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Free energy landscapes of two model peptides: α-helical and β-hairpin peptides explored with Brownian dynamics simulation
- Source :
- Molecular Simulation. 31:683-693
- Publication Year :
- 2005
- Publisher :
- Informa UK Limited, 2005.
-
Abstract
- We applied an atomistic Brownian dynamics (BD) simulation with multiple time step method for the folding simulation of a 13-mer α-helical peptide and a 12-mer β-hairpin peptide, giving successful folding simulations. In this model, the driving energy contribution towards folding came from both electrostatic and van der Waals interactions for the α-helical peptide and from van der Waals interactions for the β-hairpin peptide. Although, many non-native structures having the same or lower energy than that of native structure were observed, the folded states formed the most populated cluster when the structures obtained by the BD simulations were subjected to the cluster analysis based on distance-based root mean square deviation of side-chains between different structures. This result indicates that we can predict the native structures from conformations sampled by BD simulation.
- Subjects :
- chemistry.chemical_classification
General Chemical Engineering
Peptide
General Chemistry
Condensed Matter Physics
Folding (chemistry)
symbols.namesake
chemistry
Computational chemistry
Chemical physics
Modeling and Simulation
symbols
Brownian dynamics
Cluster (physics)
General Materials Science
Protein folding
van der Waals force
Root-mean-square deviation
Energy (signal processing)
Information Systems
Subjects
Details
- ISSN :
- 10290435 and 08927022
- Volume :
- 31
- Database :
- OpenAIRE
- Journal :
- Molecular Simulation
- Accession number :
- edsair.doi...........b82257e651d08171668575fb1cd35c01