Predicting Membrane-Active Peptide Dynamics in Fluidic Lipid Membranes

Charles H. Chen*, Karen Pepper, Jakob P. Ulmschneider, Martin B. Ulmschneider, Timothy K. Lu

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


Understanding the interactions between peptides and lipid membranes could not only accelerate the development of antimicrobial peptides as treatments for infections but also be applied to finding targeted therapies for cancer and other diseases. However, designing biophysical experiments to study molecular interactions between flexible peptides and fluidic lipid membranes has been an ongoing challenge. Recently, with hardware advances, algorithm improvements, and more accurate parameterizations (i.e., force fields), all-atom molecular dynamics (MD) simulations have been used as a “computational microscope” to investigate the molecular interactions and mechanisms of membrane-active peptides in cell membranes (Chen et al., Curr Opin Struct Biol 61:160–166, 2020; Ulmschneider and Ulmschneider, Acc Chem Res 51(5):1106–1116, 2018; Dror et al., Annu Rev Biophys 41:429–452, 2012). In this chapter, we describe how to utilize MD simulations to predict and study peptide dynamics and how to validate the simulations by circular dichroism, intrinsic fluorescent probe, membrane leakage assay, electrical impedance, and isothermal titration calorimetry. Experimentally validated MD simulations open a new route towards peptide design starting from sequence and structure and leading to desirable functions.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc
Number of pages22
Publication statusPublished - 2022

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Membrane-active peptides
  • Molecular dynamics simulations
  • Pore formation
  • Protein design
  • Protein folding


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