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At least 109 records · Page 6Linked to original sources
PubMed2006

Structural and molecular interactions of CCR5 inhibitors with CCR5.

We have characterized the structural and molecular interactions of CC-chemokine receptor 5 (CCR5) with three CCR5 inhibitors active against R5 human immunodeficiency virus type 1 (HIV-1) including the potent in vitro and in vivo CCR5 inhibitor aplaviroc (AVC). The data obtained with saturation binding assays and structural analyses delineated the key interactions responsible for the binding of CCR5 inhibitors with CCR5 and illustrated that their binding site is located in a predominantly lipophilic pocket in the interface of extracellular loops and within the upper transmembrane (TM) domain of CCR5. Mutations in the CCR5 binding sites of AVC decreased gp120 binding to CCR5 and the susceptibility to HIV-1 infection, although mutations in TM4 and TM5 that also decreased gp120 binding and HIV-1 infectivity had less effects on the binding of CC-chemokines, suggesting that CCR5 inhibition targeting appropriate regions might render the inhibition highly HIV-1-specific while preserving the CC chemokine-CCR5 interactions. The present data delineating residue by residue interactions of CCR5 with CCR5 inhibitors should not only help design more potent and more HIV-1-specific CCR5 inhibitors, but also give new insights into the dynamics of CC-chemokine-CCR5 interactions and the mechanisms of CCR5 involvement in the process of cellular entry of HIV-1.

Animals↗
PubMed2005

HBVPathDB: a database of HBV infection-related molecular interaction network.

AIM: To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. METHODS: The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). RESULTS: We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. CONCLUSION: The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

Databases, Genetic↗
PubMed2005

Mobility moment analysis of molecular interactions by capillary electrophoresis.

A new method for the quantitative evaluation of molecular interactions that are observed in electrophoresis is described. One component taking part in the interaction is labeled with a fluorescent dye and is subjected to capillary zone electrophoresis with fluorescence detection in the presence or absence of an unlabeled interacting component. Fluorescence signals are collected at constant time intervals, and the electropherograms are converted to represent the fluorescence signal against mobility. After baseline subtraction, the first statistical moment of fluorescence signals on the mobility axis is calculated. This moment represents the average mobility of a labeled component. The change in the mobility moment in the presence and absence of the unlabeled component is used to evaluate the degree of saturation of the binding site of a labeled molecule with an unlabeled molecule. Mixtures of fluorescence-labeled protein (Fab' fragment of antibody or concanavalin A) and its unlabeled interacting partner (alpha(1)-antitrypsin or succinylated ovalbumin, respectively) at various concentrations were injected into a bare-silica capillary, and zone electrophoresis was carried out. The change in the mobility moment of the fluorescence-labeled molecules was used to determine the dissociation constants of the complexes. The determined constants are comparable to those obtained by a well-established method, that is, an analysis based on the peak height of the complex. Since the mobility moment analysis is not affected by the total intensity of the signals, it should be advantageous in analyses in which multiple capillaries are used, in which the injection volume and the sensitivity of detection might be more difficult to control at constant values. The mobility moment analysis also has advantages for the analysis of heterogeneous samples, since the identification of peaks is not necessarily required.

Antigen-Antibody Reactions↗
PubMed1999

Loss of molecular interaction between cytochrome c and cardiolipin due to lipid peroxidation.

To explore the molecular mechanism underlying the translocation of cytochrome c from the mitochondrial inner membrane to the cytosol during apoptosis, we analyzed the molecular interaction between cytochrome c and cardiolipin (CL) by (1)H NMR spectroscopy. Bovine heart CL induced a drastic broadening of the linewidth of the downfield signals at 31.4 and 34.2 ppm assigned to the heme methyl group-3 and -8, respectively, of horse heart cytochrome c. In contrast, CL mono- and dihydroperoxides were less active in broadening the signals than CL, and CL trihydroperoxides induced almost no broadening of their linewidth. This finding suggests that the peroxidation of CL induces a release of cytochrome c from mitochondria into the cytosol, which release induces apoptosis in the cells.

Animals↗
PubMed1995

The molecular interaction of sulfonylureas with beta-cell ATP-sensitive K(+)-channels.

The molecular interaction of glimepiride and glibenclamide with the beta-cell sulfonylurea receptor was investigated by kinetic and steady state binding as well as photoaffinity labeling. The novel sulfonylurea, glimepiride, exhibits a significantly higher exchange rate with the sulfonylurea receptor but a 2.5-3 fold lower binding affinity compared to glibenclamide. [3H]Glimepiride was specifically incorporated into a 65-kDa polypeptide under conditions which led to predominant labeling of a 140-kDa protein by [3H]glibenclamide. Labeling of the 140-kDa protein by [3H]glibenclamide was inhibited by unlabeled glimepiride and, vice versa, glibenclamide inhibited labeling of the 65-kDa protein by [3H]glimepiride. The 65-kDa protein was also specifically photolabeled by the sulfonylurea [125I]35623, whereas an 4-azidobenzoyl derivative of glibenclamide, N3-[3H]33055, exclusively labeled a 33-kDa protein. Solubilization of beta-cell tumor membranes led to a shift of specific [3H]glibenclamide-binding from the 140-kDa to the 65-kDa protein, exclusively and to an increased labeling of the 65-kDa protein by [3H]glimepiride. The labeling of a unique protein is in agreement with similar Kd-values for binding to the sulfonylurea receptor measured for both sulfonylureas upon solubilization of beta-cell membranes. Photoaffinity labeling of intact cultured beta-cells led also to labeling of a 140-kDa protein by [3H]glibenclamide and of a 65-kDa protein by [3H]glimepiride. These studies suggest that the beta-cell sulfonylurea receptor consists of at least two protein subunits of M(r) 140,000 and 65,000 which bind sulfonylureas of different structure with different binding affinities and kinetic parameters. Furthermore, the exchange rate of a sulfonylurea determines the insulin releasing activity in vitro more closely than the binding affinity.

ATP-Binding Cassette Transporters↗
PubMed1999

Molecular interactions and kinetic properties of fats.

This article has reviewed the recent work on the molecular interactions and kinetic properties of the polymorphic transformations of the TAGs in the single and mixed states. Progress has recently been made in the molecular-level understanding of the polymorphic transformations of the TAGs. Particularly, the use of the time-resolved X-ray diffraction with Synchrotron radiation (SR-XRD) has provided precise information of the structural changes of the fat crystals at a time scale of 10 sec. Therefore, fruitful information was obtained on the kinetic and molecular aspects of crystallization and mixing processes of the various types of mixed-acid TAGs, which were not obtained with the traditional thermal and structural techniques because of their complicated structural properties. One may anticipate that, although the experimental sites and machine times are limited, the SR-XRD techniques will be more applied to the fat systems involving the following materials and systems; (a) multicomponent natural fats with and without additives of emulsifiers, proteins and carbohydrates, (b) fats in dispersed phases such as oil-in-water (O/W) and water-in-oil (W/O) emulsions, (c) crystallization and transformation processes under external influences of hydrostatic pressure and shear stress [68].

Fats↗
PubMed2006

Fluorescence cross-correlation analyses of the molecular interaction between an Aux/IAA protein, MSG2/IAA19, and protein-protein interaction domains of auxin response factors of arabidopsis expressed in HeLa cells.

Since auxin may elicit numerous developmental responses by the use of a combination of auxin response factors (ARFs) and their Aux/IAA repressors, it is important to determine the interaction between the two protein families in a quantitative manner. We transiently expressed the C-terminal protein-protein interaction domains (CTDs) of Arabidopsis ARFs, MP/ARF5 and NPH4/ARF7, and MSG2/IAA19, fused to fluorescent proteins in HeLa cells, and determined their molecular interactions with fluorescence cross-correlation spectroscopy (FCCS). Almost complete association was found between MSG2 and MP-CTD and between MSG2 and NPH4-CTD. Approximately 20% association was found for MSG2 homodimers, NPH4-CTD homodimers and MP-CTD/NPH4-CTD heterodimers. Homotypic binding of MP-CTD may be weaker than that of MSG2. MSG2 was localized in cytoplasmic compartments in HeLa cells, whereas it was localized in the nuclei in plant cells. The fact that the heterotypic interaction between MSG2 and ARF-CTDs is stronger than each of the homotypic interactions appears to be the molecular basis for tight control of the transcriptional activity of ARFs by auxin. These results also show that FCCS is useful to examine protein-protein interactions especially for transcriptional regulators.

Arabidopsis↗
PubMed2004

Fluorescence correlation spectroscopy: a new tool for quantification of molecular interactions.

Fluorescence correlation spectroscopy (FCS) provides a powerful method to measure molecular dynamics and interactions in a wide variety of experimental systems and environments. In this article we focus on the use of FCS methods to quantify molecular interactions, including the use of diffusion analysis and molecular counting. Both autocorrelation and cross-correlation FCS measurements are discussed.

Microscopy, Fluorescence, Multiphoton↗
PubMed2003

Molecular interaction of connexin 30.3 and connexin 31 suggests a dominant-negative mechanism associated with erythrokeratodermia variabilis.

Connexins are homologous four-transmembrane-domain proteins and major components of gap junctions. We recently identified mutations in either GJB3 or GJB4 genes, encoding respectively connexin 31 (Cx31) or 30.3 (Cx30.3), as causally involved in erythrokeratodermia variabilis (EKV), a mostly autosomal dominant disorder of keratinization. Despite slight differences, phenotypes of EKV Mendes Da Costa (Cx31) and EKV Cram-Mevorah (Cx30.3) show major clinical overlap and both Cx30.3 and Cx31 are expressed in the upper epidermal layers. These similarities suggested to us that Cx30.3 and Cx31 may interact at a molecular level. Indeed, expression of wild-type Cx30.3 in HeLa cell resulted only in minor amounts of protein addressed to the plasma membrane. Mutant Cx30.3 was hardly detectable and disturbed intercellular coupling. In sharp contrast, co-expression of both wild-type proteins led to a gigantic increase of stabilized heteromeric gap junctions. Furthermore, co-expressed wild-type Cx30.3 and Cx31 coprecipitate, which demonstrates a physical interaction. Inhibitor experiments revealed that this interaction begins in the endoplasmic reticulum. These results not only provide new insights into epidermal connexin synthesis and polymerization, but also allow a novel molecular explanation for the similarity of EKV phenotypes.

Cell Line↗
PubMed1996

Characterization of molecular interactions between intercellular adhesion molecule-1 and leukocyte function- associated antigen-1.

The ability of soluble ICAM-1 (sICAM-1) to inhibit ICAM-1/LFA-1 adhesion events has been reported previously by numerous investigators. sICAM-1 has been demonstrated to inhibit various in vitro assays at concentrations ranging from 2 nM to greater than 40 microM. Given the hypothesis that circulating ICAM-1 modulates immune functions, the ability of sICAM-1 to inhibit cellular functions may have significant ramifications. Considering the potential clinical importance of the interaction between ICAM-1 and its receptor, LFA-1, it is necessary to understand this receptor-ligand interaction at a molecular level. In this study, direct binding experiments were utilized to determine the affinity between biotinylated monomeric sICAM-1 and immobilized LFA-1 (approximately 130 nM). Competitive binding experiments with unlabeled sICAM-1 and a truncated form of sICAM-1 (D1D2) yielded similar affinities. The specificity of this interaction was characterized using mAbs directed against sICAM-1 or LFA-1. This assay system was extended to include multimeric species using nonblocking mAbs directed against domains D4 and D5 of sICAM-1. Dimerizing sICAM-1 with a mAb alphaD4 or alphaD5 increased the affinity for immobilized LFA-1 by two orders of magnitude (approximately 4 nM), an effect presumably due to avidity. These results indicate that while the monomeric sICAM-1/LFA-1 interaction may involve only a moderate binding affinity, multimeric ICAM-1 present on a cell surface may bind cell surface-immobilized LFA-1 with very high avidity. These sICAM-1/LFA-1 molecular assays should be useful in defining the efficacy of potential antagonists.

Binding, Competitive↗
PubMed1998

Affinity and kinetic analysis of the molecular interaction of ICAM-1 and leukocyte function-associated antigen-1.

LFA-1 is a member of the beta2 integrin family, and interacts with ICAM-1, a member of the Ig superfamily containing five Ig-like domains. Interaction of LFA-1 with ICAM-1 is important in a number of cellular events, including Ag-specific T cell activation and leukocyte transendothelial migration, which are known to be typically transient and highly regulated. In this study, we have used surface plasmon resonance technology to study the ICAM-1/LFA-1 interaction at the molecular level. A soluble form of LFA-1 (sLFA-1), normally expressed as two noncovalently associated membrane-bound subunits, has been produced, and its interaction with ICAM-1 has been examined. The kinetic analysis of a monomeric sLFA-1 binding to the first two domains of ICAM-1 expressed as a chimeric IgG fusion protein (D1D2-IgG) revealed that sLFA-1 was bound to the D1D2-IgG chimera with a Kd of 500 nM and dissociated with a k(diss) of 0.1 s(-1). Monomeric membrane-bound LFA-1 purified from plasma membranes showed a similar kinetic to sLFA-1. These results suggest that the monovalent interaction between ICAM-1 and LFA-1 has a primarily high affinity and a slow dissociation rate constant as compared with other adhesion molecules, suggesting a potential mechanism for firm adhesion.

Animals↗
PubMedDate not supplied

Virtual screening and scaffold hopping based on GRID molecular interaction fields.

In this study, a set of strategies for structure-based design using GRID molecular interaction fields (MIFs) to derive a pharmacophoric representation of a protein is reported. Thrombin, one of the key enzymes involved in the blood coagulation cascade, was chosen as the model system since abundant published experimental data are available related to both crystal structures and structurally diverse sets of inhibitors. First, a virtual screening methodology was developed either using a pharmacophore representation of the protein based on GRID MIFs or using GRID MIFs from the 3D structure of a set of chosen thrombin inhibitors. The search was done in a 3D multiconformation version of the Available Chemical Directory (ACD) database, which had been spiked with 262 known thrombin inhibitors (multiple conformers available per compound). The model managed to find 80% of the known thrombin inhibitors among the 74,291 conformers in the ACD by only searching 5% of the database; hence, a 15-fold enrichment of the library was achieved. Second, a scaffold hopping methodology was developed using GRID MIFs, giving the scaffold interaction pattern and the shape of the scaffold, together with the distance between the anchor points. The scaffolds reported by Dolle in the Journal of Combinatorial Chemistry summaries (2000 and 2001) and scaffolds built or derived from ligands cocomplexed with the thrombin enzyme were parameterized using a new set of descriptors and saved into a searchable database. The scaffold representation from the database was then compared to a template scaffold (from a thrombin crystal structure), and the thrombin-derived scaffolds included in the database were found among the top solutions. To validate the usefulness of the methodology to replace the template scaffold, the entire molecule was built (scaffold and side chains) and the resulting compounds were docked into the active site of thrombin. The docking solutions showed the same binding pattern as the cocomplexed compound, hence, showing that this method can be a valuable tool for medicinal chemists to select interchangeable core structures (scaffolds) in an easy manner and retaining the binding properties from the original ligand.

Binding Sites↗
PubMed2006

Analysis of the molecular interaction between mannosylated proteins and serum mannan-binding lectins.

The kinetics and specificity of the molecular interaction between proteins modified with varying numbers of mannose residues and isolated rabbit mannan-binding lectin (MBL) were characterized by using surface plasmon resonance spectroscopy (SPR). Mannosylated bovine serum albumin (Man-BSA) with different numbers of mannoses and other mannosylated derivatives of lysozyme (LZM), soybean trypsin inhibitor (STI), superoxide dismutase (SOD) and bovine gamma-immunoglobulin (IgG) were synthesized. Rabbit MBL was isolated by affinity column chromatography and immobilized on the SPR sensor chip via avidin-biotin binding. Binding of Man-BSAs to immobilized rabbit MBL increased with an increase in the number of mannose residues, primarily due to the reduction in dissociation rate. On the other hand, the association rate constant was similar for five mannosylated proteins investigated, whereas the dissociation rate constant differed markedly in spite of the same degree of mannosylation. Specific binding of mannosylated proteins to MBL may depend on the number of mannose residues and their steric configurations.

Animals↗
PubMed2006

IntAct--open source resource for molecular interaction data.

IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The database features over 126,000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from http://www.ebi.ac.uk/intact.

DNA↗
PubMed2006

Collective dynamics of interacting molecular motors.

The collective dynamics of N interacting processive molecular motors are considered theoretically when an external force is applied to the leading motor. We show, using a discrete lattice model, that the force-velocity curves strongly depend on the effective dynamic interactions between motors and differ significantly from those of a simple approach where the motors equally share the force. Moreover, they become essentially independent of the number of motors if N is large enough (N> or approximately 5 for conventional kinesin). We show that a two-state ratchet model has a very similar behavior to that of the coarse-grained lattice model with effective interactions. The general picture is unaffected by motor attachment and detachment events.

Computer Simulation↗
PubMedDate not supplied

Kinetic determinations of molecular interactions using Biacore--minimum data requirements for efficient experimental design.

Reliable kinetic estimates can be obtained from significantly less data than is commonly used today, particularly in the characterization of 1:1 interactions involving low molecular weight compounds and proteins. We have designed a rational and cost-effective strategy to determine kinetic constants using Biacore's surface plasmon resonance-based biosensors and show that the number of measurements necessary for accurate kinetic determinations can be greatly reduced, increasing sample throughput and saving sample material. Simulated and measured data for a range of possible 1:1 interactants were studied to find the minimum requirements of a data set for kinetic analysis. The results showed that kinetic constants in the region 10(4) < k(a) < 10(7) M(-1) s(-1) (association) and 10(-4) < k(d) < 10(-1) s(-1) (dissociation) could easily be determined in a 1:1 interaction model. Owing to the information-dense nature of Biacore data, only two sample concentrations were necessary to reliably determine the kinetics. A standard sample concentration series consisting of 10-fold dilutions between approximately 10 microM and approximately 1 nM consistently provided at least two concentrations with sufficient information about the interaction in this region. Determinations of the constants became increasingly unreliable outside this region. If the rate constants prove to be outside the specified region or the data fits poorly to the 1:1-MTL model, more experiments are required. General recommendations for the design of a cost-effective assay to deliver reliable kinetic measurements are provided.

Biosensing Techniques↗
PubMed2002

Molecular interaction and synergistic activation of a promoter by Six, Eya, and Dach proteins mediated through CREB binding protein.

Drosophila sine oculis, eyes absent, and dachshund are essential for compound eye formation and form a gene network with direct protein interaction and genetic regulation. The vertebrate homologues of these genes, Six, Eya, and Dach, also form a similar genetic network during muscle formation. To elucidate the molecular mechanism underlying the network among Six, Eya, and Dach, we examined the molecular interactions among the encoded proteins. Eya interacted directly with Six but never with Dach. Dach transactivated a multimerized GAL4 reporter gene by coproduction of GAL4-Eya fusion proteins. Transactivation by Eya and Dach was repressed by overexpression of VP16 or E1A but not by E1A mutation, which is defective for CREB binding protein (CBP) binding. Recruitment of CBP to the immobilized chromatin DNA template was dependent on FLAG-Dach and GAL4-Eya3. These results indicate that CBP is a mediator of the interaction between Eya and Dach. Contrary to our expectations, Dach binds to chromatin DNA by itself, not being tethered by GAL4-Eya3. Dach also binds to naked DNA with lower affinity. The conserved DD1 domain is responsible for binding to DNA. Transactivation was also observed by coproduction of GAL4-Six, Eya, and Dach, indicating that Eya and Dach synergy is relevant when Eya is tethered to DNA through Six protein. Our results demonstrated that synergy is mediated through direct interaction of Six-Eya and through the interaction of Eya-Dach with CBP and explain the molecular basis for the genetic interactions among Six, Eya, and Dach. This work provides fundamental information on the role and the mechanism of action of this gene cassette in tissue differentiation and organogenesis.

3T3 Cells↗