New aspects of the molecular evolution of legumains, Asn-specific cysteine proteinases

The molecular evolution of asparagine-specific cysteine proteinases, called legumains, from plants and animals was analyzed using newly available related amino acid sequences from lower eukaryotes, bacteria and Archaea. The results suggest that genuine legumains originate from prokaryote pro-legumains. The evolutionary roots of genuine legumains from plants and animals descend from Parabasalia and Alveolata before developing into their respective separate branches headed by Chlorophyta and Placozoa. The branch of legumain-like plant/animal glycosylphosphatidyl inositol transamidases separated from the general evolutionary stem of legumains at the level of lower eukaryotes. Modeling of the 3D structure of a plant genuine legumain underlined the previously suggested similarity of the active site geometry of legumains with caspases, which are Asp-specific bacterial and eukaryote proteinases.     

Plant systems for recognition of pathogen-associated molecular patterns

Research of the last decade has revealed that plant immunity consists of different layers of defense that have evolved by the co-evolutional battle of plants with its pathogens. Particular light has been shed on PAMP- (pathogen-associated molecular pattern) triggered immunity (PTI) mediated by pattern recognition receptors. Striking similarities exist between the plant and animal innate immune system that point for a common optimized mechanism that has evolved independently in both kingdoms. Pattern recognition receptors (PRRs) from both kingdoms consist of leucine-rich repeat receptor complexes that allow recognition of invading pathogens at the cell surface. In plants, PRRs like FLS2 and EFR are controlled by a co-receptor SERK3/BAK1, also a leucine-rich repeat receptor that dimerizes with the PRRs to support their function. Pathogens can inject effector proteins into the plant cells to suppress the immune responses initiated after perception of PAMPs by PRRs via inhibition or degradation of the receptors. Plants have acquired the ability to recognize the presence of some of these effector proteins which leads to a quick and hypersensitive response to arrest and terminate pathogen growth.     

Sodium cotransport systems: cellular, molecular and regulatory aspects

The sodium cotransport systems comprise an important group of transport proteins which are involved in the transport of a variety of organic and inorganic solutes across the cellular membrane of animal cells. These systems play a central role in a wide variety of cellular and biochemical processes. We summarize here the current state of knowledge regarding the variety, structure and regulation of this important group of membrane proteins.     

Oligosaccharides in molecular recognition

The development, organization and growth of complex organisms as well as their interactions with the environment involve an intricate array of molecular recognition events. There is an increased awareness of the involvement of oligosaccharides in many of these processes. In this article, studies of oligosaccharide antigenicity, and the way these have been interpreted with respect to oligosaccharide function will be discussed. In addition, examples of oligosaccharides as receptor, first, as receptors and determinants of susceptibility to an exogenous infective agent and secondly, as recognition structures possibly involved in endogenous interactions, will be described. This will be followed by a discussion of the recent hypothesis in which oligosaccharides are envisaged as recognition structures and integral components of cell growth-regulating networks. Finally, an outline of new strategies for decoding the information content in glycoprotein oligosaccharides will be given.     

Developmental aspects of kin recognition

The ability to recognise kin requires the individual to possess a variety of abilities. Individuals must produce a cue which indicates relatedness, they must process this cue to determine relatedness and then must act on this cue. Research has concentrated on the first and final stage of this process, i.e., the cues of kinship and kin correlated behaviour. Little attention has been paid to how individuals process cues to determine relatedness. This paper discusses how individuals ‘recognise’ kin, the exhibition of kin correlated behaviour and considers the role of the MHC in these processes. Two broad theories have emerged to explain how individuals recognise their kin: either a recognition gene(s) or some experiential mechanism. In mammals there is no evidence to suggest that recognition (the processing of the cue) is under genetic control but rather is the result of experience, learning about related individuals during development. Moreover studies on kin recognition in the domestic dog suggest that all kin are not recognised by the same process but different classes of kin, parents, siblings may well be recognised using different means. Studies of kin correlated behaviour suggest that the behaviour exhibited towards kin by Mongolian gerbils is mediated by the environment. Factors of environmental familiarity, sex and developmental age all affect the response of individuals to kin and non‐kin. In these situations the ability to recognise kin does not change but the exhibition of kin correlated behaviour changes according to environmental conditions. These studies indicate that kin recognition may not be the ‘unified’ process previously thought and thus any explanations of the proximate and ultimate causation of kin recognition need to encompass this complexity. The question remains of whether the MHC is complex enough to do so. This revised version was published online in July 2006 with corrections to the Cover Date.     

Target flexibility in molecular recognition

Induced-fit effects are well known in the binding of small molecules to proteins and other macromolecular targets. Among other targets, protein kinases are particularly flexible proteins, so that such effects should be considered in attempts at structure-based inhibitor design for kinase targets. This paper outlines some recent progress in methods for including target flexibility in computational studies of molecular recognition. A focus is the "relaxed complex method," in which ligands are docked to an ensemble of conformations of the target, and the best complexes are re-scored to provide predictions of optimal binding geometries. Early applications of this method have suggested a new approach to the development of inhibitors of HIV-1 Integrase.     

Dynamic aspects of diversity

Abstract. Ecological diversity is viewed as a measure of information, as the variety of messages compounded with the number of individuals belonging to different species. Two limit situations of diversity are indicated: a chemostat-like system tending to become monospecific, and a Noah's ark or museum situation with an infinite number of species each represented by just one specimen. In a dynamic approach, two differential equations for S, the number of species, and N, the number of individuals, can be considered. A new index of diversity is proposed based on these two equations. The concept of diversity spectrum is proposed for a series of diversity measurements in samples of increasing size and related to the concept of minimal area. Diversity can also be measured on non-taxonomic categories, e.g. size classes. The contrast between the two boundary types, limes convergens (ecotone) and limes divergens (ecocline), is emphasized. The nature of the difference between them is compared with that of tension zones between fluids in contact. Differences between ecosystems can be characterized through differences in the ratio P/B (Production/Biomass) and a boundary situation is imagined including two systems with P/B different values and different diversity levels. Some examples are presented from communities in streams.     

Diversity in recognition of glycans by F-type lectins and galectins: molecular, structural, and biophysical aspects

Although lectins are "hard-wired" in the germline, the presence of tandemly arrayed carbohydrate recognition domains (CRDs), of chimeric structures displaying distinct CRDs, of polymorphic genes resulting in multiple isoforms, and in some cases, of a considerable recognition plasticity of their carbohydrate binding sites, significantly expand the lectin ligand-recognition spectrum and lectin functional diversification. Analysis of structural/functional aspects of galectins and F-lectins-the most recently identified lectin family characterized by a unique CRD sequence motif (a distinctive structural fold) and nominal specificity for l-Fuc-has led to a greater understanding of self/nonself recognition by proteins with tandemly arrayed CRDs. For lectins with a single CRD, however, recognition of self and nonself glycans can only be rationalized in terms of protein oligomerization and ligand clustering and presentation. Spatial and temporal changes in lectin expression, secretion, and local concentrations in extracellular microenvironments, as well as structural diversity and spatial display of their carbohydrate ligands on the host or microbial cell surface, are suggestive of a dynamic interplay of their recognition and effector functions in development and immunity.     

Cholesterol modulates maculosin's orientation in model systems of biological membranes. Relevance towards putative molecular recognition

Fluorescence techniques were used to study (1) the extent of insertion of the bioactive cyclic dipeptide cyclo(l-tyrosyl-l-prolyl), maculosin, in model systems of membranes of 1, 2-palmitoyl-sn-glycero-3-phosphatidyl choline (DPPC) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl choline (POPC), (2) its in-depth location in those lipidic membranes, and (3) the influence of cholesterol on the dipeptides's location and orientation. Partition into lipidic bilayers is extensive, mainly for liquid crystalline phase membranes (K(p)=1.3x10(4)). Maculosin locates at the lipid head groups level regardless of the membrane system. Nevertheless, its orientation is lipid phase dependent. When maculosin was inserted in liquid crystalline phase bilayers, its phenolic ring was perpendicular to the membrane surface, whereas it changed orientation when inserted in gel phase membranes. Cholesterol was able to reverse the lipid phase influence on maculosin's orientation.     

Dynamic polymorphism of Ras observed by single molecule FRET is the basis for molecular recognition

Ras regulates signal transduction pathway function by dynamically interacting with various effectors. To understand the basis for Ras function, its conformational dynamics were measured in the absence and presence of effectors using single molecule fluorescence resonance energy transfer (FRET) between probes located on the Switch II region and GTP. The time trajectories of FRET efficiency from GTP-bound Ras showed that this conformation spontaneously varies among multiple states. Among them, a low FRET state was identified as an inactive state. The transition involving the inactive conformational state occurred in the time range of seconds. In contrast, fluctuation occurring most probably between multiple active high FRET conformational states lasted approximately 30 ms but converged to a specific conformational state upon binding to an effector. Thus, Ras conformation spontaneously fluctuates to readily interact with various effectors.     

The cysteine bonding in TSH receptor and it function in autoantibodies recognition

The majority of epitopes for TSH receptor (TSHR) stimulating autoantibodies are clustered around the Nterminal region of the TSH receptor. The characteristic feature of this region is the presence of four cysteine residues. It was proposed that cysteines in positions 29 and 41 in the receptor are connected by disulfide bonds and they are the target for receptor stimulating antibodies. The present study was aimed to check this possibility. The synthetic peptides: peptide corresponding to the part of TSHR containing the above 29-41 cysteine bond, the peptide similar to this peptide but without disulfide bond and the control peptide, containing sequence absent in the receptor were used for rabbit immunization. The thyroid status of all immunized rabbits was the same. Rabbits immunized with peptides related to TSHR generated antisera reactive with TSHR in immunoenzymatic assay. To check specificity of this reaction the influence of the peptides and the antisera on TSH binding to the receptor in competitive assay (TRAK) and their influence on adenylate cyclase activity were studied. It was found that neither synthetic peptides nor antiserum from any rabbit influenced TSH binding to the receptor in TRAK. In contrast low, but significant adenylate cyclase stimulating activity was noticed for antisera from two of six rabbit immunized by peptide containing the disulfide bond. We concluded that such a bond between cysteine residues 29 and 41 are present in TSHR in the site of stimulating antibodies epitope.     

Automated design of specificity in molecular recognition

Specific protein-protein interactions are crucial in signaling networks and for the assembly of multi-protein complexes, and represent a challenging goal for protein design. Optimizing interaction specificity requires both positive design, the stabilization of a desired interaction, and negative design, the destabilization of undesired interactions. Currently, no automated protein-design algorithms use explicit negative design to guide a sequence search. We describe a multi-state framework for engineering specificity that selects sequences maximizing the transfer free energy of a protein from a target conformation to a set of undesired competitor conformations. To test the multi-state framework, we engineered coiled-coil interfaces that direct the formation of either homodimers or heterodimers. The algorithm identified three specificity motifs that have not been observed in naturally occurring coiled coils. In all cases, experimental results confirm the predicted specificities.     

A technique to study molecular recognition in drug design: Preliminary application of free energy derivatives to inhibition of a malarial cysteine protease

We present molecular dynamics studies on model complexes of inhibitors of a malarial cysteine protease. The initial model for such complexes came from the model building of the protein using its homology with other cysteine proteases and calculations using DOCK to generate new lead compounds. Some of the initial model-built structures were quite stable for 100 psec of dynamics; others moved significantly from their model-built orientation. We also calculated the free energy derivatives at each atom in the inhibitor, both in water and in the binding site. The results of these calculations suggest directions for the design of new, more potent enzyme inhibitors and agree qualitatively with some of the experimental findings. Nonetheless, we stress that we have only used this methodology in an interpretive rather than a predictive manner.