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Quantifying Basepair Isostericity

Quantifying Basepair Isostericity Jesse Stombaugh 1 , Craig L. Zirbel 2 , Eric Westhof 4 , and Neocles B. Leontis 3,*

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Quantifying Basepair Isostericity

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  1. Quantifying Basepair Isostericity Jesse Stombaugh1, Craig L. Zirbel2, Eric Westhof4, and Neocles B. Leontis3,* 1 Department of Biological Sciences, 2 Department of Mathematics and Statistics, 3Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403. 4 Architecture et réactivité de l’ARN, Université Louis Pasteur de Strasbourg,Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084 Strasbourg, France. email: jstomba@bgsu.edu

  2. Outline • RNA Basepair Interactions • Base Edges • Geometric Basepair Families • Frequencies from 3D structures • IsoDiscrepancy Index (IDI) • Criteria • Validation • Application • 3D Structural Alignment of rRNA • Evaluation • Conclusions

  3. RNA Basepair Interactions

  4. Base Edges

  5. Geometric Basepair Families Online Basepair Catalog: http://rna.bgsu.edu/FR3D/basepairs

  6. Frequency for those bases involved in basepairing

  7. Basepair Isostericity

  8. IsoDiscrepancy Index (IDI)

  9. Criteria used for determining IDI To compute the IsoDiscrepancy index (IDI) we calculate: The difference between C1’-C1’ distances for the two basepairs, denoted by ∆c. The distance in the plane between the C1’ atoms of the second base when the first bases have the same orientation, denoting this by t1. The rotation in the plane of the second base relative to the first base (cWW and tWS) or the flipping of the second base to bring it into the same orientation as the first base

  10. Validation of the IDI • First, the IDI should be low between instances of the same basepair. • The Figure to the left shows a histogram of the IDI calculated between each distinct pair of basepair instances of the same kind from 3D structures (i.e. GC cWW with GC cWW, UA tWH with UA tWH, etc.). • The distribution peaks at IDI = ~0.6 and is narrowly distributed

  11. Validation of the IDI • Second, the IDI should be low between isosteric basepairs. • On the left, we show the IDI calculated between combinations of 200 GC and 200 UA cWW basepairs from high resolution 3D structures (< 3.0Å). • As in the first panel, the vast majority result in an IDI below 2.0 and the distribution peaks below 1.0

  12. Validation of the IDI • Third, the IDI should be of a moderate size for basepairs that are near isosteric and known to occasionally substitute for one another. • The left panel shows the IDI between 200 GC cWW and 200 GU cWW basepairs. • The peak of the histogram occurs to the right of 2.0.

  13. Validation of the IDI • Finally, the IDI should be large for basepairs which are geometrically dissimilar (non-isosteric). • The left panel shows the IDI between 200 GU cWW pairs and 200 UG cWW pairs. • This distribution peaks at IDI ~ 4.5

  14. Application of IDI: IDIs within the cWW Family

  15. 3D rRNA Structural Alignment

  16. 3D Structural Alignment for 5S Escherichia coli and Thermus thermophilus

  17. 3D Structural Alignment for 5S Escherichia coli and Thermus thermophilus

  18. IDIs from 3D alignment: Classification of IDIs from 5S, 16S and 23S rRNA 3D Structural Alignment

  19. Conclusions • We have developed a way to quantitatively measure the geometric similarity of two basepairs, which we call the IsoDiscrepancy Index. • Using the IDI we can determine whether a basepair is isosteric, near-isosteric, or non-isosteric to another basepair. • To help evaluate the validity of the IDI, we created a 3D structural alignment of the 5S, 16S and 23S rRNA for E.coli and T. thermophilus. • Based on this alignment we observed that ~98% of the aligned basepairs are either isosteric or near-isosteric.

  20. BGSU – Chemistry Neocles Leontis, P.I. BGSU – Mathematics And Statistics. Craig Zirbel Steve Dinda Institut de Biologie Moléculaire et Cellulaire du CNRS Eric Westhof U.C. – Berkeley Jamie Cate MRC Laboratory of Molecular Biology Venki Ramakrishnan Christine Dunham JS is funded by NBL’s RCE grant, which is supported by Bowling Green State University’s ‘Research Capacity Expansion Program’ with funds provided by the Ohio board of Regents Research Incentive Fund. Acknowledgements

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