Sequence-Specific Random Coil Chemical Shifts of Intrinsically Disordered Proteins

Abstract

Although intrinsically disordered proteins (IDPs) are widespread in nature and play diverse and important roles in biology, they have to date been little characterized structurally. Auspiciously, intensified efforts using NMR spectroscopy have started to uncover the breadth of their conformational landscape. In particular, polypeptide backbone chemical shifts are emerging as powerful descriptors of local dynamic deviations from the "random coil" state toward canonical types of secondary structure. These digressions, in turn, can be connected to functional or dysfunctional protein states, for example, in adaptive molecular recognition and protein aggregation. Here we describe a first inventory of IDP backbone (15)N, (1)H(N), (1)H(α), (13)C(O), (13)C(β), and (13)C(α) chemical shifts using data obtained for a set of 14 proteins of unrelated sequence and function. Singular value decomposition was used to parametrize this database of 6903 measured shifts collectively in terms of 20 amino acid-specific random coil chemical shifts and 40 sequence-dependent left- and right-neighbor correction factors, affording the ncIDP library. For natively unfolded proteins, random coil backbone chemical shifts computed from the primary sequence displayed root-mean-square deviations of 0.65, 0.14, 0.12, 0.50, 0.36, and 0.41 ppm from the experimentally measured values for the (15)N, (1)H(N), (1)H(α), (13)C(O), (13)C(β), and (13)C(α) chemical shifts, respectively. The ncIDP prediction accuracy is significantly higher than that obtained with libraries for small peptides or "coil" regions of folded proteins.

Solid-state NMR Study Reveals Collagen I Structural Modifications of Amino Acid Side Chains upon Fibrillogenesis

“…Backbone and side chain 13 C chemical shifts found in the present work are in good agreement with data extracted from a random coiled protein library (S.D. of 0.07 after calibration (22,23)). Considering all native conditions whether in acidic or neutral basic pH, the most striking difference from (iv) is a split of resonances in the carbon dimension for all detectable side chain chemical shifts.…”

The Solution Structure, Binding Properties, and Dynamics of the Bacterial Siderophore-binding Protein FepB

“…Changes to secondary structure elements upon ligand binding were evaluated with the neighbor-corrected structural propensity calculator (ncSPC) using backbone chemical shifts as input (70,71). The overall topology of apo-and holo-FepB is a mixed ␣/␤ type consisting of 10 ␣-helices and 12 ␤-strands, where each domain has a central 5-stranded ␤-sheet (Fig.…”

In-cell NMR reveals potential precursor of toxic species from SOD1 fALS mutants

“…We have shown that hCCS, by interacting Figure 6 | The unstructured form of apo-G93A SH does not have any b-strand structural propensity. Correlation plots between experimental and predicted N (a) and Ca (b) chemical shifts using random coil libraries 56 are reported for the unstructured apo-G93A SH , the native, folded apo WT SOD1 SH and the fully mature, oxidized Cu(I),Zn-SOD1 SS . The fit parameters for the function f(x) ¼ ax þ b using least-square method (R 2 and root mean square difference (RMSD)) are indicated for each plot; c) the overall secondary structure propensity (SSP) score per residue obtained by using a weighted combination of backbone secondary chemical shifts 57 is reported for unstructured apo-G93A SH , apo WT SOD1 SH and Cu(I),Zn-SOD1 SS .…”