Recognition In Biological Systems Research Articles

Quantum/Classical Mechanical Comparison of Cation−π Interactions between Tetramethylammonium and Benzene

To consider whether existing molecular force fields can adequately reproduce cation−π interactions without adding special interaction terms, theoretical calculations with geometry optimization were performed on three configurations of tetramethylammonium (TMA) interacting via one, two, or three N-methyl groups with a benzene ring, by use of density-functional theory (DFT) methods B3LYP/6-31G* and B3LYP/6-311G**, ab initio method MP2/6-31G*, and molecular mechanic methods EFF, Tinker's Amber and MM3. Only the first configuration was found to be stable from the DFT and MP2 results, and its geometry was found to be highly flexible. ESP CHELPG charges estimated from the DFT and MP2 calculations were used to modify the atomic charges of the force fields employed in the molecular mechanics calculations to improve agreement with the BSSE-corrected binding energies deduced from the DFT and MP2 results. After this modification, the molecular mechanics results were found to be in good agreement with those obtained by DFT and MP2, without a requirement to add any additional terms to the force fields. This was confirmed by comparing the energy profiles of the complex as benzene was moved away from TMA in 0.2 Å intervals. Hence it is possible to use existing force fields to represent cation−π interactions by a simple adjustment of certain partial atomic charge parameters. In this context, we discuss the high flexibility of the cation−π interactions in the framework of molecular recognition in biological systems.

Biosensors: MICREDOX - a new biosensor technique for rapid measurement of BOD and toxicity

The combination of electrochemical, optical, acoustical and other measurement techniques with the specificity of biological recognition systems has resulted in a range of new analytical devices known as biosensors. Biosensors are under intensive development worldwide because they have a multitude of potential applications, in particular, clinical medicine, environmental monitoring and process control of industrial processes. Their basic principles, mode of operation, performance requirements and current trends will be reviewed. A brief description of a novel biosensor developed at Lincoln Technology, the MICREDOX method, is outlined and applications for rapid measurement of biochemical oxygen demand and toxicity measurements are described. Preliminary data obtained using the MICREDOX method are reported for three standard toxic materials, zinc sulphate, 3, 5-dichlorophenol and sodium lauryl sulphate.

How Does Ammonium Interact with Aromatic Groups? A Density Functional Theory (DFT/B3LYP) Investigation

DFT/B3LYP calculations were carried out on complexes formed by NH4+ with aromatics, viz. benzene, phenol, pyrrole, imidazole, pyridine, indole, furane, and thiophene, to characterize the forces involved in such interactions and to gain further insight into the nature and diversity of cation−aromatic interactions. Such calculations may provide valuable information for understanding molecular recognition in biological systems and for force-field development. B3LYP/6-31G** optimization on 35 initial structures resulted in 11 different finally optimized geometries, which could be divided into three types: NH4+−π complexes, protonated heterocyclic−NH3 hydrogen bond complexes, and heterocyclic−NH4+ hydrogen bond complexes. For NH4+−π complexes, NH4+ always tilts toward the carbon−carbon bond rather than toward the heteroatom or the carbon−heteroatom bond. The calculated CHelpG charges suggest that the charge distribution of a free heterocyclic may be used to predict the geometry of its complex. Charge populati...

Generalization and the evolution of symmetry preferences

Biological displays are often symmetrical, and there is growing evidence that receivers are sensitive to these symmetries. One explanation for the evolution of such sensitivity is that symmetry reflects the quality of the signaller. An alternative is that the sensitivity may arise as a by-product of general properties of biological recognition systems. In line with the latter idea, simulations of the recognition process based on simple, artificial neural networks have suggested that generalization can give rise to preferences for particular symmetrical stimuli. However, it is not clear from these studies exactly how the preferences emerge, and to what extent the results are relevant to biological recognition systems. Here, we employ a different class of recognition models (gradient interaction models) to demonstrate more clearly how generalization can generate a preference for symmetrical variants of a display. We also point out that the predictions of the gradient interaction and network-based models regarding the effects of generalization closely match the results from empirical studies of stimulus control. Our analysis demonstrates that the effects of generalization cannot be ignored when studying the evolution of symmetry preferences and symmetric signals.

A Bifunctional Enzyme Catalyzes the First Two Steps inN-Acetylneuraminic Acid Biosynthesis of Rat Liver

N-Acetylneuraminic acid (Neu5Ac) is the precursor of sialic acids, a group of important molecules in biological recognition systems. Biosynthesis of Neu5Ac is initiated and regulated by its key enzyme, UDP-N-acetylglucosamine 2-epimerase (UDP-GlcNAc 2-epimerase, EC 5.1. 3.14)/N-acetylmannosamine kinase (ManNAc kinase, EC 2.7.1.60) in rat liver (Hinderlich, S., Stäsche, R., Zeitler, R., and Reutter, W. (1997) J. Biol. Chem. 272, 24313-24318). In the present paper we report the isolation and characterization of a cDNA clone encoding this bifunctional enzyme. An open reading frame of 2166 base pairs encodes 722 amino acids with a predicted molecular mass of 79 kDa. The deduced amino acid sequence contains exact matches of the sequences of five peptides derived from tryptic cleavage of the enzyme. The recombinant bifunctional enzyme was expressed in COS7 cells, where it displayed both epimerase and kinase activity. Distribution of UDP-GlcNAc 2-epimerase/ManNAc kinase in the cytosol of several rat tissues was investigated by determining both specific enzyme activities. Secreting organs (liver, salivary glands, and intestinal mucosa) showed high specific activities of UDP-GlcNAc 2-epimerase/ManNAc kinase, whereas significant levels of these activities were absent from other organs (lung, kidney, spleen, brain, heart, skeletal muscle, and testis). Northern blot analysis revealed no UDP-GlcNAc 2-epimerase/ManNAc kinase mRNA in the non-secreting tissues.

Samarium Diiodide Mediated Coupling of Glycosyl Phosphates with Carbon Radical or Anion Acceptors—Synthesis of C‐Glycosides

Carbohydrate mimetics for the study of carbohydrate recognition in biological systems can be C-glycosides, which can now be prepared by the SmI2-mediated coupling of glycosyl phosphates with carbon radical or carbon anion acceptors. The reaction proceeds by one-electron processes via the radical or the anion, respectively (see scheme on the right), and is complete within 15–30 min.

Weak interactions and lessons from crystallization.

Ideas derived from the study of the process of crystallization may provide insights into molecular recognition in biological systems. Both processes exploit the cooperativity which arises from the formation of a large array of weak interactions.

Molecular Cloning and Identification of N-Acyl-D-glucosamine 2-Epimerase from Porcine Kidney as a Renin-binding Protein

N-Acetylneuraminic acid (NeuAc) is an important molecule in biological recognition systems. NeuAc is known to be biosynthesized either from UDP-N-acetyl-D-glucosamine by an action of UDP-N-acetyl-D-glucosamine 2-epimerase or from N-acetyl-D-glucosamine by N-acyl-D-glucosamine 2-epimerase (GlcNAc 2-epimerase). However, the physiological function of the GlcNAc 2-epimerase in NeuAc biosynthesis has not been fully evaluated. To clarify the role of GlcNAc 2-epimerase in NeuAc biosynthesis, the enzyme and its gene were isolated from porcine kidney cortex. Escherichia coli cells transformed with the gene expressed the GlcNAc 2-epimerase having the same properties as those of the GlcNAc 2-epimerase from porcine kidney. Sequence analysis indicated that the gene was capable of synthesizing a 46.5-kDa protein (402 amino acids) with a conserved leucine zipper motif. Homology search for the cloned gene revealed that the GlcNAc 2-epimerase was identical with renin-binding protein (RnBP) in porcine kidney (Inoue, H., Fukui, K., Takahashi, S., and Miyake, Y.(1990) J. Biol. Chem. 265, 6556-6561) (identity: 99.6% in nucleotide sequence, 99.0% in amino acid sequence). That GlcNAc 2-epimerase is a RnBP was confirmed by its ability to bind porcine kidney renin and mask its protease activity. These findings provide unequivocal evidence that the enzyme GlcNAc 2-epimerase is a RnBP.

Visual object recognition.

Visual object recognition is of fundamental importance to most animals. The diversity of tasks that any biological recognition system must solve suggests that object recognition is not a single, general purpose process. In this review, we consider evidence from the fields of psychology, neuropsychology, and neurophysiology, all of which supports the idea that there are multiple systems for recognition. Data from normal adults, infants, animals, and brain damaged patients reveal a major distinction between the classification of objects at a basic category level and the identification of individual objects from a homogeneous object class. An additional distinction between object representations used for visual perception and those used for visually guided movements provides further support for a multiplicity of visual recognition systems. Recent evidence from psychophysical and neurophysiological studies indicates that one system may represent objects by combinations of multiple views, or aspects, and another may represent objects by structural primitives and their spatial interrelationships.

Molecular Recognition in Biological Systems: Phosphate Esters vs Sulfate Esters and the Mechanism of Action of Steroid Sulfatases

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Recognition in Biological Systems: Phosphate Esters vs Sulfate Esters and the Mechanism of Action of Steroid SulfatasesC. J. Anderson, Linda J. H. Lucas, and Theodore S. WidlanskiCite this: J. Am. Chem. Soc. 1995, 117, 13, 3889–3890Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://doi.org/10.1021/ja00118a034RIGHTS & PERMISSIONSArticle Views289Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (270 KB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts

18] Hydrostatic and osmotic pressure as tools to study macromolecular recognition

Clearly, hydrostatic and osmotic pressure techniques offer unique potential in the study of fundamental problems of molecular recognition in biological systems. With the recent advances in technology such investigations are rapidly becoming commonplace. We look forward to further advances and their report in succeeding compendiums such as this volume.

The DNA recognition subunit of a DNA methyltransferase is predominantly a molten globule in the absence of DNA

Enzyme-catalysed DNA methylation provides an opportunity for the modulation of protein-DNA recognition in biological systems. Recently we have demonstrated that the smaller of the two subunits of the heterodimeric, cytosine-specific DNA methyltransferase, M. AquI, is largely responsible for sequence-specific DNA recognition. Here we present evidence from a series of NMR, fluorescence and circular dichroism spectroscopy experiments that the DNA binding subunit of M. AquI has the characteristics of a molten globule in the absence of the catalytic machinery. In this metastable state this subunit retains its ability to bind DNA in a sequence-specific manner. We believe this finding offers an insight into the structural flexibility which underpins the mechansim of action of these enzymes, and may provide a possible biological role for molten globules in protein function.

Functional Group Imaging by Chemical Force Microscopy

Mapping the spatial arrangement of chemical functional groups and their interactions is of significant importance to problems ranging from lubrication and adhesion to recognition in biological systems. A force microscope has been used to measure the adhesive and friction forces between molecularly modified probe tips and organic monolayers terminating in a lithographically defined pattern of distinct functional groups. The adhesive interactions between simple CH(3)/CH(3), CH(3)/COOH, and COOH/COOH functional groups correlate directly with friction images of sample surfaces patterned with these groups. Thus, by monitoring the friction between a specifically functionalized tip and sample, one can produce friction images that display predictable contrast and correspond to the spatial distribution of functional groups on the sample surface. Applications of this chemically sensitive imaging technique are discussed.

Molecular Recognition at Interfaces

Various molecular recognition systems were investigated at the air-water interface because a study on molecular recognition in direct contact with bulk water is key to understand molecular recognition in biological systems. Monolayers with synthesized functional groups were found to recognize target molecules, such as ATP, nucleic acid base, sugars, through hydrogen bonding, while the similar recognition is known to be difficult in bulk water phase. The multi-point recognition at the air-water interface was accomplished by using mixed monolayer systems and multi-functional guests. Micellar system of the functional surfactant also showed the recognition ability in aqueous phase, which indicates the concept of specific molecular recognition found at the air-water interface can be extended to other type of interface. The theoretical approach based on quantum chemistry was applied to these systems to figure out the mechanism of molecular recognition at interfaces.

Molecular recognition in biological systems: from activation to inhibition.

A fine-tuned system of molecular recognition is a fundamental feature of all biological processes. Although the basic principles of how molecular surfaces fit together in a complementary fashion have been established to a first approximation, the details of the interplay between electrostatic, steric, entropic and solvation effects are not well understood. To provide insight into the stereochemical factors that govern recognition and packing at protein interfaces, a host of biochemical and biophysical techniques have been applied. Perhaps the most widely used of these techniques are mutagenesis and crystallography, and when used together they have proved to be extremely powerful in defining the functional elements that are important in protein interactions. Using these protein-engineering techniques we have focused our studies on the role of molecular recognition in two important, but distinctly different, biological processes: ( 1) the role of molecular recognition in receptor activation, and (2) the stereochemical factors that define specificity and provide binding energy to inhibitors that are associated with their target proteinases. Our findings, discussed below, suggest that the conventional wisdom about specificity and binding needs to be rethought.

Biosensors

Biosensors are analytical devices that respond selectively to analytes in an appropriate sample and convert their concentration into an electrical signal via a combination of a biological recognition system and an electrochemical, optical or other transducer. Such devices will find application in medicine, agriculture, environmental monitoring and the bioprocessing industries. The last few years have seen great advances in the design of sensor architectures, the marriage of biological systems with monolithic silicon and optical technologies, the development of effective electron-transfer systems and the configuration of direct immunosensors. Recent progress in these areas has already led to the introduction of new-generation biosensors into the competitive diagnostics market place.

分子認識素子を付与したリポソームの特異細胞への指向性

We have developed the coating of liposomes with a cell specific polysaccharide. Carbohydrates play a very important role in biological recognition system. In this study, galactosamin(1), 1-amino-galactose(2), 1-amino-mannose(3), 1-amino-glu-cose(4)was selected and partly replaced to be an effective sensory device on naturally occurring polysaccharide such as pullulan. The polysaccharide-coated liposomes become significantly stable both physicochemically and biochemically and also cell recognizable. Recognizabilities of the poly-saccharide-coated liposomes were confirmed by specific lectin-induced aggregation, cell-liposome interaction, and tissue distribution. Liposomes coated with pullulan derivatives(1-3)were effectively endocytosed by human neutrophils and monocytes, while liposomes coated with pullulan derivative(4) inhibited the endocytosis. When galactosamin-modified pullulan-coated liposome was intravenously administrated into mice, liver uptake increased compared with the simple pullulan-coated liposome. These findings suggest that terminal sugars of modified polysaccharides act as a potentially valuable sensory device of drug delivery system.

Introduction to the principles and applications of biosensors.

A biosensor is an analytical device that responds to an analyte in an appropriate sample and interprets its concentration as an electrical signal via a suitable combination of a biological recognition system and an electrochemical transducer. As a result of recent scientific and technological progress, such devices are likely to play an increasingly important role in generating analytical information in all sectors of human endeavour, from medicine to the military. In particular, biosensors will form the basis of cheap, simple devices for acquiring chemical information, bringing sophisticated analytical capabilities to the non-specialist and general public alike. The market opportunities for the rapid exploitation of novel developments in this sector are substantial. Biosensor research is also likely to have a significant impact on the development of modern electronics.

Biosensors: current applications and future potential.

AbstractBiological molecules such as enzymes and antibodies display a unique capacity to recognize and respond to other molecules in a way which can be exploited in the development of analytical devices. In a biosensor, the biological recognition system creates a physiochemical change proximal to a suitable transducer and thereby converts the concentration of the analyte into a quantifiable electrical signal. The design and construction of these devices requires an imaginative combination of biological, chemical, physical and engineering disciplines. Biosensors will find application in a variety of analytical fields.

人工膜による分子認識 自励発振現象の応用

In living organisms, recognition of molecules, such as by taste, smell or immunity, is essential for the maintenance of life. It is well known that the excitability of the bio-membranes is quite important to recognize various chemicals. The development of excitable artificial membranes is thus important to understand the mechanism of molecular recognition in biological systems. In this article, the history of studies of artificial membranes excitable by electrical current, voltage, hydrostatic or osmotic pressure, and chemical substances are reviewed. Among these studies, the work by the author and his collaborators shows that excitable phenomenon is applicable to the recognition of various chemical species. The development of a new type of chemical sensor capable of distinguishing chemical substances on the basis of information on the frequency, amplitude and the shapes of electrical pulses is suggested to be promising.