Sizing-up finite fluorescent particles with nanometer-scale precision by convolution and correlation image analysis

Determining the positions, shapes and sizes of finite living particles such as bacteria, mitochondria or vesicles is of interest in many biological processes. In fluorescence microscopy, algorithms that can simultaneously localize such particles as a function of time and determine the parameters of their shapes and sizes at the nanometer scale are not yet available. Here we develop two such algorithms based on convolution and correlation image analysis that take into account the position, orientation, shape and size of the object being tracked, and we compare the precision of the two algorithms using computer simulations. We show that the precision of both algorithms strongly depends on the objects size. In cases where the diameter of the object is larger than about four to five times the beam waist radius, the convolution algorithm gives a better precision than the correlation algorithm (it leads to more precise parameters), while for smaller object diameters, the correlation algorithm gives superior precision. We apply the convolution algorithm to sequences of confocal laser scanning micrographs of immobile Escherichia coli bacteria, and show that the centroid, the front end, the rear end, the left border and the right border of a bacterium can be determined with a signal-to-noise-dependent precision down to ~5 nm.     

The control of marine biofouling on xerogel surfaces with nanometer-scale topography

Mixtures of n-octadecyltrimethoxysilane (C18, 1-5 mole-%), n-octyltriethoxysilane (C8) and tetraethoxysilane (TEOS) gave xerogel surfaces of varying topography. The 1:49:50 C18/C8/TEOS xerogel formed 100-400-nm-wide, 2-7-nm deep pores by AFM while coatings with?≥3% C18 were free of such features. Segregation of the coating into alkane-rich and alkane-deficient regions in the 1:49:50 C18/C8/TEOS xerogel was observed by IR microscopy. Immersion in ASW for 48?h gave no statistical difference in surface energy for the 1:49:50 C18/C8/TEOS xerogel and a significant increase for the 50:50 C8/TEOS xerogel. Settlement of barnacle cyprids and removal of juvenile barnacles, settlement of zoospores of the alga Ulva linza, and strength of attachment of 7-day sporelings were compared amongst the xerogel formulations. Settlement of barnacle cyprids was significantly lower in comparison to glass and polystyrene standards. The 1:49:50 and 3:47:50 C18/C8/TEOS xerogels were comparable to PDMSE with respect to removal of juvenile barnacles and sporeling biomass, respectively.     

Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics

Interactive molecular dynamics, a new modeling tool for rapid investigation of the physical mechanisms of biological processes at the atomic level, is applied to study selectivity and regulation of the membrane channel protein GlpF and the enzyme glycerol kinase. These proteins facilitate the first two steps of Escherichia coli glycerol metabolism. Despite their different function and architecture the proteins are found to employ common mechanisms for substrate selectivity: an induced geometrical fit by structurally homologous binding sites and an induced rapid dipole moment reversal. Competition for hydrogen bonding sites with water in both proteins is critical for substrate motion. In glycerol kinase, it is shown that the proposed domain motion prevents competition with water, in turn regulating the binding of glycerol.     

Effect of molecular crowding on the enzymes of glycogenolysis

Cell cytoplasm contains high concentrations of macromolecules occupying a significant part of the cell volume (crowding conditions). According to modern concepts, crowding has a pronounced effect on the rate and equilibrium of biochemical reactions and stimulates the formation of more compact structures. This review considers different aspects of the crowding effect in vivo and in vitro, its role in regulation of cell volume, the effect of crowding on various interactions, such as protein-ligand and protein-protein interactions, as well as on protein denaturation, conformation transitions of macromolecules, and supramolecular structure formation. The influence of crowding arising from the presence of high concentrations of osmolytes on the interactions of the enzymes of glycogenolysis has been demonstrated. It has been established that, in accordance with predictions of crowding theory, trimethylamine N-oxide (TMAO) and betaine highly stimulate the association of phosphorylase kinase (PhK) and its interaction with glycogen. However, high concentrations of proline, betaine, and TMAO completely suppress the formation of PhK complex with phosphorylase b (Phb). The protective effect of osmolyte-induced molecular crowding on Phb denaturation by guanidine hydrochloride is shown. The influence of crowding on the interaction of Phb with allosteric inhibitor FAD has been revealed. The results show that, under crowding conditions, the equilibrium of the isomerization of Phb shifts towards a more compact dimeric state with decreased affinity for FAD.     

Myoglobin immobilization on electrodeposited nanometer-scale nickel oxide particles and direct voltammetry

Prosperity of information on the reactions of redox-active sites in proteins can be attained by voltammetric studies in which the protein sample is located on a suitable surface. This work reports the presentation of myoglobin/nickel oxide nanoparticles/glassy carbon (Mb/NiO NPs/GC) electrode, ready by electrochemical deposition of the NiO NPs on glassy carbon electrode and myoglobin immobilization on their surfaces by the potential cycling method. Images of electrodeposited NiO NPs on the surface of glassy carbon electrode were obtained by scanning electron microscopy (SEM) and atomic force microscopy (AFM). A pair of well-defined redox peaks for Mb(Fe(III)-Fe(II)) was obtained at the prepared electrode by direct electron transfer between the protein and nanoparticles. Electrochemical parameters of immobilized myoglobin such as formal potential (E(0')), charge transfer coefficient (alpha) and apparent heterogeneous electron transfer rate constant (k(s)) were estimated by cyclic voltammetry and nonlinear regression analysis. Biocatalytic activity was exemplified at the prepared electrode for reduction of hydrogen peroxide.     

The structural basis of negative cooperativity: receptors and enzymes

Crystal structures of the negatively cooperative aspartate receptor caught at intermediate stages in the binding process help to elucidate structural factors involved in ligand binding. The frequency of occurrence of negatively cooperative proteins suggests that sequential changes in binding patterns will be extensive in positively cooperative as well as in negatively cooperative and no cooperativity proteins.     

Quantitation of intracellular membrane-bound enzymes and receptors in digitonin-permeabilized cells

The distribution of membrane-bound receptors and enzymes between the cell surface and the cell interior can be determined without solubilization or gross disruption of cell organelles in the presence of the nonionic detergent digitonin. This steroid glycoside permeabilizes cells, releases cytoplasmic proteins with subunit molecular weights up to 200,000, and allows exogenous molecules to gain access to intracellular receptors. All cell types examined were affected similarly by digitonin. Permeabilization was complete within 2 min at 0°C and did not require the continued presence of digitonin. A characteristic amount of protein (～50%) was lost between 0.02 and 0.08% ($\text{w}\text{v}$) digitonin. Three independent systems were examined: the insulin receptor in 3T3 fibroblasts and the asialoglycoprotein receptor and the $\text{Na}{}^{\mathrm{+}}\text{K}{}^{\mathrm{+}}\text{-ATPase}$ in rat hepatocytes. In each case an increase in the specific activity of enzyme/receptor occurred over a range of detergent concentration in which the retention of cell protein was constant and virtually no solubilization of membrane-bound activity occurred. The binding of ¹²⁵I-asialo-orosomucoid to rat hepatocytes at 0°C in the presence of digitonin was linear with cell number and kinetically indistinguishable from binding to intact cells. Receptors exposed by digitonin were shown to be intracellular by light microscopic examination of permeabilized cells first treated with antiserum to the receptor and then with a second antibody horseradish peroxidase conjugate. The use of digitonin has many advantages over procedures which require total cell disruption or solubilization to assess intracellular receptors. The technique has already been valuable in studies on recycling and endocytosis mediated by the asialoglycoprotein receptor (P. H. Weigel and J. A. Oka (1983)J. Biol. Chem.258, 5095–5102) and should also be useful in studies with other membrane-bound receptors and enzymes in other cell types.     

Sex steroids and their receptors: molecular actions on brain cells

Sex steroids exert actions of paramount importance on brain cells. They contribute to shape the central nervous system during embryo development. They modulate the formation and the turnover of the interconnections between neurons. They control the function of glial cells. And they do it through a signaling machinery that is apparently simple, but that hides a level of complexity that has been unveiled only in part. Different receptor isoforms, different interactions between receptors and co-regulators, chains of events originating at the cell membrane and leading to effects in the nucleus (or the other way around) all interact to determine selective modulations of brain cells. All these actions end up in phenomenal effects on brain function that change through adolescence, pregnancy, adulthood, up to menopause and ageing. Many of these actions are relevant for degenerative processes and research may offer soon new strategies to counteract these diseases.     

Adrenomedullin receptors: molecular identity and function.

Since its discovery in 1993 adrenomedullin (AM) has been the subject over 600 published articles. This multifunctional peptide has powerful vasodilator actions and recent evidence from AM gene-deleted mice suggest that AM plays an essential role in vascular development. However the lack of valid AM receptor clones and non-peptide receptor ligands has considerably slowed research progress on this important peptide. In this review we have focused on the proposition that the calcitonin receptor-like receptor (CRLR) is a receptor both for AM and the related vasoactive peptide calcitonin gene-related peptide (CGRP). The receptor activity modifying proteins (RAMPs) that are essential for defining CRLR pharmacology will also be discussed. We will describe how AM receptors have been reported to signal and be regulated and to consider whether further receptors for AM beyond CRLR/RAMP combinations might exist.     

Effects of retinoid ligands on RIP140: molecular interaction with retinoid receptors and biological activity

Receptor interacting protein 140 (RIP140) interacts with retinoic acid receptor (RAR) and retinoid X receptor (RXR) constitutively, but hormone binding enhances this interaction. The ligand-independent interaction is mediated by the amino and central regions of RIP140 which contain a total of nine copies of the LXXLL motif, whereas the agonist-induced interaction is mediated by its carboxyl terminus which contains a novel motif (1063-1076, LTKTNPILYYMLQK). The ligand-independent interaction could be enhanced slightly by agonists, whereas the ligand-dependent interaction was strictly agonist dependent for both RAR and RXR. In the context of heterodimers, ligand occupancy of RXR played a more dominant role for both molecular interaction and biological activity of RIP140. Competition and mutation studies demonstrated an essential role for (1067)Asn and (1073)Met for a ligand-dependent interaction. A model was proposed to address the constitutive and agonist-dependent interaction of RIP140 with RAR/RXR.     

The influence of enzymes on the estrogen receptors of human uterus and breast carcinoma

The influence of hydrolytic enzymes on the estrogen receptor and on the estradiol-receptor complex was studied. Proteolytic enzymes (trypsin, α-chymotrypsin, papain) phospholipases A and C, and β-glucuronidase reduced the subsequent in vitro binding of estradiol-17β by the receptor; they also released bound estradiol-17β from the estradiol-receptor complex. In addition, some glycosidases had an effect on the free receptor only. The results indicate that the estrogen receptor may contain phosphorus and carbohydrate moieties.     

Plant-associated endophytic fungi as potential bio-factories for extracellular enzymes: Progress,Challenges and Strain improvement with precision approaches

There is an intricate network of relations between endophytic fungi and their hosts that affects the production of various bioactive compounds. Plant-associated endophytic fungi contain industrially important enzymes and have the potential to fulfil their rapid demand in the international market to boost business in technology. Being safe and metabolically active, they have replaced the usage of toxic and harmful chemicals and hold a credible application in biotransformation, bioremediation and industrial processes. Despite these, there are limited reports on fungal endophytes that can directly cater to the demand and supply of industrially stable enzymes. The underlying reasons include low endogenous production and secretion of enzymes from fungal endophytes which have raised concern for widely accepted applications. Hence, it is imperative to augment the biosynthetic and secretory potential of fungal endophytes. Modern state-of-the-art biotechnological technologies aiming at strain improvement using cell factory engineering as well as precise gene editing like Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its Associated proteins (Cas) systems which can provide a boost in fungal endophyte enzyme production. Additionally, it is vital to characterize optimum conditions to grow one strain with multiple enzymes (OSME). The present review encompasses various plants-derived endophytic fungal enzymes and their applications in various sectors. Furthermore, we postulate the feasibility of new precision approaches with an aim for strain improvement and enhanced enzyme production.     

A membrane network of receptors and enzymes for adenine nucleotides and nucleosides

Most cells express more than one receptor plus degrading enzymes for adenine nucleotides or nucleosides, and cellular responses to purines are rarely compatible with the actions of single receptors. Therefore, these receptors are viewed as components of a combinatorial receptor web rather than self-dependent entities, but it remained unclear to what extent they can associate with each other to form signalling units. P2Y(1), P2Y(2), P2Y(12), P2Y(13), P2X(2), A(1), A(2A) receptors and NTPDase1 and -2 were expressed as fluorescent fusion proteins which were targeted to membranes and signalled like the unlabelled counterparts. When tested by FRET microscopy, all the G protein-coupled receptors proved able to form heterooligomers with each other, and P2Y(1), P2Y(12), P2Y(13), A(1), A(2A), and P2X(2) receptors also formed homooligomers. P2Y receptors did not associate with P2X, but G protein-coupled receptors formed heterooligomers with NTPDase1, but not NTPDase2. The specificity of prototypic interactions (P2Y(1)/P2Y(1), A(2A)/P2Y(1), A(2A)/P2Y(12)) was corroborated by FRET competition or co-immunoprecipitation. These results demonstrate that G protein-coupled purine receptors associate with each other and with NTPDase1 in a highly promiscuous manner. Thus, purinergic signalling is not only determined by the expression of receptors and enzymes but also by their direct interaction within a previously unrecognized multifarious membrane network.     

Structural studies on mannose-selective glycoprotein receptors using molecular modeling techniques

Glycoproteins play important roles in various cellular events and their presence in appropriate locations in proper active conformations is essential for many biochemical functions. Recent evidences suggest that some glycoproteins may require sorting receptors for efficient exit from the endoplasmic reticulum. These receptors need the presence of calcium or other metal ions for their native activity. The three-dimensional structure of such a receptor, p58/ERGIC-53, has been recently solved by x-ray crystallography, which is a mannose-selective lectin and contains two Ca²⁺ ions. Homology search in the sequence databases indicates a large number of proteins which bear varying degrees of homology in a wide spectrum of species with this receptor. In this study we have systematically searched for such genes which are potential candidates for acting as mannose-mediated glycoprotein receptors in various species as initially inferred from their amino acid sequence homology. Structures of a number of proteins have been predicted using knowledge-based homology modeling, and their ability to act as the glycoprotein receptor has been explored by examining the nature of sugar-binding site. Tetramer of mannose was docked in the binding pockets of the modeled structures followed by energy minimization and molecular dynamics to obtain most probable structures of the complexes. Properties of these modeled complexes were studied to examine the nature of physicochemical forces involved in the complex formation and compared with p58/ERGIC-53-mannose complex.     

The molecular phylogeny of eph receptors and ephrin ligands

Background  

The tissue distributions and functions of Eph receptors and their ephrin ligands have been well studied, however less is known about their evolutionary history. We have undertaken a phylogenetic analysis of Eph receptors and ephrins from a number of invertebrate and vertebrate species.     

The origin and molecular evolution of ionotropic glutamate receptors

A review of the main approaches to the revealing molecular evolution of glutamate receptors is presented. Large amount of evidences concerning the homology of glutamate-binding proteins forming the membrane channels has been accumulated. However, the knowledge of amino acid sequences of these proteins is the necessary but not sufficient condition for clarification of their origin and the changes in the course of molecular evolution. The natural selection estimated and secured the functional validity ofligand-gated channels. Therefore the functional and molecular approaches should supplement each other. It has been shown by and example of glutamate receptor channels of vertebrate and invertebrate animals that the combined analysis of the structure and function allows to reveal the main routes of molecular evolution of this kind of synaptic receptors.     

谷氨酸受体分子的多样性及其分子机理

谷氨酸是中枢神经系统一种重要的兴奋性神经递质,它与相应受体分子相互作用,通过细胞膜对阳离子通透性的改变或与G蛋白和第二信使系统相偶联,从而引起一系列复杂的信号转导反应。近年有关谷氨酸受体分子及其基因的研究表明:由于多基因家族、选择性剪接、RNA编辑以及异聚体形成等分子机理,使谷氨酸受体分子的结构和功能具有多样性,这种多样性是生物多样性的分子基础,也在微观水平上证明了生物多样性的原理。这方面的深入探索必将为中枢神经系统该受体表达及调控以及相关神经精神疾病发病的分子机理和治疗性药物设计提供新的线索。