Biomedical subjects

J T Gerig

Publications and source records attributed to J T Gerig.

At least 19 recordsLinked to original sources

PubMed2006

TMAO promotes fibrillization and microtubule assembly activity in the C-terminal repeat region of tau.

Alzheimer's disease most closely correlates with the appearance of the neurofibrillary tangles (NFTs), intracellular fibrous aggregates of the microtubule-associated protein, tau. Under native conditions, tau is an unstructured protein, and its physical characterization has revealed no clues about the three-dimensional structural determinants essential for aggregation or microtubule binding. We have found that the natural osmolyte trimethylamine N-oxide (TMAO) induces secondary structure in a C-terminal fragment of tau (tau(187)) and greatly promotes both self-aggregation and microtubule (MT) assembly activity. These processes could be distinguished, however, by a single-amino acid substitution (Tyr(310) --> Ala), which severely inhibited aggregation but had no effect on MT assembly activity. The inability of this mutant to aggregate could be completely reversed by TMAO. We propose a model in which TMAO induces partial order in tau(187), resulting in conformers that may correspond to on-pathway intermediates of either aggregation or tau-dependent MT assembly or both. These studies set the stage for future high-resolution structural characterization of these intermediates and the basis by which Tyr(310) may direct pathologic versus normal tau function.

Amino Acid Substitution↗

PubMed2004

Structure and solvation of melittin in hexafluoroacetone/water.

Intermolecular (1)H[(19)F] and (1)H[(1)H] nuclear Overhauser effects have been used to explore interaction of solvent components with melittin dissolved in 50% hexafluoroacetone trihydrate (HFA)/water. Standard nuclear Overhauser effect experiments and an analysis of C(alpha)H proton chemical shifts confirm that the conformation of the peptide in this solvent is alpha-helical from residues Ala4 to Thr11 and from Leu13 to Arg24. The two helical regions are not collinear; the interhelix angle (144 +/- 20 degrees ) found in this work is near that observed in the solid state and previous NMR studies. Intermolecular NOEs arising from interactions between spins of the solvent and the solute indicate that both fluoroalcohol and water molecules are strongly enough bound to the peptide that solvent-solute complexes persist for > or =2 ns. Preferential interactions of HFA with many hydrophobic side chains of the peptide are apparent while water molecules appear to be localized near hydrophilic side chains. These results indicate that interactions of both HFA and water are qualitatively different from those present when the peptide is dissolved in 35% hexafluoro-2-propanol/water, a chemically similar helix-supporting solvent system.

Acetone↗

PubMed2004

Structure and solvation of melittin in 1,1,1,3,3,3-hexafluoro-2-propanol/water.

Fluorinated alcohols can induce peptides and proteins to take up helical conformations. Nuclear Overhauser effect (NOE) spectroscopy experiments and analysis of C(alpha)H proton chemical shifts show that the conformation of melittin in 35% hexafluoro-2-propanol/water is alpha-helical from residues Ile-2 to Val-8 and from Leu-13 to Gln-25. As has been found in other solvent systems, the two helical regions are not colinear; the interhelix angle (73 +/- 15 degrees ) in 35% 1,1,1,3,3,3-hexafluoro-2-propanol/water is smaller than the angle found in other fluoroalcohol-water mixtures or in the crystal. Intermolecular (1)H(19)F and (1)H(1)H nuclear Overhauser effects were used to explore interaction of solvent components with melittin dissolved in this solvent mixture. The NOEs observed indicate that fluoroalcohol and water molecules are both tightly bound to the peptide in the vicinity of the interhelix bend. For the remainder of the molecule, solute-solvent NOEs are consistent with preferential solvation of the peptide by the fluoroalcohol component of the solvent mixture.

Alcohols↗

PubMed2003

Solute-solvent interactions probed by intermolecular NOEs.

Nuclear Overhauser effects arising from the interactions of spins of solvent molecules with spins of a solute should reveal the "exposure" of solute spins to collisions with solvent. Such intermolecular NOEs could, therefore, provide information regarding conformation or structure of the solute. Determinations of solute-solvent NOEs of 1,3-di-tert-butylbenzene in solvents composed of perfluoro-tert-butyl alcohol, tetramethylsilane, and carbon tetrachloride have been carried out. A crude, but apparently reliable, method for prediction of intermolecular solvent-solute NOEs based on hard (noninteracting) spheres was developed. Comparison of experimental to predicted NOEs indicates that tetramethylsilane interacts with the solute according to the model. By contrast, intermolecular NOE data indicate attractive interactions between the solute and perfluoro-tert-butyl alcohol. All NOE results and the corresponding predictions confirm that proton H2 of the solute is protected by the flanking tert-butyl groups from interactions with solvent molecules.

Journal Article↗

PubMed2002

Intermolecular Overhauser effects in fluoroalcohol solutions of cyclo-alanylglycine.

Interactions between the diketopiperazine cyclo-alanylglycine and four fluorinated alcohols in water-fluoroalcohol mixtures were examined by (1)H[(19)F] intermolecular nuclear Overhauser effects (NOE) experiments. The alcohols studied were trifluoroethanol, hexafluoroacetone trihydrate, 1,1,1,3,3,3-hexafluoroisopropanol and perfluoro-t-butanol. The experimental methods used permit detection of solvent-solute NOEs of 0.1% or less. Solute and solvent diffusion coefficients were determined and apparent molecular radii of the fluoroalcohols estimated. Using these data, it was shown that observed (1)H[(19)F] intermolecular NOEs are consistent with expectations based on theory. A method for extending conventional theory to take into account the shape of a solute and the exposure of its hydrogens to solvent is described. This approach gives reasonable agreement with experimental results, particularly if it is assumed that solute-solvent interactions take place in such a way that the fluorines of a fluoroalcohol are preferentially oriented toward the solute during solute-solvent encounters. The results support the suggestion that intermolecular (1)H[(19)F] NOEs may become a useful tool for studies of peptide and protein conformations in fluoroalcohol-water solvent mixtures.

Alcohols↗

PubMed2001

Intermolecular (1)H[(19)F] NOEs in studies of fluoroalcohol-induced conformations of peptides and proteins.

Mixtures of fluorinated alcohols and water can selectively stabilize certain secondary structures of peptides and proteins. Such mixtures may also be of use in solubilizing hydrophobic or membrane-bound proteins. We show that intermolecular dipolar interactions between the fluorine nuclei of such solvents and the protons of a dissolved protein lead to readily detected (1)H[(19)F] nuclear Overhauser effects. These NOEs can potentially provide information about solvent exposure of particular groups as well as indicate the formation of long-lived fluoroalcohol-solute complexes. Results obtained with HEW lysozyme in solutions containing trifluoroethanol illustrate these possibilities.

Hydrogen Bonding↗

PubMed2000

Spin relaxation and chemical exchange in NMR simulations.

Theory for describing the density matrix of a spin system experiencing chemical exchange and relaxation during the steps of an NMR experiment is presented in a form suitable for computation. Features in the theory that arise from exchange are discussed in detail, and comparisons to the exchange-free situation are made. A general computer program to carry out simulations of NMR experiments is described, and several examples of its performance are presented.

Computer Simulation↗

PubMed1999

Pulsed field gradients in simulations of one- and two-dimensional NMR spectra.

A method for the inclusion of the effects of z-axis pulsed field gradients in computer simulations of an arbitrary pulsed NMR experiment with spin (1/2) nuclei is described. Recognizing that the phase acquired by a coherence following the application of a z-axis pulsed field gradient bears a fixed relation to its order and the spatial position of the spins in the sample tube, the sample is regarded as a collection of volume elements, each phase-encoded by a characteristic, spatially dependent precession frequency. The evolution of the sample's density matrix is thus obtained by computing the evolution of the density matrix for each volume element. Following the last gradient pulse, these density matrices are combined to form a composite density matrix which evolves through the rest of the experiment to yield the observable signal. This approach is implemented in a program which includes capabilities for rigorous inclusion of spin relaxation by dipole-dipole, chemical shift anisotropy, and random field mechanisms, plus the effects of arbitrary RF fields. Mathematical procedures for accelerating these calculations are described. The approach is illustrated by simulations of representative one- and two-dimensional NMR experiments.

Anisotropy↗

PubMed1997

Effects of fluorine substitution on the structure and dynamics of complexes of dihydrofolate reductase (Escherichia coli).

Fluorine NMR experiments with a protein containing fluorinated amino acid analogs can often be used to probe structure and dynamics of the protein as well as conformational changes produced by binding of small molecules. The relevance of NMR experiments with fluorine-containing materials to characteristics of the corresponding native (nonfluorinated) proteins depends upon the extent to which these characteristics are altered by the presence of fluorine. The present work uses molecular dynamics simulations to explore the effects of replacement of tryptophan by 6-fluorotryptophan in folate and methotrexate complexes of the enzyme dihydrofolate reductase (DHFR) (Escherichia coli). Simulations of the folate-native enzyme complex produce local correlation times and order parameters that are generally in good agreement with experimental values. Simulations of the corresponding fluorotryptophan-containing system indicate that the structure and dynamics of this complex are scarcely changed by the presence of fluorinated amino acids. Calculations with the pharmacologically important methotrexate-enzyme complex predict dynamical behavior of the protein similar to that of the folate complex for both the fluorinated and native enzyme. It thus appears that, on the time scale sampled by these computer simulations, substitution of 6-fluorotryptophan for tryptophan has little effect on either the structures or dynamics of DHFR in these complexes.

Amides↗

PubMed1997

Tritium NMR studies of the human carbonic anhydrase I-benzenesulfonamide complex.

Tritium NMR spectroscopy has been used to examine the complex formed by [4-3H]benzenesulfon-amide and human carbonic anhydrase I. The results show that in solution the inhibitor forms a 1:1 complex with the enzyme. A 100-spin computational model of the system, constructed with reference to crystallographic results, was used to interpret tritium relaxation behavior and 3H{1H} NOEs. The analysis shows that the rate of dissociation of the enzyme-sulfonamide complex is 0.35 s-1 and that the aromatic ring of the inhibitor undergoes rapid rotation while complexed.

Carbonic Anhydrase Inhibitors↗

PubMed1996

Cross-correlation effects on NMR lineshapes and peptide conformation.

Information about molecular structure and dynamics can potentially be obtained by studying dipole-dipole and chemical-shift anisotropy (CSA) auto-correlation and dipole-CSA cross-correlation effects in high-resolution NMR spectra. Equations for the lineshapes of the HN multiplet in the fragment- 15NH-CH- as a function of NH-CH dihedral angle are derived by including these effects within the framework of the Redfield treatment of relaxation. To test the utility of the theoretical results, 1H[15N] HSQC proton lineshape data for a variant of the enzyme staphylococcal nuclease in which all valine residues are labeled with 15N have been analyzed to obtain the conformational angle (phi) between the N-H and adjacent C-H bonds. The results are generally in good agreement with values of phi obtained from crystal structure data. Considerations in the further development of the analysis of the lineshape of the HN multiplet for experimental determinations of phi are discussed.

Algorithms↗

PubMed1995

NMR studies of the alpha-chymotrypsin-(R)-1-acetamido-2-(4-fluorophenyl)ethane-1-boronic acid complex at pH 7.

The interaction of (R)-1-acetamido-2-(4-fluorophenyl)ethane-1-boronic acid with alpha-chymotrypsin at pH 7 was studied by a variety of fluorine and proton NMR experiments and the results compared to observations made at pH 4. It was demonstrated that this compound forms a complex with a 1:1 stoichiometry at pH 7; proton NMR indicates that the boronic acid likely is coordinated to the serine-195 residue at the active site. Analysis of fluorine T1 relaxation behavior and 19F(1H) NOE data shows that the rate constant for dissociation of the complex is 4.7 s-1, somewhat faster than is observed at pH 4. The data analysis and the results of two-dimensional 19F(1H) NOE experiments show that interactions between the fluoroaromatic ring of the inhibitor and the enzyme are weaker at the higher pH value, although the motion of the fluoroaromatic ring within the complex appears to be just as restricted as is the case at pH 4.

Boronic Acids↗

PubMed1994

Structure and dynamics of tosylchymotrypsin at pH 7 examined by tritium NMR spectroscopy.

3H-NMR spectroscopy of specifically tritiated and tritiated/deuterated derivatives of tosylchymotrypsin has been used to examine the behavior of the tosyl group in this protein at pH 7. The presence of several tritiated isotopomers complicates analysis of experiments and extensive computer simulations of T1 relaxation, line widths, and various nuclear Overhauser experiments for the collection of tritiated species present in the samples were used to the interpret the observations made. These analyses suggests that the tosyl group of tosylchymotrypsin at pH 7 is largely retained within the substrate specificity pocket observed in the crystal structure. This outcome is in strong contrast to the situation observed at pH 4, where the tosyl group is mobile enough to be found outside the specificity pocket an appreciable fraction of the time, and may be the result of protein association at pH 7.

Binding Sites↗

PubMed1993

NMR studies of the alpha-chymotrypsin-(R)-1-acetamido-2-(4- fluorophenyl)ethane-1-boronic acid complex.

The interaction of (R)-1-acetamido-2-(4-fluorophenyl)ethane-1-boronic acid with alpha-chymotrypsin at pH 4 was studied by a variety of 19F-NMR experiments. It was demonstrated that this compound forms a complex with a 1:1 stoichiometry, probably because the boronic acid acts as a 'transition state' inhibitor of the enzyme. Analysis of fluorine T1 relaxation behavior and 19F[1H] NOE data shows that the rate constant for dissociation of the complex is 1.3 s-1 and that the motion of the 4-fluoroaromatic ring within the complex can be characterized by an overall rotational correlation time of 13 ns and a correlation time for rotation about its local C2 axis of 110 ns. Enzyme-induced fluorine chemical shifts, fluorine relaxation times, line width data and 2D 19F[1H] NOE results suggest that the structure of the complex in the vicinity of the fluoroaromatic ring is similar to that found in a closely similar acylated enzyme. However, the dynamics of 4-fluoroaromatic ring motions are different in the two systems, with the ring being slightly more mobile in the boronic acid complex than in the acylenzyme.

Binding Sites↗

PubMed1991

Prediction of fluorine chemical shifts in proteins.

Molecular dynamics calculations have been used in an effort to estimate the change in fluorine nmr shielding when a fluorine nucleus enters the tertiary structure of a protein. Considerations of the possible interactions that can define the shift parameter change suggest that van der Waals interactions are the leading determinant of fluorine shifts in proteins, although aromatic ring currents, other magnetic anisotropies, and electrostatic field effects could result in shift distinctions of 1 ppm or smaller. Results of our studies of a fluorine-containing analogue of the ribonuclease A S-protein/S-peptide complex indicate that static structures such as those implied by crystallographic data lead to overestimates of the magnitude of the van der Waals shielding term; molecular dynamics simulations provide indications of the effects of conformational averaging in defining this term. The treatment used predicts the correct direction of the shift change when the fluorine enters this protein environment from aqueous solution and, with an experimentally supported choice of adjustable parameters, gives agreement with the magnitude of the shift.

Anisotropy↗

PubMed1991

Structure and dynamics of alpha-chymotrypsin-N-trifluoroacetyl-4-fluorophenylalanine complexes.

Fluorine NMR lineshape, relaxation and Overhauser effect data collected at 282 and 470 MHz have been used to obtain information about the nature of complexes formed between N-trifluoroacetyl-4-fluorophenylalanine and the enzyme chymotrypsin. Systems involving both enantiomers have been examined as well as derivatives of these in which the aromatic ring hydrogens have been replaced by deuterium. The enzyme-induced fluorine chemical shift effects and the dynamics of molecular motions of the fluorophenyl ring at the respective binding sites appear to be similar in both complexes and, where comparable, the results are in agreement with data obtained at lower frequencies that have been reported by other workers. The dynamics of the fluoroaromatic ring in these complexes are significantly different from those observed in a closely related acylated enzyme.

Animals↗

PubMed1990

Conformational dynamics in fluorophenylcarbamoyl-alpha-chymotrypsins.

A series of fluorine-substituted diphenylcarbamoyl chlorides have been synthesized and used to prepare corresponding diphenylcarbamoylated derivatives of alpha-chymotrypsin. The enzyme is rapidly inactivated by these compounds, as has been previously observed for the unsubstituted chloride, and the derivatives are stable enough to permit extensive studies by fluorine NMR spectroscopy. In combination with previously reported results, these NMR experiments suggest that the aromatic rings of a diphenylcarbamoyl group attached to chymotrypsin may be found in two magnetically and dynamically distinguishable sites, with exchange between these sites taking place by a process that involves rotation about the carbamoyl N-CO bond and localized unfolding of the enzyme. The extent to which a given fluoroaromatic ring is found in one of these sites is dependent on the position of the fluorine substituent and the nature of the partner aromatic ring. It is found that a 2-fluorophenyl ring, when present, dominantly determines site occupation, while a 3-fluorophenyl ring has no effects that are detectably different from those of an unsubstituted phenyl ring. There is evidence for slow aromatic ring rotation within at least one of the phenyl ring interaction sites. Saturation transfer and lineshape methods provide information about the rates of interconversion of the N-phenyl groups between these sites. Line-width, spin-lattice relaxation times and fluorine-proton nuclear Overhauser effects determined at 282 and 470 MHz are reported for each system examined.

Binding Sites↗

PubMed1990

Conformations of N-(2-fluorophenyl)-N-phenylcarbamoyl-alpha-chymotrypsin.

N-(2-Fluorophenyl)-N-phenylcarbamoyl chloride is shown to react with alpha-chymotrypsin to give a catalytically inactive material. A crystal structure determination shows that the chloride exists in the solid state in two conformations. In both of these the aromatic rings are tilted substantially relative to the plane through the atoms of the carbamoyl chloride group; the structures differ by a 180 degrees rotation of the 2-fluorophenyl ring. Fluorine NMR studies of alpha-chymotrypsin modified with this carbamoyl chloride show that, when bound to the enzyme, one aromatic ring of the diphenylcarbamoyl group likely rotates slowly while the other rotates much more rapidly or else is frozen in one dominant conformation. In the denatured enzyme (8 M urea) at room temperature and above, both aromatic rings of the diphenylcarbamoyl group appear to be rapidly rotating although differential linewidth changes observed at lower sample temperatures suggest that rotation of one ring becomes slow under these conditions. Rotation about the carbamoyl carbon-nitrogen bond is detected in fluorine NMR spectra of both the native and the denatured modified enzymes as the sample temperature is increased. Rates of carbamoyl rotation in the chloride, in the native modified enzyme, and in the denatured enzyme at 25 degrees C are approximately 66, 10, and 200 s-1, respectively.

Binding Sites↗