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references.bib
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@misc{Jacques2008,
author = {Ongena, Marc and Jacques, Philippe},
booktitle = {Trends in Microbiology},
number = {3},
pages = {115--125},
title = {{Bacillus lipopeptides: versatile weapons for plant disease biocontrol}},
volume = {16},
year = {2008}
}
@article{Martinotti2009,
author = {Rivardo, F and Turner, R J and Allegrone, G and Ceri, H and Martinotti, M G},
doi = {10.1007/s00253-009-1987-7},
institution = {Department of Chemical, Food, Pharmaceutical and Pharmacological Sciences (DiSCAFF), Drug and Food Biotechnology Centre, University of Eastern Piedmont, Via Bovio 6, 28100 Novara, Italy.},
journal = {Appl Microbiol Biotechnol},
keywords = {Bacillus,Bacteria,Bacterial Adhesion,Bacterial Infections,Bacterial Physiological Phenomena,Biofilms,Humans,Surface-Active Agents,chemistry/metabolism,chemistry/metabolism/pharmacology,drug effects,microbiology},
language = {eng},
month = {jun},
number = {3},
pages = {541--553},
pmid = {19343338},
title = {{Anti-adhesion activity of two biosurfactants produced by Bacillus spp. prevents biofilm formation of human bacterial pathogens.}},
url = {http://dx.doi.org/10.1007/s00253-009-1987-7},
volume = {83},
year = {2009}
}
@article{RomoGrossfield2014,
author = {Romo, Tod D and Leioatts, Nicholas and Grossfield, Alan},
doi = {10.1002/jcc.23753},
institution = {Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, 14642.},
journal = {J Comput Chem},
language = {eng},
month = {dec},
number = {32},
pages = {2305--2318},
pmid = {25327784},
title = {{Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.}},
url = {http://dx.doi.org/10.1002/jcc.23753},
volume = {35},
year = {2014}
}
@article{Balaram2012,
author = {Pathak, Khyati V and Keharia, Haresh and Gupta, Kallol and Thakur, Suman S and Balaram, Padmanabhan},
journal = {Journal of the American Society for Mass Spectrometry},
number = {10},
pages = {1716--1728},
publisher = {Springer},
title = {{Lipopeptides from the banyan endophyte, Bacillus subtilis K1: mass spectrometric characterization of a library of fengycins}},
volume = {23},
year = {2012}
}
@article{Thonart2005,
author = {Ongena, Marc and Jacques, Philippe and Tour{\'{e}}, Yacine and Destain, Jacqueline and Jabrane, Abdelhamid and Thonart, Philippe},
doi = {10.1007/s00253-005-1940-3},
issn = {1432-0614},
journal = {Applied Microbiology and Biotechnology},
number = {1},
pages = {29--38},
title = {{Involvement of fengycin-type lipopeptides in the multifaceted biocontrol potential of Bacillus subtilis}},
url = {http://dx.doi.org/10.1007/s00253-005-1940-3},
volume = {69},
year = {2005}
}
@article{Avis2007,
author = {Avis, T. J.},
doi = {10.1080/07060660709507478},
issn = {17152992},
journal = {Canadian Journal of Plant Pathology},
title = {{Antifungal compounds that target fungal membranes: Applications in plant disease control}},
year = {2007}
}
@article{Jacques1999,
author = {Schneider, Jochen and Taraz, Kambiz and Budzikiewicz, Herbert and Deleu, Magali and Thonart, Philippe and Jacques, Philippe},
doi = {10.1515/znc-1999-1102},
issn = {09395075},
journal = {Zeitschrift fur Naturforschung - Section C Journal of Biosciences},
keywords = {Bacillus subtilis,Fengycin,Lipopeptides},
title = {{The structure of two fengycins from Bacillus subtilis S499}},
year = {1999}
}
@article{Wei2010,
author = {Wei, Yu Hong and Wang, Li Chuan and Chen, Wei Chuan and Chen, Shan Yu},
journal = {International journal of molecular sciences},
number = {11},
pages = {4526--4538},
title = {{Production and characterization of fengycin by indigenous Bacillus subtilis F29-3 originating from a potato farm.}},
volume = {11},
year = {2010}
}
@article{Liu2007,
author = {Wu, Cheng-Yeu and Chen, Chyi-Liang and Lee, Yu-Hsiu and Cheng, Yu-Chieh
and Wu, Ying-Chung and Shu, Hung-Yu and Götz, Friedrich and Liu, Shih-Tung},
doi = {10.1074/jbc.M609726200},
journal = {J Biol Chem},
keywords = {Bacillus subtilis,Bacterial Proteins,Lipopeptides,Lipoproteins,Multienzyme Complexes,Nucleic Acid-Independent,Peptide Biosynthesis,Peptide Synthases,biosynthesis,enzymology/genetics,genetics/metabolism,physiology},
language = {eng},
month = {feb},
number = {8},
pages = {5608--5616},
pmid = {17182617},
title = {{Nonribosomal synthesis of fengycin on an enzyme complex formed by fengycin synthetases.}},
url = {http://dx.doi.org/10.1074/jbc.M609726200},
volume = {282},
year = {2007}
}
@article{Nylander2005,
author = {Deleu, M. and Paquot, M. and Nylander, T.},
journal = {J Colloid Interface Sci},
keywords = {Air,Artificial,Bacillus subtilis,Lipopeptides,Lipoproteins,Membrane Lipids,Membranes,Molecular Structure,Surface Properties,Water,chemistry},
language = {eng},
month = {mar},
number = {2},
pages = {358--365},
pmid = {15721905},
title = {Fengycin interaction with lipid monolayers at the air-aqueous interface-implications for the effect of fengycin on biological membranes.},
url = {http://dx.doi.org/10.1016/j.jcis.2004.09.036},
volume = {283},
year = {2005}
}
@article{Roland2006,
author = {Shoemaker, D M and Simou, J and Roland, W E},
journal = {Therapeutics and Clinical Risk Management},
number = {2},
pages = {169--174},
title = {{A review of daptomycin for injection (Cubicin) in the treatment of complicated skin and skin structure infections.}},
volume = {2},
year = {2006}
}
@article{Ewald1921,
author = {Ewald, Paul Peter},
journal = {Ann. Phys},
number = {3},
pages = {253--287},
title = {{The calculation of optical and electrostatic grid potential}},
volume = {64},
year = {1921}
}
@article{Vogel2012,
author = {Olausson, Bjoern E S and Grossfield, Alan and Pitman, Michael C. and Brown, Michael F. and Feller, Scott E. and Vogel, Alexander},
journal = {Journal of the American Chemical Society},
number = {9},
pages = {4324--4331},
title = {{Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes}},
volume = {134},
year = {2012}
}
@article{Yang2007,
author = {Hu, Liang Bin and Shi, Zhi Qi and Zhang, Ting and Yang, Zhi Min},
doi = {10.1111/j.1574-6968.2007.00743.x},
institution = {College of Life Sciences, Nanjing Agricultural University, Nanjing, China.},
journal = {FEMS Microbiol Lett},
keywords = {16S,Antifungal Agents,Bacillus subtilis,Bacterial,Brassica napus,Chromatography,DNA,Fungal,Fusarium,Genes,High Pressure Liquid,Lipopeptides,Lipoproteins,Mass Spectrometry,Molecular Sequence Data,Mycelium,Nucleic Acid,Phylogeny,Plant Stems,RNA,Ribosomal,Sequence Analysis,Sequence Homology,Spores,Zea mays,chemistry/genetics,chemistry/isolation /{\&}/ purification/pharmacology,classification/isolation /{\&}/ purification/metaboli,drug effects/growth /{\&}/ development,genetics,microbiology,rRNA},
language = {eng},
month = {jul},
number = {1},
pages = {91--98},
pmid = {17490402},
title = {{Fengycin antibiotics isolated from B-FS01 culture inhibit the growth of Fusarium moniliforme Sheldon ATCC 38932.}},
url = {http://dx.doi.org/10.1111/j.1574-6968.2007.00743.x},
volume = {272},
year = {2007}
}
@article{Grossfield2011,
institution = {Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.},
journal = {Biochim Biophys Acta},
keywords = {Acylation,Anisotropy,Anti-Infective Agents,Artificial,Binding Sites,Biomolecular,Escherichia coli,Hydrogen Bonding,Lactoferrin,Membrane Lipids,Membranes,Microbial Sensitivity Tests,Molecular Conformation,Molecular Dynamics Simulation,Nuclear Magnetic Resonance,Oligopeptides,Peptide Fragments,Phosphatidylcholines,Phosphatidylethanolamines,Phosphatidylglycerols,Protein Binding,Staphylococcus aureus,Structure-Activity Relationship,chemistry,chemistry/metabolism,chemistry/metabolism/pharmacology,drug effects/growth /{\&}/ development},
language = {eng},
month = {aug},
number = {8},
pages = {2019--2030},
pmid = {21477580},
title = {{Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations.}},
url = {http://dx.doi.org/10.1016/j.bbamem.2011.03.017},
volume = {1808},
year = {2011}
}
@article{Heerklotz2011,
author = {Patel, Hiren and Tscheka, Clemens and Edwards, Katarina and Karlsson, G{\~{A}}{\P}ran and Heerklotz, Heiko},
doi = {http://dx.doi.org/10.1016/j.bbamem.2011.04.008},
issn = {0005-2736},
journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes},
keywords = {All-or-none leakage,Antibiotic peptide,Biofilm,Biosurfactant,Fungicide,Time resolved fluorescence spectroscopy},
number = {8},
pages = {2000 -- 2008},
title = {{All-or-none membrane permeabilization by fengycin-type lipopeptides from Bacillus subtilis {\{}QST713{\}}}},
url = {http://www.sciencedirect.com/science/article/pii/S0005273611001131},
volume = {1808},
year = {2011}
}
@article{Vattulainen2017,
author = {Javanainen, Matti and Martinez-Seara, Hector and Vattulainen, Ilpo},
doi = {10.1371/journal.pone.0187936},
issn = {19326203},
journal = {PLoS ONE},
title = {{Excessive aggregation of membrane proteins in the Martini model}},
year = {2017}
}
@book{Smit2002,
author = {Frenkel, Daan and Smit, Berend},
editor = {Frenkel, Daan and Klein, Michael and Parrinello, Michele and Smit, Berend},
publisher = {Academic Press},
title = {{Understanding Molecular Simulation From Algorithms to Applications}},
year = {2002}
}
@article{Grossfield2013,
author = {Horn, Joshua N. and Cravens, Aaron and Grossfield, Alan},
journal = {Biophysical Journal},
number = {7},
pages = {1612--1623},
title = {{Interactions between fengycin and model bilayers quantified by coarse-grained molecular dynamics}},
volume = {105},
year = {2013}
}
@book{Zuckerman2010,
author = {Zuckerman, Daniel M.},
booktitle = {Statistical Physics of Biomolecules: An Introduction},
doi = {10.1201/b18849},
isbn = {9781420073799},
keywords = {Zuckerman2010},
month = {jan},
pages = {1--325},
publisher = {CRC Press},
title = {{Statistical physics of biomolecules: An introduction}},
year = {2010}
}
@article{Heerklotz2008,
author = {Heerklotz, Heiko},
doi = {10.1017/S0033583508004721},
institution = {Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada M5S 3M2. [email protected]},
journal = {Q Rev Biophys},
number = {3-4},
pages = {205--264},
pmid = {19079805},
title = {{Interactions of surfactants with lipid membranes.}},
url = {http://dx.doi.org/10.1017/S0033583508004721},
volume = {41},
year = {2008}
}
@article{RomeroPerez2007,
author = {Romero, D and de Vicente, A and Olmos, J L and D{\'{a}}vila, J C and P{\'{e}}rez-Garc$\backslash$'{\{}$\backslash$i{\}}a, A},
doi = {10.1111/j.1365-2672.2007.03323.x},
institution = {Departamento de Microbiolog{\'{i}}a, Facultad de Ciencias, Universidad de M{\'{a}}laga, M{\'{a}}laga, Spain.},
journal = {J Appl Microbiol},
keywords = {Antibiosis,Antifungal Agents,Ascomycota,Bacillus subtilis,Bacterial Proteins,Biological,Conditioned,Culture Media,Electron,Fungal,Lipoproteins,Microscopy,Pest Control,Scanning,Spores,classification/metabolism/physiology,drug effects/growth /{\&}/ development/ultrastructure,methods,pharmacology,physiology},
language = {eng},
month = {oct},
number = {4},
pages = {969--976},
pmid = {17897200},
title = {Effect of lipopeptides of antagonistic strains of Bacillus subtilis on the morphology and ultrastructure of the cucurbit fungal pathogen Podosphaera fusca.},
url = {http://dx.doi.org/10.1111/j.1365-2672.2007.03323.x},
volume = {103},
year = {2007}
}
@article{Mackerell2013,
author = {Huang, Jing and Mackerell, Alexander D.},
journal = {Journal of Computational Chemistry},
keywords = {G protein B1,J-coupling,calmodulin,cold-shock protein A,empirical force field,fatty acid binding protein,lysozyme,molecular mechanics,residual dipolar coupling,ubiquitin},
number = {25},
pages = {2135--2145},
title = {CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data},
volume = {34},
year = {2013}
}
@misc{Grossfield2014,
author = {Romo, Tod D. and Grossfield, Alan},
booktitle = {Biophysical Journal},
number = {8},
pages = {1553--1554},
publisher = {Biophysical Society},
title = {{Unknown unknowns: The challenge of systematic and statistical error in molecular dynamics simulations}},
volume = {106},
year = {2014}
}
@article{WESTPA2018,
author = {Pratt, Adam and Zuckerman, Daniel M. and Chong, Lillian T.},
doi = {10.1016/j.bpj.2017.11.3650},
issn = {00063495},
journal = {Biophysical Journal},
title = {WESTPA 2.0 Advances in Sampling, Storage, and Analysis of Weighted Ensemble Simulations},
year = {2018}
}
@article{Pastor2010,
author = {Klauda, Jeffery B and Venable, Richard M and Freites, J Alfredo and O'Connor, Joseph W and Tobias, Douglas J and Mondragon-Ramirez, Carlos and Vorobyov, Igor and {MacKerell Jr}, Alexander D and Pastor, Richard W},
journal = {The journal of physical chemistry B},
number = {23},
pages = {7830--7843},
publisher = {ACS Publications},
title = {Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types},
volume = {114},
year = {2010}
}
@article{Roy2013,
author = {Roy, Anupam and Mahata, Denial and Paul, Debarati and Korpole, Suresh and Franco, Octavio L. and Mandal, Santi M.},
journal = {Frontiers in Microbiology},
keywords = {Antimicrobial activity,Bacillus thuringiensis,Fengycin,Self-assembled structure},
number = {NOV},
publisher = {Frontiers Media SA},
title = {{Purification, biochemical characterization and self-assembled structure of a fengycin-like antifungal peptide from bacillus thuringiensis strain SM}},
volume = {4},
year = {2013}
}
@article{Seguin2009,
author = {Chan, Yiu-Kwok and Savard, Marc E and Reid, Lana M and Cyr, Terry and McCormick, Wayne A and Seguin, Charles},
doi = {10.1007/s10526-008-9201-x},
issn = {1573-8248},
journal = {BioControl},
number = {4},
pages = {567--574},
title = {Identification of lipopeptide antibiotics of a Bacillus subtilis isolate and their control of Fusarium graminearum diseases in maize and wheat},
url = {http://dx.doi.org/10.1007/s10526-008-9201-x},
volume = {54},
year = {2009}
}
@article{Feller2005,
author = {Pitman, Michael C. and Grossfield, Alan and Suits, Frank and Feller, Scott E.},
journal = {Journal of the American Chemical Society},
number = {13},
pages = {4576--4577},
title = {{Role of cholesterol and polyunsaturated chains in lipid-protein interactions: Molecular dynamics simulation of rhodopsin in a realistic membrane environment}},
volume = {127},
year = {2005}
}
@article{Deleu2009,
author = {Eeman, Marc and Pegado, Luis and Dufr{\^{e}}ne, Yves F and Paquot, Michel and Deleu, Magali},
doi = {10.1016/j.jcis.2008.10.017},
journal = {J Colloid Interface Sci},
keywords = {1,2-Dipalmitoylphosphatidylcholine,Air,Bacillus subtilis,Hydrogen-Ion Concentration,Lipopeptides,Pressure,Water,chemistry},
language = {eng},
month = {jan},
number = {2},
pages = {253--264},
pmid = {18947831},
title = {Influence of environmental conditions on the interfacial organisation of fengycin, a bioactive lipopeptide produced by Bacillus subtilis.},
url = {http://dx.doi.org/10.1016/j.jcis.2008.10.017},
volume = {329},
year = {2009}
}
@article{Rahman1981,
author = {Parrinello, M. and Rahman, A.},
doi = {10.1063/1.328693},
issn = {00218979},
journal = {Journal of Applied Physics},
title = {{Polymorphic transitions in single crystals: A new molecular dynamics method}},
year = {1981}
}
@article{Romero2007,
journal = {Molecular plant-microbe interactions : MPMI},
number = {4},
pages = {430--440},
title = {The iturin and fengycin families of lipopeptides are key factors in antagonism of Bacillus subtilis toward Podosphaera fusca.},
volume = {20},
year = {2007}
}
@article{Jacques2007,
author = {Ongena, Marc and Jacques, Philippe},
journal = {Trends in Microbiology},
number = {3},
pages = {115--124},
title = {{Bacillus lipopeptides: versatile weapons for plant diseases biocontrol}},
volume = {16},
year = {2007}
}
@article{Marrink2015,
annote = {PMID: 26574417},
author = {Wassenaar, Tsjerk A and Ing{\'{o}}lfsson, Helgi I and B{\"{o}}ckmann, Rainer A and Tieleman, D Peter and Marrink, Siewert J},
doi = {10.1021/acs.jctc.5b00209},
journal = {Journal of Chemical Theory and Computation},
number = {5},
pages = {2144--2155},
title = {Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations},
url = {https://doi.org/10.1021/acs.jctc.5b00209},
volume = {11},
year = {2015}
}
@article{Kim1996,
author = {Huber, Gary A. and Kim, Sangtae},
doi = {10.1016/S0006-3495(96)79552-8},
issn = {00063495},
journal = {Biophysical Journal},
title = {{Weighted-ensemble Brownian dynamics simulations for protein association reactions}},
year = {1996}
}
@article{MantilTyler2019,
author = {Mantil, Elisabeth and Crippin, Trinda and Avis, Tyler J.},
doi = {10.1016/j.bbamem.2019.01.003},
issn = {18792642},
journal = {Biochimica et Biophysica Acta - Biomembranes},
keywords = {Antimicrobial compound,Domain distribution,Ergosterol,Fengycin,Model membranes},
title = {Domain redistribution within ergosterol-containing model membranes in the presence of the antimicrobial compound fengycin},
year = {2019}
}
@article{Nylander2008,
author = {Magali Deleu, Michel Paquot and Nylander, Tommy},
journal = {Biophysical Journal},
pages = {2667--2679},
title = {Effect of Fengycin, a Lipopeptide Produced by Bacillus subtilis, on Model Biomembranes},
volume = {94},
year = {2008}
}
@article{Menestrina1999,
author = {Serra, Mauro Dalla and Fagiuoli, Giulia and Nordera, Paola and Bernhart, Ivonne and Volpe, Claudio Della and {Di Giorgio}, Domenico and Ballio, Alessandro and Menestrina, Gianfranco},
doi = {10.1094/MPMI.1999.12.5.391},
issn = {0894-0282},
journal = {Molecular Plant-Microbe Interactions},
number = {5},
pages = {391--400},
title = {The Interaction of Lipodepsipeptide Toxins from Pseudomonas syringae pv. syringae with Biological and Model Membranes: A Comparison of Syringotoxin, Syringomycin, and Two Syringopeptins},
url = {http://dx.doi.org/10.1094/MPMI.1999.12.5.391},
volume = {12},
year = {1999}
}
@article{Andersen1983,
author = {Andersen, H C},
journal = {J. Comput. Phys.},
pages = {24--34},
title = {{RATTLE: A “velocity” version of the SHAKE algorithm for molecular dynamics calculations.}},
volume = {52},
year = {1983}
}
@article{Rosenberg1992,
author = {Kumar, S and Bouzida, D and Swendsen, R H and Kollman, P A and Rosenberg, J M},
journal = {J. Comput. Chem.},
pages = {1011--1021},
title = {The weighted histogram analysis method for free-energy calculations on biomolecules. $\backslash$ I. The method},
volume = {13},
year = {1992}
}
@article{Seelig2004,
author = {Heerklotz, Heiko and Wieprecht, Torsten and Seelig, Joachim},
journal = {The Journal of Physical Chemistry B},
number = {15},
pages = {4909--4915},
publisher = {ACS Publications},
title = {Membrane perturbation by the lipopeptide surfactin and detergents as studied by deuterium NMR},
volume = {108},
year = {2004}
}
@article{Najla2012,
author = {Hanene, REBIB and Abdeljabbar, HEDI and Marc, ROUSSET and Abdellatif, BOUDABOUS and Ferid, LIMAM and Najla, SADFI-ZOUAOUI},
doi = {10.5897/AJB11.2887},
issn = {16845315},
journal = {African Journal of Biotechnology},
number = {34},
pages = {8464--8475},
publisher = {Academic Journals},
title = {Biological control of Fusarium foot rot of wheat using fengycin-producing Bacillus subtilis isolated from salty soil},
url = {http://www.academicjournals.org/journal/AJB/article-abstract/A19468E37686},
volume = {11},
year = {2012}
}
@article{Wimley2012,
author = {Krauson, Aram J and He, Jing and Wimley, William C},
journal = {Biochimica et Biophysica Acta (BBA)-Biomembranes},
number = {7},
pages = {1625--1632},
publisher = {Elsevier},
title = {Determining the mechanism of membrane permeabilizing peptides: identification of potent, equilibrium pore-formers},
volume = {1818},
year = {2012}
}
@article{Haqq-Misra2019,
author = {Mullan, B. and Haqq-Misra, J.},
doi = {10.1016/j.futures.2018.06.009},
issn = {00163287},
journal = {Futures},
keywords = {Anthropocene,Astrobiology,Climate change,Fermi paradox,SETI,Sustainability},
title = {Population growth, energy use, and the implications for the search for extraterrestrial intelligence},
year = {2019}
}
@article{Lu2011,
author = {Tao, Yang and Bie, Xiao-mei and Lv, Feng-xia and Zhao, Hai-zhen and Lu, Zhao-xin},
doi = {10.1007/s12275-011-0171-9},
institution = {College of Food Science and Technology, Nanjing Agricultural University, Weigang, Nanjing, 210095, PR China.},
journal = {J Microbiol},
keywords = {Antifungal Agents,Biosynthetic Pathways,Cell Membrane,Cyclic,DNA,Drug Interactions,Lipopeptides,Microbial Sensitivity Tests,Organelles,Peptides,Rhizopus,drug effects,metabolism,pharmacology},
language = {eng},
month = {feb},
number = {1},
pages = {146--150},
pmid = {21369992},
title = {Antifungal activity and mechanism of fengycin in the presence and absence of commercial surfactin against Rhizopus stolonifer.},
url = {http://dx.doi.org/10.1007/s12275-011-0171-9},
volume = {49},
year = {2011}
}
@article{HornGrossfield2013,
author = {Horn, Joshua N. and Romo, Tod D. and Grossfield, Alan},
journal = {Biochemistry},
number = {33},
pages = {5604--5610},
title = {Simulating the mechanism of antimicrobial lipopeptides with all-atom molecular dynamics},
volume = {52},
year = {2013}
}
@article{Eeman2009b,
author = {Eeman, Marc and Pegado, Luis and Dufr{\^{e}}ne, Yves F. and Paquot, Michel and Deleu, Magali},
journal = {Journal of Colloid and Interface Science},
keywords = {Atomic force microscopy,Langmuir film,Molecular organisation,Nanoscale resolution,Surface pressure-area isotherms},
number = {2},
pages = {253--264},
title = {Influence of environmental conditions on the interfacial organisation of fengycin, a bioactive lipopeptide produced by Bacillus subtilis},
volume = {329},
year = {2009}
}
@article{Stoll1978,
author = {Schneider, T and Stoll, E},
journal = {Physical Review B},
number = {3},
pages = {1302},
publisher = {APS},
title = {Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions},
volume = {17},
year = {1978}
}
@article{Sansom2008,
author = {Lindahl, Eric and Sansom, Mark S P},
journal = {Current Opinion in Structural Biology},
pages = {425--431},
title = {{Membrane proteins: molecular dynamics simulation}},
volume = {18},
year = {2008}
}
@article{Heerklotz2012,
author = {Nazari, Mozhgan and Kurdi, Mustafa and Heerklotz, Heiko},
doi = {10.1016/j.bpj.2011.12.029},
institution = {Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.},
journal = {Biophys J},
keywords = {Cell Membrane,Micelles,Models,Molecular,Molecular Conformation,Phospholipids,Surface-Active Agents,chemistry,chemistry/drug effects,pharmacology},
language = {eng},
month = {feb},
number = {3},
pages = {498--506},
pmid = {22325272},
title = {Classifying surfactants with respect to their effect on lipid membrane order.},
url = {http://dx.doi.org/10.1016/j.bpj.2011.12.029},
volume = {102},
year = {2012}
}
@article{Epand2009,
author = {Epand, Richard M and Epand, Raquel F},
journal = {Biochimica et Biophysica Acta (BBA)-Biomembranes},
number = {1},
pages = {289--294},
publisher = {Elsevier},
title = {{Lipid domains in bacterial membranes and the action of antimicrobial agents}},
volume = {1788},
year = {2009}
}
@article{Ponder2003,
author = {Grossfield, Alan and Ren, Pengyu and Ponder, Jay W.},
journal = {Journal of the American Chemical Society},
number = {50},
pages = {15671--15682},
title = {Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field},
volume = {125},
year = {2003}
}
@article{Faille2009,
doi = {10.1080/08927010902977943},
institution = {Faculty of Water Engineering, Power and Water University of Technology, Tehran, Iran.},
journal = {Biofouling},
keywords = {Amino Acid Sequence,Bacillus cereus,Bacillus subtilis,Bacterial,Bacterial Adhesion,Dose-Response Relationship,Drug,Hydrophobic and Hydrophilic Interactions,Lipopeptides,Micelles,Oligopeptides,Polytetrafluoroethylene,Spores,Stainless Steel,Substrate Specificity,Surface Properties,chemistry,chemistry/isolation /{\&}/ purification/pharmacology,drug effects,drug effects/physiology},
language = {eng},
number = {6},
pages = {533--541},
pmid = {19431000},
title = {Effect of different Bacillus subtilis lipopeptides on surface hydrophobicity and adhesion of Bacillus cereus 98/4 spores to stainless steel and Teflon.},
url = {http://dx.doi.org/10.1080/08927010902977943},
volume = {25},
year = {2009}
}
@article{WESTPA2015,
author = {Zwier, Matthew C and Adelman, Joshua L and Kaus, Joseph W and Pratt, Adam J and Wong, Kim F and Rego, Nicholas B and Su{\'{a}}rez, Ernesto and Lettieri, Steven and Wang, David W and Grabe, Michael and Zuckerman, Daniel M and Chong, Lillian T},
doi = {10.1021/ct5010615},
journal = {Journal of Chemical Theory and Computation},
number = {2},
pages = {800--809},
title = {WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis},
url = {https://doi.org/10.1021/ct5010615},
volume = {11},
year = {2015}
}
@misc{Schulten2005,
author = {Phillips, James C. and Braun, Rosemary and Wang, Wei and Gumbart, James and Tajkhorshid, Emad and Villa, Elizabeth and Chipot, Christophe and Skeel, Robert D. and Kal??, Laxmikant and Schulten, Klaus},
booktitle = {Journal of Computational Chemistry},
keywords = {Biomolecular simulation,Molecular dynamics,Parallel computing},
number = {16},
pages = {1781--1802},
title = {Scalable molecular dynamics with NAMD},
volume = {26},
year = {2005}
}
@article{Tyler2014,
author = {Wise, Cody and Falardeau, Justin and Hagberg, Ingrid and Avis, Tyler J},
doi = {10.1094/PHYTO-12-13-0336-R},
journal = {Phytopathology},
language = {eng},
month = {oct},
number = {10},
pages = {1036--1041},
pmid = {24679152},
title = {Cellular Lipid Composition Affects Sensitivity of Plant Pathogens to Fengycin, an Antifungal Compound Produced by Bacillus subtilis Strain CU12.},
url = {http://dx.doi.org/10.1094/PHYTO-12-13-0336-R},
volume = {104},
year = {2014}
}
@article{Grossfield2018,
author = {Sur, S. and Romo, T.D. and Grossfield, A.},
doi = {10.1021/acs.jpcb.7b11889},
issn = {15205207},
journal = {Journal of Physical Chemistry B},
number = {8},
title = {Selectivity and Mechanism of Fengycin, an Antimicrobial Lipopeptide, from Molecular Dynamics},
volume = {122},
year = {2018}
}
@article{Alex2007,
author = {Marrink, Siewert J. and Risselada, H. Jelger and Yefimov, Serge and Tieleman, D. Peter and {De Vries}, Alex H.},
doi = {10.1021/jp071097f},
issn = {15206106},
journal = {Journal of Physical Chemistry B},
title = {The MARTINI force field: Coarse grained model for biomolecular simulations},
year = {2007}
}
@article{Eeman2009a,
author = {Eeman, M. and Francius, G. and Dufr{\^{e}}ne, Y. F. and Nott, K. and Paquot, M. and Deleu, M.},
journal = {Langmuir},
number = {5},
pages = {3029--3039},
title = {Effect of cholesterol and fatty acids on the molecular interactions of fengycin with Stratum Corneum mimicking lipid monolayers},
volume = {25},
year = {2009}
}
@article{Grossfield2011,
author = {Grossfield, Alan},
doi = {10.1016/j.bbamem.2011.03.010},
isbn = {0006-3002 (Print)$\backslash$n0006-3002 (Linking)},
issn = {0006-3002},
journal = {Biochimica et biophysica acta},
keywords = {g protein-coupled receptor},
number = {7},
pages = {1868--1878},
pmid = {21443858},
title = {Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations.},
volume = {1808},
year = {2011}
}
@article{Gawrisch2008,
author = {Grossfield, Alan and Pitman, Michael C. and Feller, Scott E. and Soubias, Olivier and Gawrisch, Klaus},
journal = {Journal of Molecular Biology},
keywords = {GPCR,NMR,hydration,molecular dynamics},
number = {2},
pages = {478--486},
title = {Internal Hydration Increases during Activation of the G-Protein-Coupled Receptor Rhodopsin},
volume = {381},
year = {2008}
}
@article{Tieleman2013,
author = {Marrink, Siewert J. and Tieleman, D. Peter},
doi = {10.1039/c3cs60093a},
issn = {14604744},
journal = {Chemical Society Reviews},
title = {Perspective on the martini model},
year = {2013}
}
@article{Deleu2005,
author = {Deleu, Magali and Paquot, Michel and Nylander, Tommy},
journal = {Journal of Colloid and Interface Science},
keywords = {BAM,DPPC,Isotherm,Lipopeptide,Thermodynamic analysis},
number = {2},
pages = {358--365},
title = {Fengycin interaction with lipid monolayers at the air-aqueous interface - Implications for the effect of fengycin on biological membranes},
volume = {283},
year = {2005}
}
@article{Eeman2009,
author = {Eeman, M and Francius, G and Dufrêne, Y F and Nott, K and Paquot, M and Deleu, M and Dufr{\^{e}}ne, Y F},
doi = {10.1021/la803439n},
isbn = {0743-7463$\backslash$n1520-5827},
issn = {0743-7463},
journal = {Langmuir},
keywords = {Atomic Force,Atomic Force: methods,Ceramides,Ceramides: chemistry,Chemical,Cholesterol,Cholesterol: chemistry,Drug Design,Epidermis,Epidermis: metabolism,Extracellular Matrix,Extracellular Matrix: metabolism,Fatty Acids,Fatty Acids: chemistry,Lipids,Lipids: chemistry,Lipopeptides,Lipopeptides: chemistry,Lipopeptides: pharmacology,Microscopy,Models,Protein Structure,Skin,Skin: drug effects,Skin: metabolism,Skin: microbiology,Statistical,Surface Properties,Tertiary,Time Factors},
number = {5},
pages = {3029--3039},
pmid = {19437771},
title = {Effect of Cholesterol and Fatty Acids on the Molecular Interactions of Fengycin withStratum CorneumMimicking Lipid Monolayers},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19437771},
volume = {25},
year = {2009}
}
@article{Parrinello2007,
author = {Bussi, Giovanni and Donadio, Davide and Parrinello, Michele},
doi = {10.1063/1.2408420},
issn = {00219606},
journal = {Journal of Chemical Physics},
title = {Canonical sampling through velocity rescaling},
year = {2007}
}
@article{Elcock2013,
author = {Stark, Austin C. and Andrews, Casey T. and Elcock, Adrian H.},
doi = {10.1021/ct400008p},
issn = {15499618},
journal = {Journal of Chemical Theory and Computation},
title = {Toward optimized potential functions for protein-protein interactions in aqueous solutions: Osmotic second virial coefficient calculations using the MARTINI coarse-grained force field},
year = {2013}
}
@article{Burke2012,
doi = {10.1073/pnas.1117280109},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
author = {Gray, Kaitlyn C. and Palacios, Daniel S. and Dailey, Ian and Endo, Matthew M. and Uno, Brice E. and Wilcock, Brandon C. and Burke, Martin D.},
title = {Amphotericin primarily kills yeast by simply binding ergosterol},
year = {2012}
}
@article{Pastor2016,
author = {Perrin, B. Scott and Pastor, Richard W.},
doi = {10.1016/j.bpj.2016.08.014},
issn = {15420086},
journal = {Biophysical Journal},
title = {Simulations of Membrane-Disrupting Peptides I: Alamethicin Pore Stability and Spontaneous Insertion},
year = {2016}
}
@article{Kirkpatrick2003,
author = {Raja, Aarti and LaBonte, Jason and Lebbos, John and Kirkpatrick, Peter},
journal = {Nature Reviews Drug Discovery},
number = {12},
pages = {943--944},
title = {{Nature Reviews Drug Discovery 2, No 12, 943-944 (2003); doi: 10.1038/nrd1258}},
volume = {2},
year = {2003}
}
@article{Tao2011,
author = {Tao, Yang and Bie, Xiao Mei and Lv, Feng Xia and Zhao, Hai Zhen and Lu, Zhao Xin},
doi = {10.1007/s12275-011-0171-9},
isbn = {8625843964},
issn = {12258873},
journal = {Journal of Microbiology},
keywords = {Antifungal activity,Commercial surfactin,Fengycin,Lipopeptide,Mechanism,Rhizopus stolonifer},
number = {1},
pages = {146--150},
pmid = {21369992},
title = {Antifungal Activity and Mechanism of Fengycin in the Presence and Absence of Commercial Surfactin Against {\textless}i{\textgreater}Rhizopus Stolonifer{\textless}/i{\textgreater}},
volume = {49},
year = {2011}
}
@article{Chong2017,
abstract = {The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling?the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes?protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.},
author = {Zuckerman, Daniel M. and Chong, Lillian T.},
doi = {10.1146/annurev-biophys-070816-033834},
issn = {1936-122X},
journal = {Annual Review of Biophysics},
title = {{Weighted Ensemble Simulation: Review of Methodology, Applications, and Software}},
year = {2017}
}
@article{Perez2007,
abstract = {Podosphaera fusca is the main causal agent of cucurbit powdery mildew in Spain. Four Bacillus subtilis strains, UMAF6614, UMAF6619, UMAF6639, and UMAF8561, with proven ability to suppress the disease on melon in detached leaf and seedling assays, were subjected to further analyses to elucidate the mode of action involved in their biocontrol performance. Cell-free supernatants showed antifungal activities very close to those previously reported for vegetative cells. Identification of three lipopeptide antibiotics, surfactin, fengycin, and iturin A or bacillomycin, in butanolic extracts from cell-free culture filtrates of these B. subtilis strains pointed out that antibiosis could be a major factor involved in their biocontrol ability. The strong inhibitory effect of purified lipopeptide fractions corresponding to bacillomycin, fengycin, and iturin A on P. fusca conidia germination, as well as the in situ detection of these lipopeptides in bacterial-treated melon leaves, provided interesting evidence of their putative involvement in the antagonistic activity. Those results were definitively supported by site-directed mutagenesis analysis, targeted to suppress the biosynthesis of the different lipopeptides. Taken together, our data have allowed us to conclude that the iturin and fengycin families of lipopeptides have a major role in the antagonism of B. subtilis toward P. fusca.},
author = {Romero, Diego and de Vicente, Antonio and Rakotoaly, Rivo H and Dufour, Samuel E and Veening, Jan-Willem and Arrebola, Eva and Cazorla, Francisco M and Kuipers, Oscar P and Paquot, Michel and P{\'{e}}rez-Garc$\backslash$'{\{}$\backslash$i{\}}a, Alejandro},
doi = {10.1094/MPMI-20-4-0430},
institution = {Departamento de Microbiolog{\'{i}}a, Facultad de Ciencias, Universidad de M{\'{a}}laga, Campus Universitario de Teatinos s/n, E-29071 M{\'{a}}laga, Spain.},
journal = {Mol Plant Microbe Interact},
keywords = {Antibiosis,Ascomycota,Bacillus subtilis,Bacterial,Cucurbitaceae,Cyclic,Lipopeptides,Lipoproteins,Mutagenesis,Peptides,Plant Diseases,Plant Leaves,Site-Directed,Spain,Transformation,chemistry/genetics/physiology,chemistry/isolation /{\&}/ purification/pharmacology/,chemistry/isolation /{\&}/ purification/physiology,drug effects/physiology,microbiology},
language = {eng},
month = {apr},
number = {4},
pages = {430--440},
pmid = {17427813},
title = {{The iturin and fengycin families of lipopeptides are key factors in antagonism of Bacillus subtilis toward Podosphaera fusca.}},
url = {http://dx.doi.org/10.1094/MPMI-20-4-0430},
volume = {20},
year = {2007}
}
@article{Marrink2008,
abstract = {Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on length and time scales that are 2–3 orders of magnitude larger compared to atomistic simulations, providing a bridge between the atomistic and the mesoscopic scale. We developed a new CG model for proteins as an extension of the MARTINI force field. Here, we validate the model for its use in peptide-bilayer systems. In order to validate the model, we calculated the potential of mean force for each amino acid as a function of its distance from the center of a dioleoylphosphatidylcholine (DOPC) lipid bilayer. We then compared amino acid association constants, the partitioning of a series of model pentapeptides, the partitioning and orientation of WALP23 in DOPC lipid bilayers and a series of KALP peptides in dimyristoylphosphatidylcholine and dipalmitoylphosphatidylcholine (DPPC) bilayers. A comparison with results obtained from atomistic models shows good agreement in all of the tests performed. We also performed a systematic investigation of the partitioning of five series of polyalanine−leucine peptides (with different lengths and compositions) in DPPC bilayers. As expected, the fraction of peptides partitioned at the interface increased with decreasing peptide length and decreasing leucine content, demonstrating that the CG model is capable of discriminating partitioning behavior arising from subtle differences in the amino acid composition. Finally, we simulated the concentration-dependent formation of transmembrane pores by magainin, an antimicrobial peptide. In line with atomistic simulation studies, disordered toroidal pores are formed. In conclusion, the model is computationally efficient and effectively reproduces peptide−lipid interactions and the partitioning of amino acids and peptides in lipid bilayers.},
author = {Monticelli, Luca and Kandasamy, Senthil K. and Periole, Xavier and Larson, Ronald G. and Tieleman, D. Peter and Marrink, Siewert Jan},
doi = {10.1021/ct700324x},
issn = {15499618},
journal = {Journal of Chemical Theory and Computation},
title = {{The MARTINI coarse-grained force field: Extension to proteins}},
year = {2008}
}
@article{Klein1994,
author = {Martyna, Glenn J and Tobias, Douglas J and Klein, Michael L},
journal = {The Journal of Chemical Physics},
number = {5},
pages = {4177--4189},
publisher = {AIP},
title = {{Constant pressure molecular dynamics algorithms}},
volume = {101},
year = {1994}
}
@inproceedings{Paquot1999,
abstract = {The fundamental surface-active properties at the oil/water interface and emulsifying properties of surfactin, iturin A and fengycin, lipopeptides from Bacillus subtilis, were investigated. All lipopeptides reduce rapidly the dynamic interfacial tension. Among lipopeptide families, surfactin is the most effective in terms of fundamental dynamic and equilibrium interfacial properties. Lipopeptides present intermediate properties in comparison with sodium dodecyl sulfate and $\beta$-lactoglobulin concerning the stabilizing effect towards creaming-flocculation and the resistance to coalescence. Among lipopeptides, iturin A seems to show the best resistance to creaming-flocculation whereas fengycin exhibits the highest resistance to coalescence properties. Copyright (C) 1999 Elsevier Science B.V.},
author = {Deleu, M. and Razafindralambo, H. and Popineau, Y. and Jacques, P. and Thonart, P. and Paquot, M.},
booktitle = {Colloids and Surfaces A: Physicochemical and Engineering Aspects},
keywords = {Emulsifying properties,Interface,Lipopeptides},
number = {1-2},
pages = {3--10},
publisher = {Elsevier Science Publishers B.V.},
title = {{Interfacial and emulsifying properties of lipopeptides from Bacillus subtilis}},
volume = {152},
year = {1999}
}
@article{BhattZuckerman2010,
abstract = {We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. A straightforward steady-state implementation of WE is directly practical for simple landscapes, but not when significant metastable intermediates states are present. We therefore develop an enhanced WE scheme, building on existing ideas, which accelerates attainment of steady state in complex systems. We apply both WE approaches to several model systems, confirming their correctness and efficiency by comparison with brute-force results. The enhanced version is significantly faster than the brute force and straightforward WE for systems with WE bins that accurately reflect the reaction coordinate(s). The new WE methods can also be applied to equilibrium sampling, since equilibrium is a steady state.},
author = {Bhatt, Divesh and Zhang, Bin W. and Zuckerman, Daniel M.},
doi = {10.1063/1.3456985},
issn = {00219606},
journal = {Journal of Chemical Physics},
title = {{Steady-state simulations using weighted ensemble path sampling}},
year = {2010}
}
@article{Zasloff1987,
abstract = {A family of peptides with broad-spectrum antimicrobial activity has been isolated from the skin of the African clawed frog Xenopus laevis. It consists of two closely related peptides that are each 23 amino acids and differ by two substitutions. These peptides are water soluble, nonhemolytic at their effective antimicrobial concentrations, and potentially amphiphilic. At low concentrations they inhibit growth of numerous species of bacteria and fungi and induce osmotic lysis of protozoa. The sequence of a partial cDNA of the precursor reveals that both peptides derive from a common larger protein. These peptides appear to represent a previously unrecognized class of vertebrate antimicrobial activities.},
author = {Zasloff, M},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Amino Acid Sequence,Animals,Anti-Bacterial Agents,Anti-Infective Agents,Anti-Infective Agents: isolation {\&} purification,Antimicrobial Cationic Peptides,Base Sequence,Candida,Candida: drug effects,Chromatography, High Pressure Liquid,Cryptococcus neoformans,Cryptococcus neoformans: drug effects,DNA,DNA: analysis,Escherichia coli,Escherichia coli: drug effects,Female,High Pressure Liquid,Magainins,Microbial Sensitivity Tests,Peptides,Peptides: genetics,Peptides: isolation {\&} purification,Protein Precursors,Protein Precursors: analysis,Protein Precursors: genetics,Proteus,Proteus: drug effects,Saccharomyces cerevisiae,Saccharomyces cerevisiae: drug effects,Skin,Skin: analysis,Wound Healing,Xenopus Proteins,Xenopus laevis,Xenopus laevis: metabolism},
number = {15},
pages = {5449--53},
title = {{Magainins, a class of antimicrobial peptides from Xenopus skin: isolation, characterization of two active forms, and partial cDNA sequence of a precursor.}},
volume = {84},
year = {1987}
}
@article{Marrink2013,
abstract = {The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here, we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley−White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of $\alpha$-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.},
author = {{De Jong}, Djurre H. and Singh, Gurpreet and Bennett, W. F.Drew and Arnarez, Clement and Wassenaar, Tsjerk A. and Sch{\"{a}}fer, Lars V. and Periole, Xavier and Tieleman, D. Peter and Marrink, Siewert J.},
doi = {10.1021/ct300646g},
issn = {15499618},
journal = {Journal of Chemical Theory and Computation},
title = {{Improved parameters for the martini coarse-grained protein force field}},
year = {2013}
}
@article{Legrve2013,
abstract = {The control of rhizomania, one of the most important diseases of sugar beet caused by the Beet necrotic yellow vein virus, remains limited to varietal resistance. In this study, we investigated the putative action of Bacillus amylolequifaciens lipopeptides in achieving rhizomania biocontrol through the control of the virus vector Polymyxa betae. Some lipopeptides that are produced by bacteria, especially by plant growth-promoting rhizobacteria, have been found to induce systemic resistance in plants. We tested the impact of the elicitation of systemic resistance in sugar beet through lipopeptides on infection by P. betae. Lipopeptides were shown to effectively induce systemic resistance in both the roots and leaves of sugar beet, resulting in a significant reduction in P. betae infection. This article provides the first evidence that induced systemic resistance can reduce infection of sugar beet by P. betae.},
author = {Desoignies, Nicolas and Schramme, Florence and Ongena, Marc and Legr??ve, Anne},
journal = {Molecular Plant Pathology},
number = {4},
pages = {416--421},
title = {{Systemic resistance induced by Bacillus lipopeptides in Beta vulgaris reduces infection by the rhizomania disease vector Polymyxa betae}},
volume = {14},
year = {2013}
}
@article{Melo2015,
abstract = {Sterols play an essential role in modulating bilayer structure and dynamics. Coarse-grained molecular dynamics parameters for cholesterol and related molecules are available for the Martini force field and have been successfully used in multiple lipid bilayer studies. In this work, we focus on the use of virtual sites as a means of increasing the stability of cholesterol and cholesterol-like structures. We improve and extend the Martini parameterization of sterols in four different ways: 1—the cholesterol parameters were adapted to make use of virtual interaction sites, which markedly improves numerical stability; 2—cholesterol parameters were also modified to address reported shortcomings in reproducing correct lipid phase behavior in mixed membranes; 3—parameters for ergosterol were created and adapted from cholesterols; and 4—parameters for the hopanoid class of bacterial polycyclic molecules were created, namely, for hopane, diploptene, bacteriohopanetetrol, and for their polycyclic base structure.},
author = {Melo, M. N. and Ing{\'{o}}lfsson, H. I. and Marrink, S. J.},
doi = {10.1063/1.4937783},
issn = {00219606},
journal = {Journal of Chemical Physics},
title = {{Parameters for Martini sterols and hopanoids based on a virtual-site description}},
year = {2015}
}
@article{Epand2012,
author = {Wadhwani, P and Epand, R F and Heidenreich, N and B{\"{u}}rck, J and Ulrich, A S and Epand, R M},
journal = {Biophysical journal},
number = {2},
pages = {265--274},
publisher = {Elsevier},
title = {{Membrane-active peptides and the clustering of anionic lipids}},
volume = {103},
year = {2012}
}
@article{Yao2007,
abstract = {Bacillus subtilis strain IB exhibiting inhibitory activity against the Fusarium head blight disease fungus Fusarium graminearum was isolated and identified. The major inhibitory compound was purified from the culture broth through anion exchange, hydrophobic interaction, and reverse phase high-performance liquid chromatography (RP-HPLC) steps. It was a 1,463-Da lipopeptide and had an amino acid composition consisting of Ala, Glx, Ile, Orn, Pro, Thr, and Tyr at a molar ratio of 1:3:1:1:1:1:2. Electrospray ionization mass spectrometry/mass spectrometry (ESI MS/MS) analyses of the natural and the ring-opened peptides showed the antagonist was fengycin, a kind of macrolactone molecule with antifungal activity produced by several Bacillus strains. Fluorescence microscopic analysis indicated this peptide permeabilized and disrupted F. graminearum hyphae.},
author = {Wang, J and Liu, J and Chen, H and Yao, J},
doi = {10.1007/s00253-007-1054-1},
institution = {Key Laboratory of Ion Beam Bioengineering, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China. [email protected]},
journal = {Appl Microbiol Biotechnol},
keywords = {Amino Acids,Antifungal Agents,Bacillus subtilis,Chromatography,Electrophoresis,Electrospray Ionization,Fluorescence,Fusarium,Ion Exchange,Lipopeptides,Lipoproteins,Mass,Microscopy,Polyacrylamide Gel,Spectrometry,analysis,chemistry/isolation /{\&}/ purification/pharmacology,chemistry/metabolism,drug effects/growth /{\&}/ development},
language = {eng},
month = {sep},
number = {4},
pages = {889--894},
pmid = {17611753},
title = {{Characterization of Fusarium graminearum inhibitory lipopeptide from Bacillus subtilis IB.}},
url = {http://dx.doi.org/10.1007/s00253-007-1054-1},
volume = {76},
year = {2007}
}
@article{Tieleman2007,
abstract = {Naturally occurring and synthetic peptides may be a novel class of clinically useful antibiotics. A large body of experimental data on structure function relationships for such peptides is available, but the molecular mechanism of their action remains elusive in most cases. Computer simulations can give detailed insights into the interactions between peptides and lipid bilayers, at least one crucial step in the antimicrobial mechanism. Here we review recent simulations of antimicrobial peptides and discuss potential future contributions of computer simulations in understanding and ultimately designing antimicrobial peptides.},
author = {Matyus, Edit and Kandt, Christian and Tieleman, D.},
doi = {10.2174/092986707782360105},
issn = {09298673},
journal = {Current Medicinal Chemistry},
title = {{Computer Simulation of Antimicrobial Peptides}},
year = {2007}
}
@article{MantilAvis2019,
abstract = {Fengycin is an antimicrobial cyclic lipopeptide known to interact with microbial cell membranes. To gain insight into the role of lipids in fengycin sensitivity, lipids extracted from Alternaria solani, Fusarium sambucinum, and Pythium sulcatum were analyzed and used in the preparation of supported lipid bilayers (SLBs). Total Internal Reflection Fluorescence Microscopy (TIRFM) was used to evaluate lipid phase separation within the SLBs and changes in domain distribution with the application of fengycin. A. solani lipid extract contained the highest quantity of ergosterol while P. sulcatum contained no ergosterol. Sterol content of SLBs was strongly correlated with increases in phase separation, suggesting ergosterol may play a role in promoting ordering of the lipid phases in the bilayer. A. solani experienced the least change in domain characteristics following fengycin exposure, suggesting ergosterol may be buffering effects of the antimicrobial compound. Factors such as lipid headgroup charge and unsaturation levels may impact fengycin's effects on domain phase separation, but these effects were generally overshadowed by the role of ergosterol. In the absence of ergosterol, in the P. sulcatum bilayers, fengycin caused an increase in lipid phase ordering.},
author = {Mantil, Elisabeth and Crippin, Trinda and Avis, Tyler J.},
doi = {10.1016/j.colsurfb.2019.02.050},
issn = {18734367},
journal = {Colloids and Surfaces B: Biointerfaces},
keywords = {Ergosterol,Extracted mold lipids,Fengycin,Supported lipid bilayers,Total internal reflection fluorescence microscopy},
title = {{Supported lipid bilayers using extracted microbial lipids: domain redistribution in the presence of fengycin}},
year = {2019}
}
@article{Schulten1996,
author = {Humphrey, W and Dalke, A and Schulten, K},
institution = {Theoretical Biophysics Group, University of Illinois, Urbana 61801, USA.},
journal = {J Mol Graph},
keywords = {Computer Graphics,Computer Simulation,Computers,Models,Molecular,Nucleic Acids,Proteins,User-Computer Interface,chemistry},
language = {eng},
month = {feb},
number = {1},
pages = {27--28, 33--38},
pmid = {8744570},
title = {{VMD: visual molecular dynamics.}},
volume = {14},
year = {1996}
}
@article{Schulten1993,
author = {{Helmut Heller}, Michael Schaefer and Schulten, Klaus},
journal = {Journal of Physical Chemistry},
pages = {8343--8360},
title = {{Molecular Dynamics of a Bilayer of 200 lipids in the gel and in the Liquid-Crystal Phases}},
volume = {97},
year = {1993}
}
@article{Wise2014,
abstract = {ABSTRACT Fengycin is an antimicrobial cyclic lipopeptide produced by various Bacillus subtilis strains, including strain CU12. Direct effects of fengycin include membrane pore formation and efflux of cellular contents leading to cell death in sensitive microorganisms. In this study, four plant pathogens were studied in order to elucidate the role of membrane lipids in their relative sensitivity to fengycin. Inhibition of mycelial growth in these pathogens varied considerably. Analysis of membrane lipids in these microorganisms indicated that sensitivity correlated with low ergosterol content and shorter phospholipid fatty acyl chains. Sensitivity to fengycin also correlated with a lower anionic/zwitterionic phospholipid ratio. Our data suggest that decreased fluidity buffering capacity, as a result of low ergosterol content, and higher intrinsic fluidity afforded by short fatty acyl chain length may increase the sensitivity of microbial membranes to fengycin. Our results also suggest that lower content in anionic phospholipids may increase fengycin insertion into the membrane through reduced electrostatic repulsion with the negatively charged fengycin. The intrinsic membrane lipid composition may contribute, in part, to the observed level of antimicrobial activity of fengycin in various plant pathogens.},
author = {Wise, Cody and Falardeau, Justin and Hagberg, Ingrid and Avis, Tyler J},
journal = {Phytopathology},
number = {10},
pages = {1036--41},
publisher = {The American Phytopathological Society},
title = {{Cellular Lipid Composition Affects Sensitivity of Plant Pathogens to Fengycin, an Antifungal Compound Produced by Bacillus subtilis Strain CU12.}},
url = {http://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-12-13-0336-R},
volume = {104},
year = {2014}
}
@article{Bie2011,
abstract = {The antagonistic activities of Bacillus subtilis fmbj against the Rhizopus stolonifer pathogen causing peach soft rot disease were studied in this paper. Bacillus subtilis fmbj exhibited a high antifungal effect on the mycelium growth, sportulation, and germ tube elongation of R. stolonifer with the inhibition rate of 86.5{\%} and 97.42{\%}, respectively, spore germination rate of 20{\%} under antagonist strain concentration of 10⁸ CFU/mL. By using of scanning electron microscope (SEM) and transmission electron microscope (TEM), it was observed that B. subtilis fmbj strain strongly induced morphological abnormalities of R. stolonifer and destroyed structure of hypha and spore. When hypha cell wall of R. stolonifer was damaged, the organelles and cytoplasms inside cell would exude, which led to cell death.},
author = {Zhou, Xiaohong and Lu, Zhaoxin and Lv, Fengxia and Zhao, Haizhen and Wang, Yu and Bie, Xiaomei},
doi = {10.1111/j.1750-3841.2011.02160.x},
issn = {00221147},
journal = {Journal of Food Science},
keywords = {Antagonistic action,Bacillus subtilifmbj,Hypha,Rhizopus stolonifer,Spore},
title = {{Antagonistic Action ofBacillus subtilisStrain fmbj on the Postharvest PathogenRhizopus stolonifer}},
year = {2011}
}
@article{ZhangZuckerman2010,
abstract = {The "weighted ensemble" method, introduced by Huber and Kim [Biophys. J. 70, 97 (1996)], is one of a handful of rigorous approaches to path sampling of rare events. Expanding earlier discussions, we show that the technique is statistically exact for a wide class of Markovian and non-Markovian dynamics. The derivation is based on standard path-integral (path probability) ideas, but recasts the weighted-ensemble approach as simple "resampling" in path space. Similar reasoning indicates that arbitrary nonstatic binning procedures, which merely guide the resampling process, are also valid. Numerical examples confirm the claims, including the use of bins which can adaptively find the target state in a simple model.},
author = {Zhang, Bin W. and Jasnow, David and Zuckerman, Daniel M.},
doi = {10.1063/1.3306345},
issn = {00219606},
journal = {Journal of Chemical Physics},
title = {{The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures}},
year = {2010}
}
@article{Brown2014,
abstract = {Rhodopsin, the mammalian dim-light receptor, is one of the best-characterized G-protein-coupled receptors, a pharmaceutically important class of membrane proteins that has garnered a great deal of attention because of the recent availability of structural information. Yet the mechanism of rhodopsin activation is not fully understood. Here, we use microsecond-scale all-atom molecular dynamics simulations, validated by solid-state (2)H nuclear magnetic resonance spectroscopy, to understand the transition between the dark and metarhodopsin I (Meta I) states. Our analysis of these simulations reveals striking differences in ligand flexibility between the two states. Retinal is much more dynamic in Meta I, adopting an elongated conformation similar to that seen in the recent activelike crystal structures. Surprisingly, this elongation corresponds to both a dramatic influx of bulk water into the hydrophobic core of the protein and a concerted transition in the highly conserved Trp265(6.48) residue. In addition, enhanced ligand flexibility upon light activation provides an explanation for the different retinal orientations observed in X-ray crystal structures of active rhodopsin.},
author = {Leioatts, Nicholas and Mertz, Blake and Mart??nez-Mayorga, Karina and Romo, Tod D. and Pitman, Michael C. and Feller, Scott E. and Grossfield, Alan and Brown, Michael F.},
journal = {Biochemistry},
number = {2},
pages = {376--385},
title = {{Retinal ligand mobility explains internal hydration and reconciles active rhodopsin structures}},
volume = {53},
year = {2014}
}
@article{Thonart2007,
author = {Ongena, Marc and Jourdan, Emmanuel and Adam, Akram and Paquot, Michel Brans, Alain and Joris, Bernard and Arpigny, Jean-Louis and Thonart, Philippe},
journal = {Environ Microbiol},
keywords = {Bacillus subtilis,Bacterial Proteins,Cyclic,Fabaceae,Lipopeptides,Lipoproteins,Lycopersicon esculentum,Peptides,Plant Diseases,Plant Roots,genetics/metabolism,genetics/metabolism/physiology,microbiology},
language = {eng},
month = {apr},
number = {4},
pages = {1084--1090},
pmid = {17359279},
title = {Surfactin and fengycin lipopeptides of Bacillus subtilis as elicitors of induced systemic resistance in plants.},
url = {http://dx.doi.org/10.1111/j.1462-2920.2006.01202.x},
volume = {9},
year = {2007}
}
@article{Thonart2004,
author = {Tour{\'{e}}, Y and Ongena, M and Jacques, P and Guiro, A and Thonart, P},
doi = {10.1111/j.1365-2672.2004.02252.x},
institution = {Service de Technologie Microbienne, CWBI, Universit{\'{e}} de Li{\`{e}}ge, Li{\`{e}}ge, Belgium.},
journal = {J Appl Microbiol},
keywords = {Antifungal Agents,Bacillus subtilis,Bacterial,Botrytis,Cyclic,Lipopeptides,Lipoproteins,Malus,Mycoses,Peptides,Pesticides,Plant Extracts,Spores,Time Factors,chemical synthesis/metabolism,metabolism,metabolism/prevention /{\&}/ control,microbiology},
language = {eng},
number = {5},
pages = {1151--1160},
pmid = {15078533},
title = {{Role of lipopeptides produced by Bacillus subtilis GA1 in the reduction of grey mould disease caused by Botrytis cinerea on apple.}},
url = {http://dx.doi.org/10.1111/j.1365-2672.2004.02252.x},
volume = {96},
year = {2004}
}
@article{Domene2015,
annote = {PMID: 26393968},
author = {Iglesias-Fernandez, Javier and Darr{\~{A}}{\textcopyright}, Leonardo and Kohlmeyer, Axel and Thomas, Robert K and Shen, Hsin-Hui and Domene, Carmen},
doi = {10.1021/acs.langmuir.5b02305},
journal = {Langmuir},
number = {40},
pages = {11097--11104},
title = {{Surfactin at the Water/Air Interface and in Solution}},
url = {http://dx.doi.org/10.1021/acs.langmuir.5b02305},