Biomedical subjects

Robert G Griffin

Publications and source records attributed to Robert G Griffin.

16 recordsLinked to original sources

PubMed2003

Measurement of multiple psi torsion angles in uniformly 13C,15N-labeled alpha-spectrin SH3 domain using 3D 15N-13C-13C-15N MAS dipolar-chemical shift correlation spectroscopy.

We demonstrate the simultaneous measurement of several backbone torsion angles psi in the uniformly (13)C,(15)N-labeled alpha-Spectrin SH3 domain using two different 3D 15N-13C-13C-15N dipolar-chemical shift magic-angle spinning (MAS) NMR experiments. The first NCCN experiment utilizes double quantum (DQ) spectroscopy combined with the INADEQUATE type 13C-13C chemical shift correlation. The decay of the DQ coherences formed between 13C'(i) and 13C(alphai) spin pairs is determined by the "correlated" dipolar field due to 15N(i)-13C(alphai) and 13C'(i)-15N(i+1) dipolar couplings and is particularly sensitive to variations of the torsion angle in the regime |psi| > 140 degrees. However, the ability of this experiment to constrain multiple psi-torsion angles is limited by the resolution of the 13C(alpha)-(13)CO correlation spectrum. This problem is partially addressed in the second approach described here, which is an NCOCA NCCN experiment. In this case the resolution is enhanced by the superior spectral dispersion of the 15N resonances present in the 15N(i+1)-13C(alphai) part of the NCOCA chemical shift correlation spectrum. For the case of the 62-residue alpha-spectrin SH3 domain, we determined 13 psi angle constraints with the INADEQUATE NCCN experiment and 22 psi constraints were measured in the NCOCA NCCN experiment.

Carbon Isotopes↗

PubMed2003

Solid-state NMR investigation of the buried X-proline peptide bonds of bacteriorhodopsin.

The role of proline residues in the photocycle of bacteriorhodopsin (bR) is addressed using solid-state NMR. (13)C and (15)N chemical shifts from X-Pro peptide bonds in bR are assigned from REDOR difference spectra of pairwise labeled samples, and correlations of chemical shifts with structure are explored in a series of X-Pro model compounds. Results for the three membrane-embedded X-Pro bonds of bR indicate only slight changes in the transition from the resting state of the protein to either the early or late M state of the protonmotive photocycle. These results suggest that the buried prolines serve a principally structural role in bR.

Bacteriorhodopsins↗

PubMed2003

Backbone and side chain assignment strategies for multiply labeled membrane peptides and proteins in the solid state.

We demonstrate that the SPECIFIC CP technique can be used to obtain heteronuclear correlation (HETCOR) spectra of peptide backbones with greater efficiency than conventional HETCOR methods. We show that similar design principles can be employed to achieve selective homonuclear polarization transfer mediated through dipolar or scalar couplings. Both approaches are demonstrated in a tripeptide with uniform 15N and 13C labeling, and with uniform 15N labeling and natural abundance 13C. In other applications, the high efficiency of the heteronuclear SPECIFIC CP transfer allows discrimination of single amide signals in the 248-residue membrane protein bacteriorhodopsin (bR). In particular, variations are detected in the ordering of the Ala81-Arg82 peptide bond among the photocycle intermediates of bR and SPECIFIC CP is used to correlate 15N and 13C signals from the three Val-Pro peptide bonds.

Bacteriorhodopsins↗

PubMed2003

Multiple-quantum magic-angle spinning spectroscopy using nonlinear sampling.

NMR spectroscopy is a relatively insensitive technique and many biomolecular applications operate near the limits of sensitivity and resolution. A particularly challenging example is detection of the quadrupolar nucleus 17O, due to its low natural abundance, large quadrupole couplings, and low gyromagnetic ratio. Yet the chemical shift of 17O spans almost 1000 ppm in organic molecules and it serves as a potentially unique reporter of hydrogen bonding in peptides, nucleic acids, and water, and as a valuable complement to 13C and 15N NMR. Recent developments including the multiple-quantum magic-angle spinning (MQMAS) experiment have enabled the detection of 17O in biological solids, but very long data acquisitions are required to achieve sufficient sensitivity and resolution. Here, we perform nonlinear sampling in the indirect dimension of MQMAS experiments to substantially reduce the total acquisition time and improve sensitivity and resolution. Nonlinear sampling prevents the use of the discrete Fourier transform; instead, we employ maximum entropy (MaxEnt) reconstruction. Nonlinearly sampled MQMAS spectra are shown to provide high resolution and sensitivity in several systems, including lithium sulfate monohydrate (LiSO(4)-H(2)17O) and L-asparagine monohydrate (H(2)17O). The combination of nonlinear sampling and MaxEnt reconstruction promises to make the application of 17O MQMAS practical in a wider range of biological systems.

Anisotropy↗

PubMed2003

Rotational resonance NMR: separation of dipolar coupling and zero quantum relaxation.

The solid state NMR technique of rotational resonance (R2) has been used extensively to measure distances approaching 5-6 A between 13C nuclei in a variety of compounds including amyloidogenic peptides and membrane proteins. The accuracy of the distance information extracted from the time-dependent spin dynamics at R2 is often limited by the accuracy with which the relevant zero-quantum lineshape parameters are estimated. Here we demonstrate that measurement of spinning frequency dependent magnetization exchange dynamics provides data from which both distance and zero-quantum relaxation parameters can be extracted independently. In addition to providing more accurate distance information, this technique allows examination of the zero-quantum lineshape, which can indicate the presence of correlated relaxation or chemical shift distributions between dipolar-coupled sites. With this approach we have separated the contribution of dipolar couplings and zero quantum relaxation to R2 exchange curves. Thus, we have significantly improved the accuracy of the measurement of the intramolecular, internuclear distances between a pair of 13C's in two model compounds (N-acetyl-D,L-valine and glycylglycine.HCl) that lie in the distance range 4.6-4.7 A.

Carbon Isotopes↗

PubMed2002

Molecular conformation of a peptide fragment of transthyretin in an amyloid fibril.

The molecular conformation of peptide fragment 105-115 of transthyretin, TTR(105-115), previously shown to form amyloid fibrils in vitro, has been determined by magic-angle spinning solid-state NMR spectroscopy. 13C and 15N linewidth measurements indicate that TTR(105-115) forms a highly ordered structure with each amino acid in a unique environment. 2D 13C-13C and 15N-13C-13C chemical shift correlation experiments, performed on three fibril samples uniformly 13C,15N-labeled in consecutive stretches of 4 aa, allowed the complete sequence-specific backbone and side-chain 13C and 15N resonance assignments to be obtained for residues 105-114. Analysis of the 15N, 13CO, 13Calpha, and 13Cbeta chemical shifts allowed quantitative predictions to be made for the backbone torsion angles phi and psi. Furthermore, four backbone 13C-15N distances were determined in two selectively 13C,15N-labeled fibril samples by using rotational-echo double-resonance NMR. The results show that TTR(105-115) adopts an extended beta-strand conformation that is similar to that found in the native protein except for substantial differences in the vicinity of the proline residue.

Amino Acid Sequence↗

PubMed2002

Determination of multiple torsion-angle constraints in U-(13)C,(15)N-labeled peptides: 3D (1)H-(15)N-(13)C-(1)H dipolar chemical shift NMR spectroscopy in rotating solids.

We demonstrate constraint of peptide backbone and side-chain conformation with 3D (1)H-(15)N-(13)C-(1)H dipolar chemical shift, magic-angle spinning NMR experiments. In these experiments, polarization is transferred from (15)N[i] by ramped SPECIFIC cross polarization to the (13)C(alpha)[i], (13)C(beta)[i], and (13)C(alpha)[i - 1] resonances and evolves coherently under the correlated (1)H-(15)N and (1)H-(13)C dipolar couplings. The resulting set of frequency-labeled (15)N(1)H-(13)C(1)H dipolar spectra depend strongly upon the molecular torsion angles phi[i], chi1[i], and psi[i - 1]. To interpret the data with high precision, we considered the effects of weakly coupled protons and differential relaxation of proton coherences via an average Liouvillian theory formalism for multispin clusters and employed average Hamiltonian theory to describe the transfer of (15)N polarization to three coupled (13)C spins ((13)C(alpha)[i], (13)C(beta)[i], and (13)C(alpha)[i - 1]). Degeneracies in the conformational solution space were minimized by combining data from multiple (15)N(1)H-(13)C(1)H line shapes and analogous data from other 3D (1)H-(13)C(alpha)-(13)C(beta)-(1)H (chi1), (15)N-(13)C(alpha)-(13)C'-(15)N (psi), and (1)H-(15)N[i]-(15)N[i + 1]-(1)H (phi, psi) experiments. The method is demonstrated here with studies of the uniformly (13)C,(15)N-labeled solid tripeptide N-formyl-Met-Leu-Phe-OH, where the combined data constrains a total of eight torsion angles (three phi, three chi1, and two psi): phi(Met) = -146 degrees, psi(Met) = 159 degrees, chi1(Met) = -85 degrees, phi(Leu) = -90 degrees, psi(Leu) = -40 degrees, chi1(Leu) = -59 degrees, phi(Phe) = -166 degrees, and chi1(Phe) = 56 degrees. The high sensitivity and dynamic range of the 3D experiments and the data analysis methods provided here will permit immediate application to larger peptides and proteins when sufficient resolution is available in the (15)N-(13)C chemical shift correlation spectra.

Carbon Isotopes↗

PubMed2002

3D TEDOR NMR experiments for the simultaneous measurement of multiple carbon-nitrogen distances in uniformly (13)C,(15)N-labeled solids.

We describe three-dimensional magic-angle-spinning NMR experiments for the simultaneous measurement of multiple carbon-nitrogen distances in uniformly (13)C,(15)N-labeled solids. The approaches employ transferred echo double resonance (TEDOR) for (13)C-(15)N coherence transfer and (15)N and (13)C frequency labeling for site-specific resolution, and build on several previous 3D TEDOR techniques. The novel feature of the 3D TEDOR pulse sequences presented here is that they are specifically designed to circumvent the detrimental effects of homonuclear (13)C-(13)C J-couplings on the measurement of weak (13)C-(15)N dipolar couplings. In particular, homonuclear J-couplings lead to two undesirable effects: (i) they generate anti-phase and multiple-quantum (MQ) spin coherences, which lead to spurious cross-peaks and phase-twisted lines in the 2D (15)N-(13)C correlation spectra, and thus degrade the spectral resolution and prohibit the extraction of reliable cross-peak intensities, and (ii) they significantly reduce cross-peak intensities for strongly J-coupled (13)C sites (e.g., CO and C(alpha)). The first experiment employs z-filter periods to suppress the anti-phase and MQ coherences and generates 2D spectra with purely absorptive peaks for all TEDOR mixing times. The second approach uses band-selective (13)C pulses to refocus J-couplings between (13)C spins within the selective pulse bandwidth and (13)C spins outside the bandwidth. The internuclear distances are extracted by using a simple analytical model, which accounts explicitly for multiple spin-spin couplings contributing to cross-peak buildup. The experiments are demonstrated in two U-(13)C,(15)N-labeled peptides, N-acetyl-L-Val-L-Leu (N-ac-VL) and N-formyl-L-Met-L-Leu-L-Phe (N-f-MLF), where 20 and 26 (13)C-(15)N distances up to approximately 5-6 A were measured, respectively. Of the measured distances, 10 in N-ac-VL and 13 in N-f-MLF are greater than 3 A and provide valuable structural constraints.

Carbon Isotopes↗

PubMed2002

Solution-state dynamic nuclear polarization at high magnetic field.

The goal of dynamic nuclear polarization (DNP) is to enhance NMR signals by transferring electron spin polarization to the nuclei. Although mechanisms such as the solid effect and thermal mixing can be used for DNP in the solid state, currently, the only practical mechanism in solutions is the Overhauser effect (OE), which usually arises due to dipolar relaxation between electrons and the nuclei. At magnetic fields greater than approximately 1 T, dipolar relaxation does not result in a useful enhancement and therefore the conventional wisdom is that DNP should not work in solutions at high magnetic fields. However, scalar relaxation due to time-dependent scalar couplings has a different magnetic field dependence and can lead to substantial OE enhancements. At room temperature and at a magnetic field of 5 T (211 MHz for protons, 140 GHz for electrons), we have observed that scalar relaxation between electrons and nuclei results in NMR signal enhancements of 180, 42, -36, and 8, for 31P, 13C, 15N, and 19F, respectively.

Magnetic Resonance Spectroscopy↗

PubMed2002

De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy.

The three-dimensional structure of the chemotactic peptide N-formyl-l-Met-l-Leu-l-Phe-OH was determined by using solid-state NMR (SSNMR). The set of SSNMR data consisted of 16 (13)C-(15)N distances and 18 torsion angle constraints (on 10 angles), recorded from uniformly (13)C,(15)N- and (15)N-labeled samples. The peptide's structure was calculated by means of simulated annealing and a newly developed protocol that ensures that all of conformational space, consistent with the structural constraints, is searched completely. The result is a high-quality structure of a molecule that has thus far not been amenable to single-crystal diffraction studies. The extensions of the SSNMR techniques and computational methods to larger systems appear promising.

N-Formylmethionine Leucyl-Phenylalanine↗

PubMed2002

Two-dimensional (13)C-(13)C correlation spectroscopy with magic angle spinning and dynamic nuclear polarization.

The sensitivity of solid-state NMR experiments can be enhanced with dynamic nuclear polarization (DNP), a technique that transfers the high Boltzmann polarization of unpaired electrons to nuclei. Signal enhancements of up to 23 have been obtained for magic angle spinning (MAS) experiments at 5 T and 85-90 K using a custom-designed high-power gyrotron. The extended stability of MAS/DNP experiments at low temperature is demonstrated with (1)H-driven (13)C spin-diffusion experiments on the amino acid proline. These (13)C-(13)C chemical shift correlation spectra are the first two-dimensional MAS/DNP experiments performed at high field (>1.4 T).

Carbon Isotopes↗

PubMed2002

Tryptophan interactions in bacteriorhodopsin: a heteronuclear solid-state NMR study.

The bulky and amphiphilic nature of tryptophan residues makes them particularly interesting components of proteins. In bacteriorhodopsin, four of the eight tryptophan residues are in the active site, forming parts of the retinal binding pocket. In this work, we use solid-state NMR to study the interactions of the tryptophan residues in wild-type bacteriorhodopsin, in the resting state, and in critical intermediates of the proton-motive photocycle. The range of the chemical shifts of the indole nitrogens suggests that all eight of them are hydrogen bonded. Using difference spectroscopy, we isolate several changes in these hydrogen bonds in the early and late M states. As found earlier for the peptide backbone, some perturbations found in the early M state relax in the transition to the late M state while new perturbations arise. Interestingly, Rotational Echo DOuble Resonance (REDOR) difference spectroscopy of [20-13C]retinal,[indole-15N]Trp-bR shows that indole of Trp182 is not involved in the significant hydrogen bond perturbations. We also use REDOR to measure dipolar interactions in [20-13C]retinal,[indole-15N]Trp-bR, and thereby determine the distance between the C20 of retinal and the indole nitrogen of Trp182. The internuclear distance changes only slightly from the light-adapted state (3.36 +/- 0.2 A) to the early M state (3.16 +/- 0.4 A).

Bacteriorhodopsins↗

PubMed2002

Chromophore distortions in the bacteriorhodopsin photocycle: evolution of the H-C14-C15-H dihedral angle measured by solid-state NMR.

In recent years, structural information about bacteriorhodopsin has grown substantially with the publication of several crystal structures. However, precise measurements of the chromophore conformation in the various photocycle states are still lacking. This information is critical because twists about the chromophore backbone chain can influence the Schiff base nitrogen position, orientation, and proton affinity. Here, we focus on the C14-C15 bond, using solid-state nuclear magnetic resonance spectroscopy to measure the H-C14-C15-H dihedral angle. In the resting state (bR(568)), we obtain an angle of 164 +/- 4 degrees, indicating a 16 degrees distortion from a planar all-trans chromophore. The dihedral angle is found to decrease to 147 +/- 10 degrees in the early M intermediate (M(o)) and to 150 +/- 4 degrees in the late M intermediate (M(n)). These results demonstrate changes in the chromophore conformation undetected by recent X-ray diffraction studies.

Bacteriorhodopsins↗

PubMed2002

NMR determination of the torsion angle psi in alpha-helical peptides and proteins: the HCCN dipolar correlation experiment.

Several existing methods permit measurement of the torsion angles phi, psi and chi in peptides and proteins with solid-state MAS NMR experiments. Currently, however, there is not an approach that is applicable to measurement of psi in the angular range -20 degree to -70 degree, commonly found in alpha-helical structures. Accordingly, we have developed a HCCN dipolar correlation MAS experiment that is sensitive and accurate in this regime. An initial REDOR driven (13)C'--(15)N dipolar evolution period is followed by the C' to C(alpha) polarization transfer and by Lee--Goldburg cross polarization recoupling of the (13)C(alpha)(1)H dipolar interaction. The difference between the effective (13)C(1)H and (13)C(15)N dipolar interaction strengths is balanced out by incrementing the (13)C--(15)N dipolar evolution period in steps that are a factor of R(R approximately omega(CH)/omega(CN)) larger than the (13)C--(1)H steps. The resulting dephasing curves are sensitive to variations in psi in the angular region associated with alpha-helical secondary structure. To demonstrate the validity of the technique, we apply it to N-formyl-[U-(13)C,(15)N] Met-Leu-Phe-OH (MLF). The value of psi extracted is consistent with the previous NMR measurements and close to that reported in diffraction studies for the methyl ester of MLF, N-formyl-[U-(13)C,(15)N]Met-Leu-Phe-OMe.

Computer Simulation↗

PubMed2002

Control of the pump cycle in bacteriorhodopsin: mechanisms elucidated by solid-state NMR of the D85N mutant.

By varying the pH, the D85N mutant of bacteriorhodopsin provides models for several photocycle intermediates of the wild-type protein in which D85 is protonated. At pH 10.8, NMR spectra of [zeta-(15)N]lys-, [12-(13)C]retinal-, and [14,15-(13)C]retinal-labeled D85N samples indicate a deprotonated, 13-cis,15-anti chromophore. On the other hand, at neutral pH, the NMR spectra of D85N show a mixture of protonated Schiff base species similar to that seen in the wild-type protein at low pH, and more complex than the two-state mixture of 13-cis,15-syn, and all-trans isomers found in the dark-adapted wild-type protein. These results lead to several conclusions. First, the reversible titration of order in the D85N chromophore indicates that electrostatic interactions have a major influence on events in the active site. More specifically, whereas a straight chromophore is preferred when the Schiff base and residue 85 are oppositely charged, a bent chromophore is found when both the Schiff base and residue 85 are electrically neutral, even in the dark. Thus a "bent" binding pocket is formed without photoisomerization of the chromophore. On the other hand, when photoisomerization from the straight all-trans,15-anti configuration to the bent 13-cis,15-anti does occur, reciprocal thermodynamic linkage dictates that neutralization of the SB and D85 (by proton transfer from the former to the latter) will result. Second, the similarity between the chromophore chemical shifts in D85N at alkaline pH and those found previously in the M(n) intermediate of the wild-type protein indicate that the latter has a thoroughly relaxed chromophore like the subsequent N intermediate. By comparison, indications of L-like distortion are found for the chromophore of the M(o) state. Thus, chromophore strain is released in the M(o)-->M(n) transition, probably coincident with, and perhaps instrumental to, the change in the connectivity of the Schiff base from the extracellular side of the membrane to the cytoplasmic side. Because the nitrogen chemical shifts of the Schiff base indicate interaction with a hydrogen-bond donor in both M states, it is possible that a water molecule travels with the Schiff base as it switches connectivity. If so, the protein is acting as an inward-driven hydroxyl pump (analogous to halorhodopsin) rather than an outward-driven proton pump. Third, the presence of a significant C [double bond] N syn component in D85N at neutral pH suggests that rapid deprotonation of D85 is necessary at the end of the wild-type photocycle to avoid the generation of nonfunctional C [double bond] N syn species.

Bacteriorhodopsins↗

PubMedDate not supplied

Soft-triple resonance solid-state NMR experiments for assignments of U-13C, 15N labeled peptides and proteins.

The process of obtaining sequential resonance assignments for heterogeneous polypeptides and large proteins by solid-state NMR (ssNMR) is impeded by extensive spectral degeneracy in these systems. Even in these challenging cases, the cross peaks are not distributed uniformly over the entire spectral width. Instead, there exist both well-resolved single resonances and distinct groups of resonances well separated from the most crowded region of the spectrum. Here, we present a series of new triple resonance experiments that exploit the non-uniform clustering of resonances in heteronuclear correlation spectra to obtain additional resolution in the more crowded regions of a spectrum. Homonuclear and heteronuclear dipolar recoupling sequences are arranged to achieve directional transfer of coherence between neighboring residues in the peptide sequence. A frequency-selective (soft) pulse is applied to select initial polarization from a limited (and potentially) well-resolved region of the spectrum. The pre-existing resolution of one or more spins is thus utilized to obtain additional resolution in the more crowded regions of the spectrum. A new protocol to utilize these experiments for sequential resonance assignments in peptides and proteins is also demonstrated.

Carbon Isotopes↗