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A hierarchical coarse-grained (all-atom-to-all-residue) computer simulation approach: self-assembly of peptides

Pandey, Ras B ; Kuang, Zhifeng ; Farmer, Barry L Permyakov, Eugene A.

PloS one, 2013-08, Vol.8 (8), p.e70847-e70847 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
A hierarchical coarse-grained (all-atom-to-all-residue) computer simulation approach: self-assembly of peptides
Autor: Pandey, Ras B ; Kuang, Zhifeng ; Farmer, Barry L
Permyakov, Eugene A.
Assuntos: Algorithms ; Amino acids ; Analysis ; Biology ; Computer applications ; Computer Science ; Computer simulation ; Computer-generated environments ; Distribution functions ; High temperature ; Knowledge ; Knowledge bases (artificial intelligence) ; Laboratories ; Low temperature ; Mass distribution ; Materials Science ; Mathematical models ; Models, Molecular ; Molecular Dynamics Simulation ; Peptides ; Peptides - chemistry ; Physics ; Protein Conformation ; Proteins ; Radial distribution ; Scaling ; Self-assembly ; Solvents ; Spatial distribution ; Structure factor ; Temperature ; Thermal response
É parte de: PloS one, 2013-08, Vol.8 (8), p.e70847-e70847
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Conceived and designed the experiments: RBP ZK BLF. Performed the experiments: RBP ZK. Analyzed the data: RBP ZK. Contributed reagents/materials/analysis tools: RBP ZK BLF. Wrote the paper: RBP ZK BLF. Designed the coarse-grained apprach: RBP. Conducted all-atom MD simulation: ZK.
Competing Interests: The authors have declared that no competing interests exist.
Descrição: A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 ((1)H (2)S (3)S (4)Y (5)W (6)Y (7)A (8)F (9)N (10)N (11)K (12)T) is considered as an example to illustrate the utility. We find that peptides assemble rather fast into globular aggregates at low temperatures and disperse as random-coil at high temperatures. The specificity of the mass distribution of the self-assembly depends on the temperature and spatial lengths which are identified from the scaling of the structure factor. Analysis of energy and mobility profiles, gyration radius of peptide, and radial distribution function of the assembly provide insight into the multi-scale (intra- and inter-chain) characteristics. Thermal response of the global assembly with the simulated residue-residue interaction is consistent with that of the knowledge-based analysis despite expected quantitative differences.
Editor: United States: Public Library of Science
Idioma: Inglês

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A hierarchical coarse-grained (all-atom-to-all-residue) computer simulation approach: self-assembly of peptides

Pandey, Ras B ; Kuang, Zhifeng ; Farmer, Barry L Permyakov, Eugene A.

United States: Public Library of Science

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