Dimer domain swapping versus monomer folding in apo-myoglobin studied by molecular simulations

Literature Information

Publication Date 2015-01-09
DOI 10.1039/C4CP05203J
Impact Factor 3.676
Authors

Koji Ono, Mashiho Ito, Shun Hirota, Shoji Takada


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Abstract

Recent experiments showed that myoglobin can form a domain-swapped dimer under certain conditions. Here, using a coarse-grained symmetrized Go model, we performed a series of folding simulations of two apo-myoglobin molecules restrained at a high density, addressing competition of formation of a domain-swapped dimer with folding to two monomer structures. In addition to the domain-swapped dimer found in X-ray crystallography, we also found some other forms of domain swapping. With the protein density, the probability of domain-swapping increased. Folding pathway analysis clarified that separation between monomer folding and domain-swapping arose at a relatively early stage, where inter-chain contacts between helices AB of one chain and helices GH of another chain tend to result in the domain swapped dimer. This resembles the mechanism of domain swapping suggested previously for cytochrome c.

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Source Journal

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
Articles per Year: 3036

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

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