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A mass weighted chemical elastic network model elucidates closed form domain motions in proteins.

ABSTRACT: 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.

SUBMITTER: Kim MH

PROVIDER: S-EPMC3649262 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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A mass weighted chemical elastic network model elucidates closed form domain motions in proteins.

Kim Min Hyeok MH Seo Sangjae S Jeong Jay Il JI Kim Bum Joon BJ Liu Wing Kam WK Lim Byeong Soo BS Choi Jae Boong JB Kim Moon Ki MK

Protein science : a publication of the Protein Society 20130318 5

An elastic network model (ENM), usually Cα 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 ...[more]

PMID: 23456820

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Project description:BackgroundOscillatory behavior is critical to many life sustaining processes such as cell cycles, circadian rhythms, and notch signaling. Important biological functions depend on the characteristics of these oscillations (hereafter, oscillation characteristics or OCs): frequency (e.g., event timings), amplitude (e.g., signal strength), and phase (e.g., event sequencing). Numerous oscillating reaction networks have been documented or proposed. Some investigators claim that oscillations in reaction networks require nonlinear dynamics in that at least one rate law is a nonlinear function of species concentrations. No one has shown that oscillations can be produced for a reaction network with linear dynamics. Further, no one has obtained closed form solutions for the frequency, amplitude and phase of any oscillating reaction network. Finally, no one has published an algorithm for constructing oscillating reaction networks with desired OCs.ResultsThis is a theoretical study that analyzes reaction networks in terms of their representation as systems of ordinary differential equations. Our contributions are: (a) construction of an oscillating, two species reaction network [two species harmonic oscillator (2SHO)] that has no nonlinearity; (b) obtaining closed form formulas that calculate frequency, amplitude, and phase in terms of the parameters of the 2SHO reaction network, something that has not been done for any published oscillating reaction network; and (c) development of an algorithm that parameterizes the 2SHO to achieve desired oscillation, a capability that has not been produced for any published oscillating reaction network.ConclusionsOur 2SHO demonstrates the feasibility of creating an oscillating reaction network whose dynamics are described by a system of linear differential equations. Because it is a linear system, we can derive closed form expressions for the frequency, amplitude, and phase of oscillations, something that has not been done for other published reaction networks. With these formulas, we can design 2SHO reaction networks to have desired oscillation characteristics. Finally, our sensitivity analysis suggests an approach to constructing a 2SHO for a biochemical system.

Dataset Information

A mass weighted chemical elastic network model elucidates closed form domain motions in proteins.

Publications

A mass weighted chemical elastic network model elucidates closed form domain motions in proteins.

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