Tuesday, May 15, 2012

Two Fresh Reviews on Nucleic Acid Simulations.

Two new reviews have just come out headed by common names in the field of modeling nucleic acids like Michael Levitt, Jiri Sponer, and Tom Cheatham.

Modeling Nucleic Acids
Adelene YL Sim, Peter Minary, Michael Levitt
Current Opinion in Structural Biology (2012), 22, 1-6

This is a very short review, so, if you're really looking for a REVIEW on modeling nucleic acids this is not a recommended read.
Levitt's group highlights what they call, degrees of freedom (DOF), as if it was a whole field, weird..., "degrees of freedom are degrees of freedom", not a subject field.
Anyhow, that DOF part is where it gets interesting, as they point out to their recent work which goes in the direction of rigid-body analysis, although, again, they wanna call it different.
They cite two of their recent articles, one called "Modeling and Design by Hierarchical Natural Moves", and the other called "Conformational Optimization with Natural Degrees of Freedom: A Novel Stochastic Chain Closure Algorithm".

The most interesting part of the review is that they claim to have solved, what they call the "lever-arm" problem, which I suspect to be closely related to the crank-shaft effect (neatly illustrated by Mr. "I solved tRNA", i.e., Sung‐Hou Kim). They go on to say that the trick is to use only degrees of freedom which affect local conformation (?) but this selection breaks the continuity of the helix, and so that forces them to use a chain-closure algorithm. All in all it's quite hard to follow what they mean, so it leaves one intrigued to look for answers in their other papers which seem to be more meaty.

Molecular Dynamics Simulations of G-DNA and Perspectives on the Simulation of Nucleic Acid Structures
Jiří Šponer, Xiaohui Cang, Thomas E. Cheatham III
Methods (2012), XX, XX-XX

This one is a proper review with specific details on molecular dynamics using explicit solvent (water).
It seems to tell in detail the very valuable information on the miss-happenings of the Orozco corrections (ff9 + parmbsc0) to the Amber force-field for nucleic acids which result in ladder-like conformations.
It also gives a good outline of the up-to-date developments of the AMBER and CHARMM force-fields, and mentions that CHARMM seems not to be stable on G-DNA simulations, of course, just using one methodology for the solvent cage, so, remains to be seen what happens by using something different to particle mesh ewald.

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