Role of Counterions in Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimers

ACS Omega
Pedro B P S ReisMiguel Machuqueiro

Abstract

Electrostatic interactions play a pivotal role in the structure and mechanism of action of most biomolecules. There are several conceptually different methods to deal with electrostatics in molecular dynamics simulations. Ionic strength effects are usually introduced using such methodologies and can have a significant impact on the quality of the final conformation space obtained. We have previously shown that full system neutralization can lead to wrong lipidic phases in the 25% PA/PC bilayer (J. Chem. Theory Comput. 2014,10, 5483-5492). In this work, we investigate how two limit approaches to the ionic strength treatment (implicitly with GRF or using full system neutralization with either GRF or PME) can influence the conformational space of the second-generation PAMAM dendrimer. Constant-pH MD simulations were used to map PAMAM's conformational space at its full pH range (from 2.5 to 12.5). Our simulations clearly captured the coupling between protonation and conformation in PAMAM. Interestingly, the dendrimer conformational distribution was almost independent of the ionic strength treatment methods, which is in contrast to what we have observed in charged lipid bilayers. Overall, our results confirm that both GRF with impli...Continue Reading

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Citations

Feb 2, 2019·Soft Matter·Jonas LandsgesellPeter Košovan
Jul 17, 2020·The Journal of Chemical Physics·Fabian GrünewaldSiewert J Marrink
Mar 26, 2019·Journal of Chemical Theory and Computation·Diogo Vila-ViçosaMiguel Machuqueiro
Mar 16, 2019·Journal of Chemical Information and Modeling·Mayk C RamosBruno A C Horta
Aug 19, 2020·Journal of Chemical Theory and Computation·Nuno F B OliveiraMiguel Machuqueiro
May 8, 2018·Journal of Chemical Theory and Computation·Diogo Vila-ViçosaMiguel Machuqueiro
Aug 29, 2020·Journal of Chemical Information and Modeling·Pedro B P S ReisMiguel Machuqueiro

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Methods Mentioned

BETA
NMR

Software Mentioned

SETTLE
DelPhi
PETIT
GROMACS
CpHMD
GROMOS
PAMAM

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