首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到20条相似文献,搜索用时 15 毫秒
1.
2.
The development of biologically active molecules based on molecular recognition is an attractive and challenging task in medicinal chemistry and the molecules that can activate/deactivate certain receptors are of great medical interest. In this contribution, selected pyrimidine/piperidine derivatives were synthesized and tested for the ability to activate/deactivate Aryl hydrocarbon receptor (AhR) and Glucocorticoid receptor (GR). Tested compounds are shown to activate the receptors but to much lesser extent than positive controls, dioxin and dexamethasone for Ahr and GR, respectively. However, some of them antagonized the positive controls action. Although further in vivo studies are needed to fully characterize the bioactivities of these compounds, the reported in vitro evidences demonstrate that they might be used as the modulators of AhR and GR activities.  相似文献   

3.
Detection and sequence-identification of nucleic acid molecules is often performed by binding, or hybridization, of specimen "target" strands to immobilized, complementary "probe" strands. A familiar example is provided by DNA microarrays used to carry out thousands of solid-phase hybridization reactions simultaneously to determine gene expression patterns or to identify genotypes. The underlying molecular process, namely sequence-specific recognition between complementary probe and target molecules, is fairly well understood in bulk solution. However, this knowledge proves insufficient to adequately understand solid-phase hybridization. For example, equilibrium binding constants for solid-phase hybridization can differ by many orders of magnitude relative to solution values. Kinetics of probe-target binding are affected. Surface interactions, electrostatics and polymer phenomena manifest themselves in ways not experienced by hybridizing strands in bulk solution. The emerging fundamental understanding provides important insights into application of DNA microarray and biosensor technologies.  相似文献   

4.
Iron acquisition is a complex, multicomponent process critical for most organisms' survival and virulence. Small iron chelating molecules, siderophores, mediate transport as key components of common pathways for iron assimilation in many microorganisms. The chemistry and biology of the extraordinary tight and specific metal binding siderophores is of general interest in terms of host/guest chemistry and is a potential target toward the development of therapeutic treatments for microbial virulence. The siderophore pathway of the moderate thermophile, Thermobifida fusca, is an excellent model system to study the process in Gram‐positive bacteria. Here we describe the structure and characterization of the siderophore periplasmic binding protein, FscJ from the fuscachelin gene cluster of T. fusca. The structure shows a di‐domain arrangement connected with a long α‐helix hinge. Several X‐ray structures detail ligand‐free conformational changes at different pH values, illustrating complex interdomain flexibility of the siderophore receptors. We demonstrated that FscJ has a unique recognition mechanism and details the binding interaction with ferric‐fuscachelin A through ITC and docking analysis. The presented work provides a structural basis for the complex molecular mechanisms of siderophore recognition and transportation. Proteins 2016; 84:118–128. © 2015 Wiley Periodicals, Inc.  相似文献   

5.
Malate dehydrogenase (l-malate:NAD+ oxidoreductase, EC 1.1.1.37) has been purified about 480-fold from crude extract of the facultative phototrophic bacterium, Rhodopseudomonas capsulata by only two purification steps, involving Red-Sepharose affinity chromatography. The enzyme has a molecular mass of about 80 kDa and consists of two subunits with identical molecular mass (35 kDa). The enzyme is susceptible to heat inactivation and loses its activity completely upon incubation at 40°C for 10 min. Addition of NAD+, NADH and oxaloacetate, but not l-malate, to the enzyme solution stabilized the enzyme. The enzyme catalyzes exclusively the oxidation of l-malate, and the reduction of oxaloacetate and ketomalonate in the presence of NAD+ and NADH, respectively, as the coenzyme. The pH optima are around 9.5 for the l-malate oxidation, and 7.75–8.5 and 4.3–7.0 for the reduction of oxaloacetate and ketomalonate, respectively. The Km values were determined to be 2.1 mM for l-malate, 48 μM for NAD+, 85 μM for oxaloacetate, 25 μM for NADH and 2.2 mM for ketomalonate. Initial velocity and product inhibition patterns of the enzyme reactions indicate a random binding of the substrates, NAD+ and l-malate, to the enzyme and a sequential release of the products: NADH is the last product released from the enzyme in the l-malate oxidation.  相似文献   

6.
In this work, we examine the hypothesis about how trapped water molecules at the interface between triosephosphate isomerase (TIM) and either of two phosphorylated inhibitors, 2-phosphoglycolate (2PG) or phosphoglycolohydroxamate (PGH), can explain the anomalous highly negative binding heat capacities (ΔCp,b) of both complexes, TIM–2PG and TIM–PGH. We performed fluorimetric titrations of the enzyme with PGH inhibitor under osmotic stress conditions, using various concentrations of either osmolyte: sucrose, ethylene glycol or glycine betaine. We also analyze the binding processes under various stressor concentrations using a novel calorimetric methodology that allows ΔCp,b determinations in single experiments: Multithermal Titration Calorimetry. The binding constant of the TIM–PGH complex decreased gradually with the concentration of all osmolytes, but at diverse extents depending on the osmolyte nature. According to the osmotic stress theory, this decrease indicates that the number of water molecules associated with the enzyme increases with inhibitor binding, i.e. some solvent molecules became trapped. Additionally, the binding heat capacities became less negative at higher osmolyte concentrations, their final values depending on the osmolyte. These effects were also observed in the TIM–2PG complex using sucrose as stressor. Our results strongly suggest that some water molecules became immobilized when the TIM-inhibitor complexes were formed. A computational analysis of the hydration state of the binding site of TIM in both its free state and its complexed form with 2PG or PGH, based on molecular dynamics (MD) simulations in explicit solvent, showed that the binding site effectively immobilized additional water molecules after binding these inhibitors.  相似文献   

7.
Mechanobiological processes are rooted in mechanics and chemistry, and such processes may be modeled in a framework that couples their governing equations starting from fundamental principles. In many biological applications, the reactants and products of chemical reactions may be electrically charged, and these charge effects may produce driving forces and constraints that significantly influence outcomes. In this study, a novel formulation and computational implementation are presented for modeling chemical reactions in biological tissues that involve charged solutes and solid-bound molecules within a deformable porous hydrated solid matrix, coupling mechanics with chemistry while accounting for electric charges. The deposition or removal of solid-bound molecules contributes to the growth and remodeling of the solid matrix; in particular, volumetric growth may be driven by Donnan osmotic swelling, resulting from charged molecular species fixed to the solid matrix. This formulation incorporates the state of strain as a state variable in the production rate of chemical reactions, explicitly tying chemistry with mechanics for the purpose of modeling mechanobiology. To achieve these objectives, this treatment identifies the specific theoretical and computational challenges faced in modeling complex systems of interacting neutral and charged constituents while accommodating any number of simultaneous reactions where reactants and products may be modeled explicitly or implicitly. Several finite element verification problems are shown to agree with closed-form analytical solutions. An illustrative tissue engineering analysis demonstrates tissue growth and swelling resulting from the deposition of chondroitin sulfate, a charged solid-bound molecular species. This implementation is released in the open-source program FEBio (www.febio.org). The availability of this framework may be particularly beneficial to optimizing tissue engineering culture systems by examining the influence of nutrient availability on the evolution of inhomogeneous tissue composition and mechanical properties, the evolution of construct dimensions with growth, the influence of solute and solid matrix electric charge on the transport of cytokines, the influence of binding kinetics on transport, the influence of loading on binding kinetics, and the differential growth response to dynamically loaded versus free-swelling culture conditions.  相似文献   

8.
Immune-mediated adverse drug reactions (ADRs) are one of the most severe drug hypersensitivity syndromes in clinical therapy. As certain drug molecules such as abacavir and carbamazepine have long been known to strongly associate with specific human leukocyte antigen (HLA) alleles to induce an array of adverse immune responses, it is fundamentally important to elucidate the molecular mechanism and biological implication underlying the direct HLA–drug interaction. In this study, a synthetic bioinformatics protocol was used to investigate the recognition and binding phenomenon of drug molecules to their associated HLA alleles. In the procedure, sophisticated molecular docking was performed to determine the intermolecular interactions of drug compounds with HLA proteins, and the resulting scores were then compared with the apparent odds ratio values extracted from clinical data. Some typical HLA–drug complexes with or without antigenic peptides were also subjected to atomistic molecular dynamics simulations, aiming at the understanding of structural details and energetic properties involved in the complex systems. It is suggested that (i) although the theoretical affinities exhibited only a moderate correlation with observed association strengths for unique HLA–drug pairs, the binding orientation and conformation of drug molecules rooting in HLA pockets contributed significantly to eliciting T-cell response and (ii) peptide antigens may play a crucial role in ADR-related HLA–drug recognition and interaction.  相似文献   

9.
Multicomponent self-diffusion data on dioleoyl(DOL)- and dipalmitoyllecithin (DPL) vesicle-water systems have been determined using a Fourier transform NMR technique. The self-diffusion of vesicles is characterized by diffusion coefficients two magnitudes lower than that of small molecules in solution. Consequently, the degree of binding of small molecules is strongly reflected in their time-averaged self-diffusion coefficient in vesicle-water systems. This provides a new basis for the determination of vesicle-water partition equilibria. The feasibility of the technique has been investigated in one anesthetic-lipid system and is found to be very good. The binding of the hydrochloride form of tetracaine to DOL vesicles at pH 3 and 7 (Kp = 30–50) is found to be very much lower than that of the neutral molecule at pH 9 (Kp = 800–900). No significant difference in the tetracaine binding characteristics was found between DOL, DOL-cholesterol and DPL systems.  相似文献   

10.
In the few last years, the need of reliable, fast and inexpensive methods for selective analysis of specific substances in complex mixtures has grown exponentially. In particular, the detection of biomolecules, such as oligonucleotides, proteins, peptides and carbohydrates is of outstanding importance in gene expression, drug design and medicine studies. To these purposes, molecular recognition on microarray-configured devices is one of the most promising tools. This technology uses a number of different substrates such as glass, silicon, alumina or gold-coated slides. The use of polymers is a very effective way to tailor surface properties introducing functional groups able to bind biomolecules and prevent denaturation and non-specific binding. Furthermore, advanced polymers, thanks to their particular physico-chemical properties, can be used to improve selectivity and sensitivity during assays. This review will provide very recent examples of polymer-mediated molecular recognition between guest molecules in solution and host molecules located at the solid phase.  相似文献   

11.
Plasmodium vivax is a very common but non-cultivable malaria parasite affecting large human population in tropical world. To develop therapeutic reagents for this malaria, the parasite molecules involved in host-parasite interaction need to be investigated as they form effective vaccine or drug targets. We have investigated here the erythrocyte binding activity of a group of 15 different Plasmodium vivax tryptophan rich antigens (PvTRAgs). Only six of them, named PvTRAg, PvTRAg38, PvTRAg33.5, PvTRAg35.2 PvTRAg69.4 and PvATRAg74, showed binding to host erythrocytes. That the PvTRAgs binding to host erythrocytes was specific was evident from the competitive inhibition and saturation kinetics results. The erythrocyte receptors for these six PvTRAgs were resistant to trypsin and neuraminidase. These receptors were also chymotrypsin resistant except the receptors for PvTRAg38 and PvATRAg74 which were partially sensitive to this enzyme. The cross-competition studies showed that the chymotrypsin resistant RBC receptor for each of these two proteins was different. Altogether, there seems to be three RBC receptors for these six PvTRAgs and each PvTRAg has two RBC receptors. Both RBC receptors for PvTRAg, PvTRAg69.4, PvTRAg33.5, and PvTRAg35.2 were common to all these four proteins. These four PvTRAgs also shared one of their RBC receptors with PvTRAg38 as well as with PvATRAg74. The erythrocyte binding activity of these six PvTRAgs was inhibited by the respective rabbit polyclonal antibodies as well as by the natural antibodies produced by the P. vivax exposed individuals. It is concluded that only selective few PvTRAgs show erythrocyte binding activity involving different receptor molecules which can be blocked by the natural antibodies. Further studies on these receptor and ligands may lead to the development of therapeutic reagents for P. vivax malaria.  相似文献   

12.
Pleckstrin homology (PH) domains mediate protein–membrane interactions by binding to phosphatidylinositol phosphate (PIP) molecules. The structural and energetic basis of selective PH–PIP interactions is central to understanding many cellular processes, yet the molecular complexities of the PH–PIP interactions are largely unknown. Molecular dynamics simulations using a coarse-grained model enables estimation of free-energy landscapes for the interactions of 12 different PH domains with membranes containing PIP2 or PIP3, allowing us to obtain a detailed molecular energetic understanding of the complexities of the interactions of the PH domains with PIP molecules in membranes. Distinct binding modes, corresponding to different distributions of cationic residues on the PH domain, were observed, involving PIP interactions at either the “canonical” (C) and/or “alternate” (A) sites. PH domains can be grouped by the relative strength of their C- and A-site interactions, revealing that a higher affinity correlates with increased C-site interactions. These simulations demonstrate that simultaneous binding of multiple PIP molecules by PH domains contributes to high-affinity membrane interactions, informing our understanding of membrane recognition by PH domains in vivo.  相似文献   

13.
The involvement of circulating hemocytes as the principal cellulareffector mediating molluscan immune responses is well established.They participate in a variety of internal defense-related activitiesincluding microbial phagocytosis, multicellular encapsulation,and cell-mediated cytotoxicity reactions that are presumed tobe initiated through foreign ligand binding to hemocyte receptorsand subsequent transduction of the binding signal through thecell resulting in appropriate (or in some cases, inappropriate)hemocyte responses. At present, however, although functionalevidence abounds as to the existence of hemocyte "recognition"receptors, few have been characterized at the molecular level.Similarly, signal transduction systems associated with variousreceptor-mediated hemocyte functions in molluscs are only beginningto be investigated and understood. This review examines whatis currently known about the molluscan hemocyte receptors andthe putative signal transduction pathways involved in regulatingtheir cellular behaviors/activities. The cumulative data impliesthe presence of various hemocyte-associated receptors capableof binding specific carbohydrates, extracellular matrix proteins,growth factors, hormones, and cytokines. Moreover, receptor-ligandinteractions appear to involve signaling molecules similar tothose already recognized in vertebrate immunocyte signal transductionpathways, such as protein kinases A and C, focal adhesion kinase,Src, Ca2+ and mitogen-activated protein kinase. Overall, theexperimental evidence suggests that molluscan immune responsesrely on molecules that share homology with those of vertebratesignaling systems. As more information regarding the molecularnature of hemocyte recognition receptors and their associatedsignaling molecules is accumulated, a clearer picture of howhemocyte immune responses to invading organisms are regulatedwill begin to emerge.  相似文献   

14.
In invertebrates, crustaceans' immune system consists of pattern recognition receptors (PRRs) instead of immunoglobulin's, which involves in the microbial recognition and initiates the protein–ligand interaction between hosts and pathogens. In the present study, PRRs namely β‐1,3 glucan binding protein (β‐GBP) from mangrove crab Episesarma tetragonum and its interactions with the pathogens such as bacterial and fungal outer membrane proteins (OMP) were investigated through microbial aggregation and computational interaction studies. Molecular recognition and microbial aggregation results of Episesarma tetragonum β‐GBP showed the specific binding affinity toward the fungal β‐1,3 glucan molecule when compared to other bacterial ligands. Because of this microbial recognition, prophenoloxidase activity was enhanced and triggers the innate immunity inside the host animal. Our findings disclose the role of β‐GBP in molecular recognition, host–pathogen interaction through microbial aggregation, and docking analysis. In vitro results were concurred with the in silico docking, and molecular dynamics simulation analysis. This study would be helpful to understand the molecular mechanism of β‐GBP and update the current knowledge on the PRRs of crustaceans. Copyright © 2014 John Wiley & Sons, Ltd.  相似文献   

15.
The solution and solid state conformations of several 6-O-methyl homoerythromycins 14 were studied using a combination of X-ray crystallography, NMR spectroscopy and molecular modelling calculations. In the solid state 1 was found to exist as the two independent molecules with similar structures termed 3-endo-folded-out. In solution a significant conformational flexibility was noticed especially in the C2 to C5 region. The compounds 1 and 2 unlike 14-membered macrolides adopted the 3-endo-folded-out conformation while 3 and 4 existed in the classical folded-out conformation. TrNOESY and STD experiments showed that 1 and 2 bound to the Escherichia coli ribosome while 3 and 4, lacking the cladinose sugar, did not exhibit binding activities, this being in accordance with biochemical data. The bound conformations were found to be very similar to the free ones, some small differences were observed and discussed. The STD experiments provided evidence on binding epitopes. The structural parts of 1 and 2 in close contact with ribosome were similar, however the degree of saturation transfer was higher for 2. The differences between tr-NOE data and STD enhancements in 1 and 2 arouse as a consequence of structural changes upon binding and a closer proximity of 2 to the ribosome surface. An understanding of the molecular mechanisms involved in the interaction of macrolides with ribosomes can help in developing strategies aiming at design of potential inhibitors.  相似文献   

16.
Upon the ligand-dependent dimerization of the epidermal growth factor receptor (EGFR), the intrinsic protein tyrosine kinase (PTK) activity of one receptor monomer is activated, and the dimeric receptor undergoes self-phosphorylation at any of eight candidate phosphorylation sites (P-sites) in either of the two C-terminal (CT) domains. While the structures of the extracellular ligand binding and intracellular PTK domains are known, that of the ∼225-amino acid CT domain is not, presumably because it is disordered. Receptor phosphorylation on CT domain P-sites is critical in signaling because of the binding of specific signaling effector molecules to individual phosphorylated P-sites. To investigate how the combination of conventional substrate recognition and the unique topological factors involved in the CT domain self-phosphorylation reaction lead to selectivity in P-site phosphorylation, we performed coarse-grained molecular simulations of the P-site/catalytic site binding reactions that precede EGFR self-phosphorylation events. Our results indicate that self-phosphorylation of the dimeric EGFR, although generally believed to occur in trans, may well occur with a similar efficiency in cis, with the P-sites of both receptor monomers being phosphorylated to a similar extent. An exception was the case of the most kinase-proximal P-site-992, the catalytic site binding of which occurred exclusively in cis via an intramolecular reaction. We discovered that the in cis interaction of P-site-992 with the catalytic site was facilitated by a cleft between the N-terminal and C-terminal lobes of the PTK domain that allows the short CT domain sequence tethering P-site-992 to the PTK core to reach the catalytic site. Our work provides several new mechanistic insights into the EGFR self-phosphorylation reaction, and demonstrates the potential of coarse-grained molecular simulation approaches for investigating the complexities of self-phosphorylation in molecules such as EGFR (HER/ErbB) family receptors and growth factor receptor PTKs in general.  相似文献   

17.
Sperm–oocyte interaction during fertilization is multiphasic, with multicomponent events, taking place between egg's glycoproteins and sperm surface receptors. Protein–carbohydrate complementarities in gamete recognition have observed in cases throughout the whole evolutionary scale. Sperm-associated α-l-fucosidases have been identified in various organisms. Their wide distribution and known properties reflect the hypothesis that fucose and α-l-fucosidases have fundamental function(s) during gamete interactions. An α-l-fucosidase has been detected as transmembrane protein on the surface of spermatozoa of eleven species across the genus Drosophila. Immunofluorescence labeling showed that the protein is localized in the sperm plasma membrane over the acrosome and the tail, in Drosophila melanogaster. In the present study, efforts were made to analyze with solid phase assays the oligosaccharide recognition ability of fruit fly sperm α-l-fucosidase with defined carbohydrate chains that can functionally mimic egg glycoconjugates. Our results showed that α-l-fucosidase bound to fucose residue and in particular it prefers N-glycans carrying core α1,6-linked fucose and core α1,3-linked fucose in N-glycans carrying only a terminal mannose residue. The ability of sperm α-l-fucosidase to bind to the micropylar chorion and to the vitelline envelope was examined in in vitro assays in presence of α-l-fucosidase, either alone or in combination with molecules containing fucose residues. No binding was detected when α-l-fucosidase was pre-incubated with fucoidan, a polymer of α-l-fucose and the monosaccharide fucose. Furthermore, egg labeling with anti-horseradish peroxidase, that recognized only core α1,3-linked fucose, correlates with α-l-fucosidase micropylar binding. Collectively, these data support the hypothesis of the potential role of this glycosidase in sperm–egg interactions in Drosophila.  相似文献   

18.
The human Monoamine oxidase (hMAO) metabolizes several biogenic amine neurotransmitters and is involved in different neurological disorders. Extensive MD simulation studies of dopamine-docked hMAO B structures have revealed the stabilization of amino-terminal of the substrate by a direct and water-mediated interaction of catalytic tyrosines, Gln206, and Leu171 residues. The catechol ring of the substrate is stabilized by Leu171(C–H)?π(Dop)?(H–C) Ile199 interaction. Several conserved water molecules are observed to play a role in the recognition of substrate to the enzyme, where W1 and W2 associate in dopamine– FAD interaction, reversible dynamics of W3 and W4 influenced the coupling of Tyr435 to Trp432 and FAD, and W5 and W8 stabilized the catalytic Tyr188/398 residues. The W6, W7, and W8 water centers are involved in the recognition of catalytic residues and FAD with the N+- site of dopamine through hydrogen bonding interaction. The recognition of substrate to gating residues is made through W9, W10, and W11 water centers. Beside the interplay of water molecules, the catalytic aromatic cage has also been stabilized by π?water, π?C–H, and π?π interactions. The topology of conserved water molecular sites along with the hydration dynamics of catalytic residues, FAD, and dopamine has added a new feature on the substrate binding chemistry in hMAO B which may be useful for substrate analog inhibitor design.  相似文献   

19.
Self-replicating molecules stand at the very boundary of chemistry with biology. This review describes the development of synthetic structures capable of self-replication from studies in molecular recognition. The weak intermolecular forces--hydrogen bonds and aromatic stacking interactions--that characterize interactions of nucleic acid components were designed into synthetic receptors for adenine. Covalent conjugates of these receptors with adenines gave self-complementary structures capable of replication. The new systems feature autocatalysis, sigmoidal product growth and even mutation. General rules for the design of replicating systems are described and these suggest that the evolution of replicating molecules was an inevitable event.  相似文献   

20.
The oxygenases - enzymes which incorporate molecular oxygen directly into organic molecules - are ubiquitous and of high metabolic significance. These enzymes play crucial roles in the degradation of drugs and foreign substances and in the biosynthesis, interconversion and degradation of amino acids, lipids, porphyrins, vitamins and hormones. Thus, they are centrally involved in the mechanisms of cytotoxicity, mutagenicity, carcinogenicity and tissue necrosis. From the standpoint of enzyme technology, the ability of these enzymes to incorporate molecular oxygen into organic substrates efficiently and selectively is highly enticing, since such reactions are poorly accomplished using conventional chemistry. This review focuses on enzymatic epoxidation reactions, one example of the many chemical transformations catalysed by oxygenases. By way of introduction, an overview of the role of enzymatic epoxidation reactions in the metabolism of polycyclic aromatic hydrocarbons, in steroid biosynthesis and interconversion, and in various other pathways is presented. Following this, enzymatic epoxidation of simple olefins is considered in detail, with emphasis on bacterial systems and discussion of both enzymology and reactivity characteristics. Finally, a number of major issues which must be confronted if complex oxygenase systems are to be utilized in enzyme technology application are briefly discussed. Among these are specialized immobilization techniques, cofactor recycling, problems of enzyme stability, and the intriguing possibility of utilizing mechanistic information in the design of non-enzymatic, chemical model systems which mimic oxygenase catalysis.  相似文献   

设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号