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Biomedical subjects

J Mack

Publications and source records attributed to J Mack.

At least 19 recordsLinked to original sources

Investigation of corannulene for molecular hydrogen storage via computational chemistry and experimentation.

Molecular simulations for hydrogen physisorption with corannulene molecules arranged according to their crystal structure result in good agreement with the weight-percent hydrogen stored as determined experimentally employing a 3-g sample of highly crystalline corannulene at ambient temperatures and 72 bar of pressure. Calculated enthalpies of adsorption for corannulene/hydrogen molecular systems obtained from ab initio calculations which take into account electron correlation via second-order Möller-Plesset perturbation theory are in good agreement with literature experimental enthalpies of adsorption for activated carbons interacting with molecular hydrogen. Ab initio results also show that corannulene molecules arranged in a sandwich structure are important for approximately doubling the binding energy of corannulene interacting with molecular hydrogen through a cooperative interaction. To test the effects of finite temperatures and pressures, stack arrays were used as input for molecular dynamics simulations and indicate that physisorption mechanisms including van der Waals forces and dipole-induced dipole interactions may yield enhanced adsorption capacity in relation to other carbon-based materials. These results will be instrumental in identifying interlayer separations of an array of corannulene or related molecules that may provide a high weight percent of physisorbed hydrogen.

Journal Article↗

Free-electron attachment to coronene and corannulene in the gas phase.

Electron attachment to the polyaromatic hydrocarbons coronene and corannulene is studied in the electron energy range of about 0-14 eV using a high-resolution crossed electron-neutral beam setup. The major anions observed are the parent anions peaking at about 0 eV with cross sections of 3.8 x 10(-20) and 1 x 10(-19) m(2), respectively. The only fragment anions formed in coronene and corannulene are the dehydrogenated coronene and corannulene anions. Other anions observed in the negative mass spectra at about 0 eV can be ascribed to impurities of the sample. High-level quantum-mechanical studies are carried out for the determination of electron affinities, hydrogen binding energies, and structures of both molecules. The behavior of coronene and corannulene upon electron attachment is compared with that of other polyaromatic hydrocarbons studied previously.

Anions↗

Promotion of neural cell adhesion by electrochemically generated and functionalized polymer films.

New strategies for spatially controllable cell adhesion have been developed for brain cells from embryonic chicken. They are based on electrochemically active phenol and pyrrole derivatives, and can be used for the selective coverage of electroconductive substrates. Besides mimicking standard laminin-related adhesion promoting mechanisms by means of an electroactive monomer-linked 18-peptide segment from laminin (SRARKQAASIKVAVSADR), electrochemically generated thin (6-30 nm) polymer films of 3-hydroxybenzyl-hydrazine (3HBH) and 2-(3-hydroxyphenyl)-ethanol (2(3HP)E) with and without mechanically entrapped or covalently linked D-lysine have proved to promote cell adhesion in serum-free medium on indium-doped tin oxide (ITO) substrates during the first 6 culturing days in vitro. The effectiveness of the peptide was strongly density-dependent. Unexpectedly, laminin itself or a combination of laminin and poly-D-lysine (PDL) did not promote cell adhesion and neuron differentiation in serum-free cultures on ITO. However, they worked perfectly well on regular polystyrene substrates in serum-free medium or on ITO when medium with serum was used. This finding might suggest that the adhesion efficiency of laminin does not depend only on the kind of medium supplement but also on the type of substrate. In contrast, the adhesion-promoting properties of "artificial" polymeric films seemed to be based on a more direct cell-film interaction, with the film masking the substrate properties.

Animals↗

An in vivo model for investigating bilateral synaptic plasticity across CA3/CA1 synapses in guinea pig dorsal hippocampus.

A method is described for concurrent investigation of long-term potentiation (LTP) in the left and right CA1 synapses in dorsal hippocampi in guinea pig in vivo. Briefly, animals are anesthetized with urethane, and small access holes are made in the skull through which electrodes are lowered to stimulate the left CA3 and record from both CA1 regions. Using this animal model, we have found that LTP is produced in both CA1 regions, following conditioning stimulation to the left CA3. However, in some animals LTP occurred in the left CA1 without concomitant synaptic potentiation in the contralateral CA1. We also observed that in some experiments synaptic potentiation in the contralateral CA1, when present, decayed to baseline levels even though LTP persisted in the ipsilateral CA1. To conclude, our data on bilateral LTP demonstrates findings that are best addressed in vivo.

Action Potentials↗

Solution structure and function of a conserved protein SP14.3 encoded by an essential Streptococcus pneumoniae gene.

Streptococcus pneumoniae is a major human pathogen that causes high mortality and morbidity rates and has developed resistance to many antibiotics. The genome of S. pneumoniae has recently been completely sequenced revealing many genes encoding hypothetical proteins of unknown function. We have found that the gene encoding one such conserved protein, SP14.3, is essential for growth of S. pneumonia. Since it is essential, SP14.3 represents a potential target for drug discovery. Here, we describe the three-dimensional solution structure of SP14.3 as determined by NMR spectroscopy. The structure consists of two domains each with an alpha/beta-fold. The N-terminal domain contains two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. The N-terminal domain of the protein contains a highly negatively charged surface and resembles the fold of the N-terminal domain of Thermus thermophilus ribosomal protein S3. The C-terminal domain has a protein fold similar to human small nuclear ribonucleoprotein Sm D3 and Haloarcula marismortui ribosomal protein L21E. The two domains of the protein tumble in solution overall as a whole with an overall molecular rotational correlation time (tau(m)) of 12.9 ns at 25 degrees C. The relative orientation of the two domains is not defined by the nuclear Overhauser effect data. Indeed, residual dipolar couplings and the structure calculations indicate that the relative orientation of the two domains is not rigidly oriented with respect to one another in solution.

Bacterial Proteins↗

Synthesis of linear and comb-like peptide constructs containing up to four copies of a T cell epitope and their capacity to stimulate T cells.

Polypeptide constructs containing up to four copies of the T cell epitope 306-318 of influenza virus haemagglutinin have been synthesized on solid phase. Between the copies, a non-natural PEG-based spacer amino acid has been introduced. The oligomeric epitopes were analysed by RP-HPLC and ES-MS. The arrangement of the epitopes within the peptide constructs was either linear or comb-like. The proliferative response in a T helper cell assay induced by these oligomerized epitopes has been tested, showing that the linearly arranged epitopes are more effective than the comb-like oligomers.

Amino Acid Sequence↗

Structure of the N-terminal region of Haemophilus influenzae H10017: implications for function.

Haemophilus influenzae is a gram-negative pathogen that causes infections ranging from asymptomatic colonization of the human upper respiratory tract to serious invasive diseases such as meningitis. Although the genome of Haemophilus influenzae has been completely sequenced, the structure and function of many of these proteins are unknown. H10017 is one of these uncharacterized proteins. Here we describe the three-dimensional solution structure of the N-terminal portion of H10017 as determined by NMR spectroscopy. The structure consists of a five-stranded antiparallel beta-sheet and two short alpha-helices. It is similar to the C-terminal domain of Diphtheria toxin repressor (DtxR). The C-terminal portion of H10017 has an amino acid sequence that closely resembles pyruvate formate-lyase--an enzyme that converts pyruvate and CoA into acetyl-CoA and formate by a radical mechanism. Based on structural and sequence comparisons, we propose that the C-terminus of H10017 functions as an enzyme with a glycyl radical mechanism, while the N-terminus participates in protein/protein interactions involving an activase (iron-sulfur protein) and/or the substrate.

Acetyltransferases↗

Completely regioselective, highly stereoselective syntheses of cis-Bisfullerene

cis-Bisfullerene[60] adducts of 6,13-disubstituted pentacenes (R = Ph, 4'-hydroxymethylphenyl) are synthesized in 75% to 85% isolated yields under kinetically controlled Diels-Alder conditions. The cycloadditions are completely regioselective and highly stereoselective, with only traces of the diastereomeric trans-bisfullerene[60] adducts forming.

Journal Article↗

pi-stacking interactions in cis-Bisfullerene

Experimental, molecular modeling, and model compound studies suggest that favorable fullerene[60] pi-stacking interactions in the ground state and in syn-transition states account for the high cis stereoselectivities observed in the reactions between C(60) and 6, 13-disubstituted pentacenes.

Journal Article↗

NMR studies of the anti-apoptotic protein Bcl-xL in micelles.

The Bcl-2 family of proteins play a pivotal role in the regulation of programmed cell death. One of the postulated mechanisms for the function of these proteins involves the formation of ion channels in membranes. As a first step to structurally characterize these proteins in a membrane environment, we investigated the structure of a Bcl-x(L) mutant protein when incorporated into small detergent micelles. This form of Bcl-x(L) lacks the loop (residues 49-88) between helix 1 and helix 2 and the putative C-terminal transmembrane helix (residues 214-237). Below the critical micelle concentration (CMC), Bcl-x(L) binds detergents in the hydrophobic groove that binds to pro-apoptotic proteins. However, above the CMC, Bcl-x(L) undergoes a dramatic conformational change. Using NMR methods, we characterized the secondary structure of Bcl-x(L) in the micelle-bound form. Like Bcl-x(L) in aqueous solution, the structure of the protein when dissolved in dodecylphosphocholine (DPC) micelles consists of several alpha-helices separated by loops. However, the length and position of the individual helices of Bcl-x(L) in micelles differ from those in aqueous solution. The location of Bcl-x(L) within the micelle was examined from the analysis of protein-detergent NOEs and limited proteolysis. In addition, the mobility of the micelle-bound form of Bcl-x(L) was investigated from NMR relaxation measurements. On the basis of these studies, a model is proposed for the structure, dynamics, and location of Bcl-x(L) in micelles. In this model, Bcl-x(L) has a loosely packed, dynamic structure in micelles, with helices 1 and 6 and possibly helix 5 partially buried in the hydrophobic interior of the micelle. Other parts of the protein are located near the surface or on the outside of the micelle.

Amino Acid Sequence↗

A streptavidin surface on planar glass substrates for the detection of biomolecular interaction.

Based on the requirements of biomolecular interaction analysis on direct optical transducers, a streptavidin surface is examined. A general protocol was developed allowing the immobilization of biotinylated compounds using the rife biotin-streptavidin system. This type of surface modification can be applied to all biosensors using glass surfaces as sensor devices. Reflectometric interference spectroscopy (RIfS), a label-free, direct optical method was used to demonstrate the quality of the transducer surfaces. The surface modification is based on an aminofunctionalized polyethylene glycol layer covalently bound to the silica surface of the transducer and shows very little nonspecific binding. Biotin molecules can be easily coupled on such layers. Streptavidin followed by a biotinylated estrone derivative was immobilized by incubation of the biotinylated transducer surface. For the streptavidin layer we obtained interference signals corresponding to a protein monolayer. Finally, using a surface prepared as described above, biomolecular interaction experiments with an antibody against estrone were carried out to show the quality of the transducer surface. With RIfS all of the affinity-based surface modifications can be detected online and time resolved.

Antibodies↗

Design of supported membranes tethered via metal-affinity ligand-receptor pairs.

Model lipid layers are very promising in investigating the complex network of recognition, transport and signaling processes at membranes. We have developed a novel and generic approach to create supported lipid membranes tethered by metal-affinity binding. By self-assembly we have generated various interfaces that display histidine sequences (6xHis) via polymer spacers. These histidine-functionalized interfaces are designed to allow specific docking and fusion of vesicles containing metal-chelating lipids. By means of surface plasmon resonance and atomic force microscopy we analyzed the formation and subsequently the structure of these solid-supported membranes. Although the affinity constant of single ligand-receptor pairs is only in the micromolar range, very stable immobilization of these membranes was observed. This behavior can be explained by multivalent interactions resembling many features of cell adhesion. The process is highly specific, because vesicle docking and bilayer formation are strictly dependent on the presence of metal-affinity ligand-receptor pairs. The surface accessibility and geometry of these tethered membranes were probed by binding of histidine-tagged polypeptides. The supported membranes show adsorption kinetics and values similar to planar supported monolayers. Using various combinations of metal-chelating and histidine-tagged lipids or thiols these metal-affinity-tethered membranes should make a great impact on probing and eventually understanding the dynamic dialog of reconstituted membrane proteins.

Affinity Labels↗

Efficient cotransduction of tumors by multiple herpes simplex vectors: implications for tumor vaccine production.

Many gene therapy strategies would be enhanced by efficient transfer of multiple genes into the same cell. Herpes simplex viral amplicon (HSV) vectors are good vehicles for gene transfer because they accommodate large pieces of foreign DNA and transfer genes rapidly and efficiently. The current studies examine whether efficient cotransduction of tumor cells can be accomplished using multiple HSV vectors in a manner useful for clinical gene therapy. Interleukin-12 (IL-12) exists as a heterodimer, with components (m35 and m40) coded for by genes on two separate chromosomes. We constructed HSV vectors carrying either IL12m35 (HSVm35) or IL12m40 (HSVm40) or both genes (HSVm75) separated by an internal ribosome entry site to assess whether gene transfer using a single HSV vector constructed to carry multiple genes has any advantage over gene transfer using multiple vectors that are each carrying single genes. Because IL-12 and IL-2 have been found to have synergistic antitumoral activity, we further analyzed the biologic activity of tumor cells cotransduced by separate HSV vectors carrying genes coding for these two cytokines. The results demonstrate that multiple genes can be inserted into the same cell efficiently using multiple HSV vectors, and that these vectors allow rapid production of tumor vaccines expressing multiple cytokine genes. Thus, gene transfer using HSV may not be limited by the size of the DNA that each vector can accommodate. Immunizations with tumors cotransduced with HSVm35 and HSVm40 were equally effective in eliciting a cytolytic T-lymphocyte response and in protecting against tumor growth in vivo as immunization with tumors treated with HSVm75. Immunization with tumors cotransduced with HSVm75 and HSVil2 was superior to immunization with tumors transduced with either alone. The combination of IL-2- and IL-12-secreting tumor cells may be used as an effective immunization strategy against solid tumors.

Animals↗

Rationale for Bcl-xL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies.

The three-dimensional structure of the anti-apoptotic protein Bcl-xL complexed to a 25-residue peptide from the death promoting region of Bad was determined using NMR spectroscopy. Although the overall structure is similar to Bcl-xL bound to a 16-residue peptide from the Bak protein (Sattler et al., 1997), the Bad peptide forms additional interactions with Bcl-xL. However, based upon site-directed mutagenesis experiments, these additional contacts do not account for the increased affinity of the Bad 25-mer for Bcl-xL compared to the Bad 16-mer. Rather, the increased helix propensity of the Bad 25-mer is primarily responsible for its greater affinity for Bcl-xL. Based on this observation, a pair of 16-residue peptides were designed and synthesized that were predicted to have a high helix propensity while maintaining the interactions important for complexation with Bcl-xL. Both peptides showed an increase in helix propensity compared to the wild-type and exhibited an enhanced affinity for Bcl-xL.

Amino Acid Sequence↗

Conformational variants of class II MHC/peptide complexes induced by N- and C-terminal extensions of minimal peptide epitopes.

Class II MHC molecules are known to exist in conformational variants. "Floppy" and "compact" forms of murine MHC molecules, for example, are discriminated by their migration behavior on SDS/PAGE and represent empty and ligand-loaded forms. Here we show that formation of distinctly faster-migrating ligand complexes (F-forms) rather than the normal compact (C-) forms of HLA-DR1 or -DR4 results from extensions of minimal peptide epitopes (such as HA306-318 or IC106-120) by approximately 10 amino acids at either the N or the C terminus. Two similar but distinct F-forms (FI and FII) were detected, depending on the site of the extension. Both F-forms were characterized by increased surface hydrophobicity and reduced SDS-stability. Native gel separations and size exclusion chromatography indicated that the F-forms had increased hydrodynamic radii compared with the C-form and an apparent size similar to that of empty MHC molecules. The regions on the ligand overhangs responsible for the effect began at a distance of approximately 5 amino acids on either side of the epitopes, comprised 4-8 amino acids (i.e., a total overhang of 9-14), and did not have a particular sequence preference. The possible functional significance of these forms is discussed.

Antigen Presentation↗