1. 3D Structures of Biological Macromolecules Part 6: A Case Study in Structural Bioinformatics – C-H…  -Interactions in Proteins Jürgen Sühnel jsuehnel@fli-leibniz.de Supplementary Material: www.fli-leibniz.de/www_bioc/3D/ Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena / Germany

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

3. C-H...  -Interactions: Well-known in small molecules 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 Except for a few reports on the occurrence of C-H...  -interactions in selected structures there has been no systematic study for proteins.

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

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

9. C-H...  -Interactions in Proteins: Aims Analysis of C-H...  -interactions occurring in proteins Geometry Geometry Which donor atom types and which  -systems are involved ? Which donor atom types and which  -systems are involved ? Where in proteins do C-H...  -interactions occur ? Where in proteins do C-H...  -interactions occur ? Are there any secondary structure and neighbourhood relations ? Are there any secondary structure and neighbourhood relations ?

10. C-H...  -Interactions in Proteins d CX fraction < 4.0 Å69% < 4.1 Å78% < 4.2 Å86% < 4.3 Å92% < 4.4 Å96% d CX 3.74 – 3.93 Å

11. C-H...  -Interactions in Proteins Donor / acceptorAro-  Am-  Ac-  Arg-  Total C  -H 1,832 437 568 712 3,549 (1,01) (0,34) (0,31)(0,99) C ali -H14,4872,6383,8612,58423,570 (1,95)(0,51)(0,52)(0,88) C aro -H 2,687 361 608 312 3,968 (3,43) (0,66) (0,77) (1,0) Total19,0063,4365,0373,60831,087 Non-redundant database of 1154 protein chains with 285,794 amino acids Acceptors Aro -aromatic ringHis, Phe, Trp, Tyr Am -amide groupAsn, Gln Ac - carboxylate groupAsp, Glu Arg - amidinium groupArg Donors C  -H -total number of aa plus number of Gly C ali -H -all alipahtic C-H groups except for C  -H C aro -H - all aromatic C-H groups

12. C-H...  -Interactions in Proteins

14. 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)

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

16. 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. C-H...  -Interactions in Proteins

17. cytochrome P450 (1bu7)

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

19. 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

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

24. 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. 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.

25. More Hydrogen Bonds for the (Structural) Biologist

26. 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. 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.

27. More Hydrogen Bonds for the (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.

28. More Hydrogen Bonds for the (Structural) Biologist C  -H...O (LYS153-Val149) C  1 -H...  (Trp238-Phe94) N-H...  (Ser63-Tyr61) “Classical” N-H...O (helix192-204) phospholipase C (PDB code: 1ah7) 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 for the (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. Incorporation of the results obtained in structure prediction and refinement programs Global Phasing Ltd. (U.K.) ??? Identification of examples for the structural and functional relevance of the new interaction types