Examination of Solvent Interactions with Trp-Cage in 1,1,1,3,3,3-Hexafluoro-2-propanol-water at 298 K through MD Simulations and Intermolecular Nuclear Overhauser Effects.

MD simulations of the peptide Trp-cage dissolved in 28% hexafluoroisopropanol (HFIP)-water have been carried out at 298 K with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross-relaxation. The work was motivated by the observation that most experimental fluoroalcohol-peptide cross-relaxation terms at 298 K are small, both positive and negative, and not always well predicted from simulations. The cross-relaxation terms for hydrogens of the caged tryptophan residue of Trp-cage are substantially negative, a result consistent with simulations. It was concluded that hexafluoroisopropanol interactions near this part of the peptide are particularly long-lived. While both HFIP and water are present in all regions of the simulation box, the composition of the solvent mixture is not homogeneous throughout the system. HFIP generally accumulates near the peptide surface, while water molecules are preferentially found in regions that are more than 1.5 nm from the surface of the peptide. However, some water remains in higher-than-expected amounts in the solvent layer surrounding 6Trp, 9Asp, Ser13, and Ser14 residues in the helical region of Trp-cage. As observed in simulations of this system at 278 K, HFIP molecules aggregate into clusters that continually form and re-form. Translational diffusion of both HFIP and water appears to be slowed near the surface of the peptide with reduction in diffusion near the 6Trp residue 2- to 3-fold larger than calculated for solvent interactions with other regions of Trp-cage.

Examination of Interactions of Hexafluoro-2-propanol with Trp-Cage in Hexafluoro-2-propanol-Water by MD Simulations and Intermolecular Nuclear Overhauser Effects.

All-atom molecular dynamic simulations of the peptide Trp-cage in 30% hexafluoro-2-propanol- water (V/V) at 278 K have been carried out with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross relaxation. Force field parameters for HFIP reported by Fioroni et al. along with the fluorine parameters of the TFE5 model reported by this lab were used. Water was represented by the TIP5P-Ew model. Peptide modeling used the AMBER99SB-ILDN force field. Translational diffusion coefficients of solution components at 278 K were predicted to within 35% of experimental values using these parameter sets. The simulations indicate that the solvent mixture is not homogeneous, with HFIP molecules clustered into aggregates as large as 53 fluoroalcohol molecules. The solvent environment of surface atoms of Trp-cage fluctuates between being HFIP-rich and more water-rich about every 10 ns. In accord with previous studies by other groups, the average concentration of HFIP near the surface of the peptide is significantly enhanced over the concentration of HFIP in the bulk solvent. In the simulations, ∼7% of the initial contacts between HFIP molecules and Trp-cage develop into peptide-fluoroalcohol interactions that persist for times as long as 8 ns. Most of the available experimental nuclear spin cross-relaxation rates (ΣHF) for hydrogens of the Trp-cage in 30% HFIP-water are reproduced from the MD trajectories to within uncertainties of the experimental data and the simulations. However, a few calculated ΣHF values for hydrogens of the Trp-cage do not agree with experiment. These tend to be situations where long-lived peptide-HFIP interactions are predicted. The disagreements between observed and calculated ΣHF in these instances signal defects in the modeling parameters and procedures that are presently unrecognized.

Examination of Trifluoroethanol Interactions with Trp-Cage in Trifluoroethanol-Water at 298 K through Molecular Dynamics Simulations and Intermolecular Nuclear Overhauser Effects.

Molecular dynamics simulations of the protein model Trp-cage in 42% trifluoroethanol (TFE)-water at 298 K have been carried out with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross-relaxation. The TFE5 model of TFE developed in a previous work was used with the TIP5P-Ew model of water. System densities and component translational diffusion coefficients predicted by the simulations were within 20% of the experimental values. Consideration of the calculated relative amounts of TFE and water surrounding the hydrogens of Trp-cage indicated that the composition of the solvent mixture beyond ∼1.5 nm from the van der Waals surface of the peptide is close to the composition of the bulk solvent, but as observed by others, TFE accumulates preferentially near the peptide surface. In the simulations, both TFE and water molecules make contacts with the peptide surface; water molecules predominate in contacts with the peptide backbone atoms and TFE molecules generally preferentially interact with side chains. Translational diffusion of solvent molecules appears to be slowed near the surface of the peptide. Depending on the location in the structure, TFE molecules form complexes with the peptide that may persist for up to ∼7 ns. Many of the peptide spin-solvent fluorine cross-relaxation parameters (ΣHF) for which experimental values are available are reasonably well-predicted from the simulations. However, the calculated ΣHF values were too small for some hydrogens of the 6Trp indole ring and the amino acid hydrogens near this residue in the native structure, whereas ΣHF values for hydrogens on the side chains of 1Asn, 4Ile, and 7Leu are too large. In 42% TFE-water, persistent conformations of Trp-cage are found, which differ from the conformation found in water by the orientation of the 3Tyr ring.

Examination of Trifluoroethanol Interactions with Trp-Cage through MD Simulations and Intermolecular Nuclear Overhauser Effects.

Molecular dynamics simulations of the protein model Trp-cage in 42% 2,2,2-trifluoroethanol (TFE)-water at 318 K have been carried out with the goal of exploring solvent fluorine-peptide hydrogen nuclear spin cross-relaxation. TFE5 and TFE6 models of TFE developed in previous work from this laboratory were used with the TIP5PE model of water. System densities and component translational diffusion coefficients were well predicted by the simulations, as were many of the cross-relaxation parameters (ΣHF) for which experimental values are available. However, the calculated ΣHF values were too small for some hydrogens of the Trp6 indole ring and for amino acid hydrogens near this residue in the native structure. Simulations carried out with unfolded versions of Trp-cage suggest that underestimates of ΣHF are the result of insufficient sampling of conformational motions that expose these hydrogens to interactions with solvent molecules during simulations of the native peptide. Consideration of the relative amounts of TFE and water surrounding the Trp-cage structure indicates that the composition of the solvent mixture at distances beyond ∼1.5 nm from the surface of the peptide is close to the composition of the bulk solvent, but, as observed by others, TFE tends to accumulate preferentially near the surface of the peptide. Both TFE and water molecules make contacts with the peptide surface; water molecules predominate in contacts with the peptide backbone atoms, and TFE molecules generally preferentially interact with side chains. Translational diffusion of solvent molecules appears to slow down near the surface of the peptide.

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.

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.

The effect of sample viscosity on the deacylation of p-fluoro-trans-cinnamoylchymotrypsin.

The deacylation of p-fluoro-trans-cinnamoylchymotrypsin at pH 5.0 in the presence of variable amounts of polyvinylpyrrolidone has been examined. The sample viscosity at the highest polymer concentration used was over 200 times greater than that of pure buffer but no effects on the deacylation kinetics were observed.

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.

Fluorine nuclear magnetic resonance spectra of rabbit carbonmonoxyhemoglobin.

Carbonmonoxyhemoglobin prepared from protein isolated from rabbits maintained on a diet supplemented with 4-fluorophenylalanine (Phe (4F)) has been studied by fluorine NMR spectroscopy. Substitution of Phe(4F) appears to take place randomly at the sixteen nonequivalent phenylalanine positions of the globins; examination of hybrid hemoglobins in which only one type of globin chain contained the fluorinated amino acid, as well as changes in the spectrum upon exposure to oxygen, aided in the assignment of fluorine resonances from the alpha- or beta-globin chains. The effects of modification of Cys-beta-93 with a spin label and variation of pH and sample temperature on the spectrum were also examined. These data in association with theoretical estimates of aromatic ring current and van der Waals effects on chemical shifts were used to support tentative assignments of several signals observed to specific amino acid residues. Evidence suggesting the presence of two conformational forms of the protein, possibly due to disorder of the heme groups, is described.

Fluorine-NMR studies of chimpanzee hemoglobin.

It has been demonstrated that 4-fluorophenylalanine, a known inhibitor of protein synthesis, becomes incorporated into hemoglobin when present in the diet of a chimpanzee. 19F-NMR spectra of various forms of this protein show well-resolved lines, each line presumably corresponding to a unique phenylalanine/fluorophenylalanine position of the primary sequence. Fluorine chemical shifts and, by implication, tertiary structures vary with the oxidation state and ligand.

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.

Modification of human serum albumin with N-(2,5-dinitro-4-fluorophenyl)-4-amino-2,2,6,6-tetramethyl-piperidinooxy radical.

Human serum albumin has been treated with the spin-labeling reagent indicated in the title. Ultraviolet spectral studies of the protein so modified suggest that reaction takes place at lysine and tyrosine sidechains; kinetic experiments indicate that there are two especially reactive amino groups of the protein which are preferentially modified. Evidence is presented that these groups include the one acetylated by aspirin (Lys-199) or those arylated by 2.6-dinitro-4-trifluoromethylbenzenesulfonate. Esr experiments show that bound spin labels have about the same correlation time expected for overall tumbling of the protein; ESR observations indicate that molecular freedom near the spin labels is not increased when the protein is transferred to 8 M urea.

Reactions of 2,6-dinitro-4-trifluoromethylbenzenesulfonate with human serum albumin.

The reaction of the title compound with human serum albumin has been examined at various concentrations of the sulfonate. Kinetic data suggest that there are two highly reactive lysine amino groups on the protein, five lysine residues which are less reactive and an undetermined number of additional nucleophilic groups that react very slowly with the reagent at pH 7.5. One of the rapidly reacting lysines is tentatively identified as lysine-199 in the protein sequence. Fluorine NMR experiments indicate the presence of tight binding sites on the protein for the sulfonate which are not near reactive functional groups.

NMR studies of fluorophenylalanine-containing carbonic anhydrase.

Rabbits ingesting 4-fluorophenylalanine are known to incorporate small amounts of this fluorinated amino acid into their proteins. Carbonic anhydrase I isolated from the erythrocytes of animals so maintained exhibits a well-resolved fluorine NMR signal for each phenylalanine in the sequence. The chemical shifts of most of these signals respond to the binding of inhibitors, suggesting that most if not all of the tertiary structure of the enzyme adjusts to the presence of inhibitors at the active site.

Measurement of cytosolic calcium using 19F NMR.

Fluorine-19 nuclear magnetic resonance (NMR) studies of cells and perfused organs loaded with fluorinated ion chelators represent a new approach to determining cytosolic free calcium levels in situ. The molecular basis for this approach and the relative advantages and disadvantages of the NMR technique are discussed in this paper. Results obtained on perfused normoxic and ischemic rat hearts are presented, indicating that ischemia is associated with an elevation in the level of cytosolic free calcium before the onset of irreversible cell injury. The results are therefore consistent with this elevation playing a causative role in the mediation of myocardial cell injury resulting from ischemia.

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.

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.

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.

Toward a molecular dynamics force field for simulations of 40% trifluoroethanol-water.

Various computational models of trifluoroethanol (TFE) and water have been explored with the goal of finding a system for molecular dynamics (MD) simulations that reliably predict properties of 40% TFE-water (v/v) and can be used in studies of peptide-solvent nuclear cross-relaxation. Models derived by modification of TFE parameters developed by Fioroni et al. (J. Phys. Chem. B 2000, 104, 12347), in combination with either TIP4P-Ew or TIP5P-E water, were most successful. Simulations of 40% TFE-TIP4P-Ew water evidenced separation of the system into large TFE-rich and water-rich domains. With TIP5P-E water, simulations showed aggregation of each solvent component into small clusters. Nuclear spin dipolar interactions between solvent fluorines and the methyl hydrogens of acetate ion dissolved in 40% TFE-water were calculated. The cross-relaxation parameter σHF reckoned for the TFE-TIP5P-E system agreed with experiment while the value calculated using the TFE-TIP4P-Ew system was too low. While the TFE-TIP5P-E model of 40% TFE-water leads to good predictions of the system density, translational diffusion coefficients, and a solvent-solute cross-relaxation parameter, this model performs poorly in predicting the enthalpy of mixing. Preliminary studies of 20% TFE-water and 50% TFE-water suggest that the model will perform with the same characteristics for mixtures that have compositions near 40% TFE-water.

Investigation of ethanol-peptide and water-peptide interactions through intermolecular nuclear overhauser effects and molecular dynamics simulations.

Molecular dynamics simulations have been used to explore solvent-solute intermolecular nuclear Overhauser effects (NOEs) on NMR (nuclear magnetic resonance) signals of [val5]angiotensin dissolved in 35% ethanol-water (v/v). Consideration of chemical shift, coupling constant and intramolecular NOE data suggest that conformations of the peptide are adequately sampled by simulations of up to 0.6 µs duration. Calculated cross relaxation terms at 0 and 25 °C are compared to experimental values and to terms predicted using a particulate model of the solvent. Many calculated solvent NOEs are in agreement with experimental results; disagreements are particularly striking for hydrogens of the Phe8 residue of the peptide. Calculations show that individual molecules of either solvent component can spend many ns in association with the peptide but dipolar interactions within such a complex account for only a few percent of an observed cross relaxation rate. Most parts of the peptide interact selectively with ethanol. Diffusion of both solvent components is slowed when they are close to the peptide. Solvent-solute cross relaxation terms for acetic acid in the same solvent obtained from simulations agree with experiment. Preferential interactions of solvent molecules with acetic acid are largely absent, as are effects of this solute on solvent diffusion rates.