Notes on the Treatment of Charged Particles for Studying Cyclotide/Membrane Interactions with Dissipative Particle Dynamics

ORCID
0000-0001-8973-8463
Affiliation
Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany;
Bänsch, Felix;
GND
128763922
ORCID
0000-0001-6966-0814
Affiliation
Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessing Str. 8, 07743 Jena, Germany;
Steinbeck, Christoph;
ORCID
0000-0003-0722-4229
Affiliation
Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany;
Zielesny, Achim

Different charge treatment approaches are examined for cyclotide-induced plasma membrane disruption by lipid extraction studied with dissipative particle dynamics. A pure Coulomb approach with truncated forces tuned to avoid individual strong ion pairing still reveals hidden statistical pairing effects that may lead to artificial membrane stabilization or distortion of cyclotide activity depending on the cyclotide’s charge state. While qualitative behavior is not affected in an apparent manner, more sensitive quantitative evaluations can be systematically biased. The findings suggest a charge smearing of point charges by an adequate charge distribution. For large mesoscopic simulation boxes, approximations for the Ewald sum to account for mirror charges due to periodic boundary conditions are of negligible influence.

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