analysis in the mixed‐wood boreal forest demonstrates that patterns of upland vegetation distribution are correlated to soil moisture and nutrient gradients. Variation in species abundance with time since the last fire is removed from the gradient analysis in order to avoid confounding the physical environment gradients. The physical‐environment gradients are related to qualitative positions on the hill slope i.e. crest, mid‐slope, bottom‐slope. However, hill‐slope shape can be quantitatively described and compared by fitting allometric equations to the slope profiles. Using these equations, we show that hill‐slope profiles on similar surficial materials have similar parameters, despite coming from widely separated locations. We then quantitatively link the moisture and nutrient gradients to the equations. Moisture and nutrients significantly increase as distance down‐slope from the ridgeline increases. Corresponding vegetation composition changes too. These relationships characterize the general pattern of vegetation change down most hill slopes in the area. Since hill slopes are a universal feature of all landscapes, these principles may characterize landscape scale spatial patterns of vegetation in many environments.     

Microbe-plant interactions: principles and mechanisms

The present status of research on the molecular basis of microbe-plant interactions is discussed. Principles and mechanisms which play a role in the interactions of microbial pathogens, biofertilizers, phytostimulators, rhizoremediators and biocontrol agents with the plants are treated. Special emphasis is given to colonization, phase variation, two-component systems, quorum sensing, complex regulation of the syntheses of extracellular enzymes and secondary metabolites, Type 4 pili and Type III and Type IV secretion systems. This revised version was published online in August 2006 with corrections to the Cover Date.