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Literature DB >> 23410475

Folding and association of a homotetrameric protein complex in an all-atom Go model.

Abstract

The 84-residue homotetrameric BBAT1 is one of the smallest stable protein complexes and therefore is a good test system to study the self-assembly of multimeric proteins. We have researched for this protein the interplay between the folding of monomers and their assembly into tetramers. Replica exchange molecular dynamics simulations relying on a Go model are compared with earlier simulations that use the physics-based coarse-grained UNRES model.

Entities: Chemical Species

Mesh：

Substances：
Proteins

Year: 2013 PMID： 23410475 PMCID： PMC4201375 DOI： 10.1103/PhysRevE.87.014701

Source DB: PubMed Journal: Phys Rev E Stat Nonlin Soft Matter Phys ISSN： 1539-3755

23 in total

1. Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

Authors: N Koga; S Takada
Journal: J Mol Biol Date: 2001-10-12 Impact factor: 5.469

2. Non-native interactions, effective contact order, and protein folding: a mutational investigation with the energetically frustrated hydrophobic model.

Authors: Werner L Treptow; Marco Aurélio A Barbosa; Leandro G Garcia; Antônio F Pereira de Araújo
Journal: Proteins Date: 2002-11-01

3. The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations.

Authors: Yaakov Levy; Amedeo Caflisch; Jose N Onuchic; Peter G Wolynes
Journal: J Mol Biol Date: 2004-06-25 Impact factor: 5.469

4. X-ray structure analysis of a designed oligomeric miniprotein reveals a discrete quaternary architecture.

Authors: Mayssam H Ali; Ezra Peisach; Karen N Allen; Barbara Imperiali
Journal: Proc Natl Acad Sci U S A Date: 2004-08-09 Impact factor: 11.205

5. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains.

Authors: Adam Liwo; Mey Khalili; Harold A Scheraga
Journal: Proc Natl Acad Sci U S A Date: 2005-01-26 Impact factor: 11.205

Folding and association of a homotetrameric protein complex in an all-atom Go model.

1. Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

2. Non-native interactions, effective contact order, and protein folding: a mutational investigation with the energetically frustrated hydrophobic model.

3. The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations.

4. X-ray structure analysis of a designed oligomeric miniprotein reveals a discrete quaternary architecture.

5. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains.

6. Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding.

Review 7. Biomolecular simulation: a computational microscope for molecular biology.

Review 8. 3D domain swapping: a mechanism for oligomer assembly.

9. Folding and self-assembly of a small protein complex.

10. Biomolecular dynamics: order-disorder transitions and energy landscapes.

1. Folding and self-assembly of a small heterotetramer.