A Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface.

Beitrag in einer Fachzeitschrift
(Originalarbeit)


Details zur Publikation

Autor(en): Pluhackova K, Sandoval-Pérez G, Böckmann R
Zeitschrift: Journal of Chemical Theory and Computation
Jahr der Veröffentlichung: 2017
ISSN: 1549-9626
Sprache: Englisch


Abstract


Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parameterized and validated on thermodynamic observables and structural characteristics of individual compounds, e.g. of soluble proteins or lipid bilayers. Less strictly, due to the added complexity and missing experimental data to compare to, force fields have hardly been tested on the properties of mixed systems, e.g. on protein-lipid systems. Their selection and combination for mixed system is further complicated by the partially differing parameterization strategies. Additionally, the presence of other compounds in the system may shift the subtle balance of force field parameters. Here, we assessed the protein-lipid interactions as described in the four atomistic force fields GROMOS54a7, CHARMM36, and the two force field combinations Amber14sb/Slipids and Amber14sb/Lipid14. Four observables were compared, focusing on the membrane-water interface: the conservation of the secondary structure of transmembrane proteins, the positioning of a transmembrane peptide relative to the lipid bilayer, the insertion depths of side chains of unfolded peptides absorbed at the membrane interface, and the ability to reproduce experimental insertion energies of Wimley-White peptides at the membrane interface. Significant differences between the force fields were observed that affect e.g. membrane insertion depth and tilting of transmembrane peptides.



FAU-Autoren / FAU-Herausgeber

Böckmann, Rainer Prof. Dr.
Professur für Computational Biology
Pluhackova, Kristyna Dr.
Professur für Computational Biology
Sandoval-Pérez, Gloria
Professur für Computational Biology


Zitierweisen

APA:
Pluhackova, K., Sandoval-Pérez, G., & Böckmann, R. (2017). A Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface. Journal of Chemical Theory and Computation. https://dx.doi.org/10.1021/acs.jctc.7b00001

MLA:
Pluhackova, Kristyna, Gloria Sandoval-Pérez, and Rainer Böckmann. "A Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface." Journal of Chemical Theory and Computation (2017).

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Zuletzt aktualisiert 2018-11-08 um 02:29