Journal
PROTEIN SCIENCE
Volume 22, Issue 5, Pages 605-613Publisher
WILEY
DOI: 10.1002/pro.2244
Keywords
elastic network model; normal mode analysis; protein dynamics; closed protein conformation
Categories
Funding
- World Class University Program [R33-10079]
- National Research Foundation of Korea, Ministry of Education, Science, and Technology [2011-0014584]
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An elastic network model (ENM), usually C coarse-grained one, has been widely used to study protein dynamics as an alternative to classical molecular dynamics simulation. This simple approach dramatically saves the computational cost, but sometimes fails to describe a feasible conformational change due to unrealistically excessive spring connections. To overcome this limitation, we propose a mass-weighted chemical elastic network model (MWCENM) in which the total mass of each residue is assumed to be concentrated on the representative alpha carbon atom and various stiffness values are precisely assigned according to the types of chemical interactions. We test MWCENM on several well-known proteins of which both closed and open conformations are available as well as three -helix rich proteins. Their normal mode analysis reveals that MWCENM not only generates more plausible conformational changes, especially for closed forms of proteins, but also preserves protein secondary structures thus distinguishing MWCENM from traditional ENMs. In addition, MWCENM also reduces computational burden by using a more sparse stiffness matrix.
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