Literature DB >> 23528098

Conformational states of melittin at a bilayer interface.

Magnus Andersson1, Jakob P Ulmschneider, Martin B Ulmschneider, Stephen H White.   

Abstract

The distribution of peptide conformations in the membrane interface is central to partitioning energetics. Molecular-dynamics simulations enable characterization of in-membrane structural dynamics. Here, we describe melittin partitioning into dioleoylphosphatidylcholine lipids using CHARMM and OPLS force fields. Although the OPLS simulation failed to reproduce experimental results, the CHARMM simulation reported was consistent with experiments. The CHARMM simulation showed melittin to be represented by a narrow distribution of folding states in the membrane interface.
Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2013        PMID: 23528098      PMCID: PMC3602767          DOI: 10.1016/j.bpj.2013.02.006

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  21 in total

1.  Structure, location, and lipid perturbations of melittin at the membrane interface.

Authors:  K Hristova; C E Dempsey; S H White
Journal:  Biophys J       Date:  2001-02       Impact factor: 4.033

2.  Canonical sampling through velocity rescaling.

Authors:  Giovanni Bussi; Davide Donadio; Michele Parrinello
Journal:  J Chem Phys       Date:  2007-01-07       Impact factor: 3.488

Review 3.  Experimentally determined hydrophobicity scale for proteins at membrane interfaces.

Authors:  W C Wimley; S H White
Journal:  Nat Struct Biol       Date:  1996-10

4.  Folding of beta-sheet membrane proteins: a hydrophobic hexapeptide model.

Authors:  W C Wimley; K Hristova; A S Ladokhin; L Silvestro; P H Axelsen; S H White
Journal:  J Mol Biol       Date:  1998-04-17       Impact factor: 5.469

5.  Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations.

Authors:  Jakob P Ulmschneider; Jeremy C Smith; Martin B Ulmschneider; Anne S Ulrich; Erik Strandberg
Journal:  Biophys J       Date:  2012-08-08       Impact factor: 4.033

6.  Hydrogen-bond energetics drive helix formation in membrane interfaces.

Authors:  Paulo F Almeida; Alexey S Ladokhin; Stephen H White
Journal:  Biochim Biophys Acta       Date:  2011-07-22

7.  Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations.

Authors:  Ryan W Benz; Hirsh Nanda; Francisco Castro-Román; Stephen H White; Douglas J Tobias
Journal:  Biophys J       Date:  2006-09-01       Impact factor: 4.033

8.  Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.

Authors:  Jeffery B Klauda; Richard M Venable; J Alfredo Freites; Joseph W O'Connor; Douglas J Tobias; Carlos Mondragon-Ramirez; Igor Vorobyov; Alexander D MacKerell; Richard W Pastor
Journal:  J Phys Chem B       Date:  2010-06-17       Impact factor: 2.991

9.  Energetics, stability, and prediction of transmembrane helices.

Authors:  S Jayasinghe; K Hristova; S H White
Journal:  J Mol Biol       Date:  2001-10-05       Impact factor: 5.469

10.  United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field.

Authors:  Jakob P Ulmschneider; Martin B Ulmschneider
Journal:  J Chem Theory Comput       Date:  2009-07-14       Impact factor: 6.006

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  22 in total

Review 1.  Computational studies of peptide-induced membrane pore formation.

Authors:  Richard Lipkin; Themis Lazaridis
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-08-05       Impact factor: 6.237

Review 2.  Membrane-active peptides: binding, translocation, and flux in lipid vesicles.

Authors:  Paulo F Almeida
Journal:  Biochim Biophys Acta       Date:  2014-04-25

3.  The structure of a melittin-stabilized pore.

Authors:  John M Leveritt; Almudena Pino-Angeles; Themis Lazaridis
Journal:  Biophys J       Date:  2015-05-19       Impact factor: 4.033

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

Authors:  Sanjay K Upadhyay; Yukun Wang; Tangzhen Zhao; Jakob P Ulmschneider
Journal:  J Membr Biol       Date:  2015-05-12       Impact factor: 1.843

5.  Hydrogen Exchange Mass Spectrometry of Proteins at Langmuir Monolayers.

Authors:  Gregory F Pirrone; Briana C Vernon; Michael S Kent; John R Engen
Journal:  Anal Chem       Date:  2015-07-02       Impact factor: 6.986

6.  PackMem: A Versatile Tool to Compute and Visualize Interfacial Packing Defects in Lipid Bilayers.

Authors:  Romain Gautier; Amélie Bacle; Marion L Tiberti; Patrick F Fuchs; Stefano Vanni; Bruno Antonny
Journal:  Biophys J       Date:  2018-07-05       Impact factor: 4.033

Review 7.  Computational modeling of membrane proteins.

Authors:  Julia Koehler Leman; Martin B Ulmschneider; Jeffrey J Gray
Journal:  Proteins       Date:  2014-11-19

8.  Folding a viral peptide in different membrane environments: pathway and sampling analyses.

Authors:  Shivangi Nangia; Jason G Pattis; Eric R May
Journal:  J Biol Phys       Date:  2018-04-11       Impact factor: 1.365

9.  The importance of the membrane interface as the reference state for membrane protein stability.

Authors:  Jakob P Ulmschneider; Jeremy C Smith; Stephen H White; Martin B Ulmschneider
Journal:  Biochim Biophys Acta Biomembr       Date:  2018-09-20       Impact factor: 3.747

Review 10.  Mechanisms of integral membrane protein insertion and folding.

Authors:  Florian Cymer; Gunnar von Heijne; Stephen H White
Journal:  J Mol Biol       Date:  2014-09-30       Impact factor: 5.469

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