PMID- 16884212
OWN - NLM
STAT- MEDLINE
DCOM- 20070913
LR  - 20131121
IS  - 1520-6106 (Print)
IS  - 1520-5207 (Linking)
VI  - 110
IP  - 31
DP  - 2006 Aug 10
TI  - Mixed atomistic and coarse-grained molecular dynamics: simulation of a 
      membrane-bound ion channel.
PG  - 15045-8
AB  - The recently developed multiscale coarse-graining (MS-CG) method (Izvekov, S.; 
      Voth, G. A. J. Phys. Chem. B 2005, 109, 2469; J. Chem. Phys. 2005, 123, 134105) 
      is used to build a mixed all-atom and coarse-grained (AA-CG) model of the 
      gramicidin A (gA) ion channel embedded in a dimyristoylphosphatidylcholine (DMPC) 
      lipid bilayer and water environment. In this model, the gA peptide was described 
      in full atomistic detail, while the lipid and water molecules were described 
      using coarse-grained representations. The atom-CG and CG-CG interactions in the 
      mixed AA-CG model were determined using the MS-CG method. Molecular dynamics (MD) 
      simulations were performed using the resulting AA-CG model. The results from 
      simulations of the AA-CG model compare very favorably to those from all-atom MD 
      simulations of the entire system. Since the MS-CG method employs a general and 
      systematic approach to obtain effective interactions from the underlying all-atom 
      models, the present approach to rigorously develop mixed AA-CG models has the 
      potential to be extended to many other systems.
FAU - Shi, Qiang
AU  - Shi Q
FAU - Izvekov, Sergei
AU  - Izvekov S
FAU - Voth, Gregory A
AU  - Voth GA
LA  - eng
GR  - 1 S10 RR17214-01/RR/NCRR NIH HHS/United States
GR  - R01 GM63796/GM/NIGMS NIH HHS/United States
PT  - Letter
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
RN  - 0 (Ion Channels)
RN  - 0 (Lipid Bilayers)
RN  - 0 (Peptides)
RN  - 059QF0KO0R (Water)
RN  - 1405-97-6 (Gramicidin)
RN  - U86ZGC74V5 (Dimyristoylphosphatidylcholine)
SB  - IM
MH  - *Computer Simulation
MH  - Dimyristoylphosphatidylcholine/chemistry
MH  - Gramicidin/*chemistry
MH  - Ion Channels/chemistry
MH  - Lipid Bilayers/chemistry
MH  - Models, Molecular
MH  - Peptides/*chemistry
MH  - Protein Conformation
MH  - Quantum Theory
MH  - Water/chemistry
EDAT- 2006/08/04 09:00
MHDA- 2007/09/14 09:00
CRDT- 2006/08/04 09:00
PHST- 2006/08/04 09:00 [pubmed]
PHST- 2007/09/14 09:00 [medline]
PHST- 2006/08/04 09:00 [entrez]
AID - 10.1021/jp062700h [doi]
PST - ppublish
SO  - J Phys Chem B. 2006 Aug 10;110(31):15045-8. doi: 10.1021/jp062700h.