Sugar ring pucker: Difference between revisions
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==Describing conformations with a pseudorotation angle== | ==Describing conformations with a pseudorotation angle== | ||
To classify conformations unambiguously, the pseudorotation angle and amplitude are used. There are two definitions in the literature that lead to very similar results.[https://x3dna.org/articles/conformation-of-the-sugar-ring-in-nucleic-acid-structures] Once the pseudoration angle is calculated, you can name the conformation and plot it in a pseudorotation diagram (see e.g. [https://www.researchgate.net/publication/297890156_Insights_into_Furanose_Solution_Conformations_Beyond_the_Two-State_Model/figures?lo=1]). | [[Image:Pseudorotation cyclopentane.PNG|400px]] | ||
To classify conformations unambiguously, the pseudorotation angle and amplitude are used. The image above shows conformations of cyclopentane ordered by pseudorotation angle. The pentagons represent the five-membered ring, with atoms above the plane shown as blue circles, those below the plane shown as orange circles, and the three or four others in the plane. Conformations close in pseudorotation angle are also close in root mean square distances of corresponding atoms. There are two definitions in the literature that lead to very similar results.[https://x3dna.org/articles/conformation-of-the-sugar-ring-in-nucleic-acid-structures] Once the pseudoration angle is calculated, you can name the conformation and plot it in a pseudorotation diagram (see e.g. [https://www.researchgate.net/publication/297890156_Insights_into_Furanose_Solution_Conformations_Beyond_the_Two-State_Model/figures?lo=1]). This [https://www.youtube.com/watch?v=AtC4EfYENAc dance performance] shows how the conformations change as the pseudorotation angle changes. | |||
==Conformations of ribose rings== | ==Conformations of ribose rings== | ||