Quantifying Protein-Protein Interactions in Molecular Simulations.

Alfredo Jost Lopez,Jürgen Köfinger,Patrick K Quoika,Max Linke,Gerhard Hummer

doi:10.1021/acs.jpcb.9b11802

Alfredo Jost Lopez, Jürgen Köfinger + Show 3 more

Open Access

https://doi.org/10.1021/acs.jpcb.9b11802

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Abstract

Interactions among proteins, nucleic acids, and other macromolecules are essential for their biological functions and shape the physicochemcial properties of the crowded environments inside living cells. Binding interactions are commonly quantified by dissociation constants Kd, and both binding and nonbinding interactions are quantified by second osmotic virial coefficients B2. As a measure of nonspecific binding and stickiness, B2 is receiving renewed attention in the context of so-called liquid–liquid phase separation in protein and nucleic acid solutions. We show that Kd is fully determined by B2 and the fraction of the dimer observed in molecular simulations of two proteins in a box. We derive two methods to calculate B2. From molecular dynamics or Monte Carlo simulations using implicit solvents, we can determine B2 from insertion and removal energies by applying Bennett’s acceptance ratio (BAR) method or the (binless) weighted histogram analysis method (WHAM). From simulations using implicit or explicit solvents, one can estimate B2 from the probability that the two molecules are within a volume large enough to cover their range of interactions. We validate these methods for coarse-grained Monte Carlo simulations of three weakly binding proteins. Our estimates for Kd and B2 allow us to separate out the contributions of nonbinding interactions to B2. Comparison of calculated and measured values of Kd and B2 can be used to (re-)parameterize and improve molecular force fields by calibrating specific affinities, overall stickiness, and nonbinding interactions. The accuracy and efficiency of Kd and B2 calculations make them well suited for high-throughput studies of large interactomes.

Highlights

In biological cells, most protein, DNA, and RNA molecules have to bind to specific binding partners to perform their biological functions
Nonspecific interactions shape the physicochemical properties of the crowded environments inside cells.[3]
We focus on protein−protein interactions, but all of our results are generally applicable to other specific and nonspecific binding interactions

Summary

Introduction

Most protein, DNA, and RNA molecules have to bind to specific binding partners to perform their biological functions. These specific interactions compete with nonspecific interactions, and cells have evolved various mechanisms to minimize wasteful nonspecific binding.[1,2] nonspecific interactions shape the physicochemical properties of the crowded environments inside cells.[3] The quantification of binding affinities and interaction strengths of biological macromolecules is crucial for the understanding and modeling of cellular processes. The interaction strength of pairs of proteins in binding and nonbinding configurations can be quantified by measuring the second osmotic virial coefficient Bij, which relates the microscopic protein interactions to the macroscopic osmotic pressure.[5−7] the second osmotic virial coefficient is related to solubility and used as a predictor for protein scerydsimtalelinztaattiioonn1c0o−n1d2 itainodnss.8iz,9e-Ienxcelxupseiorinmcehnrtos,mBaijtoisgrmapehasyu.8reSdcabtytering experiments, such as static light scattering (SLS) and small-angle X-ray scattering (SAXS) experiments, can provide approximate estimates for Bij.[13,14]

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