Modification of the CHARMM force field for DMPC lipid bilayer

被引:56
作者
Hogberg, Carl-Johan [1 ]
Nikitin, Alexei M. [1 ,2 ]
Lyubartsev, Alexander P. [1 ]
机构
[1] Stockholm Univ, Arrhenius Lab, Div Phys Chem, SE-10691 Stockholm, Sweden
[2] Russian Acad Sci, VA Engelhardt Mol Biol Inst, Moscow 119991, Russia
关键词
molecular dynamics; lipid bilayers; force field; DMPC; hydration;
D O I
10.1002/jcc.20974
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of the headgroup charges on the basis of HF/6-311 (d,p) ab-initio computations. Both rigid TIP3P and flexible SPC water models were used with the new lipid model, showing similar results. The new model in a 75 ns simulation has shown a correct value of the area per lipid at zero surface tension, as well as good agreement with the experiment for the electron density, structure factor, and order parameters, including those in the headgroup part of lipids. (C) 2008 Wiley Periodicals, Inc.
引用
收藏
页码:2359 / 2369
页数:11
相关论文
共 45 条
[1]  
Allen MP, 1987, COMPUTER SIMULATIONS, DOI DOI 10.2307/2938686
[2]   MOLECULAR-DYNAMICS SIMULATION OF DIELECTRIC-PROPERTIES OF WATER [J].
ANDERSON, J ;
ULLO, JJ ;
YIP, S .
JOURNAL OF CHEMICAL PHYSICS, 1987, 87 (03) :1726-1732
[3]   Methodological issues in lipid bilayer simulations [J].
Anézo, C ;
de Vries, AH ;
Höltje, HD ;
Tieleman, DP ;
Marrink, SJ .
JOURNAL OF PHYSICAL CHEMISTRY B, 2003, 107 (35) :9424-9433
[4]   Detailed structure and dynamics of bicelle phospholipids using selectively deuterated and perdeuterated labels.: 2H NMR and molecular mechanics study [J].
Aussenac, F ;
Laguerre, M ;
Schmitter, JM ;
Dufourc, EJ .
LANGMUIR, 2003, 19 (25) :10468-10479
[5]   A WELL-BEHAVED ELECTROSTATIC POTENTIAL BASED METHOD USING CHARGE RESTRAINTS FOR DERIVING ATOMIC CHARGES - THE RESP MODEL [J].
BAYLY, CI ;
CIEPLAK, P ;
CORNELL, WD ;
KOLLMAN, PA .
JOURNAL OF PHYSICAL CHEMISTRY, 1993, 97 (40) :10269-10280
[6]   Experimental validation of molecular dynamics simulations of lipid bilayers:: A new approach [J].
Benz, RW ;
Castro-Román, F ;
Tobias, DJ ;
White, SH .
BIOPHYSICAL JOURNAL, 2005, 88 (02) :805-817
[7]   Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature [J].
Berger, O ;
Edholm, O ;
Jahnig, F .
BIOPHYSICAL JOURNAL, 1997, 72 (05) :2002-2013
[8]   QUANTITATIVE-DETERMINATION OF HYDROCARBON CHAIN CONFORMATIONAL ORDER IN BILAYERS OF SATURATED PHOSPHATIDYLCHOLINES OF VARIOUS CHAIN LENGTHS BY FOURIER-TRANSFORM INFRARED-SPECTROSCOPY [J].
CASAL, HL ;
MCELHANEY, RN .
BIOCHEMISTRY, 1990, 29 (23) :5423-5427
[9]   APPLICATION OF RESP CHARGES TO CALCULATE CONFORMATIONAL ENERGIES, HYDROGEN-BOND ENERGIES, AND FREE-ENERGIES OF SOLVATION [J].
CORNELL, WD ;
CIEPLAK, P ;
BAYLY, CI ;
KOLLMAN, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993, 115 (21) :9620-9631
[10]   A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES [J].
CORNELL, WD ;
CIEPLAK, P ;
BAYLY, CI ;
GOULD, IR ;
MERZ, KM ;
FERGUSON, DM ;
SPELLMEYER, DC ;
FOX, T ;
CALDWELL, JW ;
KOLLMAN, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) :5179-5197