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Biomedical subjects

Milan Mrksich

Publications and source records attributed to Milan Mrksich.

At least 37 records · Page 2Linked to original sources
PubMed2004

Peptide arrays: towards routine implementation.

Peptide arrays have attracted wide interest as tools for discovering biochemical interactions. Because many protein binding and enzyme activities are directed towards peptides, the preparation of arrays having hundreds to thousands of immobilized peptides offers an unprecedented opportunity for identifying interactions of proteins. This short opinion reviews recent progress in the preparation of peptide arrays and their use in the characterization of biomolecular interactions and the discovery of new reagents for biological researches. This body of work establishes the feasibility of this technology and suggests that it will find much wider use in research groups.

Biotechnology↗
PubMed2004

Discovery of a small molecule that inhibits the interaction of anthrax edema factor with its cellular activator, calmodulin.

The catalytic efficiency of adenylyl cyclase activity of edema factor (EF) from Bacillus anthracis is enhanced by approximately 1000-fold upon its binding to mammalian protein calmodulin (CaM). A tandem cell-based and protein binding-based screen of a 10,000 member library identified a molecule that inhibits the EF-CaM interaction and therefore the adenylyl cyclase activity. A combination of fluorescence spectroscopy and photolabeling studies showed that the molecule targets the CaM binding region of EF. A series of related compounds were synthesized and evaluated to identify one compound, 4-[4-(4-nitrophenyl)-thiazolylamino]-benzenesulfonamide, that maintained activity against EF but showed minimal toxicity to two cultured cell lines. This compound represents an important reagent to study the role of EF in anthrax pathology and may represent a drug lead against anthrax infection.

Adenylyl Cyclase Inhibitors↗
PubMed2003

Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough.

Edema factor (EF) and CyaA are adenylyl cyclase toxins secreted by pathogenic bacteria that cause anthrax and whooping cough, respectively. Using the structure of the catalytic site of EF, we screened a data base of commercially available, small molecular weight chemicals for those that could specifically inhibit adenylyl cyclase activity of EF. From 24 compounds tested, we have identified one quinazoline compound, ethyl 5-aminopyrazolo[1,5-a]quinazoline-3-carboxylate, that specifically inhibits adenylyl cyclase activity of EF and CyaA with approximately 20 microm Ki. This compound neither affects the activity of host resident adenylyl cyclases type I, II, and V nor exhibits promiscuous inhibition. The compound is a competitive inhibitor, consistent with the prediction that it binds to the adenine portion of the ATP binding site on EF. EF is activated by the host calcium sensor, calmodulin. Surface plasmon resonance spectroscopic analysis shows that this compound does not affect the binding of calmodulin to EF. This compound is dissimilar from a previously described, non-nucleoside inhibitor of host adenylyl cyclase. It may serve as a lead to design antitoxins to address the role of adenylyl cyclase toxins in bacterial pathogenesis and to fight against anthrax and whooping cough.

Adenylate Cyclase Toxin↗
PubMed2003

Electrochemical desorption of self-assembled monolayers noninvasively releases patterned cells from geometrical confinements.

This report describes a method to pattern mammalian cells using self-assembled monolayers (SAMs), and then to use electrochemical desorption of these monolayers to release cells from their patterns. This method uses an oligo(ethyleneglycol)-terminated SAM to prevent,-and a methyl-terminated SAM to allow-adsorption of proteins and attachment of bovine capillary endothelial cells. Electrochemical removal of the oligo(ethyleneglycol)-terminated SAM allowed proteins to adsorb onto areas that had been previously inert and enabled cells to migrate into these areas. This straightforward technique is useful in bioassays for drug screening and for fundamental studies in cell biology.

Animals↗
PubMed2002

Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins.

Edema factor (EF) and CyaA are calmodulin (CaM)-activated adenylyl cyclase exotoxins involved in the pathogenesis of anthrax and whooping cough, respectively. Using spectroscopic, enzyme kinetic and surface plasmon resonance spectroscopy analyses, we show that low Ca(2+) concentrations increase the affinity of CaM for EF and CyaA causing their activation, but higher Ca(2+) concentrations directly inhibit catalysis. Both events occur in a physiologically relevant range of Ca(2+) concentrations. Despite the similarity in Ca(2+) sensitivity, EF and CyaA have substantial differences in CaM binding and activation. CyaA has 100-fold higher affinity for CaM than EF. CaM has N- and C-terminal globular domains, each binding two Ca(2+) ions. CyaA can be fully activated by CaM mutants with one defective C-terminal Ca(2+)-binding site or by either terminal domain of CaM while EF cannot. EF consists of a catalytic core and a helical domain, and both are required for CaM activation of EF. Mutations that decrease the interaction of the helical domain with the catalytic core create an enzyme with higher sensitivity to Ca(2+)-CaM activation. However, CyaA is fully activated by CaM without the domain corresponding to the helical domain of EF.

Adenylyl Cyclases↗
PubMed2002

Selective immobilization of proteins to self-assembled monolayers presenting active site-directed capture ligands.

This paper describes a method for the selective and covalent immobilization of proteins to surfaces with control over the density and orientation of the protein. The strategy is based on binding of the serine esterase cutinase to a self-assembled monolayer presenting a phosphonate ligand and the subsequent displacement reaction that covalently binds the ligand to the enzyme active site. Surface plasmon resonance (SPR) spectroscopy showed that cutinase binds irreversibly to a monolayer presenting the capture ligand at a density of 1% mixed among tri(ethylene glycol) groups. The covalent immobilization is specific for cutinase, and the glycol-terminated monolayer effectively prevents unwanted nonspecific adsorption of proteins. To demonstrate that the method could be used to immobilize proteins of interest, a cutinase-calmodulin fusion protein was constructed and immobilized to the monolayer. SPR showed that calcineurin selectively associated with the immobilized calmodulin. This capture ligand immobilization method combines the advantages that the immobilization reaction is highly selective for the intended protein, the tether is covalent and, hence, stable, and the method avoids the need for synthetic modification and rigorous purification of proteins before immobilization. These characteristics make the method well suited to a range of applications and, in particular, for constructing protein microarrays.

Binding Sites↗
PubMed2002

Protein nanoarrays generated by dip-pen nanolithography.

Dip-pen nanolithography was used to construct arrays of proteins with 100- to 350-nanometer features. These nanoarrays exhibit almost no detectable nonspecific binding of proteins to their passivated portions even in complex mixtures of proteins, and therefore provide the opportunity to study a variety of surface-mediated biological recognition processes. For example, reactions involving the protein features and antigens in complex solutions can be screened easily by atomic force microscopy. As further proof-of-concept, these arrays were used to study cellular adhesion at the submicrometer scale.

3T3 Cells↗
PubMed2002

Dependence of the rate of an interfacial Diels-Alder reaction on the steric environment of the immobilized dienophile: an example of enthalpy-entropy compensation.

This paper describes a physical organic study of the relationship between the rate for an interfacial Diels-Alder reaction and the steric environment around the reacting molecules. The study used as a model reaction the cycloaddition of cyclopentadiene with a self-assembled monolayer (SAM) presenting benzoquinone groups surrounded by hydroxyl-terminated alkanethiolates. The accessibility of the quinone was varied by preparing monolayers from hydroquinone-terminated alkanethiols of different lengths [HS(CH(2))(n)-HQ, n = 6-14] and a hydroxyl-terminated alkanethiol [HS(CH(2))(11)-OH] of constant length. Cyclic voltammetry was used to measure the rate of the reaction by monitoring the decay of the redox-active quinone. The second-order rate constant showed a modest change as the position of quinone was varied relative to the hydroxyl groups of the monolayer. For monolayers wherein the quinone groups were extended from the interface, the rate constants oscillated near 0.20 M(-1) s(-1) with an even-odd dependence on the length of the alkanethiol. For monolayers that positioned the quinone groups below the surrounding hydroxyl groups, the rate constants decreased by approximately 8-fold. Examination of the activation parameters revealed that the quinone groups that were positioned below the interface (and in a crowded environment) reacted with an enthalpy of activation that was 4 kcal/mol greater than did the quinones that were accessible at the interface. The reaction of the buried quinone, however, proceeded with an entropy of activation that was more favorable by 13 eu, and therefore with a similar free energy of activation. The combination of SAMs for preparing model interfaces and cyclic voltammetry for measuring rates provides a new opportunity for physical organic studies of interfacial reactions.

Journal Article↗
PubMed2002

Towards quantitative assays with peptide chips: a surface engineering approach.

The development of peptide and protein microarrays has created enormous opportunities in biomedical research. Current chip-based assays are well suited for identifying candidate protein or enzyme activities but still require conventional solution phase experiments to validate hits. Here, three surface-engineering strategies for microarray design are described and are illustrated in the development of a peptide chip for the quantitative analysis of kinase activity on solid support. These strategies promise to widen the application of microarrays by permitting the evaluation of hits in a chip-based format.

Amino Acid Sequence↗
PubMed2002

Carbohydrate arrays for the evaluation of protein binding and enzymatic modification.

This paper reports a chemical strategy for preparing carbohydrate arrays and utilizes these arrays for the characterization of carbohydrate-protein interactions. Carbohydrate chips were prepared by the Diels-Alder-mediated immobilization of carbohydrate-cyclopentadiene conjugates to self-assembled monolayers that present benzoquinone and penta(ethylene glycol) groups. Surface plasmon resonance spectroscopy showed that lectins bound specifically to immobilized carbohydrates and that the glycol groups prevented nonspecific protein adsorption. Carbohydrate arrays presenting ten monosaccharides were then evaluated by profiling the binding specificities of several lectins. These arrays were also used to determine the inhibitory concentrations of soluble carbohydrates for lectins and to characterize the substrate specificity of beta-1,4-galactosyltransferase. Finally, a strategy for preparing arrays with carbohydrates generated on solid phase is shown. This surface engineering strategy will permit the preparation and evaluation of carbohydrate arrays that present diverse and complex structures.

Binding, Competitive↗
PubMed2002

What can surface chemistry do for cell biology?

Recent research has enhanced the development of substrates that serve as models of extracellular matrix and their use in studies of cell adhesion and migration. Advances include the development of methods to prepare substrates having ligands immobilized in controlled densities and patterns, and recent work that is developing dynamic substrates which can modulate, in real-time, the activities of ligands. These technologies are providing new opportunities for studies of cell-extracellular-matrix interactions.

Adsorption↗
PubMed2002

Protein chips: from concept to practice.

A series of exciting reports over the past two years has established the usefulness of protein chips and made important advances in preparing protein arrays. However, several technical challenges must still be addressed to make these tools available to the wider community of researchers. Here, we discusses these challenges and survey recent opportunities for creating quantitative assays, preparing and immobilizing large numbers of proteins, using detection methods to analyze the results of chip-based experiments, and using informatics tools to interpret these results.

Biotechnology↗