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PubMed2006

A network analysis of changes in molecular interactions in cellular signaling.

Multiprotein complexes play an essential role in the propagation and integration of cellular signals. However, systems level analyses of signaling-dependent changes in the pattern of molecular interactions are still missing. Signaling in T-lymphocytes is one prominent example in which multiprotein complexes orchestrate signal transduction. We implemented peptide microarrays comprising a set of interaction motifs of signaling proteins for network-based analyses of signaling-dependent changes in molecular interactions. Lysates of resting or stimulated cells were incubated on these arrays, and the binding of signaling proteins was detected by immunofluorescence. Signaling-dependent complex formation led to changes of signals on the microarrays in two ways. 1) Masking of a binding site of a signaling protein for a peptide on the array resulted in a signal decrease. 2) Interaction of a protein with a second protein, which in turn binds to a peptide on the array, resulted in a signal increase for the first protein. Dissipation of complexes led to the reverse changes. Competition with peptides corresponding to interaction motifs provided detailed information on the architecture of complexes; lack of individual signaling proteins revealed the functional interdependence of interactions in the network. We show that complex formation through phosphorylation of the scaffolding protein LAT (linker for activation of T-cells) acted as a signal amplifier. PLCgamma1 deficiency increased the resting state levels of LAT-dependent complexes and augmented the recruitment of the phosphatase SHPTP2 into complexes. For the analysis of signaling networks, the parallel detection of changes in interactions enabled the identification of functional interdependencies with minimum a priori knowledge.

Adaptor Proteins, Signal Transducing↗

PubMed1998

The emergence of flow cytometry for sensitive, real-time measurements of molecular interactions.

The analysis of macromolecular interactions is an essential element of biomedical research. Flow cytometry is uniquely capable of making sensitive and quantitative measurements of molecular interactions. These measurements can be made in real time with subsecond kinetic resolution using purified biomolecules or living cells. Combined with automated sample handling, these features make flow cytometry a versatile and robust technology for the analysis of molecular interactions.

Antigens, Surface↗

PubMed2003

A Bayesian molecular interaction library.

We describe a library of molecular fragments designed to model and predict non-bonded interactions between atoms. We apply the Bayesian approach, whereby prior knowledge and uncertainty of the mathematical model are incorporated into the estimated model and its parameters. The molecular interaction data are strengthened by narrowing the atom classification to 14 atom types, focusing on independent molecular contacts that lie within a short cutoff distance, and symmetrizing the interaction data for the molecular fragments. Furthermore, the location of atoms in contact with a molecular fragment are modeled by Gaussian mixture densities whose maximum a posteriori estimates are obtained by applying a version of the expectation-maximization algorithm that incorporates hyperparameters for the components of the Gaussian mixtures. A routine is introduced providing the hyperparameters and the initial values of the parameters of the Gaussian mixture densities. A model selection criterion, based on the concept of a 'minimum message length' is used to automatically select the optimal complexity of a mixture model and the most suitable orientation of a reference frame for a fragment in a coordinate system. The type of atom interacting with a molecular fragment is predicted by values of the posterior probability function and the accuracy of these predictions is evaluated by comparing the predicted atom type with the actual atom type seen in crystal structures. The fact that an atom will simultaneously interact with several molecular fragments forming a cohesive network of interactions is exploited by introducing two strategies that combine the predictions of atom types given by multiple fragments. The accuracy of these combined predictions is compared with those based on an individual fragment. Exhaustive validation analyses and qualitative examples (e.g., the ligand-binding domain of glutamate receptors) demonstrate that these improvements lead to effective modeling and prediction of molecular interactions.

Algorithms↗

PubMed2004

Investigation of molecular interactions between paclitaxel and DPPC by Langmuir film balance and differential scanning calorimetry.

Molecular interactions between paclitaxel and dipalmitoylphosphatidyl choline (DPPC) were investigated by Langmuir film balance and differential scanning calorimetry (DSC). Both the lipid monolayer at the air-water interface and that in the lipid bilayer vesicles (liposomes) were employed as model cell membranes. Thermodynamic and kinetic analyses of the DPPC/pacltaxel monolayer system and the paclitaxel penetration into the DPPC monolayer showed that DPPC and paclitaxel can form a nonideal miscible system in the lipid monolayer over a wide range of the DPPC/paclitaxel molar ratios. Paclitaxel exerts an area-condensing effect on the DPPC monolayer at small molecular areas and an area-expanding effect at large molecular areas on the pi-A behavior of the DPPC monolayer, which can be explained by the intermolecular forces and geometric accommodation between paclitaxel and DPPC. Based on a calculation of the excess free energy of the mixed monolayer system, the most stable state of the system occurs at the monolayer composition of 5% paclitaxel. Penetration kinetics showed that the paclitaxel penetration into the DPPC monolayer increases with increasing the drug concentration in the subphase, but there is a limit of approximately 500 ng/mL. Any further increase in paclitaxel concentration had no additional significant effects on the drug penetration. Differential scanning calorimetry showed that paclitaxel caused broadening of the main phase transition. There was no significant change in the peak melting temperature of the DPPC bilayers, which demonstrated that paclitaxel was localized in the outer hydrophobic cooperative zone of the bilayer.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1992

[Molecular interaction in pharmaceutical solution, solubilization, partition, and stability of drugs].

The pharmaceutical studies carried out by the author during 40 years were reviewed from the viewpoint of molecular interaction. Included subjects are: electrostatic interaction between drug ions, ion pair formation and its partition to organic phase, drug solubilization by adjuvants, partition of drugs between aqueous and micellar phases, cyclodextrin inclusions, human serum albumin binding and drug stability related to the esterase-like activity of the albumin, and oral liposome preparation of vitamin K1. The drug stabilities related to those molecular interactions were emphasized.

Drug Stability↗

PubMed1978

Molecular interaction between E-prostaglandins and selected polymers and its potential utilization in oral dosage form design.

Coacervate formation was observed between some E-prostaglandins and povidone in acetonitrile. This molecular interaction was studied using differential scanning calorimetry, IR spectrophotometry, and light microscopy. The structural requirements for coacervate formation between E-prostaglandins and povidone were investigated. Possible utilization of this molecular interaction in the development of E-prostaglandin formulations was explored. The dissolution rate of some insoluble E-prostaglandin esters increased when they were coprecipitated with povidone and polyethylene glycol. For example, the p-hydroxybenzaldehyde semicarbazone ester of 16,16-dimethyldinoprostone dissolved about 200 times faster as a povidone coprecipitate than did the control mixture. Enhancement of the dissolution rate was observed for the povidone coprecipitates of dinoprostone and its p-acetylphenyl and beta-naphthyl exters but not for the p-phenylphenyl ester. Fast dissolving dispersions of the E-prostaglandin esters also could be prepared with the water-insoluble cross-linked polyvinylpyrrolidone. This type of dispersion was nonglassy and easily dispersible in water. Thus, it might have certain advantages over the classical soluble povidone coprecipitates in terms of ease of handling. The degree of enhancement in dissolution of dispersions of cross-linked polyvinylpyrrolidone and E-prostaglandin esters is apparently dependent on the structure of the esters. The potential dissolution enhancement may be related to the strength of the interaction between the macromolecule and the esters, as indicated by the qualitative relationship between the extent of adsorption of the prostaglandins to cross-linked polyvinylpyrrolidone and the dissolution rate enhancement.

Administration, Oral↗

PubMedDate not supplied

Improvement in ductility of chitosan through blending and copolymerization with PEG: FTIR investigation of molecular interactions.

Chitosan is an important biomaterial used widely in medical applications. One of the key concerns about its use is the fragile nature of chitosan films. By comparing the component molecular interactions using FTIR, this study attempts to understand how the ductility of chitosan can be improved by blending and copolymerizing with poly(ethylene glycol) (PEG). An improvement in ductility was obtained for all compositions of blend as manifested by a decrease in modulus and an increase in strain at break. For comparable PEG composition (approximately 30%), the properties of the solution-cast blend were better than those of the grafted copolymer. Therefore, blending may be a more efficient way to improve ductility of chitosan. FTIR characterization of the materials revealed subtle decreases in molecular interactions upon annealing the partially miscible blend. These may not be apparent in DSC or X-ray diffraction, yet they play a key role in the mechanical behavior. It appears that in the case of the graft copolymer the improvement in the properties comes from suppression of the crystallinity of each component and not from component interactions. On the other hand, in the blend, the improvement appears to come predominantly from the "well-dispersed", "kinetically trapped" phase morphology and from the intermolecular interactions. Therefore, annealing the blend leads to decreased intermolecular interactions, phase coarsening, and deterioration in properties.

Binding Sites↗

PubMed1988

Molecular interaction of bovine kininogen and its derivatives with papain.

The molecular interaction of bovine kininogen and its derivatives with papain was investigated. High-molecular-weight kininogen (HMWK) or low-molecular-weight kininogen (LMWK) and inactive papain treated with N-[N-(L-3-trans-carboxyoxiran-2-carbonyl)-L-leucyl]agmatine (E-64) formed, respectively, a complex, which was dissociable on sodium dodecyl sulfate polyacrylamide-gel electrophoresis (SDS-PAGE). The densitometric determination of the bands separated on SDS-PAGE and amino acid analysis of the samples extracted from the electrophoresis gel revealed that the complex between kininogen and papain is formed in a molar ratio of one to one. Moreover, analysis of the inhibition of the caseinolytic activity of papain by these kininogens indicated that HMWK, LMWK, and kinin-free derivatives obtained from both kininogens inhibit active papain with a stoichiometry of 1:1. On the other hand, the papain activity was inhibited by two kinds of cyanogen bromide fragments isolated from the heavy chain of HMWK. These two fragments with Ki values of 38 and 0.64 nM corresponded, respectively, to residue Nos. 47 to 243 and Nos. 244-360 of the HMWK heavy chain. These results suggest that in the intact HMWK and LMWK, one of the two potential reactive sites interacts with papain to form a complex and that the other reactive site becomes active only after separation of the two sites.

Amino Acids↗

PubMed2001

Identification of the molecular interaction site of amyloid beta peptide by using a fluorescence assay.

Beta-amyloid peptides (Abeta) are the main protein components of neuritic plaques and are important in the pathogenesis of Alzheimer's disease. It is reported that Abeta itself is not toxic; however, it becomes toxic to neuronal cells once it has aggregated into amyloid fibrils by peptide-peptide interactions. In this study, to specify the molecular mechanism of aggregation, a novel fluorescence assay was designed. For this purpose, possible partial peptides (38 types of 5-mer) were synthesized on solid-phase. The molecular interactions were examined by a fluorescence probe possessing Lys-Leu-Val-Phe-Phe (KLVFF) as a molecular recognition site. KLVFF is known to be a minimum sequence for formation of the Abeta aggregate. A specific interaction was observed between labeled and immobilized KLVFF. It suggests that the aggregation of Abeta was controlled by the recognition of KLVFF itself by hydrophobic and electrostatic interactions.

Alzheimer Disease↗

PubMed1988

Molecular interactions between sphingomyelin and phosphatidylcholine in phospholipid vesicles.

The molecular interactions between DPPC and sphingomyelin have been examined using differential scanning calorimetry and Fourier transform infrared spectroscopy (FT-IR). It has been observed using DSC that the mixtures of DPPC and sphingomyelin show a single peak, which indicates that they are very miscible. It has been shown, by means of FT-IR, that the incorporation of sphingomyelin into DPPC does not modify the gauche/all-trans ratio at temperatures either above or below that of the phase transition. However, the librational motion of the fatty acyl chains was affected, although only above the phase transition. Mixing sphingomyelin and DPPC induced a conformational change in the polar region of DPPC, as deduced from the changes observed in the frequencies of the sn-1 and sn-2 C = O groups of DPPC with relation to pure DPPC and also in the polar region of sphingomyelin as deduced from the change in the frequency of the amide band. The phosphate group of sphingomyelin was observed to participate in hydrogen bonds between the molecules of sphingomyelin and, possibly, DPPC. Some possibilities of the interaction between the molecules of DPPC and sphingomyelin are discussed.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2004

Use of magnetic nanoparticles as nanosensors to probe for molecular interactions.

Biocompatible magnetic nanosensors have been designed to detect molecular interactions in biological media. Upon target binding, these nanosensors cause changes in the spin-spin relaxation times of neighboring water molecules, which can be detected by magnetic resonance (NMR/MRI) techniques. These magnetic nanosensors have been designed to detect specific mRNA, proteins, enzymatic activity, and pathogens (e.g., virus) with sensitivity in the low femtomole range (0.5-30 fmol).

Biocompatible Materials↗

PubMed2005

Lewis acidity/basicity of pi-electron systems: theoretical study of a molecular interaction between a pi system and a Lewis acid/base.

Molecular interactions between pi systems having different pi-electron character (benzene, hexafluorobenzene, and borazine), and a Lewis acid/base (borane and ammonia) were theoretically studied. An attractive interaction between benzene, the electron-rich pi system, and borane was observed. On the other hand, repulsive interactions between benzene and ammonia was observed when the lone pair of nitrogen points toward the benzene ring. In contrast, an attractive interaction between hexafluorobenzene, an electron-deficient pi system, and ammonia was observed. Unexpectedly, a weak attractive interaction between hexafluorobenzene and borane was also observed. Borazine shows an interaction both to borane and ammonia. The attraction between the nitrogen atom of borazine and borane was larger than that between the boron atom of borazine and ammonia.

Journal Article↗

PubMed2004

Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks.

Molecular interaction maps (MIMs) use a clear, accurate, and versatile graphical language to depict complex biological processes. Here, we discuss the main features of the MIM language and its potential uses. MIMs can be used as database resources and simulation guides, and can serve to generate new hypotheses regarding the roles of specific molecules in the bioregulatory networks that control progression through the cell cycle, differentiation, and cell death.

Animals↗

PubMed2005

Targeting chk2 kinase: molecular interaction maps and therapeutic rationale.

Most anticancer drugs presently used clinically target genomic DNA. The selectivity of these anticancer drugs for tumor tissues is probably due to tumor-specific defects suppressing cell cycle checkpoints and DNA repair, and enhancing apoptotic response in the tumor. We will review the molecular interactions within the ATM-Chk2 pathway implicating the DNA damage sensor kinases (ATM, ATR and DNA-PK), the adaptor BRCT proteins (Nbs1, Brca1, 53BP1, MDC1) and the effector kinases (Chk2, Chk1, Plk3, JNK, p38). The molecular interaction map convention (MIM) will be used for presenting this molecular network (http://discover.nci.nih.gov/mim/). A characteristic of the ATM-Chk2 pathway is its redundancy. First, ATM and Chk2 phosphorylate common substrates including p53, E2F1, BRCA1, and Chk2 itself, which suggests that Chk2 (also known as CHECK2, Cds1 in fission yeast, and Dmchk2 or Dmnk or Loki in the fruit fly) acts as a relay for ATM and/or as a salvage pathway when ATM is inactivated. Secondly, redundancy is apparent for the substrates, which can be phosphorylated/activated at similar residues by Chk2, Chk1, and the polo kinases (Plk's). Functionally, Chk2 can activate both apoptosis (via p53, E2F1 and PML) and cell cycle checkpoint (via Cdc25A and Cdc25C, p53, and BRCA1). We will review the short list of published Chk2 inhibitors. We will also propose a novel paradigm for screening interfacial inhibitors of Chk2. Chk2 inhibitors might be used to enhance the tumor selectivity of DNA targeted agents in p53-deficient tumors, and for the treatment of tumors whose growth depends on enhanced Chk2 activity.

Animals↗

PubMed2005

Peptide microarrays for the detection of molecular interactions in cellular signal transduction.

The formation of protein complexes is a hallmark of cellular signal transduction. Here, we show that peptide microarrays provide a robust and quantitative means to detect signalling-dependent changes of molecular interactions. Recruitment of a protein into a complex upon stimulation of a cell leads to the masking of an otherwise exposed binding site. In cell lysates this masking can be detected by reduced binding to a microarray carrying a peptide that corresponds to the binding motif of the respective interaction domain. The method is exemplified for the lymphocyte-specific tyrosine kinase 70 kDa zeta-associated protein binding to a bis-phosphotyrosine-motif of the activated T-cell receptor via its tandem SH2 domain. Compared to established techniques, the method provides a significant shortcut to the detection of molecular interactions.

Animals↗

PubMed2002

Magnetic relaxation switches capable of sensing molecular interactions.

Highly sensitive, efficient, and high-throughput biosensors are required for genomic and proteomic data acquisition in complex biological samples and potentially for in vivo applications. To facilitate these studies, we have developed biocompatible magnetic nanosensors that act as magnetic relaxation switches (MRS) to detect molecular interactions in the reversible self-assembly of disperse magnetic particles into stable nanoassemblies. Using four different types of molecular interactions (DNA-DNA, protein-protein, protein-small molecule, and enzyme reactions) as model systems, we show that the MRS technology can be used to detect these interactions with high efficiency and sensitivity using magnetic relaxation measurements including magnetic resonance imaging (MRI). Furthermore, the magnetic changes are detectable in turbid media and in whole-cell lysates without protein purification. The developed magnetic nanosensors can be used in a variety of biological applications such as in homogeneous assays, as reagents in miniaturized microfluidic systems, as affinity ligands for rapid and high-throughput magnetic readouts of arrays, as probes for magnetic force microscopy, and potentially for in vivo imaging.

Base Sequence↗

PubMed2004

[The molecular interaction between P53 and telomeric repeat binding protein 1 in vitro].

OBJECTIVE: Cellular proliferate inhibition, senescence or apoptosis are induced by telomere shortening through the activation of P53 pathway, but so far, little is known of the mechanism. This study aimed to clarify the molecular regulation of P53 through telomere pathway by the investigation of molecular interaction between P53 and the main telomere associated protein telomeric repeat binding protein 1(TRBP1) in vitro. METHODS: Glutathione S-transferase (GST) alone and 4 different human P53-GST fusion proteins were expressed in E.coli. and purified through glutathione Sepharose (TM)4B by affinity chromatography, P53s were wild type P53 (1-393), N terminal truncated form P53 2C (95-393), C terminal truncated form P53 N5 (2-293) and single amino acid mutant P53 R175H (175 arginine to histidine). Glutathione Sepharose (TM)4B, purified GST alone and P53 fusions were mixed with human breast cancer cell line MCF-7 cellular protein extracts through in vitro binding assay-pull down, the molecular interaction between P53 and TRBP1 were detected by Western blot. RESULTS: SDS-PAGE and Coomassie brilliant blue staining showed that the molecular weights of all the purified proteins were as expected and purities were over 90%. Western blot of TRBP1 showed that both wild type P53 and P53 R175H could bind to TRBP1 of MCF-7 cells, and their binding capacities are similar, whereas GST alone and Glutathione Sepharose(TM) 4B beads could not. Compared with both of them, the interaction between P53 2C and TRBP1 enhanced dramatically, but between P53 N5 and TRBP1 reduced significantly. CONCLUSION: P53 can interact with TRBP1 directly and in vitro, C terminus of P53 (293-393) is the structural domain of their interaction. This C terminus domain dependent interaction between P53 and TRBP1 may be related to the cellular activities induced by telomere dynamic changing.

Adenocarcinoma↗

PubMed2006

Depicting combinatorial complexity with the molecular interaction map notation.

To help us understand how bioregulatory networks operate, we need a standard notation for diagrams analogous to electronic circuit diagrams. Such diagrams must surmount the difficulties posed by complex patterns of protein modifications and multiprotein complexes. To meet that challenge, we have designed the molecular interaction map (MIM) notation (http://discover.nci.nih.gov/mim/). Here we show the advantages of the MIM notation for three important types of diagrams: (1) explicit diagrams that define specific pathway models for computer simulation; (2) heuristic maps that organize the available information about molecular interactions and encompass the possible processes or pathways; and (3) diagrams of combinatorially complex models. We focus on signaling from the epidermal growth factor receptor family (EGFR, ErbB), a network that reflects the major challenges of representing in a compact manner the combinatorial complexity of multimolecular complexes. By comparing MIMs with other diagrams of this network that have recently been published, we show the utility of the MIM notation. These comparisons may help cell and systems biologists adopt a graphical language that is unambiguous and generally understood.

Combinatorial Chemistry Techniques↗