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(-) General Aspects

In protein structures the planar peptide bond occurs predominantly in the trans conformation
[Ramachandran & Sasisekharan, Adv. Prot. Chem. 23(1968)283]. Proline residues have a rela-
tively high intrinsic probability of having the cis conformation. The cis/trans-isomerisation
of the peptide bonds on the N-terminal side of proline residues plays an important role in the
folding process of a protein [Schmid & Baldwin, Proc. Nat. Aca. Sci. USA 75(1978)4764]. The
isomerisation of the peptide bond preceeding proline residues may limit the refolding rate of
proteins in vitro and in vivo [Brandts et al. Biochemistry 14(1975)4953, Steinmann et al. J.Biol.
Chem. 266(1991)1299, Fischer & Schmid Biochemistry 29(1990)2205, Schmid Annu.Rev.Bio-
phys. Biomol. Struct. 22(1993)123].
A class of enzymes, the peptidyl-prolyl cis/trans isomerases (PPIases) are able to catalyse pro-
tein folding by accelaration the isomerisation of peptidyl-prolyl bonds [Schmid et al. Adv.Prot.
Chem. 44(1993)25].
An overwiew "Fit for Live? Evolution of chaperones and folding catalysts parallels the develop-
ment of complex organisms" is given on this page.

The cis/trans isomerisation of a peptidyl-prolyl bond leads to a different propagation direction
of the polypeptide backbone in each isomer.
"The cis/trans isomerisation at the peptide bond N-terminal to proline resembles a molecular
switch with the following characteristics:
1. There are two switch positions, other positions are unstable
2. The energy needed to operate the switch is high on the energy scale for bio-
logical recognition processes.
3. Operation of the switch leads to an amplification of an effect at the place
where the signal arrives. In the case of the proline switch this amplification
manifests itself chiefly in the form of a mechanical movement, which may
be the movement of a segment of the protein backbone.
4. Isomerisatin catalysts such as the PPIases act as variable components for
reducing the switch resistant, and in the presents of many switches they
assure extra selectivity. The switching resistance (rotational barriers) is
controlled by varying the enzyme concentration and the selection of switching
elements by means of the enzyme specificy."

[G. Fischer, Angew. Chem. Int. Ed. Engl. 33(1994)1415]

(-) Peptidyl-prolyl Bonds in Peptides and Proteins

Basic information about the amino acid proline can be obtained from 'The Principles of
Protein Structure' Course at the Birkbeck College (University of London)

The following data on the occurence of cis prolyl bonds in proteins were derived from a set
of non-redundant protein structures from the Brookhaven PDB. For analysing the structural
parameters (peptide bond angle omega, secondary structure) the program package Iditis
(Oxford Molecular, Version 2.1, data base 9.0) was used.

The distribution of the peptide bond angle omega for peptidyl-prolyl bonds in proteins
shows significant peaks at 180 deg. (trans peptide bond) and 0 deg. (cis peptide bond).

There are some differences between the data on the cis content in Xaa-Pro bonds (Xaa:
amino acid N-terminal to proline) derived from different data bases [Stewart et al. J.Mol.
Biol. 214(1990)253, McArthur & Thornton J.Mol.Biol. 218(1991)397, Iditis 6.0, Iditis 9.0,
data from the actual Brookhaven PDB will be added as soon as possible]. McArthur and
Thornton found three types of peptidyl-prolyl bonds which do not occur in cis conformation
(Cys, Met, Trp). Stewart et al. showed only Trp-Pro to take no cis conformation. From the
Iditis 2.1, data base 9.0 data for all amino acids were received. In some cases the cis content
decreases from 1990 to 1995 (Arg, Leu), in the most cases deviations show no regularity.
These results teach a careful approach to statistical data derived from the Brookhaven
PDB.

Investigations on 'peptidyl-prolyl bonds and secondary structure' show, that trans petidyl-
prolyl bonds are distributed in all types of secondary structure. Cis peptidyl are found pri-
marily in bends and turns, suggesting a specific structural role for this type of bonding.
[Stewart et al. J.Mol.Biol. 214(1990)253].

From NMR investigations on proline containig peptides results a correlation between
the cis content of peptidyl-prolyl bonds in peptides and proteins [Reimer et al. J.Mol.Biol.
279(1998)449].

(-) Peptidyl-prolyl Cis/Trans Isomerases (PPIases)

(-) Definition

Peptidyl-prolyl cis/trans isomerases are enzymes that catalyse the isomerisation of
peptidyl-prolyl bonds. Three families of proteins with PPIase activity are known:

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

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

Parvulins

(-) Cyclophilins in the Brookhaven PDB

From the following representatives the three dimensional structures are known:

1ak4 HUMAN CYCLOPHILIN A BOUND TO THE N-TERMINAL DOMAIN OF HIV-1 CAPSID PROTEIN
1clh CYCLOPHILIN (NMR, 12 STRUCTURES)
1cyn CYCLOPHILIN B COMPLEXED WITH [D-(CHOLINYLESTER)SER8]-CYCLOSPORIN
1fgl CYCLOPHILIN A COMPLEXED WITH A FRAGMENT OF HIV-1 GAG PROTEIN
1lop CYCLOPHILIN A COMPLEXED WITH SUCCINYL-ALA-PRO-ALA-P-NITROANILIDE
1mik CYCLOPHILIN A
1oca HUMAN CYCLOPHILIN A, UNLIGATED, NMR, 20 STRUCTURES
1rmh RECOMBINANT CYCLOPHILIN A FROM HUMAN T CELL
2cpl CYCLOPHILIN A
2cyh CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE ALA-PRO
2rma CYCLOPHILIN A (E.C.5.2.1.8) COMPLEXED WITH CYCLOSPORIN A
2rmb CYCLOPHILIN A (E.C.5.2.1.8) COMPLEXED WITH DIMETHYL-CYCLOSPORIN A
2rmc CYCLOPHILIN C COMPLEXED WITH CYCLOSPORIN A
3cyh CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE SER-PRO
3cys CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A (NMR, 22 STRUCTURES)
4cyh CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE HIS-PRO
5cyh CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE GLY-PRO

(-) FKBP's in the Brookhaven PDB

From the following representatives the three dimensional structures are known:

1bkf FK506 BINDING PROTEIN FKBP MUTANT R42K/H87V COMPLEX WITHFK506
1fap THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMYCINE
1fkb FK506 BINDING PROTEIN (FKBP) COMPLEX WITH IMMUNOSUPPRESSANT RAPAMYCINE
1fkf FK506 BINDING PROTEIN (FKBP) COMPLEX WITH IMMUNOSUPPRESSANT FK506
1fkg FK506 BINDING PROTEIN (FKBP) COMPLEX WITH ROTAMASE INHIBITOR
1fkh FK506 BINDING PROTEIN (FKBP) COMPLEX WITH ROTAMASE INHIBITOR
1fki FK506 BINDING PROTEIN (FKBP) COMPLEX WITH ROTAMASE INHIBITOR
1fkj ATOMIC STRUCTURE OF FKBP12-FK506
1fkk ATOMIC STRUCTURE OF FKBP12, AN IMMUNOPHILIN BINDING PROTEIN
1fkl ATOMIC STRUCTURE OF FKBP12-RAPAYMYCIN
1fkr FK506 AND RAPAMYCIN-BINDING PROTEIN (FKBP12) (NMR, 20 STRUCTURES)
1fks FK506 AND RAPAMYCIN-BINDING PROTEIN (FKBP12) (NMR)
1fkt FK506 AND RAPAMYCIN-BINDING PROTEIN (FKBP12) (NMR)
1nsg THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12- RAPAMYCINE
1pbk HOMOLOGOUS DOMAIN OF HUMAN FKBP25
1rot STRUCTURE OF FKBP59-I, THE N-TERMINAL DOMAIN OF A 59 KDA FK506-BINDING PROTEIN
1rou STRUCTURE OF FKBP59-I, THE N-TERMINAL DOMAIN OF A 59 KDA FK506-BINDING PROYEIN
1tco TERNARY COMPLEX OF A CALCINEURIN A FRAGMENT, CALCINEURIN B, FKBP12

(-) Mechanistical Aspects of the Cis/Trans Isomerisation

The elementary step in the catalysis of the cis/trans isomerisation of a peptidyl-prolyl
bond is a reduction in the double bond character of the C-N bond. Some plausible re-
action mechanisms are present in this scheme [G. Fischer, Angew. Chem. Int. Ed. Engl.
33(1994)1415]. Details of these mechanisms by which PPIase catalyzed prolyl isomeri-
sation occur still remain to be clarified.
In general, the C-N amide bond is conjugated with the carbonyl group. The double bond
character of the C-N bond results from this conjugation. Any factors which can weaken
the double bond character of the amide bond are expected to accelerate the isomerisation.

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?