Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins

Abstract

Intrinsically disordered proteins (IDPs) lack well-defined three-dimensional structures, thus challenging the archetypal notion of structure-function relationships. Determining the ensemble of conformations that IDPs explore under physiological conditions is the first step towards understanding their diverse cellular functions. Here, we quantitatively characterize the structural features of IDPs as a function of sequence and length using coarse-grained simulations. For diverse IDP sequences, with the number of residues (N T ) ranging from 24 to 441, our simulations not only reproduce the radii of gyration (R g ) obtained from experiments, but also predict the full scattering intensity profiles in very good agreement with Small Angle X-ray Scattering experiments.The R g values are well-described by the standard Flory scaling law,with ν ≈ 0.588, making it tempting to assert that IDPs behave as polymers in a good solvent. However, clustering analysis reveals that the menagerie of structures explored by IDPs is diverse, with the extent of heterogeneity being highly sequence-dependent, even though ensemble-averaged properties, such as the dependence of R g on chain length, may suggest synthetic polymer-like behavior in a good solvent. For example, we show that for the highly charged Prothymosin-α, a substantial fraction of conformations is highly compact. Even if the sequence compositions are similar, as is the case for α-Synuclein and a truncated construct from the Tau protein, there are substantial differences in the conformational heterogeneity. Taken together, these observations imply that metrics based on net charge or related quantities alone, cannot be used to anticipate the phases of IDPs, either in isolation or in complex with partner IDPs or RNA. Our work sets the stage for probing the interactions of IDPs with each other, with folded protein domains, or with partner RNAs, which are critical for describing the structures of stress granules and biomolecular condensates with important cellular functions.

Thermal Compaction of Disordered and Elastin-like Polypeptides: A Temperature-Dependent, Sequence-Specific Coarse-Grained Simulation Model

“…In spite of good agreement with SAXS described above, and the known ability of the SOP-IDP model to capture both R g and R h for other IDPs (e.g. α-Synuclein) to acceptable accuracy 81 as discussed in previous sections. We refer the reader to the Appendix section, where we provide further discussion on this observed deviation.…”

“…In order to incorporate temperature-dependence of inter-residue interactions in a CG model, it is practical and convenient to develop a model that describes the ambienttemperature phases of disordered polypeptides for diverse sequence compositions. The recently developed SOP-IDP model has been shown to reproduce the radii of gyration (R g ), as well as the small angle X-ray scattering (SAXS) profiles at room temperatures for diverse sequence compositions, including highly charged, fully polar, and predominantly hydrophobic sequences 81 . We thus chose the SOP-IDP model, devoid of any explicit temperature-dependence of inter-residue interactions, as the template to build the temperature-dependence upon.…”

“…The charge of an amino acid is assigned to the side-chain bead. Details on the significance these terms, in the context of both folded proteins and disordered sequences, can be found elsewhere 81,82,84,85 .…”

“…First, given that the SOP-IDP model has been shown to capture the chain dimensions under ambient conditions for diverse polypeptide sequences 81,82 , it is not surprising that the temperature-independent model results are already in fair agreement with experiments, with deviations in R h from the experimental values ∼(8-15)%. It is gratifying to observe, that the temperature-dependent parameterization of the model results in improved agreement with experimental values, with maximum deviation now limited to <9%.…”

Flexible Players within the Sheaths: The Intrinsically Disordered Proteins of Myelin in Health and Disease

“…CD and NMR spectroscopy are powerful tools in directly probing disorder [274,275]. Small-angle scattering methods are sensitive to aggregation, but useful in probing conformational sampling in solution [276], complementing especially Förster resonance energy transfer experiments and computational methods [277,278]. Techniques that require isotope labelling, such as neutron methods and NMR spectroscopy, face their own challenges during protein production.…”