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MD simulation VS. Continuum mechanical model Of protein

Hi, all

Molecular dynamics (or MC) is a powerful tool in the protein research. There're lots of scientific works in this field, which deepen our understanding gradually. My question follows, "how about the continuum mechaics in protein research".

Any discussions and advices are appreciated.


Kong    5th Sep 2007



Xi Chen's picture

See which is a top-down approach. More publications along such direction are forthcoming.

As far as I know, there are very few works on continuum description on protein molecules. Very recently, as Prof. Chen commented, he and his collaborators have proposed the multi-scale model of protein, i.e. mechano-sensitive ion channel, based on combination of MD simulation and FE model (See here).

Except Prof. Chen's work, the continuum descriptions on single-molecule chain (e.g. DNA) have been proposed by Kratky and Porod, renowned as Worm-Like-Chain (WLC) model. WLC model has succeeded in depicting the nonlinear elastic behavior of single-stranded DNA based on pulling experiments by Bustamante group (See paper by Bustamante et al., Science, 265, p1599-1600, 1994). Such model has recently enabled Frey and coworkers to study the mechanical properties (bending properties) of microtubule based on real-time observation of microtubule tip connected to a bead with optical apparatus (for details, see here). Based on their experiments with comparison to WLC model, they showed that WLC model allows for depicting the bending behavior of microtubule as a function of contour length.

Such chain model have also allowed me and my advisors (Prof. Makarov and Prof. Rodin) to understand the mechanical properties of cross-linked single-molecule chain, which provides the insight into remarkable mechanical properties of some mechanical proteins such as titin Ig domain (See Refs: Ref at JPC and Ref at PRE).

More recently, the single-molecule experiments on spider silk fiber and spider silk protein by Hansma and coworkers have revealed that the mechanical behaviors of both spider silk fiber and spider silk protein are well delineated by scaling law, indicating that fiber consists of single-molecule chain in a hierarchical manner (See here). Such experimental results have resulted in the emergence of hierarchical model of spider silk fiber based on single-molecule chain (e.g., See here). Such hierarchical model based on single-molecule chain such as WLC has enabled the quantitative descriptions on the nonlinear elastic behavior of biological gels such as actin, collagen, neurofilament, etc. (for details, see here). In the issue of last week (Aug. 30, 2007) at PRL, the cover article is about the model of a fiber made of WLC chains with chirality (see here).

As shown above, the continuum-like model for a fiber made of single-molecules in a hierarchical manner has been one of hot issues in recent modeling researches in biomolecules. Such issue may be intriguing mechanicist, physicist, and chemists whose backgrounds are based on both theory and experiments.

Dear Prof. Chen and Prof. Eom,

Thanks a lot for your very useful comments. 


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