Abstract
The populations and transitions between Ramachandran basins are studied for combinations of the standard 20 amino acids in monomers, dimers and trimers using an implicit solvent Langevin dynamics algorithm and employing seven commonly used force-fields. Both the basin populations and inter-conversion rates are influenced by the nearest neighbor's conformation and identity, contrary to the Flory isolated-pair hypothesis. This conclusion is robust to the choice of force-field, even though the use of different force-fields produces large variations in the populations and inter-conversion rates between the dominant helical, extended beta, and polyproline II basins. The computed variation of conformational and dynamical properties with different force-fields exceeds the difference between explicit and implicit solvent calculations using the same force-field. For all force-fields, the inter-basin transitions exhibit a directional dependence, with most transitions going through extended beta conformation, even when it is the least populated basin. The implications of these results are discussed in the context of estimates for the backbone entropy of single residues, and for the ability of all-atom simulations to reproduce experimental protein folding data.
Keywords
Ramachandran plotPolyproline helixForce field (fiction)Langevin dynamicsChemistryStatistical physicsMolecular dynamicsThermodynamicsChemical physicsPhysicsComputational chemistryProtein structurePeptide
MeSH Terms
AlgorithmsComputer SimulationEntropyKineticsModelsChemicalModelsMolecularMotionPeptidesPliabilityProtein ConformationProtein Folding
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Publication Info
- Year
- 2003
- Type
- article
- Volume
- 331
- Issue
- 3
- Pages
- 693-711
- Citations
- 123
- Access
- Closed
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Cite This
Muhammad H. Zaman,
Min‐Yi Shen,
R. Stephen Berry
et al.
(2003).
Investigations into Sequence and Conformational Dependence of Backbone Entropy, Inter-basin Dynamics and the Flory Isolated-pair Hypothesis for Peptides.
Journal of Molecular Biology
, 331
(3)
, 693-711.
https://doi.org/10.1016/s0022-2836(03)00765-4
Identifiers
- DOI
- 10.1016/s0022-2836(03)00765-4
- PMID
- 12899838