Cyclophilins (Cyp) - inhibited by Cyclosporin A (CsA)

FK506 Binding Proteins (FKBP's) - inhibited by FK506

Parvulins

Experimental studies of intramolecular catalysis of amide isomerisation in model systems
shows an evidence for a hydrogen bond between the side chain and the prolyl imide
nitrogen in a cis peptidomimetic [Cox et al. J.Am.Chem.Soc. 119(1997)2307].
MO and force field calculations on proline containing dipeptides shows, that the C-ter-
minal amide proton interacts favorably with the imide nitrogen of the proline moiety.
This calculations indicate a cis/trans barrier lowering of 1.4 kcal/mol due to intramole-
cular catalysis [Fischer & Karplus J.Am.Chem.Soc. 116(1994)11931].
Folding experiments and mutagenic analysis of dihydrofolate reductase show that the rate
limiting step of refolding, the isomerisation of the proline 66 residue can be intramole-
cularly ctalyzed by the side chain of the arginine 44 residue. The guanidinium group NH2
nitrogen of this residue forms a hydrogen bond to the imide nitrogen of the proline
residue.
Metal ions (Lewis Acids) in small amounts can catalyse the the isomerisation of amides.
The side chain of substituted prolines acts as a binding site for Cu(II) ions to catalyse the
prolyl isomerisation [Cox et al. J.Am.Chem.Soc. 118(1996)5332].
The data discussed above indicate a general acid catalysis of the cis/trans isomerisation
of a peptidyl-prolyl bond (equation 2 in the scheme).

In the structure of the PPIase cyclophilin compexed with a substrate, the guanidinium
group of an arginine in the active site can form a hydrogen bond with the lone pair
electrons of the peptidyl-prolyl bond in the substrate peptide. The structure of different
complexes of cyclophilin with inihibitors, substrate peptides and protein fragments may
provide insight into the mechanism of the enzymatic catalysis of the prolyl isomerisa-
tion.

1. The cyclophilin-substrate complex:

The first three figures show the recombinant cyclophilin A from human T cell (Cyp)
complexed with the model peptide Suc-Ala-Ala-Pro-Phe-pNA (AAPF);
PDB code: 1rmh

Figure 1: The Cyp-AAPF complex

Figure 2: The active site (proline binding pocket, Conolly surface)
of the Cyp-AAPF complex

Figure 3: The active site (proline binding pocket, Conolly surface transparent)
of the Cyp-AAPF complex

The following figures shows the recombinant cyclophilin A from human T cell (Cyp)
complexed with a fragment of the HIV-1 GAG protein (PDB code 1fgl). This protein
play an essential role in the replication of the HIV (movie from the Microbiology Video
Library at the Department of Microbiology & Immunology, University of Leicester).

Figure 4: The HIV-1 GAG-fragment - Cyp complex

Figure 5: The active site (proline binding pocket, Conolly surface, the fragment
of the HIV-1 GAG protein is shown as a yellow colored solid ribbon)
of this complex

Figure 6: The active site (proline binding pocket, Conolly surface transparent)
of this complex

The side chain of the substrate proline sits in the hydrophobic pocket made up of the side
chains of Phe60, Met61, Phe113, Ile122 (red colored region on the Conolly surface). The
Arg55 residue hydrogen bonds to the lone pair electrons of the amide nitrogen. Zhao & Ke
[Biochemistry 35(1996)7356] proposed on the basis of the crystal structure, that the hydro-
gen bond deconjugates the resonance of the amide bond during catalysis. The C-terminal
region of the proline interacts with hydrophilic amino acids (Arg55, His126, blue colored
region on the Conolly surface). These facts provide the mechanism shown in equation 2 in
the scheme discussed mentioned above.
The mutant cyclophilin protein in which the arginine residue is replaced by alanine (R55A)
shows dramatically lower PPIase activity below 1% of the wild type enzyme [Zydowski
et al. Protein Science 1(1992)1092]. If the histidine residue in the active site is replaced
by glutamine (H126Q), the PPIase activity decreases (0.5% of wild type activity) [Zydows-
ki et al.].
A general acid catalysis of the enzymatic cis/trans isomerisation (for cyclophilin) by Arg55
is not in conflict with the observed pH independence [Harrison & Stein Biochemistry 29
(1990)3813]. The Arg55 is expected to be protonated at a pH range of 5.5-9.0.

2. The position of Arg55 in different complexes
[derived from Zhao & Ke ; Biochemistry 35(1996)7356]

The structures of the cyclophilin complexed with the dipeptides Ala-Pro, Ser-Pro, His-Pro
and Gly-Pro (2cyh, 3cyh, 4cyh, 5cyh) are very similar to the unligated protein (2cpl). The
superposition of the amino acids forming the proline binding site from uncomplexed cyclo-
philin (2cpl) and the protein ligated with the Ala-Pro (2cyh) dipeptide revealed only small
displacements (Fig. 7)

Figure 7: Superposition of the active sites in Cyp and the complex Cyp-AlaPro
(2cpl: red, 2cyh: yellow)

In all complexes the two carboxy-terminal oxygens of the dipeptide form hydrogen bonds to
the Arg55 (Fig. 8). The position of the Arg55 in the cyclophilin complexed with cyclosporin A (2rma) is very similar to the structures discussed above (Fig. 9).

Figure 8: Superposition of all dipeptide-Cyp structures
(dipeptides [stick] and Arg55 [ball & stick] colored by atoms)

Figure 9: Superposition of the Cyp-AlaPro (yellow) and the Cyp-cyclosporin A complex (red)

The overall binding of the dipeptides to cyclophilin also closely resembles that of the substrate
tetrapeptide Suc-AlaAlaProPhe-pNA (AAPF) and the binding region of the HIV-1 GAG pro-
tein. In these cases, the residue Arg55 form one hydrogen bond to the carbonyl oxygen an one to
the imide nitrogen atom of the substrate proline (Fig. 10).

Figure 10: Superposition of the two Cyp-substrate structures
(Cyp-AAPF yellow, Cyp-HIV-1 GAG protein red)

In comparision to the dipeptide binding the hydrogen bonding pattern of the proline, the orienta-
tion of the proline in the proline binding pocket and the conformation of the side chain of Arg55
is changed (Fig.11).

Figure 11: Superposition of the Cyp-AAPF (red) and the Cyp-AlaPro
(yellow, proline is colored by atoms)

Only in the cyclophilin-substrate structures, the guanidinium group of Arg55 interacts via hydro-
gen bond with the imide nitrogen of the substrate proline.

The similarity between the orientation of the active side residues in cyclophilin, the cyclophilin-
cyclosporin A complex (inhibitor) and the dipeptide complexes imply these questions:

"Are dipeptides inhibitors for cyclophilins or do they have a different catalytic mechanism from
the substrate-petides AAPF and HIV-1 GAG fragment? [Zhao & Ke]"

Which role play the amino acid Arg55 in the catalytic mechanism of this enzyme?
Which role play the amino acid His126 in the catalytic mechanism of this enzyme?