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1. Kinetic advantage of intrinsically disordered proteins in coupled folding–binding process: a critical assessment of the “fly-casting” mechanism

The coupling of folding with binding through a “fly-casting” mechanism has been proposed by P. G. Wolynes et al. to account for the fast binding kinetics of Intrinsically disordered proteins (IDPs). Although there are growing experimental studies on the kinetics of the coupled folding–binding process, it remains poorly determined whether IDPs possess higher binding rates than ordered proteins and whether the speeding effect operates via the “fly-casting” mechanism. In our recent work, we collated experimental data from the literature to verify the kinetic advantages of IDPs, and conducted molecular simulations to clarify the origin of the kinetic advantages. We showed that the kinetic advantage of IDPs is not only due to the greater capture radii of IDPs since the slower translational diffusion of IDPs hamper the capture rate. The true origin of the faster binding for IDPs is the fewer encounter times required before the formation of the final binding complex.

The work has been published as: Yongqi Huang and Zhirong Liu, J. Mol. Biol. 393, 1143 (2009). It was recommended by Vladimir N. Uversky in Faculty of 1000 Biology (http://f1000biology.com/article/id/1226965), and was selected as “Papers of Interest” in the 2009.11 issue of Biophysical Society Newsletter.

2. Models for how type-2 topoisomerases untangle DNA?

How does the global topology affect local interactions and, conversely, how do locally acting type-2 topoisomerases guard against detrimental global entanglements of a DNA that is orders of magnitude larger than the enzyme? Collaborating with Prof. Hue Sun Chan of University of Toronto and Prof. Lynn Zechiedrich from Baylor College of Medicine, we conducted simulations to test a model that topoisomerases remove disentangle by acting selectively on preformed “hooked” juxtapositions, and showed that local juxtaposition geometry contains rich information of global topology which provides a statistical mechanical basis for type-2 topoisomerase action not only in decatenating and unknotting, but in suppressing the equilibrium distribution of supercoils as well.

The work has been published as: Phys. Rev. E. 81, 031902 (2010); J. Mol. Biol. 400, 963 (2010). We were invited to write a review paper as Nucleic Acids Res. 37, 661 (2009), which was selected as the cover paper of the issue.

 

3. Modification of gap in graphene

A strategy to open a gap in graphene is to constructing periodic holes on graphene to form graphene antidot lattices (GALs). Theoretical calculations have predicted that the induced gap in GALs is approximately proportional to the hole diameter and inversely proportional to the superlattice cell area. On examining the published theoretical works of GALs in the literature, we noticed that a half of the possible GALs patterns were unintentionally missed. By constructing complete patterns, we found that the bandgap of the GALs was sensitive to the width of the wall between the neighboring holes. A nonzero bandgap was opened in hexagonal GALs with even width, while the bandgap remained closed in those with odd width. The work was published as: ACS Nano 5, 4023 (2011).

We have also investigated other means to modify the gap of graphene by other means, such as the strain (Nano Res. 3, 545 (2010), where a tight-binding analytic framework is combined with first-principles calculations to reveal the mechanism underlying the strain effects on electronic structures of graphene and graphene nanoribbons) and chlorination (J. Phys. Chem. C 116, 844 (2012)), as well as how the transport behavior of zigzag graphene nanoribbons are tailored by strain (AIP Adv. 2, 012103 (2012)).

 

 

 

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