Alexander A. Nevzorov

Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state NMR spectroscopy

The atomic resolution structure of fd coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles differs from that previously determined by x-ray fiber diffraction. Most notably, the 50-residue protein is not a single curved helix, but rather is a nearly ideal straight helix between residues 7 and 38, where there is a distinct kink, and then a straight helix with a different orientation between residues 39 and 49. Residues 1–5 have been shown to be mobile and unstructured, and proline 6 terminates the helix. The structure of the coat protein in virus particles, in combination with the structure of the membrane-bound form of the same protein in bilayers, also recently determined by solid-state NMR spectroscopy, provides insight into the viral assembly process. In addition to their roles in molecular biology and biotechnology, the filamentous bacteriophages continue to serve as model systems for the development of experimental methods for determining the structures of proteins in biological supramolecular assemblies. New NMR results include the complete sequential assignment of the two-dimensional polarization inversion spin-exchange at the magic angle spectrum of a uniformly 15N-labeled 50-residue protein in a 1.6 × 107 Da particle in solution, and the calculation of the three-dimensional structure of the protein from orientational restraints with an accuracy equivalent to an rms deviation of ≈1Å.

Influence of cholesterol on dynamics of dimyristoylphosphatidylcholine bilayers as studied by deuterium NMR relaxation

Investigation of the deuterium (2H) nuclear magnetic resonance (NMR) relaxation rates of lipid bilayers containing cholesterol can yield new insights regarding its role in membrane function and dynamics. Spin-lattice (R1Z) and quadrupolar order (R1Q) 2H NMR relaxation rates were measured at 46.1 and 76.8 MHz for macroscopically oriented bilayers of 1,2-diperdeuteriomyristoyl-sn-glycero-3-phosphocholine (DMPC-d54) containing cholesterol (1/1 molar ratio) in the liquid-ordered phase at 40 °C. The data for various segmental positions along the DMPC-d54 acyl chain were simultaneously fitted to a composite membrane deformation model, including fast segmental motions which preaverage the coupling tensor along the lipid acyl chain, slow molecular reorientations, and small-amplitude collective fluctuations. In contrast to pure DMPC-d54 in the liquid-crystalline (Lα) phase, for the DMPC-d54:cholesterol (1/1) system a linear square-law functional dependence of the relaxation rates on the order parameter (quadrupola...

Dynamics of lipid bilayers from comparative analysis of 2H and 13C nuclear magnetic resonance relaxation data as a function of frequency and temperature

Analysis of the nuclear spin relaxation rates of lipid membranes provides a powerful means of studying the dynamics of these important biological representatives of soft matter. Here, temperature- and frequency-dependent 2H and 13C nuclear magnetic resonance (NMR) relaxation rates for vesicles and multilamellar dispersions of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) in the liquid–crystalline state have been fitted simultaneously to various dynamic models for different positions of the acyl chains. The data include 2H R1Z rates (Zeeman order of electric quadrupolar interaction) acquired at 12 external magnetic field strengths from 0.382 to 14.6 T, corresponding to a frequency range from ωD/2π=2.50–95.3 MHz; and 2H R1Q rates (quadrupolar order of electric quadrupolar interaction) at 15.3, 46.1, and 76.8 MHz. Moreover, 13C R1Z data (Zeeman order of magnetic dipolar interaction) for DMPC are included at six magnetic field strengths, ranging from 1.40 to 17.6 T, thereby enabling extension of the freq...

Structural basis of the temperature transition of Pf1 bacteriophage

The filamentous bacteriophage Pf1 undergoes a reversible temperature‐dependent transition that is also influenced by salt concentrations. This structural responsiveness may be a manifestation of the important biological property of flexibility, which is necessary for long, thin filamentous assemblies as a protection against shear forces. To investigate structural changes in the major coat protein, one‐ and two‐dimensional solid‐state NMR spectra of concentrated solutions of Pf1 bacteriophage were acquired, and the structure of the coat protein determined at 0°C was compared with the structure previously determined at 30°C. Despite dramatic differences in the NMR spectra, the overall change in the coat protein structure is small. Changes in the orientation of the C‐terminal helical segment and the conformation of the first five residues at the N‐terminus are apparent. These results are consistent with prior studies by X‐ray fiber diffraction and other biophysical methods.

A Resonance Assignment Method for Oriented-Sample Solid-State NMR of Proteins

A general sequential assignment strategy for uniformly (15)N-labeled uniaxially aligned membrane proteins is proposed. Mismatched Hartmann-Hahn magnetization transfer is employed to establish proton-mediated correlations among the neighboring (15)N backbone spins. Magnetically aligned Pf1 phage coat protein was used to illustrate the method. Exchanged and nonexchanged separated local field spectra were acquired and overlaid to distinguish the cross-peaks from the main peaks. Most of the original assignments from the literature were confirmed without selectively labeled samples. This method is applicable to proteins with arbitrary topology and will find use in assigning solid-state NMR spectra of oriented membrane proteins for their subsequent structure determination.

Spin relaxation by dipolar coupling: From motional narrowing to the rigid limit

A coupled system of two molecules bearing spins of 1/2, which are allowed to diffuse relative to each other, is considered. By using a symmetry-adapted basis operator set, the overall density matrix equation is decoupled into two equations for the time-resolved isochromat components, the sum of which yields the observed signal. The appropriate stochastic Liouville equation is solved by a combination of eigenfunction expansion and finite-differences for the angular and radial relative motions, respectively. A full range of spectra from classic Pake patterns in the rigid limit to motionally narrowed Lorentzians is recovered. As an extension of the above approach, the solid-echo experiment is described in terms of the ensemble-averaged isochromats. Homogeneous transverse relaxation times (T2) as a function of the translational diffusion coefficient (DT) are obtained from simulating SECSY (spin-echo correlation spectroscopy) signals, which show distinct T2 minima vs DT. The present method of separating the qu...

Mismatched Hartmann-Hahn Conditions Cause Proton-Mediated Intermolecular Magnetization Transfer between Dilute Low-Spin Nuclei in NMR of Static Solids

Mismatched Hartmann-Hahn conditions between the protons and dilute spins (such as 15N) are found to cause intermolecular magnetization transfer between the low-gamma nuclei over long distances. This transfer is purely proton mediated and occurs even in the absence of direct 15N-15N couplings. This has been demonstrated experimentally using a static single crystal of n-acetyl Leucine with intermolecular distances between the 15N nuclei exceeding 6.5 A. A quantum-mechanical explanation of this phenomenon is given based on the average-Hamiltonian theory which was confirmed by detailed numerical many-spin simulations. The theory and experiment presented in the present paper may help in the development of solid-state NMR methods for studying interhelical contacts in membrane proteins, as well as for their spectral assignment.

Repetitive cross-polarization contacts via equilibration-re-equilibration of the proton bath: Sensitivity enhancement for NMR of membrane proteins reconstituted in magnetically aligned bicelles.

Thermodynamic limit of magnetization corresponding to the intact proton bath usually cannot be transferred in a single cross-polarization contact. This is mainly due to the finite ratio between the number densities of the high- and low-gamma nuclei, quantum-mechanical bounds on spin dynamics, and Hartmann-Hahn mismatches due to rf field inhomogeneity. Moreover, for fully hydrated membrane proteins refolded in magnetically oriented bicelles, short spin-lock relaxation times (T1ρ) and rf heating can further decrease cross polarization efficiency. Here we show that multiple equilibrations-re-equilibrations of the high- and low-spin reservoirs during the preparation period yield an over twofold gain in the magnetization transfer as compared to a single-contact cross polarization (CP), and up to 45% enhancement as compared to the mismatch-optimized CP-MOIST scheme for bicelle-reconstituted membrane proteins. This enhancement is achieved by employing the differences between the spin-lattice relaxation times for the high- and low-gamma spins. The new technique is applicable to systems with short T1ρs, and speeds up acquisition of the multidimensional solid-state NMR spectra of oriented membrane proteins for their subsequent structural and dynamic studies.

Grid-free powder averages: On the applications of the Fokker-Planck equation to solid state NMR

We demonstrate that Fokker-Planck equations in which spatial coordinates are treated on the same conceptual level as spin coordinates yield a convenient formalism for treating magic angle spinning NMR experiments. In particular, time dependence disappears from the background Hamiltonian (sample spinning is treated as an interaction), spherical quadrature grids are avoided completely (coordinate distributions are a part of the formalism) and relaxation theory with any linear diffusion operator is easily adopted from the Stochastic Liouville Equation theory. The proposed formalism contains Floquet theory as a special case. The elimination of the spherical averaging grid comes at the cost of increased matrix dimensions, but we show that this can be mitigated by the use of state space restriction and tensor train techniques. It is also demonstrated that low correlation order basis sets apparently give accurate answers in powder-averaged MAS simulations, meaning that polynomially scaling simulation algorithms do exist for a large class of solid state NMR experiments.

Orientational and Motional Narrowing of Solid-State NMR Lineshapes of Uniaxially Aligned Membrane Proteins

A unified theory for the NMR line shapes of aligned membrane proteins arising from uniaxial disorder (mosaic spread) and global rotational diffusion about the director axis is presented. A superoperator formalism allows one to take into account the effects of continuous radiofrequency irradiation and frequency offsets in the presence of dynamics. A general method based on the Stochastic Liouville Equation makes it possible to bridge the static and dynamic limits in a single model. Simulations of solid-state NMR spectra are performed for a uniform α helix by considering orientational disorder and diffusion of the helix as a whole relative to the alignment axis. The motional narrowing of the resonance lines is highly inhomogeneous and can be used as an additional angular restraint in structure calculations. Experimental solid-state NMR spectra of Pf1 coat protein support the conclusions of the theory for two limiting cases. The static disorder dominates the (15)N NMR spectra of Pf1 aligned on a phage, while fast uniaxial diffusion provides a line narrowing mechanism for the Pf1 protein reconstituted in magnetically aligned bicelles.