Book chapter
Molecular simulations of diffusion and association in multimacromolecular systems
Numerical Computer Methods, Part D, Vol.383, pp.166-198
Methods in enzymology, 383, Academic Press
2004
DOI: 10.1016/S0076-6879(04)83008-8
PMID: 15063651
Abstract
This chapter analyzes the molecular simulations of diffusion and association in multimacromolecular systems. The purpose of Brownian dynamics (BD) is, like any other dynamic simulation method, to model the time-dependent behavior of a system of molecules. The most well-known molecular simulation method is molecular dynamics (MD), which in its usual form is used to simulate the internal dynamics of macro-molecules, such as proteins and nucleic acids in water. The hydrophobic effect naturally arise in MD simulations that include explicit water molecules and simple hydrocarbons, such as methane or ethane show a pronounced affinity for one another in aqueous phase MD simulations. A common approach is to model the magnitude of hydrophobic interactions as being proportional to the amount of solvent-accessible surface area that becomes buried when the molecules contact each other. It is suggested that simulating the diffusion and association of three or more proteins is feasible with BD and, in principle, would be as simple as placing all the proteins in a box and letting them diffuse until they form stable complexes.
Details
- Title: Subtitle
- Molecular simulations of diffusion and association in multimacromolecular systems
- Creators
- Adrian H Elcock - Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, USA
- Resource Type
- Book chapter
- Publication Details
- Numerical Computer Methods, Part D, Vol.383, pp.166-198
- Publisher
- Academic Press; United States
- Series
- Methods in enzymology; 383
- DOI
- 10.1016/S0076-6879(04)83008-8
- PMID
- 15063651
- ISSN
- 0076-6879
- eISSN
- 1557-7988
- Language
- English
- Date published
- 2004
- Academic Unit
- Physics and Astronomy; Biochemistry and Molecular Biology
- Record Identifier
- 9984024409802771
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