PMID- 17850132
OWN - NLM
STAT- MEDLINE
DCOM- 20071206
LR  - 20131121
IS  - 1520-6106 (Print)
IS  - 1520-5207 (Linking)
VI  - 111
IP  - 39
DP  - 2007 Oct 4
TI  - Multiscale coarse-graining of monosaccharides.
PG  - 11566-75
AB  - A systematic multiscale coarse-graining (MS-CG) algorithm is applied to build 
      coarse-grained models for monosaccharides in aqueous solution. The methodology is 
      demonstrated for the example of alpha-D-glucopyranose. The nonbonded interactions 
      are directly derived from the force-matching approach, whereas the bonded 
      interactions are obtained through Boltzmann statistical analyses of the 
      underlying atomistic trajectory. The MS-CG model is shown to reproduce many 
      structural and thermodynamic properties in the constant NPT ensemble. Although 
      the model is derived at a single temperature, pressure, and concentration, it is 
      shown to be reasonably transferable to other thermodynamic states. In this model, 
      long-range interactions are effectively mapped into short-range forces with a 
      moderate cutoff and are evaluated by table look-up. As a result, molecular 
      dynamics employing the MS-CG model is approximately 3 orders of magnitude more 
      efficient than its atomistic counterpart. Consequently, the model is particularly 
      suitable for simulating carbohydrate systems at large length and long time 
      scales. Results for an alpha-(1-->4)-d-glucan with 14 glucose units are also 
      presented, demonstrating that the MS-CG algorithm is also applicable to the 
      coarse-graining of other saccharide systems.
FAU - Liu, Pu
AU  - Liu P
AD  - Center for Biophysical Modeling and Simulation and Department of Chemistry, 
      University of Utah, Salt Lake City, Utah 84112-0850, USA.
FAU - Izvekov, Sergei
AU  - Izvekov S
FAU - Voth, Gregory A
AU  - Voth GA
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20070913
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
RN  - 0 (Monosaccharides)
RN  - 0 (Solutions)
RN  - 059QF0KO0R (Water)
RN  - IY9XDZ35W2 (Glucose)
SB  - IM
MH  - Algorithms
MH  - Glucose/*analogs & derivatives/*chemistry
MH  - *Models, Chemical
MH  - Models, Molecular
MH  - Monosaccharides/*chemistry
MH  - Solutions
MH  - Thermodynamics
MH  - Water/chemistry
EDAT- 2007/09/14 09:00
MHDA- 2007/12/07 09:00
CRDT- 2007/09/14 09:00
PHST- 2007/09/14 09:00 [pubmed]
PHST- 2007/12/07 09:00 [medline]
PHST- 2007/09/14 09:00 [entrez]
AID - 10.1021/jp0721494 [doi]
PST - ppublish
SO  - J Phys Chem B. 2007 Oct 4;111(39):11566-75. doi: 10.1021/jp0721494. Epub 2007 Sep 
      13.