arXiv subjects

Julie D. Forman-Kay

Publications and source records attributed to Julie D. Forman-Kay.

6 recordsLinked to original sources

arXiv2024

Electrostatics of Salt-Dependent Reentrant Phase Behaviors Highlights Diverse Roles of ATP in Biomolecular Condensates

Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The multifaceted electrostatic effects in these biomolecular condensates are exemplified here by experimental and theoretical investigations of the different salt- and ATP-dependent LLPSs of an IDR of messenger RNA-regulating protein Caprin1 and its phosphorylated variant pY-Caprin1, exhibiting, e.g., reentrant behaviors in some instances but not others. Experimental data are rationalized by physical modeling using analytical theory, molecular dynamics, and polymer field-theoretic simulations, indicating that interchain ion bridges enhance LLPS of polyelectrolytes such as Caprin1 and the high valency of ATP-magnesium is a significant factor for its colocalization with the condensed phases, as similar trends are observed for other IDRs. The electrostatic nature of these features complements ATP's involvement in $\pi$-related interactions and as an amphiphilic hydrotrope, underscoring a general role of biomolecular condensates in modulating ion concentrations and its functional ramifications.

q-bio.BM↗

arXiv2020

Comparative Roles of Charge, $π$ and Hydrophobic Interactions in Sequence-Dependent Phase Separation of Intrinsically Disordered Proteins

Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular condensates underlain by liquid-liquid phase separation (LLPS), we conducted multiple-chain simulations of the N-terminal intrinsically disordered region (IDR) of DEAD-box helicase Ddx4, as a test case, to assess the roles of electrostatic, hydrophobic, cation-$π$, and aromatic interactions in amino acid sequence-dependent LLPS. We evaluated 3 residue-residue interaction schemes with a shared electrostatic potential. Neither a common hydrophobicity scheme nor one augmented with arginine/lysine-aromatic cation-$π$ interactions consistently accounted for the experimental LLPS data on the wildtype, a charge-scrambled, an FtoA, and an RtoK mutant of Ddx4 IDR. In contrast, interactions based on contact statistics among folded globular protein structures reproduce the overall experimental trend, including that the RtoK mutant has a much diminished LLPS propensity. Consistency between simulation and LLPS experiment was also found for RtoK mutants of P-granule protein LAF-1, underscoring that, to a degree, the important LLPS-driving $π$-related interactions are embodied in classical statistical potentials. Further elucidation will be necessary, however, especially of phenylalanine's role in condensate assembly because experiments on FtoA and YtoF mutants suggest that LLPS-driving phenylalanine interactions are significantly weaker than those posited by common statistical potentials. Protein-protein electrostatic interactions are modulated by relative permittivity, which depends on protein concentration. Analytical theory suggests that this dependence entails enhanced inter-protein interactions in the condensed phase but more favorable protein-solvent interactions in the dilute phase. The opposing trends lead to a modest overall impact on LLPS.

q-bio.BM↗

arXiv2019

Extended Experimental Inferential Structure Determination Method for Evaluating the Structural Ensembles of Disordered Protein States

Characterization of proteins with intrinsic or unfolded state disorder comprises a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. We introduce a comprehensive Bayesian framework, the Extended Experimental Inferential Structure Determination (X-EISD) method, that calculates the maximum log-likelihood of a protein structural ensemble by accounting for the uncertainties of a wide range of experimental data and back-calculation models from structures, including NMR chemical shifts, J-couplings, Nuclear Overhauser Effects, paramagnetic relaxation enhancements, residual dipolar couplings, and hydrodynamic radii, single molecule fluorescence Förster resonance energy transfer efficiencies and small angle X-ray scattering intensity curves. We apply X-EISD to the drkN SH3 unfolded state domain and show that certain experimental data types are more influential than others for both eliminating structural ensemble models, while also finding equally probable disordered ensembles that have alternative structural properties that will stimulate further experiments to discriminate between them.

physics.bio-ph↗

arXiv2017

Charge Pattern Matching as a "Fuzzy" Mode of Molecular Recognition for the Functional Phase Separations of Intrinsically Disordered Proteins

Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for distributing different IDP sequences into various cellular membraneless compartments. Pertinent physics was addressed recently by applying random-phase-approximation (RPA) polymer theory to electrostatics, which is a major energetic component governing IDP phase properties. RPA accounts for charge patterns and thus has advantages over Flory-Huggins and Overbeek-Voorn mean-field theories. To make progress toward deciphering the phase behaviors of multiple IDP sequences, the RPA formulation for one IDP species plus solvent is hereby extended to treat polyampholyte solutions containing two IDP species. The new formulation generally allows for binary coexistence of two phases, each containing a different set of volume fractions $(ϕ_1,ϕ_2)$ for the two different IDP sequences. The asymmetry between the two predicted coexisting phases with regard to their $ϕ_1/ϕ_2$ ratios for the two sequences increases with increasing mismatch between their charge patterns. This finding points to a multivalent, stochastic, "fuzzy" mode of molecular recognition that helps populate various IDP sequences differentially into separate phase compartments. An intuitive illustration of this trend is provided by Flory-Huggins models, whereby a hypothetical case of ternary coexistence is also explored. Augmentations of the present RPA theory with a relative permittivity $ε_{\rm r}(ϕ)$ that depends on IDP volume fraction $ϕ=ϕ_1+ϕ_2$ lead to higher propensities to phase separate, in line with the case with one IDP species we studied previously. ...

q-bio.BM↗

arXiv2016

Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) are typically low in nonpolar/hydrophobic but relatively high in polar, charged, and aromatic amino acid compositions. Some IDPs undergo liquid-liquid phase separation in the aqueous milieu of the living cell. The resulting phase with enhanced IDP concentration can function as a major component of membraneless organelles that, by creating their own IDP-rich microenvironments, stimulate critical biological functions. IDP phase behaviors are governed by their amino acid sequences. To make progress in understanding this sequence-phase relationship, we report further advances in a recently introduced application of random-phase-approximation (RPA) heteropolymer theory to account for sequence-specific electrostatics in IDP phase separation. Here we examine computed variations in phase behavior with respect to block length and charge density of model polyampholytes of alternating equal-length charge blocks to gain insight into trends observed in IDP phase separation. As a real-life example, the theory is applied to rationalize/predict binodal and spinodal phase behaviors of the 236-residue N-terminal disordered region of RNA helicase Ddx4 and its charge-scrambled mutant for which experimental data are available. Fundamental differences are noted between the phase diagrams predicted by RPA and those predicted by mean-field Flory-Huggins and Overbeek-Voorn/Debye-Hückel theories. In the RPA context, a physically plausible dependence of relative permittivity on protein concentration can produce a cooperative effect in favor of IDP-IDP attraction and thus a significant increased tendency to phase separate. Ramifications of these findings for future development of IDP phase separation theory are discussed.

q-bio.BM↗

arXiv2016

Sequence-specific polyampholyte phase separation in membraneless organelles

Liquid-liquid phase separation of charge/aromatic-enriched intrinsically disordered proteins (IDPs) is critical in the biological function of membraneless organelles. Much of the physics of this recent discovery remains to be elucidated. Here we present a theory in the random phase approximation to account for electrostatic effects in polyampholyte phase separations, yielding predictions consistent with recent experiments on the IDP Ddx4. The theory is applicable to any charge pattern and thus provides a general analytical framework for studying sequence dependence of IDP phase separation.

q-bio.BM↗