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Items: 1 to 20 of 120

1.

Insertion of the Ca²⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations.

Bucher D, Hsu YH, Mouchlis VD, Dennis EA, McCammon JA.

PLoS Comput Biol. 2013;9(7):e1003156. doi: 10.1371/journal.pcbi.1003156. Epub 2013 Jul 25.

2.

The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations.

Wee CL, Balali-Mood K, Gavaghan D, Sansom MS.

Biophys J. 2008 Aug;95(4):1649-57. doi: 10.1529/biophysj.107.123190. Epub 2008 May 9.

3.

Interaction of monotopic membrane enzymes with a lipid bilayer: a coarse-grained MD simulation study.

Balali-Mood K, Bond PJ, Sansom MS.

Biochemistry. 2009 Mar 17;48(10):2135-45. doi: 10.1021/bi8017398.

PMID:
19161285
4.

Molecular dynamics simulations of the dimerization of transmembrane alpha-helices.

Psachoulia E, Marshall DP, Sansom MS.

Acc Chem Res. 2010 Mar 16;43(3):388-96. doi: 10.1021/ar900211k.

PMID:
20017540
5.

Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates.

Mouchlis VD, Bucher D, McCammon JA, Dennis EA.

Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):E516-25. doi: 10.1073/pnas.1424651112. Epub 2015 Jan 26.

6.

Coarse-grained molecular dynamics study of cyclic peptide nanotube insertion into a lipid bilayer.

Hwang H.

J Phys Chem A. 2009 Apr 23;113(16):4780-7. doi: 10.1021/jp8080657.

PMID:
19035669
7.

A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations.

Wang ZJ, Deserno M.

J Phys Chem B. 2010 Sep 2;114(34):11207-20. doi: 10.1021/jp102543j. Erratum in: J Phys Chem B. 2012 Mar 29;116(12):3907.

8.

Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer.

Pluhackova K, Wassenaar TA, Kirsch S, Böckmann RA.

J Phys Chem B. 2015 Mar 26;119(12):4396-408. doi: 10.1021/acs.jpcb.5b00434. Epub 2015 Mar 12.

PMID:
25719673
9.

Fluoroketone inhibition of Ca(2+)-independent phospholipase A2 through binding pocket association defined by hydrogen/deuterium exchange and molecular dynamics.

Hsu YH, Bucher D, Cao J, Li S, Yang SW, Kokotos G, Woods VL Jr, McCammon JA, Dennis EA.

J Am Chem Soc. 2013 Jan 30;135(4):1330-7. doi: 10.1021/ja306490g. Epub 2013 Jan 16. Erratum in: J Am Chem Soc. 2013 Apr 17;135(15):5932.

10.

A multiscale coarse-graining method for biomolecular systems.

Izvekov S, Voth GA.

J Phys Chem B. 2005 Feb 24;109(7):2469-73.

PMID:
16851243
11.

Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel.

Shi Q, Izvekov S, Voth GA.

J Phys Chem B. 2006 Aug 10;110(31):15045-8.

PMID:
16884212
12.

Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.

Wassenaar TA, Ingólfsson HI, Priess M, Marrink SJ, Schäfer LV.

J Phys Chem B. 2013 Apr 4;117(13):3516-30. doi: 10.1021/jp311533p. Epub 2013 Mar 6.

13.

Interaction of human synovial phospholipase A2 with mixed lipid bilayers: a coarse-grain and all-atom molecular dynamics simulation study.

Qin SS, Yu YX, Li QK, Yu ZW.

Biochemistry. 2013 Feb 26;52(8):1477-89. doi: 10.1021/bi3012687. Epub 2013 Feb 12.

PMID:
23343574
14.

Molecular dynamics methods to predict peptide locations in membranes: LAH4 as a stringent test case.

Farrotti A, Bocchinfuso G, Palleschi A, Rosato N, Salnikov ES, Voievoda N, Bechinger B, Stella L.

Biochim Biophys Acta. 2015 Feb;1848(2):581-92. doi: 10.1016/j.bbamem.2014.11.002. Epub 2014 Nov 13.

15.

Coarse-grained molecular dynamics simulations of membrane proteins and peptides.

Bond PJ, Holyoake J, Ivetac A, Khalid S, Sansom MS.

J Struct Biol. 2007 Mar;157(3):593-605. Epub 2006 Oct 20.

PMID:
17116404
16.

Atomistic mechanisms of huntingtin N-terminal fragment insertion on a phospholipid bilayer revealed by molecular dynamics simulations.

Côté S, Wei G, Mousseau N.

Proteins. 2014 Jul;82(7):1409-27. doi: 10.1002/prot.24509. Epub 2014 Feb 18.

PMID:
24415136
17.

Ca(2+) bridging of apposed phospholipid bilayers.

Issa ZK, Manke CW, Jena BP, Potoff JJ.

J Phys Chem B. 2010 Oct 21;114(41):13249-54. doi: 10.1021/jp105781z.

PMID:
20836527
18.

Localizing the membrane binding region of Group VIA Ca2+-independent phospholipase A2 using peptide amide hydrogen/deuterium exchange mass spectrometry.

Hsu YH, Burke JE, Li S, Woods VL Jr, Dennis EA.

J Biol Chem. 2009 Aug 28;284(35):23652-61. doi: 10.1074/jbc.M109.021857. Epub 2009 Jun 25.

19.

Cell cycle dependence of group VIA calcium-independent phospholipase A2 activity.

Manguikian AD, Barbour SE.

J Biol Chem. 2004 Dec 17;279(51):52881-92. Epub 2004 Sep 22.

20.

The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials.

Lu L, Voth GA.

J Chem Phys. 2011 Jun 14;134(22):224107. doi: 10.1063/1.3599049.

PMID:
21682507
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