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At least 55 records · Page 3Linked to original sources
PubMed1993

Evidence of the specific molecular interactions between naringenin, NODD and nod-promoter.

This paper presents evidence that specific molecular interactions occur between three nod regulation elements: naringenin, NODD and nod-promoter. No such interactions were observed when the concentration of naringenin was less than 0.4 mM. However, remarkable molecular interactions were observed when naringenin was at 4.0 mM. The interactions were highly specific because no such interactions have been observed when naringenin was exposed at various concentrations to other promoter-regulatory protein system (e.g., the protease regulatory system of Xanthomonas campestris, although, like NODD-nod-promoter system, specific binding occurs between the protease promoter and the corresponding regulatory protein).

Endopeptidases↗
PubMedDate not supplied

Selective infection of E. coli as a function of a specific molecular interaction.

Selective infection of phage is when the bacterial infection depends on the specific molecular interaction between an antigen and a phage-displayed protein sequence such as an antibody. Engineering of the normal infection into pathways, directed by a specific protein--protein interaction, has raised several mechanistic questions. Here, we address the type of display and the affinity between the interacting pairs. The deleted phage R408d3 was used for the first time in selective infection and was shown to exhibit a superior performance compared to the VCSM13 phage. Furthermore, the affinity between the interacting pairs also affected the selective infection process and a correlation between affinity and infection efficiency was detected, thus implying that selective infection is the method of choice for selection of rare high-affinity interactions in molecular libraries.

Bacteriophages↗
PubMed2006

Detecting molecular interactions that stabilize native bovine rhodopsin.

Using single-molecule force spectroscopy we probed molecular interactions within native bovine rhodopsin and discovered structural segments of well-defined mechanical stability. Highly conserved residues among G protein-coupled receptors were located at the interior of individual structural segments, suggesting a dual role for these segments in rhodopsin. Firstly, structural segments stabilize secondary structure elements of the native protein, and secondly, they position and hold the highly conserved residues at functionally important environments. Two main classes of force curves were observed. One class corresponded to the unfolding of rhodopsin with the highly conserved Cys110-Cys187 disulfide bond remaining intact and the other class corresponded to the unfolding of the entire rhodopsin polypeptide chain. In the absence of the Cys110-Cys187 bond, the nature of certain molecular interactions within folded rhodopsin was altered. These changes highlight the structural importance of this disulfide bond and may form the basis of dysfunctions associated with its absence.

Animals↗
PubMed2002

Real-time analysis of molecular interaction of retinoid receptors and receptor-interacting protein 140 (RIP140).

Receptor interacting protein 140 (RIP140) is a coregulator for a large number of transcription factors. RIP140 interacts with retinoic acid receptor (RAR) and retinoid X receptor (RXR) with or without ligands. The C-terminal domain of RIP140 (RIP-C') contains a novel sequence (1063-1076, LTKTNPILYYMLQK) and has been shown to interact with RAR and RXR ligand dependently in two-hybrid interaction and pull-down assays. To examine the kinetic characteristics of molecular interaction of RIP-C' with RAR and RXR, a surface plasmon resonance technology (BIAcore) was applied for real-time analyses of this molecular interaction with highly purified proteins. A modified pull-down assay using purified proteins was also conducted to obtain supporting data. The effect of retinoid ligands on this type of interaction was addressed. By using receptor mutants, it was demonstrated that the activation function-2 domain and the ability to form dimers of the receptors are required for an efficient interaction of receptor with RIP140. Finally, with a mutagenesis approach, we determined the effects of specific point mutations on the kinetics of RIP-C' interaction with RAR/RXR.

Adaptor Proteins, Signal Transducing↗
PubMed2001

Molecular interactions with nuclear factor kappaB (NF-kappaB) transcription factors of a PNA-DNA chimera mimicking NF-kappaB binding sites.

The decoy approach against nuclear factor kappaB (NF-kappaB) is a useful tool to alter NF-kappaB dependent gene expression using synthetic oligonucleotides (ODNs) carrying NF-kappaB specific cis-elements. Unfortunately, ODNs are not stable and need to be be extensively modified to be used in vivo or ex vivo. We have previously evaluated the possible use of peptide nucleic acids (PNAs) as decoy molecules. The backbone of PNAs is composed of N-(2-aminoethyl)glycine units, rendering these molecules resistant to both nucleases and proteases. We found that the binding of NF-kappaB transcription factors to PNAs was either very low (binding to PNA-PNA hybrids) or exhibited low stability (binding to PNA-DNA hybrids). The main consideration of the present paper was to determine whether PNA-DNA chimeras mimicking NF-kappaB binding sites are capable of stable interactions with proteins belonging to the NF-kappaB family. Molecular modeling was employed for the design of PNA-DNA chimeras; prediction of molecular interactions between chimeras and NF-kappaB nuclear proteins were investigated by molecular dynamics simulations, and interactions between PNA-DNA chimeras and NF-kappaB proteins were studied by gel shifts. We found significant differences between the structure of duplex NF-kappaB PNA-DNA chimera and duplex NF-kappaB DNA-DNA. However, it was found that these differences do not prevent the duplex PNA-DNA chimera from binding to NF-kappaB transcription factors, being able to suppress the molecular interactions between HIV-1 LTR and p50, p52 and nuclear factors from B-lymphoid cells. Therefore, these results demonstrate that the designed NF-kappaB DNA-PNA chimeras could be used for a decoy approach in gene therapy.

Animals↗
PubMedDate not supplied

Automatic annotation of BIND molecular interactions from three-dimensional structures.

Software to automate the process of extracting molecular interactions from three-dimensional (3D) structures has been developed that records these as Biomolecular Interaction Network Database (BIND) pairwise interaction records. Full annotation of BIND records is provided through a database processing tool called MMDBind, including detailed atom-atom and residue-residue level interaction information. BIND three-dimensional interaction annotation is synthesized by combining information from the Molecular Modeling Database (MMDB), and the HET (heterogen) group dictionary of small molecules in the macromolecular Crystallographic Information Format (mmCIF). Interactions are validated using the Protein Quaternary Structure (PQS) system. A total of 18,166 interactions were removed as being redundant or biologically irrelevant after PQS validation. This first pass MMDBind annotation creates two new divisions of BIND, 3D Biopolymers (BIND-3DBP) comprising 16,737 initial interaction records, and 3D Small Molecules (BIND-3DSM) comprising 48,219 records. Visualization of interacting residues and nucleotides within a macromolecular structure is possible directly from the BIND database owing to added 3D feature annotation within the BIND records that can be conveniently seen using Cn3D ("see-in-3D") after query from the BIND Data Manager. These interaction records provide a further demonstration of the completeness of the BIND data specification and its capabilities as storage and exchange format for all kinds of molecular interactions, including RNA, DNA, protein, and small molecules. Data from the 3DBP and 3DSM sets are available for downloading in Abstract Syntax Notation.1 (ASN.1) or Extensible Markup Language (XML) formats at ftp://ftp.bind.ca/DB/MMDBBind. Data from the 3DBP set is available for interactive query from the BIND Data Manager at www.bind.ca.

Crystallography, X-Ray↗
PubMed2004

Spectroscopic studies of the molecular interactions in n-ethylamines and 2-nitropropane/n-ethylamine mixtures.

New experimental results are reported on molecular interactions in the n-ethylamines and 2-nitropropane (2-NP)/n-ethylamine mixtures studied by Raman spectroscopy under pressure in a diamond anvil cell (0-50 GPa) and, at ambient pressure, by infrared spectroscopy. Modifications of the infrared spectra in 2-NP in presence of triethylamine (TEA) or diethylamine (DEA) have been observed at ambient pressure and interpreted as a specific molecular interaction. High-pressure fluorescence in the vicinity of the liquid-solid phase transition of the 2-NP/DEA and 2-NP/monoethylamine mixtures, is highlighted and discussed.

Ethylamines↗
PubMed2004

Study of molecular interactions between a phospholipidic layer and a pH-sensitive polymer using the Langmuir balance technique.

Molecular interactions between a terminally alkylated pH-sensitive N-isopropylacrylamide copolymer DODA-poly(NIPAM-co-MAA) and a monolayer of distearoylphosphatidylcholine (DSPC) at the air/water interface are investigated using the Langmuir balance technique. The compression isotherms ofthe copolymer monolayer at the air-water interface confirm that the copolymer undergoes a structural transition with a change in pH ranging from an extended coil state at neutral pH to a collapsed globular state at a pH corresponding to the pH of the polymer phase transition. Adsorption kinetics of DODA-poly(NIPAM-co-MAA) in the DSPC monolayer is analyzed using a first-order kinetics model allowing an effective interaction area Ax between DSPC and DODA-poly(NIPAM-co-MAA) molecules to be evaluated. The results clearly indicate that the interaction area increases with a decrease in pH. The results also suggest that the penetration of the DODA-poly(NIPAM-co-MAA) within the phospholipid monolayer is enhanced by a decrease in pH which causes a change in the copolymer structure and an increase in specific attractive interactions between the copolymer and the phospholipid. Therefore, the copolymer can trigger the destabilization or rupture of the phospholipidic layer through a simple variation in its structure associated with a variation in molecular interactions when coupled or inserted within the membrane. This study greatly supports the prospects of the copolymer-functionalized liposomes as stable and tunable carrier systems for in vivo applications in drug delivery.

Acrylamides↗
PubMedDate not supplied

Role of molecular interaction in stability of celecoxib-PVP amorphous systems.

Stabilization of an amorphous solid against devitrification can be achieved using additives that interact specifically with the parent molecule, and restrain it from rearranging into a crystal lattice. The amorphous form of celecoxib (CEL) was stabilized by poly(vinylpyrrolidone) (PVP), both in the solid state and during dissolution. A comprehensive characterization of CEL-PVP binary amorphous systems by thermal, spectroscopic, and computer simulation techniques provided greater insight into the molecular interaction between the two species. PVP antiplasticized the amorphous CEL, thus raising its glass transition temperature (T(g)) and restricting the molecular mobility. The T(g)()mix values for CEL-PVP binary amorphous systems of varying composition showed positive deviation from those predicted through the Gordon-Taylor/ Kelley-Bueche equation, thus indicating a molecular interaction between CEL and PVP. This was further substantiated by shifts observed in DSC melting endotherms of CEL, and FTIR bands for C=O stretching vibrations in PVP for CEL-PVP binary amorphous systems. Computer simulation showed stronger H-bonds between amido protons of CEL and carbonyl O of a monomeric unit of PVP, compared to those observed in pure amorphous CEL. These molecular interactions between CEL and PVP supported the stabilizing action of PVP for the amorphous form of CEL.

Calorimetry, Differential Scanning↗
PubMed2000

Molecular interactions with mercury in the kidney.

Mercury is unique among the heavy metals in that it can exist in several physical and chemical forms, including elemental mercury, which is a liquid at room temperature. All forms of mercury have toxic effects in a number of organs, especially in the kidneys. Within the kidney, the pars recta of the proximal tubule is the most vulnerable segment of the nephron to the toxic effects of mercury. The biological and toxicological activity of mercurous and mercuric ions in the kidney can be defined largely by the molecular interactions that occur at critical nucleophilic sites in and around target cells. Because of the high bonding affinity between mercury and sulfur, there is particular interest in the interactions that occur between mercuric ions and the thiol group(s) of proteins, peptides and amino acids. Molecular interactions with sulfhydryl groups in molecules of albumin, metallothionein, glutathione, and cysteine have been implicated in mechanisms involved in the proximal tubular uptake, accumulation, transport, and toxicity of mercuric ions. In addition, the susceptibility of target cells in the kidneys to the injurious effects of mercury is modified by a number of intracellular and extracellular factors relating to several thiol-containing molecules. These very factors are the theoretical basis for most of the currently employed therapeutic strategies. This review provides an update on the current body of knowledge regarding the molecular interactions that occur between mercury and various thiol-containing molecules with respect to the mechanisms involved in the renal cellular uptake, accumulation, elimination, and toxicity of mercury.

Animals↗
PubMed1989

[Molecular composite resins reinforced with polyaramides (Part 1). Molecular interaction between N-Octylated-Poly-p-Phenylene Terephthalamide (PPTA) as core molecule and PMMA and Polystyrene (PS) as matrices].

Molecular composite PMMA resin (Oct-PPTA-PMMA) can be reinforced with poly-N-octyl-p-phenylene terephthalamide (Oct-PPTA) as rigid core molecule. Compounding 3 wt% of Oct-PPTA to PMMA increased compressive, diametral and bending strength by 10 to 15%. The molecular interaction between Oct-PPTA as the core molecule and PMMA as a polar matrix and polystyrene (PS) as a non-polar matrix was examined with respect to dynamic viscoelasticity. Compounding 3 wt% of Oct-PPTA (Oct-PPTA-PS) to PS decreased compressive, diametral and bending strength by 15 to 30%. The dynamic storage modulus (G') value of Oct-PPTA-PS is lower than G' of PS in the region from rubbery state to viscous flow state. These results reveal a significant effect of the polar groups on the molecular interaction between the core molecule and matrices in the molecular composites compounding Oct-PPTA as core molecule.

Chemical Phenomena↗
PubMed2005

Effects of lipid chain unsaturation and headgroup type on molecular interactions between paclitaxel and phospholipid within model biomembrane.

Molecular interactions between paclitaxel, an anticancer drug, and phospholipids of various chain unsaturations and headgroup types were investigated in the present study by Langmuir film balance and differential scanning calorimetry. Both the lipid monolayer at the air-water interface and the lipid bilayer vesicles (liposomes) were employed as model cell membranes. It was found that, regardless of the difference in molecular structure of the lipid chains and headgroup, the drug can form nonideal, miscible systems with the lipids at the air-water interface over a wide range of paclitaxel mole fractions. The interaction between paclitaxel and phospholipid within the monolayer was dependent on the molecular area of the lipids at the interface and can be explained by intermolecular forces or geometric accommodation. Paclitaxel is more likely to form thermodynamically stable systems with 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine (DPPC) and 1,2-dielaidoyl-sn-glycero-3-phosphocholine (DEPC) than with 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC). Investigation of the drug penetration into the lipid monolayer showed that DPPC and DEPC have higher incorporation abilities for the drug than DPPE and DSPC. A similar trend was also evidenced by DSC investigation with liposomes. While little change of DSC profiles was observed for the DPPE/paclitaxel and DSPC/paclitaxel liposomes, paclitaxel caused noticeable changes in the thermographs of DPPC and DEPC liposomes. Paclitaxel was found to cause broadening of the main phase transition without significant change in the peak melting temperature of the DPPC bilayers, which demonstrates that paclitaxel was localized in the outer hydrophobic cooperative zone of the bilayer, i.e., in the region of the C1-C8 carbon atoms of the acyl chain or binding at the polar headgroup site of the lipids. However, it may penetrate into the deeper hydrophobic zone of the DEPC bilayers. These findings provide useful information for liposomal formulation of anticancer drugs as well as for understanding drug-cell membrane interactions.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2006

Chk2 molecular interaction map and rationale for Chk2 inhibitors.

To organize the rapidly accumulating information on bioregulatory networks related to the histone gamma-H2AX-ATM-Chk2-p53-Mdm2 pathways in concise and unambiguous diagrams, we used the molecular interaction map notation (http://discover.nci.nih.gov/min). Molecular interaction maps are particularly useful for networks that include protein-protein binding and posttranslational modifications (e.g., phosphorylation). Both are important for nearly all of the proteins involved in DNA double-strand break signaling. Visualizing the regulatory circuits underlying cellular signaling may help identify key regulatory reactions and defects that can serve as targets for anticancer drugs.

Antineoplastic Agents↗
PubMed2005

Molecular interaction map of the p53 and Mdm2 logic elements, which control the Off-On switch of p53 in response to DNA damage.

The molecular network that controls responses to genotoxic stress is centered at p53 and Mdm2. Recent findings have shown this network to be more complex than previously envisioned. Using a notation specifically designed for circuit diagram-like representations of bioregulatory networks, we have prepared an updated molecular interaction map of the immediate connections of p53 and Mdm2, which are described as logic elements of the network. We use the map as the basis for a comprehensive review of current concepts of signal processing by these logic elements (an interactive version of the maps-eMIMs can be examined at ). We also used molecular interaction maps to propose a p53 Off-On switch in response to DNA damage.

Apoptosis↗
PubMed2004

Effects of lipid chain length on molecular interactions between paclitaxel and phospholipid within model biomembranes.

Molecular interactions between an anticancer drug, paclitaxel, and phosphatidylcholine (PC) of various chain lengths were investigated in the present work by the Langmuir film balance technique and differential scanning calorimetry (DSC). Both the lipid monolayer at the air-water interface and lipid bilayer vesicles (liposomes) were employed as model biological cell membranes. Measurement and analysis of the surface pressure versus molecular area curves of the mixed monolayers of phospholipids and paclitaxel under various molar ratio showed that phospholipids and paclitaxel formed a nonideal miscible system at the interface. Paclitaxel exerted an area-condensing effect on the lipid monolayer at small molecular surface areas and an area-expanding effect at large molecular areas, which could be explained by the intermolecular forces and geometric accommodation between the two components. Paclitaxel and phospholipids could form thermodynamically stable monolayer systems: the stability increased with the chain length in the order DMPC (C14:0)>DPPC (C16:0)>DSPC (C18:0). Investigation of paclitaxel penetration into the pure lipid monolayer showed that DMPC had a higher ability to incorporate paclitaxel and the critical surface pressure for paclitaxel penetration also increased with the chain length in the order DMPC>DPPC>DSPC. A similar trend was testified by DSC studies on vesicles of the mixed paclitaxel/phospholipids bilayer. Paclitaxel showed the greatest interaction with DMPC while little interaction could be measured in the paclitaxel/DSPC liposomes. Paclitaxel caused broadening of the main phase transition without significant change at the peak melting temperature of the phospholipid bilayers, which demonstrated that paclitaxel was localized in the outer hydrophobic cooperative zone of the bilayer. The interaction between paclitaxel and phospholipid was nonspecific and the dominant factor in this interaction was the van der Waals force or hydrophobic force. As the result of the lower net van der Waals interaction between hydrocarbon chains for the shorter acyl chains, paclitaxel interacted more readily with phospholipids of shorter chain length, which also increased the bilayer intermolecular spacing.

Calorimetry, Differential Scanning↗
PubMed2006

Microparadigms: chains of collective reasoning in publications about molecular interactions.

We analyzed a very large set of molecular interactions that had been derived automatically from biological texts. We found that published statements, regardless of their verity, tend to interfere with interpretation of the subsequent experiments and, therefore, can act as scientific "microparadigms," similar to dominant scientific theories [Kuhn, T. S. (1996) The Structure of Scientific Revolutions (Univ. Chicago Press, Chicago)]. Using statistical tools, we measured the strength of the influence of a single published statement on subsequent interpretations. We call these measured values the momentums of the published statements and treat separately the majority and minority of conflicting statements about the same molecular event. Our results indicate that, when building biological models based on published experimental data, we may have to treat the data as highly dependent-ordered sequences of statements (i.e., chains of collective reasoning) rather than unordered and independent experimental observations. Furthermore, our computations indicate that our data set can be interpreted in two very different ways (two "alternative universes"): one is an "optimists' universe" with a very low incidence of false results (<5%), and another is a "pessimists' universe" with an extraordinarily high rate of false results (>90%). Our computations deem highly unlikely any milder intermediate explanation between these two extremes.

Computer Simulation↗
PubMed2005

Transcriptional activity of Sp1 is regulated by molecular interactions between the zinc finger DNA binding domain and the inhibitory domain with corepressors, and this interaction is modulated by MEK.

Sp1 activates the transcription of many cellular and viral genes with the GC-box in either the proximal promoter or the enhancer. Sp1 is composed of several functional domains, such as the inhibitory domain (ID), two serine/threonine-rich domains, two glutamine-rich domains, three C2H2-type zinc finger DNA binding domains (ZFDBD), and a C-terminal D domain. The ZDDBD is the most highly conserved domain among the Sp-family transcription factors and plays a critical role in GC-box recognition. In this study, we investigated the protein-protein interactions occurring at the Sp1ZFDBD and the Sp1ID, and the molecular mechanisms controlling the interaction. Our results found that Sp1ZFDBD and Sp1ID repressed transcription once they were targeted to the proximal promoter of the pGal4 UAS reporter fusion gene system, suggesting molecular interaction with the repressor molecules. Indeed, mammalian two-hybrid assays, GST fusion protein pull-down assays, and co-immunoprecipitation assays showed that Sp1ZFDBD and Sp1ID are able to interact with corepressor proteins such as SMRT, NcoR, and BCoR. The molecular interactions appear to be regulated by MAP kinase/Erk kinase kinase (MEK). The molecular interactions between Sp1ID and the corepressor might explain the role of Sp1 as a repressor under certain circumstances. The siRNA-induced degradation of the corepressors resulted in an up-regulation of Sp1-dependent transcription. The cellular context of the corepressors and the regulation of molecular interaction between corepressors and Sp1ZFDBD or Sp1ID might be important in controlling Sp1 activity.

Animals↗
PubMed1985

Refined crystal structure of deoxyhemoglobin S. II. Molecular interactions in the crystal.

The refined crystal structure of deoxyhemoglobin S (Padlan, E. A., and Love, W. E. (1985) J. Biol. Chem. 260, 8272-8279) was used to analyze in detail the molecular interactions between hemoglobin tetramers in the crystal. The analysis confirms the close similarity and also the nonequivalence of the molecular interactions involving the two independent tetramers in the asymmetric unit of the crystal. The residue at the site of the hemoglobin S mutation, beta 6, is intimately involved in the lateral contacts between adjacent molecules. The molecular contacts in the crystals of deoxyhemoglobin S, deoxyhemoglobin A, and deoxyhemoglobin F were compared; some contacts involve the same regions of the molecule although the details of the interactions are very different. The effect of introducing an R state tetramer into the deoxyhemoglobin S strands was investigated using the known structure of carbon monoxyhemoglobin A. It was found that substituting a molecule of carbon monoxyhemoglobin A for one of the deoxyhemoglobin S tetramers results in extensive molecular interpenetration.

Carboxyhemoglobin↗