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Modeling of protein turns and derivation of NMR parameters related to turn structure

Modeling of protein turns and derivation of NMR parameters related to turn structure. Megan Chawner BRITE REU Program Advisor: Dr. Dimitrios Morikis Department of Bioengineering University of California, Riverside. Outline. Background My Project Results Conclusions Acknowledgements.

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Modeling of protein turns and derivation of NMR parameters related to turn structure

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  1. Modeling of protein turns and derivation of NMR parameters related to turn structure Megan Chawner BRITE REU Program Advisor: Dr. Dimitrios Morikis Department of Bioengineering University of California, Riverside

  2. Outline • Background • My Project • Results • Conclusions • Acknowledgements

  3. Protein Structure: All proteins are made up of twenty amino acid building blocks into a sequence = primary structure

  4. Protein structure: sequence folds into b-sheet, a-helix, random coil loops and various types of turns stabilized by atomic interactions (e.g., H-bonds) = secondary structure Strand 1 Anti-parallel b-sheet Inter-strandH-bonds Strand 2 Primary structure: EKQKPDGVFQE a-helix C=O(i)…H-N(i+4) H-bonds 1 helix turn = 3.6 a.a. Primary structure: GPLLNKFLTT

  5. Protein Structure: three-dimensional protein folds are stabilized by long range interactions = tertiary structure Turns introduce reversibility in the direction of other elements of secondary structure, such as a-helices or b-sheets • 3 amino acids = g-turn • 4 amino acids = b-turn g-turn b-turn

  6. Backbone torsion angles: j, y, w i-1 i+1 i ji yi wi Turns Ramachandran plot (j, y) plot defines secondary structure b-sheet a-helix

  7. Protein Structure Determination: uses Nuclear magnetic resonance (NMR) spectroscopy to get NMR observables, • which are converted to NMR-derived structural parameters • Nuclear Overhauser effects (NOEs) inter-proton distances • 3J(HN-Ha)-coupling constants j-torsion angles NOE equation (Wuthrich, 1986) ri,j inter-proton distance tc  rotational correlation time NOE < 5 Å through-space interactions  inter-proton distances 3J(HN-Ha) = 3-chemical bond coupling through-bond interactions j-torsions Karplus Equation (Karplus, 1959, J Chem Phys) A=6.98, B=-1.38, C=1.72 (Wang and Bax, 1996, JACS)

  8. Relations of experimental observables andstructural parameters Amino Acid i Amino Acid i+1 R O R O N Ca C N Ca C ji+1 wi yi+1 yi ji H H H H daN (i,i+1) 3J(HN-Ha) Ha(i)-HN(i+1) dNa (i,i) HN(i)-Ha(i) daa (i,i+1) dNa (i,i) Ha(i)-Ha(i+1) HN(i)-HN(i+1) dNN (i,i+1) HN(i)-Ha(i+1) 3J(HN-Ha) = 3-bond  j-torsion NOE < 5 Å  distance in space

  9. Solution of Karplus equation using MatLab C C = = O O C C = = O O N N H H H H b b C C C C = = O O C C = = O O N N H H b b C C H H Cis Cis Cis Trans Trans Trans Cis Cis Trans Trans C C C C H H C C C C C C C C a N N C C a a a a N N N N C C C C q a a N N C C a a a a N N N N C C C C j j j j H H H H j j j j q q C C C C H H Newman Projections Trans q=180o j=-120o Cis q=0o j=60o b-sheet 3J(HN-Ha) (Hz) q=-90o j=-30o q=90o j=150o a-helix j (o) Chawner & Morikis, in preparation

  10. My Project Goals: To use NMR-derived parameters (inter-proton distances and j-torsion angles) to create databases of expected NMR observables (NOEs and 3J(HN-Ha)-coupling constants) for ideal b- and g- turns with statistical deviations. Bottom line: we are back-calculating NMR observables. Remember,during structure determination, NMR-derived parameters are obtained from NMR spectroscopic observables, NOEs and 3J(HN-Ha)-coupling constants. Use: Rapid protein turn structure identification by examination of raw NMR observables, without a complete structure calculation.

  11. Computational modeling of ideal b-and g-turns according to torsion angles using DeepView 2 2 3 3 j j y y 3 3 j j 2 2 y y 2 2 3 3 I I H H - - bond bond I’ I’ 1 1 4 4 a a a a C C - - C C Color code: Color code: Blue: N Blue: N II’ II’ II II Light blue: H Light blue: H Gray: C Gray: C Red: O Red: O b-turns VIII VIII Chawner & Morikis, in preparation Classic b-turn criteria Distance: Ca(1)-Ca(4) < 7 Å C=O(1)…H-N(4) H-bonded Distance:O(1)-N(4) < 3.3 Å Distance:O(1)-HN(4) < 2.4 Å Angle: O(1)-H(4)-N(4) almost linear ± 35o

  12. direct inverse Computational modeling of ideal b-and g-turns according to torsion angles g-turns Chawner & Morikis, in preparation Classic g-turn criteria

  13. Nuclear Overhauser effects (NOEs)  inter-proton distances b-turn g-turn Characteristic g-turn distances Ha(1)-HN(3): (i, i+2) Ha(1)-HN(2): (i, i+1) Ha(2)-HN(3): (i, i+1) HN(1)-HN(2): (i, i+1) HN(2)-HN(3): (i, i+1) Characteristic b-turn distances Ha(2)-HN(4): (i, i+2) Ha(2)-HN(3): (i, i+1) Ha(3)-HN(4): (i, i+1) HN(2)-HN(3): (i, i+1) HN(3)-HN(4): (i, i+1)

  14. Test of compliance of molecular models with ideal turn criteria H-bondpresent Not present Marginal H-bonds present because of larger deviations from linearity Chawner & Morikis, in preparation

  15. Molecular models: measured distances corresponding to characteristic NOEs Ideal b-turns Idealg-turns

  16. Relative classification of NOE intensities We classified the inter-proton distances as corresponding to strong, medium, weak and very weak NOE intensities: 1.8-2.6 Å = strong 2.7-3.5 Å = medium 3.6-4.4 Å = weak 4.5-5.0 Å = very weak b-turns 1.8 Å: sum of van der Waals radii with some overlap Chawner & Morikis, in preparation

  17. Relative classification of NOE intensities We classified the inter-proton distances: 1.8-2.6 Å = strong 2.7-3.5 Å = medium 3.6-4.4 Å = weak 4.5-5.0 Å = very weak g-turns

  18. Solution of Karplus equation: calculations of characteristic 3J(HN-Ha)-coupling constants b-turns g-turns Chawner & Morikis, in preparation

  19. b-sheet a-helix We classified the turn’s 3J(HN-Ha)-coupling constants as stronger or weaker relative to itself, so that the different types can be differentiated comparatively b-turns g-turns Caution: small variations in j-torsion angles result to very large variations in j-coupling constants. In general, the use of j-coupling constants is not as helpful as NOE intensity patterns and connectivities. Chawner & Morikis, in preparation

  20. Conclusions • NOE intensity patterns and connectivities can be used to distinguish turn type without a complete structure determination. We have created small NOE intensity databases that discriminate Type I, I’, II, II’, and VIII b-turns, and direct and inverse g-turns. • Caution: Classification of strong, medium, weak, and very weak NOEs is relative. • Small variations of the characteristic j-torsion angles introduce very large variations in the 3J(HN-Ha)-coupling constant values, sometimes spanning the whole range of possible solutions for the Karplus equation and the whole allowed region of the Ramachandran plot. • Why? the small variations in j-torsion angles are owed to the dynamic character of turns in proteins and peptides and to conformational averaging. • Overall, NOEs are more useful than J-coupling constants.

  21. Acknowledgements • Dr. Dimitrios Morikis • Li Zhang • Coordinators of BRITE Program • Fellow BRITE students

  22. Trans q=180o j=-120o C C = = O O C C = = O O N N H H H H b b C C C C = = O O C C = = O O N N H H b b C C H H q=-90o j=-30o Cis q=0o j=60o Newman Projection Solution of Karplus equation 3J(HN-Ha) q=90o j=150o j

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