How reliable are molecular dynamics simulations of membrane active antimicrobial peptides?
| Autor: | Jakob P. Ulmschneider, Yukun Wang, Erik Strandberg, Dong-Qing Wei, Anne S. Ulrich, Tangzheng Zhao |
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| Rok vydání: | 2014 |
| Předmět: |
Models
Molecular Antimicrobial peptide PGLa Lipid Bilayers Antimicrobial peptides Molecular Conformation Biophysics Nanotechnology MD force field Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences Biochemistry Force field (chemistry) BP100 Mice 03 medical and health sciences Molecular dynamics Anti-Infective Agents Animals Humans Lipid bilayer membrane Computer Simulation Statistical physics Protein Precursors Maculatin 030304 developmental biology 0303 health sciences Chemistry Melittin Cell Biology Melitten 0104 chemical sciences Oligopeptides Antimicrobial Cationic Peptides |
| Zdroj: | Biochimica et Biophysica Acta (BBA) - Biomembranes. 1838:2280-2288 |
| ISSN: | 0005-2736 |
| DOI: | 10.1016/j.bbamem.2014.04.009 |
| Popis: | Membrane-active antimicrobial peptides (AMPs) are challenging to study experimentally, but relatively easy to investigate using molecular dynamics (MD) computer simulations. For this reason, a large number of MD studies of AMPs have been reported over recent years. Yet relatively little effort has focused on the validity of such simulations. Are these results reliable, and do they agree with what is known experimentally? And how much meaningful information can be obtained? To answer these questions, we demonstrate here some of the requirements and limitations of running MD simulations for several common AMPs: PGLa, melittin, maculatin and BP100. The two most important findings are: (a) simulation results depend strongly on force field parameters, making experimental verification of the simulations obligatory, and (b) slow orientational and conformational fluctuations mean that much longer sampling timescales (multi-μs) are needed if quantitative agreement between simulation averages and experimental data is to be achieved. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. |
| Databáze: | OpenAIRE |
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