PMID- 21905717
OWN - NLM
STAT- MEDLINE
DCOM- 20120215
LR  - 20111014
IS  - 1520-5207 (Electronic)
IS  - 1520-5207 (Linking)
VI  - 115
IP  - 41
DP  - 2011 Oct 20
TI  - Exploration of transferability in multiscale coarse-grained peptide models.
PG  - 11911-26
LID - 10.1021/jp204455g [doi]
AB  - Coarse-grained models can facilitate the efficient simulation of complex 
      biological systems. In earlier studies the multiscale coarse-graining (MS-CG) 
      method was employed to examine the folding landscape for two small peptides. In 
      those studies, MS-CG force fields specific to each peptide were employed. We 
      extend here the scope of that work with the goal of obtaining a transferable 
      MS-CG force field which can be used to simulate the folded conformations of 
      peptides with disparate structural motifs. Information obtained via MS-CG 
      modeling was used to understand the characteristics of CG interactions which 
      govern their capacity to be transferred between different peptide systems. We 
      find that polar CG groups are least transferable in general, with interactions 
      between CG sites representing the CO and NH groups on the peptide backbone being 
      particularly resistant to facile transfer. Our results additionally suggest that, 
      while there are limitations to the approach, the MS-CG method may provide a 
      systematic path toward obtaining rigorously defined CG interactions with at least 
      some degree of transferability. These studies also indicate that it may be 
      possible to enhance the transferability of the MS-CG approach by identifying 
      novel ways to combine information from different MS-CG force fields.
FAU - Thorpe, Ian F
AU  - Thorpe IF
AD  - Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United 
      States.
FAU - Goldenberg, David P
AU  - Goldenberg DP
FAU - Voth, Gregory A
AU  - Voth GA
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20110923
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
RN  - 0 (Peptides)
SB  - IM
MH  - Amino Acid Sequence
MH  - *Models, Molecular
MH  - Molecular Sequence Data
MH  - Peptides/*chemistry
MH  - Protein Structure, Secondary
MH  - Thermodynamics
EDAT- 2011/09/13 06:00
MHDA- 2012/02/16 06:00
CRDT- 2011/09/13 06:00
PHST- 2011/09/13 06:00 [entrez]
PHST- 2011/09/13 06:00 [pubmed]
PHST- 2012/02/16 06:00 [medline]
AID - 10.1021/jp204455g [doi]
PST - ppublish
SO  - J Phys Chem B. 2011 Oct 20;115(41):11911-26. doi: 10.1021/jp204455g. Epub 2011 
      Sep 23.