Biology subjects

Wand, A. J.

Publications and source records attributed to Wand, A. J..

3 recordsLinked to original sources

bioRxiv2026

The cytokine structural homologs IL-1β and IL-1Ra have distinct dynamical character that potentially influence their roles in allosteric regulation of the IL-1 receptor.

Interleukin-1{beta} (IL-1{beta}) and the interleukin-1 receptor antagonist (IL-1Ra) share the {beta}-trefoil fold, engage the same receptor (IL-1R), but produce opposite biological outcomes. IL-1{beta} recruits the accessory protein IL-1RAcP to initiate inflammatory signaling while IL-1Ra occupies the receptor without supporting co-receptor recruitment. Seeking the origin of this divergence in properties not apparent from static structures, we used solution NMR relaxation to characterize fast internal motion in both proteins. Rigorous treatment of macromolecular tumbling shows both to be nearly maximally triaxial, which admits two near-degenerate axially symmetric solutions. This ambiguity was propagated throughout and found to have negligible impact. Complete replicate data sets from independently prepared IL-1{beta} samples establish the experimental precision directly. Backbone amide and methyl-bearing side chain order parameters are indistinguishable between the two proteins, the latter averaging 0.484 {+/-} 0.030 and 0.486 {+/-} 0.033, indicating essentially equivalent residual conformational entropy. Their spatial distributions are uncorrelated when projected onto the shared fold. Importantly, the difference between the proteins is concentrated at the receptor interface, where methyl probes lying on the IL-1{beta} footprint are considerably more mobile than those of IL-1Ra. It is therefore the agonist, not the antagonist, that presents an anomalously mobile binding surface. IL-1Ra also buries some 16% less surface while ostensibly binding IL-1R more tightly, the signature of an interface predisposed toward productive contact. Conformational entropy can thus distinguish protein function where structure and average flexibility are conserved, and the distinction resides not in how much entropy a protein has but in where it is kept.

biophysics↗

bioRxiv2026

Harmonizing Peak Matching Between Multidimensional NMR Spectra

A common task in analysis of multidimensional NMR is the mapping of cross-peaks from one spectrum to another. In some situations, only a subset of coordinates of cross-peaks are to be matched such as in comparing corresponding dimensions of triple resonance assignment spectra. In other cases, the sample is perturbed in some way, and the task is to map corresponding cross-peaks that potentially change in any and all dimensions. This exercise is commonly done "by hand" and is both time-consuming and subjective. It is difficult for an individual to consider all possible interpretations of deviations between two multidimensional NMR spectra. Furthermore, in regions of high degeneracy, cross-peak matchings between spectra can be ambiguous. Ideally, a mapping algorithm should reflect a confidence of its matchings to indicate the reliability of proposed matchings and should do so while harmonizing all potential mappings in the spectrum. Critically, this process should be automated using criteria that are both well-defined, consistent and provide a measure of reliability. Here we develop a novel model describing the distribution of apparent deviations between cross-peaks of two multidimensional NMR spectra to random noise and true deviations to harmonize the cross-peak matching. Bayesian inference is employed to provide confidence estimates. The resulting algorithm (pHarmony) is tested in a variety of ways such as mapping between pairs of triple resonance spectra and between two- and three-dimensional heteronuclear NMR spectra generated by a fragment-based ligand discovery screen.

biophysics↗

bioRxiv2020

Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy

For a variety of reasons, the internal motions of integral membrane proteins have largely eluded comprehensive experiential characterization. Here, the fast side chain dynamics of the 7-transmembrane helix protein sensory rhodopsin II and the beta-barrel bacterial outer membrane channel protein W have been characterized in lipid bilayers and detergent micelles by solution NMR relaxation techniques. Though of quite different topologies, both proteins are found to have a similar and striking distribution of methyl-bearing amino acid side chain motion that is independent of membrane mimetic. The methyl-bearing side chains of both proteins, on average, are more dynamic in the ps-ns time regime than any soluble protein characterized to date. Approximately one third of methyl-bearing side chains exhibit extreme rotameric averaging on this timescale. Accordingly, both proteins retain an extraordinary residual conformational entropy in the folded state, which provides a counterbalance to the absence of the hydrophobic effect that normally stabilizes the folded state of water-soluble proteins. Furthermore, the large reservoir of conformational entropy that is observed provides the potential to greatly influence the thermodynamics underlying a plethora of membrane protein functions including ligand binding, allostery and signaling.

biophysics↗