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Analysis of the dynamical flexibility of bis-peptide nanostructures

Pornsuwan, Oraya and Schafmeister, Christian E. and Saxena, Sunil (2008) Analysis of the dynamical flexibility of bis-peptide nanostructures. JOURNAL OF PHYSICAL CHEMISTRY C, 112 (5). pp. 1377-1384.

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We present an approach to predict the overall structure and flexibility of bis-peptide nanostructures from electron spin resonance (ESR) distance measurements. These molecules are composed of conformationally restricted monomers, and results on a series of bis-peptide oligomers containing four to eight monomers are presented. On the basis of molecular dynamics (MD), a joint-stiff segment model is generated to represent the bis-peptide backbones. A scheme is established to exploit information on end-to-end distance distribution functions obtained by ESR to optimize the force fields used in the joint-stiff segment model. The model provides end-to-end distribution functions for the oligomers that better fit the ESR results than those originally obtained from MD simulations. The results also provide information on the distribution of orientations of a monomer with respect to the preceding monomer. An optimized orientational angle of γγ0 was −21.06°. The other angles were consistent with MD predictions. The optimized force constants of kα = 2.144 kcal/(mol·rad2), kβ = 3.245 kcal/(mol·rad2), kγ = 2.876 kcal/(mol·rad2), and kββ = 3.041 kcal/(mol·rad2) were found. Information of these orientational parameters enhances our ability to predict the shapes and flexibility of new oligomers constructed using an arbitrary number of this monomer.

Item Type:Article
Subjects:Material Science > Bio materials
Material Science > Nanochemistry
ID Code:5979
Deposited By:IoN
Deposited On:06 Aug 2009 10:17
Last Modified:06 Aug 2009 10:17

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