PMID- 17400700
OWN - NLM
STAT- MEDLINE
DCOM- 20070726
LR  - 20181227
IS  - 0006-3495 (Print)
IS  - 1542-0086 (Electronic)
IS  - 0006-3495 (Linking)
VI  - 92
IP  - 12
DP  - 2007 Jun 15
TI  - Coarse-grained peptide modeling using a systematic multiscale approach.
PG  - 4289-303
AB  - A systematic new approach to derive multiscale coarse-grained (MS-CG) models has 
      been recently developed. The approach employs information from atomistically 
      detailed simulations to derive CG forces and associated effective potentials. In 
      this work, the MS-CG methodology is extended to study two peptides representing 
      distinct structural motifs, alpha-helical polyalanine and the beta-hairpin 
      V(5)PGV(5). These studies represent the first known application of this approach 
      to peptide systems. Good agreement between the MS-CG and atomistic models is 
      achieved for several structural properties including radial distribution 
      functions, root mean-square deviation, and radius of gyration. The new MS-CG 
      models are able to preserve the native states of these peptides within 
      approximately 1 A backbone root mean-square deviation during CG simulations. The 
      MS-CG approach, as with most coarse-grained models, has the potential to increase 
      the length and timescales accessible to molecular simulations. However, it is 
      also able to maintain a clear connection to the underlying atomistic-scale 
      interactions.
FAU - Zhou, Jian
AU  - Zhou J
AD  - Center for Biophysical Modeling and Simulation, Department of Chemistry, 
      University of Utah, Salt Lake City, Utah.
FAU - Thorpe, Ian F
AU  - Thorpe IF
FAU - Izvekov, Sergey
AU  - Izvekov S
FAU - Voth, Gregory A
AU  - Voth GA
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20070330
PL  - United States
TA  - Biophys J
JT  - Biophysical journal
JID - 0370626
RN  - 0 (Peptides)
SB  - IM
MH  - *Algorithms
MH  - Computer Simulation
MH  - *Models, Chemical
MH  - *Models, Molecular
MH  - Peptides/*chemistry
MH  - Protein Conformation
PMC - PMC1877786
EDAT- 2007/04/03 09:00
MHDA- 2007/07/27 09:00
PMCR- 2008/06/15
CRDT- 2007/04/03 09:00
PHST- 2007/04/03 09:00 [pubmed]
PHST- 2007/07/27 09:00 [medline]
PHST- 2007/04/03 09:00 [entrez]
PHST- 2008/06/15 00:00 [pmc-release]
AID - S0006-3495(07)71230-4 [pii]
AID - 94425 [pii]
AID - 10.1529/biophysj.106.094425 [doi]
PST - ppublish
SO  - Biophys J. 2007 Jun 15;92(12):4289-303. doi: 10.1529/biophysj.106.094425. Epub 
      2007 Mar 30.