Calculating the bimolecular rate of protein-protein association with interacting crowders

Eng Hui Yap, Teresa Head-Gordon

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

We have recently introduced a method termed Poisson-Boltzmann semianalytical method (PB-SAM) for solving the linearized Poisson-Boltzmann equation for large numbers of arbitrarily shaped dielectric cavities with controlled precision. In this work we extend the applicability of the PB-SAM approach by deriving force and torque expressions that fully account for mutual polarization in both the zero- and first-order derivatives of the surface charges, that can now be embedded into a Brownian dynamics scheme to look at electrostatic-driven mesoscale assembly and kinetics. We demonstrate the capabilities of the PB-SAM approach by simulating the protein concentration effects on the bimolecular rate of association of barnase and barstar, under periodic boundary conditions and evaluated through mean first passage times. We apply PB-SAM to the pseudo-first-order reaction rate conditions in which either barnase or barstar are in great excess relative to the other protein (124:1). This can be considered a specific case in which the PB-SAM approach can be applied to crowding conditions in which crowders are not inert but can form interactions with other molecules.

Original languageEnglish (US)
Pages (from-to)2481-2489
Number of pages9
JournalJournal of Chemical Theory and Computation
Volume9
Issue number5
DOIs
StatePublished - May 14 2013

Fingerprint

Association reactions
proteins
Proteins
crowding
Boltzmann equation
Surface charge
Reaction rates
torque
Electrostatics
reaction kinetics
Torque
assembly
Boundary conditions
Polarization
electrostatics
boundary conditions
Derivatives
cavities
Molecules
Kinetics

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Calculating the bimolecular rate of protein-protein association with interacting crowders. / Yap, Eng Hui; Head-Gordon, Teresa.

In: Journal of Chemical Theory and Computation, Vol. 9, No. 5, 14.05.2013, p. 2481-2489.

Research output: Contribution to journalArticle

@article{df7f51e017794a2a90e68cec6762bd56,
title = "Calculating the bimolecular rate of protein-protein association with interacting crowders",
abstract = "We have recently introduced a method termed Poisson-Boltzmann semianalytical method (PB-SAM) for solving the linearized Poisson-Boltzmann equation for large numbers of arbitrarily shaped dielectric cavities with controlled precision. In this work we extend the applicability of the PB-SAM approach by deriving force and torque expressions that fully account for mutual polarization in both the zero- and first-order derivatives of the surface charges, that can now be embedded into a Brownian dynamics scheme to look at electrostatic-driven mesoscale assembly and kinetics. We demonstrate the capabilities of the PB-SAM approach by simulating the protein concentration effects on the bimolecular rate of association of barnase and barstar, under periodic boundary conditions and evaluated through mean first passage times. We apply PB-SAM to the pseudo-first-order reaction rate conditions in which either barnase or barstar are in great excess relative to the other protein (124:1). This can be considered a specific case in which the PB-SAM approach can be applied to crowding conditions in which crowders are not inert but can form interactions with other molecules.",
author = "Yap, {Eng Hui} and Teresa Head-Gordon",
year = "2013",
month = "5",
day = "14",
doi = "10.1021/ct400048q",
language = "English (US)",
volume = "9",
pages = "2481--2489",
journal = "Journal of Chemical Theory and Computation",
issn = "1549-9618",
publisher = "American Chemical Society",
number = "5",

}

TY - JOUR

T1 - Calculating the bimolecular rate of protein-protein association with interacting crowders

AU - Yap, Eng Hui

AU - Head-Gordon, Teresa

PY - 2013/5/14

Y1 - 2013/5/14

N2 - We have recently introduced a method termed Poisson-Boltzmann semianalytical method (PB-SAM) for solving the linearized Poisson-Boltzmann equation for large numbers of arbitrarily shaped dielectric cavities with controlled precision. In this work we extend the applicability of the PB-SAM approach by deriving force and torque expressions that fully account for mutual polarization in both the zero- and first-order derivatives of the surface charges, that can now be embedded into a Brownian dynamics scheme to look at electrostatic-driven mesoscale assembly and kinetics. We demonstrate the capabilities of the PB-SAM approach by simulating the protein concentration effects on the bimolecular rate of association of barnase and barstar, under periodic boundary conditions and evaluated through mean first passage times. We apply PB-SAM to the pseudo-first-order reaction rate conditions in which either barnase or barstar are in great excess relative to the other protein (124:1). This can be considered a specific case in which the PB-SAM approach can be applied to crowding conditions in which crowders are not inert but can form interactions with other molecules.

AB - We have recently introduced a method termed Poisson-Boltzmann semianalytical method (PB-SAM) for solving the linearized Poisson-Boltzmann equation for large numbers of arbitrarily shaped dielectric cavities with controlled precision. In this work we extend the applicability of the PB-SAM approach by deriving force and torque expressions that fully account for mutual polarization in both the zero- and first-order derivatives of the surface charges, that can now be embedded into a Brownian dynamics scheme to look at electrostatic-driven mesoscale assembly and kinetics. We demonstrate the capabilities of the PB-SAM approach by simulating the protein concentration effects on the bimolecular rate of association of barnase and barstar, under periodic boundary conditions and evaluated through mean first passage times. We apply PB-SAM to the pseudo-first-order reaction rate conditions in which either barnase or barstar are in great excess relative to the other protein (124:1). This can be considered a specific case in which the PB-SAM approach can be applied to crowding conditions in which crowders are not inert but can form interactions with other molecules.

UR - http://www.scopus.com/inward/record.url?scp=84877759822&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84877759822&partnerID=8YFLogxK

U2 - 10.1021/ct400048q

DO - 10.1021/ct400048q

M3 - Article

AN - SCOPUS:84877759822

VL - 9

SP - 2481

EP - 2489

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 5

ER -