Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins

Abstract

Phase separation is thought to underlie spatial and temporal organization that is required for controlling biochemical reactions in cells. Multivalence of interaction motifs, also known as stickers, is a defining feature of proteins that drive phase separation. Intrinsically disordered proteins with stickers uniformly distributed along the linear sequence can serve as scaffold molecules that drive phase separation. The sequence-intrinsic contributions of disordered proteins to phase separation can be discerned by computing or measuring sequence-specific phase diagrams. These help to delineate the combinations of protein concentration and a suitable control parameter, such as temperature, that support phase separation. Here, we present an approach that combines detailed simulations with a numerical adaptation of an analytical Gaussian cluster theory to enable the calculation of sequence-specific phase diagrams. Our approach leverages the known equivalence between the driving forces for single-chain collapse in dilute solutions and the driving forces for phase separation in concentrated solutions. We demonstrate the application of the theory-aided computations through calculation of phase diagrams for a set of archetypal intrinsically disordered low-complexity domains. We also leverage theories to compute sequence-specific percolation lines and thereby provide a thermodynamic framework for hardening transitions that have been observed for many biomolecular condensates.

Deciphering how naturally occurring sequence features impact the phase behaviors of disordered prion-like domains

“…Additionally, PLCDs are flexible, finite-sized heteropolymers, and yet they have been shown to behave in a manner that is similar to effective homopolymers 17 , whereby the determinants for the collapse of each chain in dilute solutions are the same as those for driving phase separation 36 . This “strong coupling” between the determinants of conformational and phase equilibria of PLCDs has been attributed to the uniform distribution of aromatic stickers along the linear sequence 17, 37 . The sequence titrations that we deploy in this work allow us to quantify the impact of changes to sticker versus spacer grammars on the coupling between single-chain dimensions and the driving forces for phase separation.…”

Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures

“…An alternative approach, which we adopt in this work, is to leverage the corollary of LCST behavior at the single chain limit 27 . At temperatures that are proximal to the LCST, the system of chain of interest will undergo a coil-to-globule transition in a dilute solution 28 . This is because the chain collapse is a manifestation of the physics of phase separation at the single chain limit.…”

“…We use the ABSINTH implicit solvation model 20 and forcefield paradigm 34 to model the linkage between conformational equilibria and solvent-mediated interactions among polypeptide atoms. This allows us to perform simulations of temperature dependent coil-to-globule transitions, extract parameters to the Gaussian cluster theory 32 , and deploy these parameters in numerical calculations to generate full phase diagrams for the IDP of interest 28 (1)…”

“…The theta temperatures extracted from these simulations are presented in the main text.Analysis of coil-globule transitions, extraction of parameters, and calculation of phase diagrams using the Gaussian Cluster Theory:The profiles of RgN 0.5 vs. T were analyzed to extract the theta temperature (Tq) for each of the four sequences. For this, we used a method that we described recently by Zeng et al,28 . Only three of the four sequences have coil-globule transition profiles for which a robust estimate of the theta temperature can be made.…”

“…The methods we present here are a start toward the integration of supervised learning to leverage information gleaned from systematic characterizations of IDP phase behavior and physical chemistry based computations that combined all-atom simulations with improvements such as ABSINTH-T, and theoretical calculations that allow us to connect single chain coil-globule transitions to full phase diagrams28 . The heuristic we have extracted from IS limit simulations helps with discriminating sequences with LCST vs. UCST phase behavior.…”