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Jack H Freed

Publications and source records attributed to Jack H Freed.

At least 19 recordsLinked to original sources
PubMed2006

Dynamics of the nitroxide side chain in spin-labeled proteins.

The dynamics of the tether linking methanethiosulfonate (MTSSL) spin probes to alpha-helices has been investigated with the purpose of rationalizing its effects on ESR line shapes. Torsional profiles for the chain bonds have been calculated ab initio, and steric interactions with the alpha-helix and the neighboring residues have been introduced at the excluded-volume level. As a consequence of the restrictions deriving from chain geometry and local constraints, a limited number of allowed conformers has been identified that undergo torsional oscillations and conformational jumps. Torsional fluctuations are described as damped oscillations, while transition rates between conformers are calculated according to the Langer multidimensional extension of the Kramers theory. The time scale and amplitude of the different motions are compared; the major role played by rotations of the outermost bonds of the side chain emerges, along with the effects of substituents in the pyrroline ring on the conformer distribution and dynamics. The extent and symmetry of magnetic tensor averaging produced by the side chain motions are estimated, the implications for the ESR spectra of spin-labeled proteins are discussed, and suggestions for the introduction of realistic features of the spin probe dynamics into the line shape simulation are presented.

Models, Molecular↗
PubMed2006

Modeling the effects of structure and dynamics of the nitroxide side chain on the ESR spectra of spin-labeled proteins.

In the companion paper (J. Phys. Chem. B 2006, 110, jp0629487), a study of the conformational dynamics of methanethiosulfonate spin probes linked at a surface-exposed alpha-helix has been presented. Here, on the basis of this analysis, X-band ESR spectra of these spin labels are simulated within the framework of the Stochastic Liouville equation (SLE) methodology. Slow reorientations of the whole protein are superimposed on fast chain motions, which have been identified with conformational jumps and fluctuations in the minima of the chain torsional potential. Fast chain motions are introduced in the SLE for the protein reorientations through partially averaged magnetic tensors and relaxation times calculated according to the motional narrowing theory. The 72R1 and 72R2 mutants of T4 lysozyme, which bear the spin label at a solvent-exposed helix site, have been taken as test systems. For the side chain of the R2 spin label, only a few noninterconverting conformers are possible, whose mobility is limited to torsional fluctuations, yielding almost identical spectra, typical of slightly mobile nitroxides. In the case of R1, more complex spectra result from the simultaneous presence of constrained and mobile chain conformers, with relative weights that can depend on the local environment. The model provides an explanation for the experimentally observed dependence of the spectral line shapes on temperature, solvent, and pattern of substituents in the pyrroline ring. The relatively simple methodology presented here allows the introduction of realistic features of the spin probe dynamics into the simulation of ESR spectra of spin-labeled proteins; moreover, it provides suggestions for a proper account of such dynamics in more sophisticated approaches.

Electron Spin Resonance Spectroscopy↗
PubMed2006

Collective fluctuations in ordered fluids investigated by two-dimensional electron-electron double resonance spectroscopy.

Two-dimensional electron-electron double resonance (2D-ELDOR) is a technique that is sensitive to the dynamical processes affecting spin labels in complex fluid environments. In ordered fluids, such as membrane vesicles, the 2D-ELDOR experiment is affected by the molecular tumbling in the locally ordered environment. This motion occurs on two different time scales, the faster molecular motion relative to the local director, and the slower collective fluctuations of the director field. In the experimental study of Patyal, Crepeau, and Freed (Biophys. J. 1997, 73, 2201), it was found that the widths of the autopeaks of the 2D-ELDOR spectrum increased as a function of the mixing time. In the present work, a theory is developed for the effects of director fluctuations on the autopeaks in the 2D-ELDOR experiment by employing an analytical solution of the stochastic Liouville equation for which the director field is treated as a multidimensional Gaussian process, as previously developed by Frezzato, Kothe, and Moro (J. Phys. Chem. B 2001, 105, 1281 and J. Phys. Chem. B 2004, 108, 9505). Good agreement is found between theory and experiment, notably the only adjustable parameter is k, the bending elastic modulus of the membrane. The values of k = 11 x 10(-20) J for 1,2-dipalmitoyl-sn-glycero-phosphatidylcholine (DPPC) vesicles and k = 15 x 10(-20) J for DPPC/gramicidin A (5:1) vesicles, both at 45 degrees C, were found from the analysis and agree well with previous related measurements by other physical techniques. This establishes 2D-ELDOR as a useful technique to study the elastic properties of biological membranes.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2006

Methyl dynamics in proteins from NMR slowly relaxing local structure spin relaxation analysis: A new perspective.

NMR spin relaxation of (2)H nuclei in (13)CH(2)D groups is a powerful method for studying side-chain motion in proteins. The analysis is typically carried out with the original model-free (MF) approach adapted to methyl dynamics. The latter is described in terms of axial local motions around, and of, the methyl averaging axis, mutually decoupled and independent of the global motion of the protein. Methyl motion is characterized primarily by the axial squared order parameter, S(axis)2, associated with fluctuations of the methyl averaging axis. This view is shown to be oversimplified by applying to typical experimental data the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (Adv. Chem. Phys. 1993, 83, 89) which can be considered the generalization of the MF approach. Neglecting mode coupling and the asymmetry of the local ordering and treating approximately features of local geometry imply inaccurate values of S(axis)2, hence of the residual configurational entropy derived from it. S(axis)2, interpreted as amplitude of motion, was found to range from near disorder to almost complete order. Contrary to this picture, we find with the SRLS approach a moderate distribution in the magnitude of asymmetric local ordering and significant variation in its symmetry. The latter important property can be associated implicitly with the contribution of side-chain rotamer jumps. This is consistent with experimental residual dipolar coupling studies and theoretical work based on molecular dynamics simulations and molecular mechanics considerations. Configurational entropy is obtained in the SRLS approach directly from experimentally determined asymmetric potentials. Inconsistency between order parameters from 2H relaxation and from eta(HC-HH) cross-correlation and increase in order parameters with increasing temperature were observed with the MF approach. These discrepancies are reconciled, and physically tenable temperature dependence is obtained with the SRLS approach.

Biophysics↗
PubMed2006

Inter-helix distances in lysophospholipid micelle-bound alpha-synuclein from pulsed ESR measurements.

We demonstrate the use of pulsed ESR spectroscopy to measure intramolecular distances in the Parkinson's disease-associated protein alpha-synuclein bound to detergent and lysophospholipid micelles. We show that the inter-helical separation between the two helices formed upon binding to micelles is dependent on micelle composition, with micelles formed from longer acyl chains leading to an increased splaying of the two helices. Our data suggest that the topology of alpha-synuclein is not strongly constrained by the linker region between the two helices and instead depends on the geometry of the surface to which the protein is bound.

Electron Spin Resonance Spectroscopy↗
PubMed2006

Protein dynamics from NMR: the slowly relaxing local structure analysis compared with model-free analysis.

(15)N-(1)H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multifield data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the slowly relaxing local structure (SRLS) approach, which accounts rigorously for mode mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulas are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF analysis force-fits the experimental data because mode mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multifield multitemperature data analyzed with the MF approach may lead to the detection of incorrect phenomena, and conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS spectral densities comply with this requirement.

Computer Simulation↗
PubMed2006

Reconstruction of the chemotaxis receptor-kinase assembly.

In bacterial chemotaxis, an assembly of transmembrane receptors, the CheA histidine kinase and the adaptor protein CheW processes environmental stimuli to regulate motility. The structure of a Thermotoga maritima receptor cytoplasmic domain defines CheA interaction regions and metal ion-coordinating charge centers that undergo chemical modification to tune receptor response. Dimeric CheA-CheW, defined by crystallography and pulsed ESR, positions two CheWs to form a cleft that is lined with residues important for receptor interactions and sized to clamp one receptor dimer. CheW residues involved in kinase activation map to interfaces that orient the CheW clamps. CheA regulatory domains associate in crystals through conserved hydrophobic surfaces. Such CheA self-contacts align the CheW receptor clamps for binding receptor tips. Linking layers of ternary complexes with close-packed receptors generates a lattice with reasonable component ratios, cooperative interactions among receptors and accessible sites for modification enzymes.

Bacterial Proteins↗
PubMed2006

Coexisting domains in the plasma membranes of live cells characterized by spin-label ESR spectroscopy.

The importance of membrane-based compartmentalization in eukaryotic cell function has become broadly appreciated, and a number of studies indicate that these eukaryotic cell membranes contain coexisting liquid-ordered (L(o)) and liquid-disordered (L(d)) lipid domains. However, the current evidence for such phase separation is indirect, and so far there has been no direct demonstration of differences in the ordering and dynamics for the lipids in these two types of regions or their relative amounts in the plasma membranes of live cells. In this study, we provide direct evidence for the presence of two different types of lipid populations in the plasma membranes of live cells from four different cell lines by electron spin resonance. Analysis of the electron spin resonance spectra recorded over a range of temperatures, from 5 to 37 degrees C, shows that the spin-labeled phospholipids incorporated experience two types of environments, L(o) and L(d), with distinct order parameters and rotational diffusion coefficients but with some differences among the four cell lines. These results suggest that coexistence of lipid domains that differ significantly in their dynamic order in the plasma membrane is a general phenomenon. The L(o) region is found to be a major component in contrast to a model in which small liquid-ordered lipid rafts exist in a 'sea' of disordered lipids. The results on ordering and dynamics for the live cells are also compared with those from model membranes exhibiting coexisting L(o) and L(d) phases.

Animals↗
PubMed2006

Electron spin resonance microscopy applied to the study of controlled drug release.

We describe our recent developments towards 3D micron-scale imaging capability, based on electron spin resonance (ESR), and its application to the study of controlled release. The method, termed ESR microscopy (ESRM), is an extension of the conventional "millimeter-scale" ESR imaging technique. It employs paramagnetic molecules (such as stable radicals or spin-labeled drugs) and may enable one to obtain accurate 3D spatially resolved information about the drug concentration, its self-diffusion tensor, rotational correlation time and the pH in the release matrix. Theoretical calculations, along with initial experimental results, suggest that a 3D resolution of approximately 1 microm is feasible with this method. Here we were able to image successfully a high spin concentration sample with a resolution of approximately 3 x 3 x 8 microm and subsequently study a single approximately 120 microm biodegradable microsphere, internalized with a dilute solution of trityl radical, with a resolution of approximately 12.7 x 13.2 x 26 microm. Analysis of the microsphere ESR imaging data revealed a likely increase in the viscosity inside the sphere and/or binding of the radical molecule to the sphere matrix. Future directions for progress are also discussed.

Drug Delivery Systems↗
PubMed2005

EPR distance measurements support a model for long-range radical initiation in E. coli ribonucleotide reductase.

The class I E. coli ribonucleotide reductase, composed of homodimers of R1 and R2, catalyzes the conversion of nucleoside diphosphates to deoxynucleoside diphosphates. The reduction process involves the tyrosyl radical on R2 that generates a transient thiyl radical on R1 over a proposed distance of 35 A. A mechanism-based inhibitor, 2'-azido-2'-deoxyuridine-5'-diphosphate, that reduces the tyrosyl radical on R2 and forms a nitrogen-centered radical on R1 has provided a method to measure the diagonal distance between the two subunits. PELDOR and DQC paramagnetic resonance methods give rise to a distance of 48 A, similar to that calculated from a docking model of the R1 and R2 structures.

Electron Spin Resonance Spectroscopy↗
PubMed2005

Effects of finite pulse width on two-dimensional Fourier transform electron spin resonance.

Two-dimensional (2D) Fourier transform ESR techniques, such as 2D-ELDOR, have considerably improved the resolution of ESR in studies of molecular dynamics in complex fluids such as liquid crystals and membrane vesicles and in spin labeled polymers and peptides. A well-developed theory based on the stochastic Liouville equation (SLE) has been successfully employed to analyze these experiments. However, one fundamental assumption has been utilized to simplify the complex analysis, viz. the pulses have been treated as ideal non-selective ones, which therefore provide uniform irradiation of the whole spectrum. In actual experiments, the pulses are of finite width causing deviations from the theoretical predictions, a problem that is exacerbated by experiments performed at higher frequencies. In the present paper we provide a method to deal with the full SLE including the explicit role of the molecular dynamics, the spin Hamiltonian and the radiation field during the pulse. The computations are rendered more manageable by utilizing the Trotter formula, which is adapted to handle this SLE in what we call a "Split Super-Operator" method. Examples are given for different motional regimes, which show how 2D-ELDOR spectra are affected by the finite pulse widths. The theory shows good agreement with 2D-ELDOR experiments performed as a function of pulse width.

Electron Spin Resonance Spectroscopy↗
PubMed2005

Maximum entropy: a complement to Tikhonov regularization for determination of pair distance distributions by pulsed ESR.

Tikhonov regularization (TIKR) has been demonstrated as a powerful and valuable method for the determination of distance distributions of spin-pairs in bi-labeled biomolecules directly from pulsed ESR signals. TIKR is a direct method, which requires no iteration, and, therefore, provides a rapid and unique solution. However, the distribution obtained tends to exhibit oscillatory excursions with negative portions in the presence of finite noise, especially in the peripheral regions of the distribution. The Shannon-Jaynes entropy of a probability distribution provides an intrinsic non-negativity constraint on the probability distribution and an unbiased way of obtaining information from incomplete data. We describe how the maximum entropy regularization method (MEM) may be applied to solve the ill-posed nature of the dipolar signal in pulsed ESR. We make use of it to suppress the negative excursions of the distance distribution and to increase the tolerance to noise in the dipolar signal. Model studies and experimental data are investigated, and they show that, with the initial or "seed" probability distribution that is required for MEM taken as the TIKR result, then MEM is able to provide a regularized solution, subject to the non-negativity constraint, and it is effective in dealing with noise that is problematic for TIKR. In addition we have incorporated into our MEM method the ability to extract the intermolecular dipolar component, which is embedded in the raw experimental data. We find that MEM minimization, which is implemented iteratively, is greatly accelerated using the TIKR result as the seed, and it converges more successfully. Thus we regard the MEM method as a complement to TIKR by securing a positive pair distance distribution and enhancing the accuracy of TIKR.

Cytochromes c↗
PubMed2005

New method for determining tie-lines in coexisting membrane phases using spin-label ESR.

A full description of coexisting phases includes their respective compositions, which are provided by the thermodynamic tie-lines. Fluorescence microscopy enables visualization of coexisting lipid phases in giant unilamellar phases, but the composition information is missing. For cholesterol-containing lipid mixtures, knowledge of the compositions of the coexisting phases is important for understanding the nature of "membrane rafts". We propose and demonstrate a new method, based on ESR spectroscopy, for determining tie-lines in regions of two-phase coexistence in a ternary lipid mixture. Over 100 different lipid compositions containing the spin-labeled phospholipid 16-PC in or near the two-phase coexistence region of the liquid-disordered and the gel phases of dipalmitoyl-PC/dilauroyl-PC/cholesterol (DPPC/DLPC/Chol) were studied to determine five tie-lines, spread over virtually the full range of this coexistence region. The method is based on the facts that (1) along a tie-line the ESR spectrum must be a superposition of the two ESR spectra from the respective single phases at the phase boundaries (connected by the tie-line) in a ratio given by the lever rule; (2) along a tie-line the partition coefficient, K(p), for the spin-label, which is also determined in our method, must be constant. We do find that K(p) for 16-PC is close to unity, but its value depends on the particular tie-line. The coexisting phases in equilibrium are characterized by the K(p) of the spin-label and its respective dynamic parameters obtained from fitting the ESR spectra to dynamical models.

Cholesterol↗
PubMed2005

High-frequency ESR at ACERT.

High-field ESR offers many advantages in exploring fundamental questions of structure and dynamics in chemical, biological and physical samples. We provide a review of recent work performed at ACERT demonstrating the utility and flexibility of our methods for extracting both qualitative and quantitative information from a variety of systems. In particular, we emphasize the utility of multi-frequency ESR techniques for unraveling the details of the complex dynamical modes of proteins in solution and in heterogeneous systems such as lipid bilayers. We also include indications of directions for future work where appropriate.

Dimerization↗
PubMed2005

The determination of pair distance distributions by pulsed ESR using Tikhonov regularization.

Pulsed ESR techniques with the aid of site-directed spin labeling have proven useful in providing unique structural information about proteins. The determination of distance distributions in electron spin pairs directly from the dipolar time evolution of the pulsed ESR signals by means of the Tikhonov regularization method is reported. The difficulties connected with numerically inverting this ill-posed mathematical problem are clearly illustrated. The Tikhonov regularization with the regularization parameter determined by the L-curve criterion is then described and tested to confirm its accuracy and reliability. The method is applied to recent experimental results on doubly labeled proteins that have been studied using two pulsed ESR techniques, double quantum coherence (DQC) ESR and double electron-electron resonance (DEER). The extracted distance distributions are able to provide valuable information about the conformational constraints in various partially folded states of proteins. This study supplies a mathematically reliable method for extracting pair distributions from pulsed ESR experimental data and has extended the use of pulsed ESR to provide results of greater value for structural biology.

Cytochromes c↗
PubMed2005

A variable temperature EPR study of Mn(2+)-doped NH(4)Cl(0.9)I(0.1) single crystal at 170 GHz: zero-field splitting parameter and its absolute sign.

EPR measurements have been carried out on a single crystal of Mn(2+)-doped NH(4)Cl(0.9)I(0.1) at 170-GHz in the temperature range of 312-4.2K. The spectra have been analyzed (i) to estimate the spin-Hamiltonian parameters; (ii) to study the temperature variation of the zero-field splitting (ZFS) parameter; (iii) to confirm the negative absolute sign of the ZFS parameter unequivocally from the temperature-dependent relative intensities of hyperfine sextets at temperatures below 10K; and (iv) to detect the occurrence of a structural phase transition at 4.35K from the change in the structure of the EPR lines with temperature below 10K.

Ammonium Chloride↗
PubMed2004

Spin-labeled gramicidin a: channel formation and dissociation.

Gramicidin A was studied by continuous wave electron spin resonance (CW-ESR) and by double-quantum coherence electron spin resonance (DQC-ESR) in several lipid membranes (using samples that were macroscopically aligned by isopotential spin-dry ultracentrifugation) and vesicles. As a reporter group, the nitroxide spin-label was attached at the C-terminus yielding the spin-labeled product (GAsl). ESR spectra of aligned membranes containing GAsl show strong orientation dependence. In DPPC and DSPC membranes at room temperature the spectral shape is consistent with high ordering, which, in conjunction with the observed high polarity of the environment of the nitroxide, is interpreted in terms of the nitroxide moiety being close to the membrane surface. In contrast, spectra of GAsl in DMPC membranes indicate deeper embedding and tilt of the NO group. The GAsl spectrum in the DPPC membrane at 35 degrees C (the gel to Pbeta phase transition) exhibits sharp changes, and above this temperature becomes similar to that of DMPC. The dipolar spectrum from DQC-ESR clearly indicates the presence of pairs in DMPC membranes. This is not the case for DPPC, rapidly frozen from the gel phase; however, there are hints of aggregation. The interspin distance in the pairs is 30.9 A, in good agreement with estimates for the head-to-head GAsl dimer (the channel-forming conformation), which matches the hydrophobic thickness of the DMPC bilayer. Both DPPC and DSPC, apparently as a result of hydrophobic mismatch between the dimer length and bilayer thickness, do not favor the channel formation in the gel phase. In the Pbeta and Lalpha phases of DPPC (above 35 degrees C) the channel dimer forms, as evidenced by the DQC-ESR dipolar spectrum after rapid freezing. It is associated with a lateral expansion of lipid molecules and a concomitant decrease in bilayer thickness, which reduces the hydrophobic mismatch. A comparison with studies of dimer formation by other physical techniques indicates the desirability of using low concentrations of GA (approximately 0.4-1 mol %) accessible to the ESR methods employed in the study, since this yields non-interacting dimer channels.

Electron Spin Resonance Spectroscopy↗