2012 - 3D Structures of Biological Macromolecules

1. 2012 - • 3D Structuresof Biological Macromolecules • Part 2: A Case Study in Structural Bioinformatics – • C-H…-Interactions in Proteins Jürgen Sühnel jsuehnel@fli-leibniz.de Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena / Germany Supplementary Material: www.fli-leibniz.de/www_bioc/3D/

2. C-H...-Interactions in Proteins -system C | H

3. C-H...-Interactions:Well-known in smallmolecules Kooijman et al, Acta Cryst. C. 2000, 56, 481-483 Benzene and analogous compounds dissolve exothermically in chlorofom. M. Tamres. Aromatic compounds as donor molecules in hydrogen bonding. J. Am. Chem. Soc.1952, 74, 3375-3378.

4. C-H...-Interactions in Proteins Exceptfor a fewreports on theoccurrenceof C-H...-interactions in selectedstructures therehasbeennosystematicstudyforproteins.

5. C-H...-Interactions in Proteins:Database Crystal structures with a resolution of 3.0 Å or better R-factor: 25% or lower Minimal chain length: 40 Maximum amino acid identity: 25% PISCES web server

6. C-H...-Interactions in Proteins

7. C-H...-Interactions in Proteins

8. C-H...-Interactions in Proteins

9. C-H...-Interactions in Proteins: GeometricalSelection Distance C-X< 4.5 Å Distance Hp-X < 1.2 Å (aro), 1.0 Å (non-aro) Angle C-H-X > 120 º

10. C-H...-Interactions in Proteins: Aims Analysis of C-H...-interactionsoccurring in proteins • Whichinteractionssatisfythegeometricalcriteriaadopted? • Whichdonoratomtypesandwhich -systemsareinvolved ? • Where in proteins do C-H... -interactionsoccur ? • Are thereanysecondarystructureandneighbourhoodrelations ?

11. C-H...-Interactions in Proteins dCX fraction < 4.0 Å 69% < 4.1 Å 78% < 4.2 Å 86% < 4.3 Å 92% < 4.4 Å 96% dCX 3.74 – 3.93 Å

12. C-H...-Interactions in Proteins Donor / acceptor Aro- Am- Ac- Arg- Total C-H 1,832 437 568 712 3,549 (1,01) (0,34) (0,31) (0,99) Cali-H14,487 2,638 3,861 2,584 23,570 (1,95) (0,51) (0,52) (0,88) Caro-H2,687 361 608 312 3,968 (3,43) (0,66) (0,77) (1,0) Total 19,006 3,436 5,037 3,608 31,087 Donors C-H - total number of aa plus number of Gly Cali-H - all alipahtic C-H groups except for C-H Caro-H - all aromatic C-H groups Acceptors Aro - aromatic ring His, Phe, Trp, Tyr Am - amide group Asn, Gln Ac - carboxylate group Asp, Glu Arg - amidinium group Arg Non-redundant database of 1154 protein chains with 285,794 amino acids

13. C-H...-Interactions in Proteins

14. C-H...-Interactions in Proteins

15. The 15 interactions identified occur in all parts of the protein. Some of them are completely buried and others are partially exposed to the solvent. B-eye-lens-crystallin (1amm, 1.2 Å)

16. Interactions are referred to as local if the sequence distance is smaller than 10. 41% of C-H...-interactions are local.

17. C-H...-Interactions in Proteins • 63% of this interaction type are local. • 89% of the –3 peak interactions occur in helices. • This interaction may be a major stabilizing element • in -helices.

18. cytochrome P450 (1bu7)

19. L-aminopeptidase D-Ala-esterase/amidase (1b65)

20. C-H...-Interactions in Proteins M. Brandl, M. S. Weiss, A. Jabs, J. Sühnel, R. Hilgenfeld. C-H... interactions in proteins. J. Mol. Biol.2001, 307, 357-377

24. C-H...-Interactions in Proteins C-H... and C-H...O/N interactions are opportunistic ???

25. C-H...-Interactions in Proteins • Most prominent are interactions between aliphatic or aromatic C-H donors and aromatic acceptors. • About three quarters of all Trp-rings, half of all Phe- and Tyr-rings and a quarter of His-rings are involved as acceptors in C-H...-interactions. • On the donor side there is a preference for aromatic C-H groups, for prolines and for the long extended aliphatic amino acids Lys, Arg and Met. • C-H...-interactions involving aromatic groups either as donor or as acceptor are found mostly in the interior of the protein. The more hydrophilic the participating groups are, the closer to the surface are the interactions located. • It is likely that C-H...-interactions contribute significantly to overall protein stability. M. Brandl, M. S. Weiss, A. Jabs, J. Sühnel, R. Hilgenfeld. C-H... interactions in proteins. J. Mol. Biol.2001, 307, 357-377.

26. More Hydrogen Bonds forthe (Structural) Biologist

27. More Hydrogen Bonds forthe (Structural) Biologist A general concept of hydrogen bonding in proteins is emerging. This concept involves not only N-H and O-H donor groups, but also C-H, and not only N and O as acceptor groups, but also -systems. We postulate that the incorporation of the entirety of these interactions leads to a more complete description of protein structures. M. S. Weiss, M. Brandl, J. Sühnel, D. Pal, R. Hilgenfeld. More hydrogen bonds for the (structural) biologist. Trends Biochem. Sci. 2001, 26, 521-523.

28. More Hydrogen Bonds forthe (Structural) Biologist M. S. Weiss, M. Brandl, J. Sühnel, D. Pal, R. Hilgenfeld. More hydrogen bonds for the (structural) biologist. Trends Biochem. Sci. 2001, 26, 521-523.

29. More Hydrogen Bonds forthe (Structural) Biologist phospholipase C (PDB code: 1ah7) “Classical” N-H...O (helix192-204) C-H...O (LYS153-Val149) C1-H... (Trp238-Phe94) N-H... (Ser63-Tyr61) M. S. Weiss, M. Brandl, J. Sühnel, D. Pal, R. Hilgenfeld. More hydrogen bonds for the (structural) biologist. Trends Biochem. Sci. 2001, 26, 521-523.

30. More Hydrogen Bonds forthe (Structural) Biologist • Incorporation of the results obtained in • structure prediction and refinement programs • Identification of examples for the structural and functional relevance of • the new interaction types M. S. Weiss, M. Brandl, J. Sühnel, D. Pal, R. Hilgenfeld. More hydrogen bonds for the (structural) biologist. Trends Biochem. Sci. 2001, 26, 521-523.