Accelerated Molecular Dynamics Applied to the Peptaibol Folding Problem

Tripleurin XIIc: Peptide Folding Dynamics in Aqueous and Hydrophobic Environment Mimic Using Accelerated Molecular Dynamics

(2019) Chetna Tyagi et al.   MOLECULES

Effects of Amiloride, an Ion Channel Blocker, on Alamethicin Pore Formation in Negatively Charged, Gold-Supported, Phospholipid Bilayers: A Molecular View

(2019) Fatemeh Abbasi et al.   LANGMUIR

PACKMOL-Memgen: A simple-to-use generalized workflow for membrane-protein/lipid-bilayer system building

(2019) Stephan Schott-Verdugo et al.   Journal of Chemical Information and Modeling

Structural Diversity and Bioactivities of Peptaibol Compounds From the Longibrachiatum Clade of the Filamentous Fungal Genus Trichoderma

(2019) Tamás Marik et al.   Frontiers in Microbiology

Glycine Perturbs Local and Global Conformational Flexibility of a Transmembrane Helix

(2018) Philipp Högel et al.   BIOCHEMISTRY

Electrophysiological interrogation of asymmetric droplet interface bilayers reveals surface-bound alamethicin induces lipid flip-flop

(2018) Graham Taylor et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation

(2018) Yu-ming M. Huang et al.   Journal of Chemical Theory and Computation

In situ electrochemical and PM-IRRAS studies of alamethicin ion channel formation in model phospholipid bilayers

(2018) ZhangFei Su et al.   JOURNAL OF ELECTROANALYTICAL CHEMISTRY

Monitoring the Orientational Changes of Alamethicin during Incorporation into Bilayer Lipid Membranes

(2018) Enrico Forbrig et al.   LANGMUIR

Alamethicin self-assembling in lipid membranes: concentration dependence from pulsed EPR of spin labels

(2018) Victoria N. Syryamina et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Enhanced solubility and antimicrobial activity of alamethicin in aqueous solution by complexation with γ-cyclodextrin

(2018) Meng-Ke Zhang et al.   Journal of Functional Foods

Pore forming properties of alamethicin in negatively charged floating bilayer lipid membranes supported on gold electrodes

(2018) Fatemeh Abbasi et al.   LANGMUIR

Molecular dynamics modeling of Pseudomonas aeruginosa outer membranes

(2018) Ao Li et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Communication: Alamethicin can capture lipid-like molecules in the membrane

(2017) Ekaterina F. Afanasyeva et al.   JOURNAL OF CHEMICAL PHYSICS

Antimicrobial peptides at work: interaction of myxinidin and its mutant WMR with lipid bilayers mimicking the P. aeruginosa and E. coli membranes

(2017) Lucia Lombardi et al.   Scientific Reports

Permeability across lipid membranes

(2016) Wataru Shinoda   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Exploring the Membrane Potential of Simple Dual-Membrane Systems as Models for Gap-Junction Channels

(2016) Yerko Escalona et al.   BIOPHYSICAL JOURNAL

Simulations of Membrane-Disrupting Peptides I: Alamethicin Pore Stability and Spontaneous Insertion

(2016) B. Scott Perrin et al.   BIOPHYSICAL JOURNAL

Alamethicin Supramolecular Organization in Lipid Membranes from 19 F Solid-State NMR

(2016) Evgeniy S. Salnikov et al.   BIOPHYSICAL JOURNAL

Incorporation of β-Silicon-β3-Amino Acids in the Antimicrobial Peptide Alamethicin Provides a 20-Fold Increase in Membrane Permeabilization

(2016) Julie L. H. Madsen et al.   CHEMISTRY-A EUROPEAN JOURNAL

Antimicrobial Peptides: An Emerging Category of Therapeutic Agents

(2016) Margit Mahlapuu et al.   Frontiers in Cellular and Infection Microbiology

Structure and orientation of antibiotic peptide alamethicin in phospholipid bilayers as revealed by chemical shift oscillation analysis of solid state nuclear magnetic resonance and molecular dynamics simulation

(2015) Takashi Nagao et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Mechanical properties of lipid bilayers from molecular dynamics simulation

(2015) Richard M. Venable et al.   CHEMISTRY AND PHYSICS OF LIPIDS

A Comment on the Reweighting Method for Accelerated Molecular Dynamics Simulations

(2015) Zhifeng Jing et al.   Journal of Chemical Theory and Computation

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

(2015) Yinglong Miao et al.   Journal of Chemical Theory and Computation

A thermodynamic approach to alamethicin pore formation

(2014) Asif Rahaman et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

(2014) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Conformational and Thermodynamic Properties of Non-Canonical α,α-Dialkyl Glycines in the Peptaibol Alamethicin: Molecular Dynamics Studies

(2014) Tarsila G. Castro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Membrane protein orientation and refinement using a knowledge-based statistical potential

(2013) Timothy Nugent et al.   BMC BIOINFORMATICS

Recent Results in Alamethicin Research

(2013) László Kredics et al.   CHEMISTRY & BIODIVERSITY

Direct visualization of the alamethicin pore formed in a planar phospholipid matrix

(2012) P. Pieta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

(2011) Enguerran Vanquelef et al.   NUCLEIC ACIDS RESEARCH

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

(2010) François-Yves Dupradeau et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The Trichoderma brevicompactum clade: a separate lineage with new species, new peptaibiotics, and mycotoxins

(2008) Thomas Degenkolb et al.   MYCOLOGICAL PROGRESS