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Conformational Space of Nucleic Acids

Conformational Space of Nucleic Acids. Bohdan Schneider Institute of Organic Chemistry and Biochemistry AS Czech Republic bohdan@uochb.cas.cz Supported by the grant LC512 from MŠ M T to the Center for Biomolecules and Complex Molecular Systems. Motivation.

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Conformational Space of Nucleic Acids

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  1. Conformational Space of Nucleic Acids • Bohdan Schneider • Institute of Organic Chemistry and Biochemistry AS Czech Republic • bohdan@uochb.cas.cz Supported by the grant LC512 from MŠ MT • to the Center for Biomolecules and Complex Molecular Systems

  2. Motivation • Nucleic acids have key biological functions • Folding realized via the backbone conformational variability • Function might be connected to fold

  3. Data for the Analysis • NA backbone analyzed across the NDB archive: • DNA: About Eight thousand nt units • RNA: About Four thousand nt units

  4. Analysis of Multidimensional Space • One nucleotide has 7 torsion angles ~ 7D conformational space • Largest variability at the phosphodiester link • A minimal unit for analysis >>ribose-to-ribose<< • Analyze several 3D slices through the 14D space

  5. Averaging of 3D distributions by Fourier averaging Point distribution Pseudoelectron representation

  6. Fourier transforms of 3D torsion distributions • Calculated ~fifteen 3D maps • In all, fit peaks, assign residues to peaks • Sorted residues by lexicographical clustering: • 6 primary maps for clustering • 5 to monitor quality of proposed clusters • 6 more or less ignored in the analysis

  7. Clustering by Peak Names

  8. Protocol • Select structural data • Fourier-transform 3D distributions of torsions • Localize peak positions in all maps • Fit and name peaks • Name di-nts by nearby peaks • Cluster di-nts by their names • Check clusters by overlap in real 3D • Well overlapping dints form conformational family

  9. DNA is conformationally compact

  10. RNA is conformationally diverse

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