PMID- 18808094
OWN - NLM
STAT- MEDLINE
DCOM- 20090106
LR  - 20081010
IS  - 1520-6106 (Print)
IS  - 1520-5207 (Linking)
VI  - 112
IP  - 41
DP  - 2008 Oct 16
TI  - Peptide folding using multiscale coarse-grained models.
PG  - 13079-90
LID - 10.1021/jp8015968 [doi]
AB  - The multiscale coarse-graining (MS-CG) method has been previously used to 
      describe the equilibrium properties of peptides. The present study reveals that 
      MS-CG models of alpha-helical polyalanine and the beta-hairpin V 5PGV 5 possess 
      the capacity to efficiently refold in simulations initiated from unfolded 
      configurations. The MS-CG peptides exhibit free energy landscapes that are 
      funneled toward folded configurations and two-state folding behavior, consistent 
      with the known characteristics of small, rapidly folding peptides. Moreover, the 
      models demonstrate enhanced sampling capabilities when compared to systems with 
      full atomic detail. The significance of these observations with respect to the 
      theoretical basis of the MS-CG approach is discussed. The MS-CG peptides were 
      used to reconstruct atomically detailed configurations in order to evaluate the 
      extent to which MS-CG ensembles embody all-atom peptide free energy landscapes. 
      Ensembles obtained from these reconstructed configurations display good agreement 
      with the all-atom simulation data used to generate the MS-CG models and also 
      corroborate the presence of features observed in the MS-CG peptide free energy 
      landscapes. These findings suggest that MS-CG models may be of significant 
      utility in the study of peptide folding.
FAU - Thorpe, Ian F
AU  - Thorpe IF
AD  - Center for Biophysical Modeling and Simulation, Department of Chemistry, 
      University of Utah, Salt Lake City, UT 84112-0850, USA.
FAU - Zhou, Jian
AU  - Zhou J
FAU - Voth, Gregory A
AU  - Voth GA
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20080920
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
RN  - 0 (Peptides)
RN  - 25191-17-7 (polyalanine)
SB  - IM
MH  - Computer Simulation
MH  - Hydrogen Bonding
MH  - *Models, Chemical
MH  - *Models, Molecular
MH  - Peptides/*chemistry
MH  - Protein Renaturation
MH  - Thermodynamics
EDAT- 2008/09/24 09:00
MHDA- 2009/01/07 09:00
CRDT- 2008/09/24 09:00
PHST- 2008/09/24 09:00 [pubmed]
PHST- 2009/01/07 09:00 [medline]
PHST- 2008/09/24 09:00 [entrez]
AID - 10.1021/jp8015968 [doi]
PST - ppublish
SO  - J Phys Chem B. 2008 Oct 16;112(41):13079-90. doi: 10.1021/jp8015968. Epub 2008 
      Sep 20.