Unfolded states of proteins and native states of intrinsically disordered proteins (IDPs) populate heterogeneous conformational ensembles in solution. The average sizes of these heterogeneous systems, quantified by the radius of gyration (R G ), can be measured by small-angle X-ray scattering (SAXS). Another parameter, the mean dye-to-dye distance (R E ) for proteins with fluorescently labeled termini, can be estimated using single-molecule Förster resonance energy transfer (smFRET). A number of studies have reported inconsistencies in inferences drawn from the two sets of measurements for the dimensions of unfolded proteins and IDPs in the absence of chemical denaturants. These differences are typically attributed to the influence of fluorescent labels used in smFRET and to the impact of high concentrations and averaging features of SAXS. By measuring the dimensions of a collection of labeled and unlabeled polypeptides using smFRET and SAXS, we directly assessed the contributions of dyes to the experimental values R G and R E . For chemically denatured proteins we obtain mutual consistency in our inferences based on R G and R E , whereas for IDPs under native conditions, we find substantial deviations. Using computations, we show that discrepant inferences are neither due to methodological shortcomings of specific measurements nor due to artifacts of dyes. Instead, our analysis suggests that chemical heterogeneity in heteropolymeric systems leads to a decoupling between R E and R G that is amplified in the absence of denaturants. Therefore, joint assessments of R G and R E combined with measurements of polymer shapes should provide a consistent and complete picture of the underlying ensembles.single-molecule FRET | intrinsically disordered proteins | denatured-state ensemble | protein folding | polymer theory Q uantitative characterizations of the sizes, shapes, and amplitudes of conformational fluctuations of unfolded proteins under denaturing and native conditions are directly relevant to advancing our understanding of the collapse transition during protein folding. These types of studies are also relevant to furthering our understanding of the functions and interactions of intrinsically disordered proteins (IDPs) in physiologically relevant conditions (1). Polymer physics theories provide the conceptual foundations for analyzing conformationally heterogeneous systems such as IDPs and unfolded ensembles of autonomously foldable proteins (2-4). Specifically, order parameters in theories of coil-toglobule transitions and analytical descriptions of conformational ensembles (5, 6) are based on ensemble-averaged values of radii of gyration (R G ) and amplitudes of fluctuations measured by end-toend distances (R E ).Estimates of R G are accessible through small-angle X-ray scattering (SAXS) measurements because scattering intensities are directly related to the global protein size (Fig. 1) (7, 8). At finite concentrations, assuming the absence of intermolecular interactions, R G is proportional to the square root o...

Nuclear pore complexes (NPCs) lined with intrinsically disordered FG-domains act as selective gatekeepers for molecular transport between the nucleus and the cytoplasm in eukaryotic cells. The underlying physical mechanism of the intriguing selectivity is still under debate. Here, we probe the transport of ions and transport receptors through biomimetic NPCs consisting of Nsp1 domains attached to the inner surface of solid-state nanopores. We examine both wildtype FG-domains and hydrophilic SG-mutants. FG-nanopores showed a clear selectivity as transport receptors can translocate across the pore whereas other proteins cannot. SG mutant pores lack such selectivity. To unravel this striking difference, we present coarse-grained molecular dynamics simulations that reveal that FG-pores exhibit a high-density, nonuniform protein distribution, in contrast to a uniform and significantly less-dense protein distribution in the SG-mutant. We conclude that the sequence-dependent density distribution of disordered proteins inside the NPC plays a key role for its conductivity and selective permeability.

The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize artificial NPC mimics that allows controlling the type and copy number of FG-Nups. We constructed 34 nm-wide 3D DNA origami rings and attached different numbers of NSP1, a model yeast FG-Nup, or NSP1-S, a hydrophilic mutant. Using (cryo) electron microscopy, we find that NSP1 forms denser cohesive networks inside the ring compared to NSP1-S. Consistent with this, the measured ionic conductance is lower for NSP1 than for NSP1-S. Molecular dynamics simulations reveal spatially varying protein densities and conductances in good agreement with the experiments. Our technique provides an experimental platform for deciphering the collective behavior of IDPs with full control of their type and position.

Nuclear transport is facilitated by the Nuclear Pore Complex (NPC) and is essential for life in eukaryotes. The NPC is a long-lived and exceptionally large structure. We asked whether NPC quality control is compromised in aging mitotic cells. Our images of single yeast cells during aging, show that the abundance of several NPC components and NPC assembly factors decreases. Additionally, the single-cell life histories reveal that cells that better maintain those components are longer lived. The presence of herniations at the nuclear envelope of aged cells suggests that misassembled NPCs are accumulated in aged cells. Aged cells show decreased dynamics of transcription factor shuttling and increased nuclear compartmentalization. These functional changes are likely caused by the presence of misassembled NPCs, as we find that two NPC assembly mutants show similar transport phenotypes as aged cells. We conclude that NPC interphase assembly is a major challenge for aging mitotic cells.

We report molecular dynamics (MD) simulations of the water/clean rutile TiO2 (110) interface using polarizable and non-surface polarity force field models. The effect of surface polarity on the water dynamics near the TiO2(110) surface is addressed, specifically by calculating the water hydrogen bond and reorientational dynamics. The hydrogen bond lifetime of interfacial water molecules is several times longer than that of bulk water due to the strong water-TiO2 interactions. A comparison of the dynamics simulated with the polarizable and non-surface polarity models shows that, while the hydrogen bond lifetime between the interfacial water and TiO2 surface is insensitive to the surface polarity, the reorientational dynamics around this hydrogen bond axis is significantly influenced by the surface polarity; the surface polarity of the TiO2 increases the water-TiO2 interactions, stabilizing the local structure of the interfacial water molecules and restricting their rotational motion. This reorientation occurs predominantly by rotation around the O-H group hydrogen bonded to the TiO2 surface. Furthermore, we correlate the dynamics of the induced charge on the TiO2 surface with the interfacial water dynamics. Our results show that the timescale of correlations of the atom charges induced by the local electric field in bulk water is influenced by the rotational motion, hydrogen bond rearrangement and translational motion, while the induced charge dynamics of the TiO2 surface is governed primarily by the rotational dynamics of the interfacial water molecules. This study demonstrates that the solid surface polarity has a significant impact on the dynamics of water molecules near TiO2 surfaces.