Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study

SPICA Force Field for Proteins and Peptides

(2022) Shuhei Kawamoto et al.   Journal of Chemical Theory and Computation

Lipid Headgroup Charge Controls Melittin Oligomerization in Membranes: Implications in Membrane Lysis

(2021) Sreetama Pal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Correlation between Single Molecular Dynamics and Biological Functions of Antimicrobial Peptide Melittin

(2020) Cheng Xu et al.   Journal of Physical Chemistry Letters

Free energy analysis of membrane pore formation process in the presence of multiple melittin peptides

(2019) Yusuke Miyazaki et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model

(2019) Yusuke Miyazaki et al.   Journal of Chemical Theory and Computation

Effects of Peptide Charge, Orientation, and Concentration on Melittin Transmembrane Pores

(2018) Almudena Pino-Angeles et al.   BIOPHYSICAL JOURNAL

Molecular details on the intermediate states of melittin action on a cell membrane

(2018) Jiaojiao Liu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Peptide-Lipid Interaction Sites Affect Vesicles’ Responses to Antimicrobial Peptides

(2018) Yu Shi et al.   BIOPHYSICAL JOURNAL

SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol

(2018) Sangjae Seo et al.   Journal of Chemical Theory and Computation

Potential of mean force for insertion of antimicrobial peptide melittin into a pore in mixed DOPC/DOPG lipid bilayer by molecular dynamics simulation

(2017) Yuan Lyu et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic Structure and Orientation of Melittin Bound to Acidic Lipid Bilayers, As Revealed by Solid-State NMR and Molecular Dynamics Simulation

(2017) Kazushi Norisada et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Simulations of Melittin-Induced Membrane Pores

(2017) Delin Sun et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Lipid topology and electrostatic interactions underpin lytic activity of linear cationic antimicrobial peptides in membranes

(2017) David J. Paterson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parameters for Martini sterols and hopanoids based on a virtual-site description

(2015) M. N. Melo et al.   JOURNAL OF CHEMICAL PHYSICS

Insights from Micro-second Atomistic Simulations of Melittin in Thin Lipid Bilayers

(2015) Sanjay K. Upadhyay et al.   JOURNAL OF MEMBRANE BIOLOGY

Multistep Molecular Dynamics Simulations Identify the Highly Cooperative Activity of Melittin in Recognizing and Stabilizing Membrane Pores

(2015) Delin Sun et al.   LANGMUIR

Amphipathic Membrane-Active Peptides Recognize and Stabilize Ruptured Membrane Pores: Exploring Cause and Effect with Coarse-Grained Simulations

(2015) Delin Sun et al.   LANGMUIR

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Conformational States of Melittin at a Bilayer Interface

(2013) Magnus Andersson et al.   BIOPHYSICAL JOURNAL

Melittin Creates Transient Pores in a Lipid Bilayer: Results from Computer Simulations

(2013) Kolattukudy P. Santo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Process of inducing pores in membranes by melittin

(2013) M.-T. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determining the mechanism of membrane permeabilizing peptides: Identification of potent, equilibrium pore-formers

(2012) Aram J. Krauson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Binding and reorientation of melittin in a POPC bilayer: Computer simulations

(2012) Sheeba J. Irudayam et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Computer simulation studies of self-assembling macromolecules

(2012) Wataru Shinoda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Difference between Magainin-2 and Melittin Assemblies in Phosphatidylcholine Bilayers: Results from Coarse-Grained Simulations

(2012) Kolattukudy P. Santo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Gain-of-Function Analogues of the Pore-Forming Peptide Melittin Selected by Orthogonal High-Throughput Screening

(2012) Aram J. Krauson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A New Coarse-Grained Force Field for Membrane–Peptide Simulations

(2011) Zhe Wu et al.   Journal of Chemical Theory and Computation

CD Spectroscopy of Peptides and Proteins Bound to Large Unilamellar Vesicles

(2010) Alexey S. Ladokhin et al.   JOURNAL OF MEMBRANE BIOLOGY

Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field

(2010) Wataru Shinoda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

(2010) Semen O. Yesylevskyy et al.   PLoS Computational Biology

Thermodynamics of Melittin Binding to Lipid Bilayers. Aggregation and Pore Formation†

(2009) Gabriela Klocek et al.   BIOCHEMISTRY

Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids

(2009) Russell DeVane et al.   Journal of Chemical Theory and Computation

PACKMOL: A package for building initial configurations for molecular dynamics simulations

(2009) L. Martínez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Cause and Effect of Melittin-Induced Pore Formation: A Computational Approach

(2009) Moutusi Manna et al.   LANGMUIR

Toroidal pores formed by antimicrobial peptides show significant disorder

(2008) Durba Sengupta et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

On the Mechanism of Pore Formation by Melittin

(2008) Geert van den Bogaart et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Coarse-grained molecular modeling of non-ionic surfactant self-assembly

(2008) Wataru Shinoda et al.   Soft Matter