Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities

Abstract

The properties of disordered proteins are thought to depend on intrinsic conformational propensities for polyproline II (PP II) structure. While intrinsic PP II propensities have been measured for the common biological amino acids in short peptides, the ability of these experimentally determined propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs) has not been established. Presented here are results from molecular simulations of disordered proteins showing that the hydrodynamic radius (R h) can be predicted from experimental PP II propensities with good agreement, even when charge-based considerations are omitted. The simulations demonstrate that R h and chain propensity for PP II structure are linked via a simple power-law scaling relationship, which was tested using the experimental R h of 22 IDPs covering a wide range of peptide lengths, net charge, and sequence composition. Charge effects on R h were found to be generally weak when compared to PP II effects on R h. Results from this study indicate that the hydrodynamic dimensions of IDPs are evidence of considerable sequence-dependent backbone propensities for PP II structure that qualitatively, if not quantitatively, match conformational propensities measured in peptides.

The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction

“…These data are consistent with size-exclusion chromatography and dynamic light scattering measurements that reveal an averaged hydrodynamic radius of 37.7 Å, compared to an expected value of ~20 Å for a typical globular protein of equivalent length. These data are accurately predicted by a power-law scaling relationship [42] described for IDPs and based upon intrinsic PPII propensities, which provides additional evidence that the Aap PGR has an unusually high PPII content compared to other characterized IDPs. Interestingly, we find that PGR resists the compaction typically induced in IDPs by elevated temperature or cosolvents such as TFE and TMAO.…”

“…If PGR were a globular protein, its R h would correspond to an apparent MW of 53.6 kDa, nearly four times larger than its actual MW. Furthermore, a plot of log R h vs log N where N is the number of residues, shows distinct linear trends for IDPs [42] (Table S4) and globular proteins [51, 53] (Table S5); PGR clearly falls in the IDP region in this plot (Fig. 2c).…”

“…This led to the conclusion that salt bridges do not stabilize PPII helices [105]. Tomasso et al [42] have modeled the impact of coulombic interactions on the radius of hydration ( R h ). They reported modest effects on R h due to charge-charge interactions, with the PPII propensity being the major factor on R h .…”

“…In addition to the high proline content, PGR is rich in disorder-promoting residues such Glu and Lys; these residues are highly represented in experimentally proven intrinsically disordered proteins [110]. Previously, it was shown that a simple power-law scaling relationship relates the R h of IDPs to N , the number of residues, and f PPII , the fractional number of residues in the PPII conformation as estimated from intrinsic PPII propensities [42, 51] (Eq. 7).…”

“…7). Tomasso et al compared experimental PPII propensity scales and found that the Hilser scale [111] or a composite scale combining Hilser, Kallenbach [112], and Creamer [113] PPII propensity scales could accurately predict experimental R h values for a large dataset of IDPs ranging from 73 to 260 residues in length and varying in sequence composition and net charge (from 1 to 43) [42]. Another variation on the power-law scaling relationship was proposed by Marsh and Forman-Kay, which takes into account the fraction of proline residues and the absolute net charge [53].…”