Multiple Alignment Tensors from a Denatured Protein

Abstract

NMR spectroscopy has been shown to be useful in the study of denatured proteins, although the amount of structural information is limited by the absence of long-range NOEs. In recent years, large residual dipolar couplings (RDCs) from denatured proteins have been observed under alignment conditions produced by bicelles and strained polyacrylamide gels. [1][2][3][4] Unlike theoretical predictions based upon a random coil conformation, 5 denatured proteins display surprisingly variable couplings as a function of position along the chain, suggesting that residual structure is present. In the case of staphylococcal nuclease, the structure of the denatured state in buffer (∆131∆) has been determined to have a nativelike topology by over 600 distance measurements based on paramagnetic relaxation enhancement from 14 spin labels. 6 This observation, in combination with a highly significant correlation between RDCs in buffer and in 8 M urea, led to the conclusion that a nativelike topology persists in this denatured protein, even under strongly denaturing conditions. 1 Denatured proteins, unlike native proteins, show a skewing of RDCs to one sign, a trend that becomes more pronounced as denaturing conditions become more severe. 1 Several explanations for this skewing have been proposed in the literature, such as (1) segments of extended or polyproline II secondary structure that align independently 4 or (2) enrichment of extended and polyproline II φ/ψ values along the long molecular axis. In two recently published reports, very simple computational models were able to correctly predict some of the position-dependent variations in RDC profiles for several denatured proteins. 7,8 The success of such models suggests that a single set of RDCs obtained from a single alignment tensor may contain a rather limited amount of information and therefore does not necessarily report on the presence of significant long-range structure in denatured proteins.In this report, we describe efforts to extend our picture of the residual structure in denatured nuclease by measuring RDCs with multiple alignment tensors. The residual dipolar interaction tensor corresponding to each NH bond requires five parameters for its specification. 9,10 If RDC datasets can be acquired encompassing five independent alignment conditions, it is possible to determine all five elements of the residual dipolar coupling tensor for each NH bond. 11 These tensors contain information about the orientational probability distribution for each bond and are usually rendered into a specific description of mean bond orientation, generalized order parameters, and motional asymmetry parameters. The challenge to obtain multiple alignments from denatured proteins is the seeming insensitivity of RDCs to different alignment conditions. As initial attempts to alter ∆131∆ s alignment with highly charged gels gave ambiguous results, the new method based on composite phage/polyacrylamide gels developed by Ruan and Tolman 12 was applied to denatured nuclease. This method involves the...

Conformational distributions of unfolded polypeptides from novel NMR techniques

“…51 This study took conformers calculated using FM, and predicted RDCs aligned in bacteriophage using a simplified alignment model that approximates the electrostatic interaction between an unfolded protein and an ordered liquidcrystal particle as that between the protein sidechain charges and the electric field of the phage, and again averaged the resulting RDCs over all protein conformers. The potential for extracting meaningful information from additional, differently aligning media has also been recently demonstrated by Gebel et al 72 An additional approach to a better definition of local conformational sampling in unfolded proteins is to measure more RDCs from the peptide chain. Although the study of protein X described above reproduced both 1 D NH and 2 D C Ј NH RDCs, relatively few studies have extended the investigation of RDCs beyond the analysis of 1 D NH couplings.…”

De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media

“…The diagonal matrix W, containing the singular values of the data matrix D, reports on the relative weights of different orthogonal combinations within the data as a whole. RDC datasets which exhibit perfect linear independence can be constructed according to (Ruan and Tolman 2005;Gebel et al 2006), (5) Note that the above equation differs slightly from previous formulations by a constant scaling factor. We refer to these independent RDC datasets as orthogonal linear combination (OLC)-RDCs.…”