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

Pengyu Ren,Rohit V. Pappu,Chengwen Liu,Martin J. Fossat,Ashutosh Chilkoti,Xiangze Zeng

doi:10.1063/5.0037438

Abstract

Many naturally occurring elastomers are intrinsically disordered proteins (IDPs) built up of repeating units and they can demonstrate two types of thermoresponsive phase behavior. Systems characterized by lower critical solution temperatures (LCST) undergo phase separation above the LCST whereas systems characterized by upper critical solution temperatures (UCST) undergo phase separation below the UCST. There is congruence between thermoresponsive coil-globule transitions and phase behavior whereby the theta temperatures above or below which the IDPs transition from coils to globules serve as useful proxies for the LCST / UCST values. This implies that one can design sequences with desired values for the theta temperature with either increasing or decreasing radii of gyration above the theta temperature. Here, we show that the Monte Carlo simulations performed in the so-called intrinsic solvation (IS) limit version of the temperature-dependent the ABSINTH (self-Assembly of Biomolecules Studied by an Implicit, Novel, Tunable Hamiltonian) implicit solvation model, yields a useful heuristic for discriminating between sequences with known LCST versus UCST phase behavior. Accordingly, we use this heuristic in a supervised approach, integrate it with a genetic algorithm, combine this with IS limit simulations, and demonstrate that novel sequences can be designed with LCST phase behavior. These calculations are aided by direct estimates of temperature dependent free energies of solvation for model compounds that are derived using the polarizable AMOEBA (atomic multipole optimized energetics for biomolecular applications) forcefield. To demonstrate the validity of our designs, we calculate coil-globule transition profiles using the full ABSINTH model and combine these with Gaussian Cluster Theory calculations to establish the LCST phase behavior of designed IDPs.

Highlights

We show that the Monte Carlo simulations performed in the so-called intrinsic solvation (IS) limit version of the temperature dependent self-Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian (ABSINTH) implicit solvation model yield a useful heuristic for discriminating between sequences with known lower critical solution temperatures (LCSTs) and upper critical solution temperatures (UCSTs) phase behavior
Results from atomic multipole optimized energetics for biomolecular applications (AMOEBA)-based free energy calculations for model compounds: We performed temperature dependent free energy calculations based on the Bennett Acceptance Ratio (BAR) free energy estimator56 for the direct investigation of how ∆μh varies with temperature
Our method is aided by a learned heuristic that was shown to provide clear segregation between sequences with known LCST vs UCST phase behavior. This heuristic is the slope m of the change in RgN−0.5 vs T from simulations of sequences performed in the IS limit of the ABSINTH-T model

Summary

Introduction

Disordered proteins (IDPs) that undergo thermoresponsive phase transitions are the basis of many naturally occurring elastomeric materials. These naturally occurring scaffold IDPs2 serve as the basis of ongoing efforts to design thermoresponsive materials. Well-known examples of disordered regions derived from elastomeric proteins include the repetitive sequences from proteins such as resilins, elastins, proteins from spider silks, titin, and neurofilament sidearms. Elastin-like polypeptides have served as the benchmark systems for the development of responsive disordered proteins that can be adapted for use in various biotechnology settings. The multi-way interplay of sequence-encoded intermolecular interactions, chain–solvent interactions, and chain and solvent entropy gives rise to thermoresponsive phase transitions that lead to the formation of coacervates. Here, we show that one can scitation.org/journal/apm expand the “materials genome” through de novo design strategies that are based on heuristics anchored in the physics of thermoresponsive transitions and efficient simulation engines that apply the learned heuristics in a supervised approach. Disordered proteins (IDPs) that undergo thermoresponsive phase transitions are the basis of many naturally occurring elastomeric materials.. Disordered proteins (IDPs) that undergo thermoresponsive phase transitions are the basis of many naturally occurring elastomeric materials.1 These naturally occurring scaffold IDPs2 serve as the basis of ongoing efforts to design thermoresponsive materials.. Well-known examples of disordered regions derived from elastomeric proteins include the repetitive sequences from proteins such as resilins, elastins, proteins from spider silks, titin, and neurofilament sidearms.. Elastin-like polypeptides have served as the benchmark systems for the development of responsive disordered proteins that can be adapted for use in various biotechnology settings.. We report the development of a genetic algorithm (GA) and show how it can be applied in conjunction with multiscale computations to design thermoresponsive IDPs with lower critical solution temperature (LCST) phase behavior.

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