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Biomedical subjects

Mark R Spaller

Publications and source records attributed to Mark R Spaller.

11 recordsLinked to original sources
PubMed2006

Expanding the synthetic method and structural diversity potential for the intramolecular Aza Diels-Alder cyclization.

New experimental facets have been examined to expand upon the known methods for an aromatic variant of the intramolecular Aza Diels-Alder cyclization. The specific transformation under study is one that uses functionalized anilines and an aldehyde-olefin tether to provide tetrahydroquinoline cycloadducts under mild acidic conditions. Variations investigated encompass the use of N-alkylated anilines, including one with ring-constrained nitrogen, in the context of glycine, phenylalanine, and glyoxyl ester bridging elements; bridge components with structural perturbations; modified dienophile segments; and different acid catalysts. Substituted tetrahydroquinolines obtained from many of the preceding experiments were obtained in good chemical yield, generally in excess of 80%. Designed as a platform for combinatorial chemical synthesis, this reaction manifold accommodates a range of starting materials with structurally and electronically distinct characteristics. The results of this report, in combination with the discoveries from previous work in this area, enhance the ability of the intramolecular Aza Diels-Alder transformation to generate a diverse array of quinolinic structures with multiple stereogenic centers, many of which resemble lignan and arylnaphthalene-type natural products.

Aldehydes↗
PubMed2006

Monomeric yeast frataxin is an iron-binding protein.

Friedreich's ataxia, an autosomal cardio- and neurodegenerative disorder that affects 1 in 50,000 humans, is caused by decreased levels of the protein frataxin. Although frataxin is nuclear-encoded, it is targeted to the mitochondrial matrix and necessary for proper regulation of cellular iron homeostasis. Frataxin is required for the cellular production of both heme and iron-sulfur (Fe-S) clusters. Monomeric frataxin binds with high affinity to ferrochelatase, the enzyme involved in iron insertion into porphyrin during heme production. Monomeric frataxin also binds to Isu, the scaffold protein required for assembly of Fe-S cluster intermediates. These processes (heme and Fe-S cluster assembly) share requirements for iron, suggesting that monomeric frataxin might function as the common iron donor. To provide a molecular basis to better understand frataxin's function, we have characterized the binding properties and metal-site structure of ferrous iron bound to monomeric yeast frataxin. Yeast frataxin is stable as an iron-loaded monomer, and the protein can bind two ferrous iron atoms with micromolar binding affinity. Frataxin amino acids affected by the presence of iron are localized within conserved acidic patches located on the surfaces of both helix-1 and strand-1. Under anaerobic conditions, bound metal is stable in the high-spin ferrous state. The metal-ligand coordination geometry of both metal-binding sites is consistent with a six-coordinate iron-(oxygen/nitrogen) based ligand geometry, surely constructed in part from carboxylate and possibly imidazole side chains coming from residues within these conserved acidic patches on the protein. On the basis of our results, we have developed a model for how we believe yeast frataxin interacts with iron.

Chromatography, Gel↗
PubMed2006

Act globally, think locally: systems biology addresses the PDZ domain.

Interaction networks, cartography and mapping, wiring and circuitry, whichever metaphor is invoked, the cardinal questions regarding cellular proteins are the same: What are they? How much is there? What do they do, and to whom do they do it? One of the more recent proteomics tools to pursue these lines of inquiry is the protein microarray, and a current report has unleashed this formidable technique upon a target of considerable biological interest, the PDZ domain family of signaling molecules.

Amino Acid Sequence↗
PubMed2006

The interplay between structure-based design and combinatorial chemistry.

The two most lauded drug design approaches from the past century--structure-based design and combinatorial chemistry--are increasingly experiencing integration, whereby the three-dimensional coordinates of a receptor supports the development of combinatorial-based ligand design. A selective polling of the recent literature demonstrates that this can be actualized in many ways.

Combinatorial Chemistry Techniques↗
PubMed2006

Dual role of the exocyst in AMPA receptor targeting and insertion into the postsynaptic membrane.

Intracellular membrane trafficking of glutamate receptors at excitatory synapses is critical for synaptic function. However, little is known about the specialized trafficking events occurring at the postsynaptic membrane. We have found that two components of the exocyst complex, Sec8 and Exo70, separately control synaptic targeting and insertion of AMPA-type glutamate receptors. Sec8 controls the directional movement of receptors towards synapses through PDZ-dependent interactions. In contrast, Exo70 mediates receptor insertion at the postsynaptic membrane, but it does not participate in receptor targeting. Thus, interference with Exo70 function accumulates AMPA receptors inside the spine, forming a complex physically associated, but not yet fused with the postsynaptic membrane. Electron microscopic analysis of these complexes indicates that Exo70 mediates AMPA receptor insertion directly within the postsynaptic density, rather than at extrasynaptic membranes. Therefore, we propose a molecular and anatomical model that dissects AMPA receptor sorting and synaptic delivery within the spine, and uncovers new functions of the exocyst at the postsynaptic membrane.

Animals↗
PubMed2005

Bridged peptide macrocycles as ligands for PDZ domain proteins.

[reaction: see text] Conformationally constrained side chain-bridged cyclic peptides were prepared using bis-carboxylic acid ring spacers. These macrocyles were designed to inhibit protein-protein interactions mediated by the third PDZ domain (PDZ3) of a mammalian neuronal protein, PSD-95. Isothermal titration calorimetry (ITC) experiments measured dissociation constants in the low micromolar range. For each compound, the change in entropy (TdeltaS) of binding either is comparable in magnitude to the enthalpy change (deltaH) or is the predominant driving force for association.

Amino Acid Sequence↗
PubMed2004

Thermodynamic analysis of a hydrophobic binding site: probing the PDZ domain with nonproteinogenic peptide ligands.

[structure: see text] Isothermal titration calorimetry (ITC) is used to study the thermodynamic consequences of systematically modifying the hydrophobic character of a single residue in a series of protein-binding ligands. By substituting standard and nonproteinogenic aliphatic amino acids for the C-terminal valine of the hexapeptide KKETEV, binding to the third PDZ domain (PDZ3) of the PSD-95 protein is characterized by distinct changes in the Gibbs free energy (DeltaG), enthalpy (DeltaH), and entropy (TDeltaS) parameters. One notable observation is that peptide binding affinity can be improved with a nonstandard residue.

Amino Acids↗
PubMed2004

Thermodynamic profiling of conformationally constrained cyclic ligands for the PDZ domain.

Inspired by structure-based design and tailored for combinatorial preparation, a series of novel cyclic peptides has been developed to yield binding ligands for the third PDZ domain (PDZ3) of PSD-95. These side chain-side chain bridged peptides permit the systematic expansion or contraction of ring size, which is intended to maximize the conformational diversity of the ensemble. Isothermal titration calorimetry (ITC) was used to measure the dissociation constants (K(d)) and associated thermodynamic binding parameters.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Targeting specific PDZ domains of PSD-95; structural basis for enhanced affinity and enzymatic stability of a cyclic peptide.

A cyclic peptide, Tyr-Lys-c[-Lys-Thr-Glu(betaAla)-]-Val, incorporating a beta-Ala lactam side chain linker and designed to target the PDZ domains of the postsynaptic density protein 95 (PSD-95), has been synthesized and structurally characterized by NMR while free and bound to the PDZ1 domain of PSD-95. While bound, the lactam linker of the peptide makes a number of unique contacts outside the canonical PDZ binding motif, providing a novel target for PDZ-domain specificity as well as producing a 10-fold enhancement in binding affinity. Additionally, the cyclization greatly enhances the enzymatic stability, increasing the duration that the peptide inhibits the association between PSD-95 and glutamate receptors, effectively inhibiting the clustering of kainate receptors for over 14 hr after application. Highly specific regulation of kainate receptor action may provide a novel route for treatment of drug addiction and epilepsy.

Enzyme Stability↗
PubMedDate not supplied

Combinatorial synthetic design. Solution and polymer-supported synthesis of heterocycles via intramolecular aza Diels-Alder and imino alcohol cyclizations.

A flexible synthetic strategy for combinatorial chemical applications has been developed on the basis of an aldehyde-bridge-alkene motif as the key component in several intramolecular cycloaddition reactions. This strategy was explored most extensively with the formal aza Diels-Alder cyclization, which affords a series of configurationally and functionally diverse heterocyclic compounds. The substrates included substituted salicylaldehydes, glyoxylic esters and amides, and N-acyl-alpha-aminoaldehydes; all reacted with a variety of anilines to yield different tetrahydroquinoline products. The cyclization of the aminoaldehydes was also translated from solution and optimized for solid phase. The stepwise mechanism of this cycloaddition suggested that the cationic intermediate from initial ring closure could be trapped by a variety of nucleophiles. This suggestion was confirmed by cyclization of amino alcohols and related compounds.

Alcohols↗