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Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design.

ABSTRACT: Conformationally restricted amino acids are promising candidates to serve as basic pieces in redesigned protein motifs which constitute the basic modules in synthetic nanoconstructs. Here we study the ability of constrained cyclic amino acid 1-aminocyclohexane-1-carboxylic acid (Ac6c) to stabilize highly regular beta-helical motifs excised from naturally occurring proteins. Calculations indicate that the conformational flexibility observed in both the ring and the main chain is significantly higher than that detected for other 1-aminocycloalkane-1-carboxylic acids (Acnc, where n refers to the size of the ring) with smaller cycles. Incorporation of Ac6c into the flexible loops of beta-helical motifs indicates that the stability of such excised building blocks as well as the nanoassemblies derived from them is significantly enhanced. Thus, the intrinsic Ac6c tendency to adopt folded conformations combined with the low structural strain of the cyclohexane ring confers the ability to both self-adapt to the beta-helix motif and to stabilize the overall structure by absorbing part of its conformational fluctuations. Comparison with other Acnc residues indicates that the ability to adapt to the targeted position improves considerably with the ring size, i.e., when the rigidity introduced by the strain of the ring decreases.

SUBMITTER: Rodriguez-Ropero F

PROVIDER: S-EPMC2771322 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature

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Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design.

Rodríguez-Ropero Francisco F Zanuy David D Casanovas Jordi J Nussinov Ruth R Alemán Carlos C

Journal of chemical information and modeling 20080117 2

Conformationally restricted amino acids are promising candidates to serve as basic pieces in redesigned protein motifs which constitute the basic modules in synthetic nanoconstructs. Here we study the ability of constrained cyclic amino acid 1-aminocyclohexane-1-carboxylic acid (Ac6c) to stabilize highly regular beta-helical motifs excised from naturally occurring proteins. Calculations indicate that the conformational flexibility observed in both the ring and the main chain is significantly hig ...[more]

PMID: 18201062

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Project description:BackgroundThe premature loss of primary teeth is a common problem in pediatric dentistry, resulting in disruption of the arch integrity. Hence, space maintainers (SM) used for maintaining spaces are necessary. However, current methods of making removable space maintainers (RSM) have some limitations.MethodsDigital models of dentition defects were obtained by using a scanning technique coupled with laser medical image reconstruction. The digital RSMs were designed using the 3Shape software. They were manufactured using two methods: polyetheretherketone (PEEK), and conventional methods (20 RSMs per group). For qualitative evaluation, the Likert five-point scale was used by 10 experts to obtain a score for 40 RSMs. The spaces between the tissue surfaces of the RSMs and the models were replaced using silicone, and the maximum and mean distances, as well as the standard deviation, were measured. A three-dimensional variation analysis was used to measure these spaces. The student's t-test and Satterthwaite t-test were used to compare the differences in the spaces for the various materials.ResultsThe PEEK RSMs were found to fit the models well. In the qualitative assessment, the mean experts' scores for the PEEK and conventional groups were 1.80 ± 0.40 and 1.82 ± 0.40, and there was no significant difference between the two groups (p = 0.875). In the quantitative assessment, the mean spaces for the PEEK digital RSMs and the conventional RSMs were 44.32 ± 1.75 μm, and 137.36 ± 18.63 μm, respectively, and the differences were statistically significant (p < 0.001). In addition, there were significant differences in the maximum space and the standard deviation between the two groups.ConclusionDigitally designed and integrated RSMs were found to be superior to those produced using the conventional method. 3D variation analysis results showed that the mean distances and standard deviations of the PEEK groups were significantly smaller than those of conventional group (p < 0.01). A PEEK-manufactured RSM produced using CAD/CAM would be extremely suitable for clinical applications.

Dataset Information

Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design.

Publications

Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design.

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