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Joel R Tolman

Publications and source records attributed to Joel R Tolman.

8 recordsLinked to original sources
PubMed2006

Multiple alignment tensors from a denatured protein.

The structural content of the denatured state has yet to be fully characterized. In recent years, large residual dipolar couplings (RDCs) from denatured proteins have been observed under alignment conditions produced by bicelles and strained polyacrylamide gels. In this report, we describe efforts to extend our picture of the residual structure in denatured nuclease by measuring RDCs with multiple alignment tensors. Backbone amide 15N-1H RDCs were collected from 4 M urea for a total of eight RDC data sets. The RDCs were analyzed by singular value decomposition (SVD) to determine the number of independent alignment tensors present in the data. On the basis of the resultant singular values and propagated error estimates, it is clear that there are at least three independent alignment tensors. These three independent RDC datasets can be reconstituted as orthogonal linear combinations, (OLC)-RDC datasets, of the eight actually recorded. The first, second, and third OLC-RDC datasets are highly robust to the removal of any single experimental RDC dataset, establishing the presence of three independent alignment tensors, sampled well above the level of experimental uncertainty. The observation that the RDC data span three or more dimensions of the five-dimensional parameter space demonstrates that the ensemble average structure of denatured nuclease must be asymmetric with respect to these three orthogonal principal axes, which is not inconsistent with earlier work demonstrating that it has a nativelike topology.

Bacteriophage Pf1↗
PubMed2005

Composite alignment media for the measurement of independent sets of NMR residual dipolar couplings.

The measurement of independent sets of NMR residual dipolar couplings (RDCs) in multiple alignment media can provide a detailed view of biomolecular structure and dynamics, yet remains experimentally challenging. It is demonstrated here that independent sets of RDCs can be measured for ubiquitin using just a single alignment medium composed of aligned bacteriophage Pf1 particles embedded in a strained polyacrylamide gel matrix. Using this composite medium, molecular alignment can be modulated by varying the angle between the directors of ordering for the Pf1 and strained gel matrix, or by varying the ionic strength or concentration of the Pf1 particles. This approach offers significant advantages in that greater experimental control can be exercised over the acquisition of multi-alignment RDC data while a homogeneous chemical environment is maintained across all of the measured RDC data.

Bacteriophage Pf1↗
PubMed2004

Triple quantum decoherence under multiple refocusing: slow correlated chemical shift modulations of C' and N nuclei in proteins.

A new experiment allows the identification of residues that feature slow conformational exchange in macromolecules. Rotations about dihedral angles that are slower than the global correlation time tau(c) cause a modulation of the isotropic chemical shifts of the nuclei. If these fluctuations are correlated they induce a differential line broadening between three-spin single-quantum and triple-quantum coherences involving three nuclei such as the carbonyl C', the neighbouring amide nitrogen N and the amide proton H(N) belonging to a pair of consecutive amino acids. A cross-correlated relaxation rate R (CS/CS)(C'N) can be determined that corresponds to the sum of the isotropic and anisotropic contributions to the chemical shift modulations of the carbonyl carbon and nitrogen nuclei. Only the isotropic contributions depend on the pulse repetition rate of a multiple-refocusing sequence. An attenuation of the relaxation rate with increasing pulse repetition rate can therefore be attributed to slow motions. The asparagine N25 residue of ubiquitin, located in the first alpha-helix, is shown to feature significant slow conformational exchange.

Algorithms↗
PubMed2003

De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy.

We report the de novo determination of 15N-1H bond orientations and motional order parameters for the protein ubiquitin with high accuracy based solely on NMR residual dipolar coupling measurements made in six distinct alignment media. The resulting bond orientations are in agreement with RDC-refined orientations of either solid or solution state coordinates to within approximately 2 degrees , which is also the estimated precision of the resulting orientations. The squared generalized order parameters, which reflect amplitudes of motion spanning the picosecond to millisecond time scales, exhibit a correlation with picosecond time scale order parameters derived from conventional NMR 15N spin relaxation methods. Provided that RDC measurements can be obtained using many different alignment media, this approach (called direct interpretation of dipolar couplings) may significantly impact the attainable accuracy and the molecular weight range accessible to NMR structure determination in the solution state, as well as provide a route for the study of motions occurring on the nanosecond to microsecond time scales, which have been traditionally difficult to study at atomic resolution.

Crystallography, X-Ray↗
PubMed2002

A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy.

The interpretation of residual dipolar couplings in terms of molecular properties of interest is complicated because of difficulties in separating structural and dynamic effects as well as the need to estimate alignment tensor parameters a priori. An approach is introduced here that allows many of these difficulties to be circumvented when data are acquired in multiple alignment media. The method allows the simultaneous extraction of both structural and dynamic information directly from the residual dipolar coupling data, in favorable cases even in the complete absence of prior structural knowledge. Application to the protein ubiquitin indicates greater amplitudes of internal motion than expected from traditional (15)N spin relaxation analysis.

Computer Simulation↗
PubMed2002

Accurate measurement of residual dipolar couplings in anisotropic phase.

The determination of residual dipolar couplings (RDCs) by quantitative J spectroscopy methods such as Heteronuclear Single Quantum Correlation with Phase Encoded Coupling (HSQC-PEC) is prone to systematic errors that may be caused by differential attenuation during the conversion of orthogonal density operator components into observable terms. The attenuation may be caused by miscalibration of radio-frequency pulses and by relaxation effects. A simple method is presented that allows one to remove most of these systematic errors without losses in sensitivity or resolution.

Anisotropy↗