falciparum arginase has a strong depen-dency between trimer formation, enzyme activity and metal co-ordination.. falciparum arginase thus appears to be an obligate trimer and interfering
Trang 1is mediated by a novel inter-monomer salt-bridge
between Glu295–Arg404
Gordon A Wells1, Ingrid B Mu¨ller2, Carsten Wrenger2 and Abraham I Louw1
1 Department of Biochemistry, University of Pretoria, South Africa
2 Department of Biochemical Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
The polyamines putrescine, spermine and spermidine
are near ubiquitous polycationic aliphatic amines
required for a number of essential cellular processes,
particularly in organisms undergoing rapid
prolifera-tion [1–3] These processes involve the stabilizaprolifera-tion of
macromolecules [4–6] and progression through the cell
cycle [7] Additionally, certain secondary metabolites,
such as the post-translationally modified amino acid,
hypusine [1,8], and the glutathione analogue,
trypano-thione, in Trypanosoma [9], require polyamines for their biosynthesis Polyamine biosynthesis has been identified as a possible therapeutic target for various parasitic diseases [10,11], cancers [12] and even HIV via the requirement for hypusine [13] Putrescine is synthesized by the decarboxylation of ornithine (orni-thine decarboxylase) and serves as substrate for the addition of aminopropyl groups to form spermidine and spermine The aminopropyl groups are donated
Keywords
arginase; malaria; metal; modelling; trimer
Correspondence
A I Louw, Department of Biochemistry,
University of Pretoria, Lynwood Road,
Pretoria 0002, South Africa
Fax: +27 (0)12 362 5302
Tel: +27 (0)12 420 2480
E-mail: braam.louw@up.ac.za
(Received 27 January 2009, revised 26
March 2009, accepted 23 April 2009)
doi:10.1111/j.1742-4658.2009.07073.x
A recent study implicated a role for Plasmodium falciparum arginase in the systemic depletion of arginine levels, which in turn has been associated with human cerebral malaria pathogenesis Arginase (EC 3.5.3.1) is a multimeric metallo-protein that catalyses the hydrolysis of arginine to ornithine and urea by means of a binuclear spin-coupled Mn2+ cluster in the active site
A previous report indicated that P falciparum arginase has a strong depen-dency between trimer formation, enzyme activity and metal co-ordination Mutations that abolished Mn2+ binding also caused dissociation of the trimer; conversely, mutations that abolished trimer formation resulted
in inactive monomers By contrast, the monomers of mammalian (and therefore host) arginase are also active P falciparum arginase thus appears
to be an obligate trimer and interfering with trimer formation may there-fore serve as an alternative route to enzyme inhibition In the present study, the mechanism of the metal dependency was explored by means of homology modelling and molecular dynamics When the active site metals are removed, loss of structural integrity is observed This is reflected by a larger equilibration rmsd for the protein when the active site metal is removed and some loss of secondary structure Furthermore, modelling revealed the existence of a novel inter-monomer salt-bridge between Glu295 and Arg404, which was shown to be associated with the metal dependency Mutational studies not only confirmed the importance of this salt-bridge in trimer formation, but also provided evidence for the indepen-dence of P falciparum arginase activity on trimer formation
Abbreviations
NP, constant number of atoms and constant pressure; NPT, constant number of atoms, constant pressure and temperature; PfArg, Plasmodium falciparum arginase.
Trang 2from decarboxylated S-adenosylmethionine, the
prod-uct of S-adenosylmethionine decarboxylase [2,14]
Arginase (EC 3.5.3.1) catalyses the hydrolysis of
l-arginine to l-ornithine and urea The arginase fold is
part of the ureohydrolase superfamily, which also
includes agmatinase [15,16], histone de-acetylase and
acetylpolyamine amidohydrolase [17] Agmatine is
formed by decarboxylation of arginine (arginine
decar-boxylase) and is converted by agmatinase to putrescine
and urea Arginase is thus part of one of two
alterna-tive biosynthetic routes to putrescine Polyamine
bio-synthesis enzymes characterized in the malaria
parasite, Plasmodium falciparum, include the
bifunc-tional S-adenosylmethionine decarboxylase⁄ ornithine
decarboxylase [18–22], spermidine synthase [23] and
arginase [24] In P falciparum, the agmatinase route
to putrescine has not been identified, thus making
arginase the sole biosynthetic route to putrescine in
the malaria parasite [24]
In mammals, two isoforms of arginase have been
identified: arginase I is cytosolic and largely hepatic
where it catalyses the final step of the urea cycle
[25,26]; arginase II is nonhepatic and occurs in the
mitochondrial matrix [27–29] and is involved in
homeostasis of ornithine for the further production of
proline and glutamate [30] Both isoforms have been
implicated in regulating NO biosynthesis as a result of
competition for the common substrate arginine with
inducible NO synthase [31] In bacteria, there is a
single arginase isoform, whereas more than one exists
in yeast [32] The yeast isoforms have been linked
to glutamate accumulation during germination and
asexual spore development [33,34]
Arginase is a multimeric metallo-enzyme with a
binuclear spin-coupled Mn2+cluster in each active site
that is restricted to a single a⁄ b monomer The metal
cluster is located in a 15 A˚ deep cleft with the Mn2+
atoms 3.3 A˚ apart and bridged by a solvent molecule
[35] Structures from the bacteria Bacillus caldovelox
[36,37], human arginase I [38] and II [39], rat arginase
I [35,40] and Thermus thermophilus [Protein Data
Bank (PDB) codes: 2EF4, 2EF5 and 2EIV] have been
determined In the mechanism proposed by Kanyo
et al [35], the metal bridging solvent is an activated
hydroxyl, which attacks the guanidium carbon of
arginine, followed by collapse of the tetrahedral
inter-mediate to release ornithine and urea However, ab
initio modelling of the active site suggests that the
bridging solvent may be a neutral water molecule
instead [41]
Eukaryotic arginases are trimeric, whereas bacterial
arginases are hexameric [42] However, the trimeric
arginase from Saccharomyces cerevisiae forms a
regulatory complex with trimeric ornithine transcarba-moylase, thus forming a hexameric complex [43] In mammals, monomers retain substantial activity if tri-mer formation is disrupted [44,45] In recent studies, disrupting metal binding has no reported effect on the quaternary structure [40,46,47] However, previously, it was reported that oligomerization of human arginase I could be disturbed by chelating out Mn2+ but sub-stantially similar kinetics could be restored to nylon-immobilized monomers after reincubation with Mn2+ [48,49] Removal of the active site metals in yeast not only abolishes enzyme activity, but also affects the maintenance of the quaternary structure and sensitivity
to temperature [43,50]
To date, the strongest metal dependency has been reported for the arginase from P falciparum, where mutations that abolish metal binding or removal of the metal ions cause dissociation of the trimer into inactive monomers Conversely, a mutation that abol-ishes a conserved inter-monomer interaction located away from the active site results in inactive monomers [24] These host–parasite differences may thus provide
a novel non-active site based strategy for inhibiting
P falciparum arginase (PfArg) Essentially, disturbing trimer formation may serve as a novel means of inhib-iting PfArg Thus, the mechanism of this structural dependency was investigated by homology modelling and molecular dynamics, aiming to establish an
in silicosystem for exploiting this dependency
Results
Sequence alignment and homology modelling Searching online Plasmodium genome resource, moDB [51], revealed the arginase sequences for Plas-modium vivax, PlasPlas-modium yoelii, PlasPlas-modium knowlesi and Plasmodium berghei, in addition to the previously characterized PfArg From the automated alignments, two parasite-specific inserts were revealed in the vari-ous Plasmodium arginases (Fig 1) In both reference alignments, the positions of the inserts do not differ markedly In the final model of the study, insert 1 is predicted to run from residues 77–151 (75 residues), and insert 2 from residues 377–388 (12 residues) The exact positions vary slightly depending on the align-ment used for modelling Insert 1 varies considerably
in sequence and length between different Plasmodium species, ranging from approximately 100 residues (P vivax) to only 15 residues (P berghei) It is pre-dicted to lie between the second b-strand and second a-helix of the model on the outer edge of the trimer
By contrast, insert 2 is highly conserved in length and
Trang 3sequence in all Plasmodium species Insert 2 is located
between the last b-strand and the last a-helix The
sequence identity between the P falciparum and
tem-plates was approximately 35%, 30% and 27%,
respec-tively, for the bacterial, rat and human arginases Even
a slight difference in the alignment used for insert 2
was found to have a significant effect on its
conforma-tion Modelling with insert 2 shifted one residue
upstream (fugue derived alignment; see Experimental
procedures) caused the insert to fold away from
the trimer interface, interacting with its respective
monomer (Fig 2)
The model preserves standard active site residues
observed in other arginase structures All Mn2+
coor-dinating residues (discussed below) previously
identi-fied are conserved in the model The only substitutions
are in second shell ligands when compared with the
bacterial template, where Ser176 and Glu268 (B
cald-ovelox) are replaced by Asp272 and Asp365 (P
falci-parum), respectively Residues implicated in substrate
binding are also highly conserved There is only one
conservative substitution compared to the mammalian
templates, and none compared to the bacterial
tem-plate Thr135 (rat) is replaced by Ser227 in the model
In the model, Mg2+ was modelled instead of Mn2+
as a result of limitations of the forcefield, which
was not parameterized for Mn2+ (see Experimental
procedures)
Visual inspection of the model suggested that a
novel inter-monomer salt-bridge forms between
Glu295x and Arg404y (where subscripts designate
dif-ferent monomers) (Fig 3) In multiple sequence
alignments, Glu295 aligns with conserved acidic
resi-dues in the bacterial and mammalian templates
P falciparum Glu295 aligns with an Asp in mam-mals (human arginase II: Asp223; rat arginase I: Asp204), fungi and bacteria (B caldovelox arginase: Asp199) In the other Plasmodium species, Glu295
Fig 1 Alignment used for modelling P falciparum (pfam), H sapiens (human), R norvegicus (rat) and B caldovelox (bacc) The positions of the Plasmodium-specific inserts are indicated Identical residues are shaded dark grey, and similar residues indicated by lighter shades Heli-ces are indicated by rods, and b-strands by arrows.
Fig 2 Effect of alignment on conformation of insert 2 When mov-ing the insert one residue upstream, the insert folds away from the trimer interface (yellow) compared to making contact (red) The active site Mg 2+ atoms are indicated in green Monomers are dis-tinguished by different shades of blue The image was generated using PYMOL.
Trang 4aligns either with Asp (P yoelii and P berghei) or
Glu (P knowlesi and P vivax) The only exception is
in plants, where Glu295 aligns with Ser instead
(Arabidopsis thaliana arginase I: Ser247) In the
model, Glu295 forms an interaction with the
adjacent monomer via partner residues that do not
align in sequence in the mammalian and bacterial
templates In mammalian arginases, the Asp223⁄ 204x
(rat arginase I⁄ human arginase II) cognate forms an
inter-monomer salt-bridge with Arg308⁄ 327y This
salt-bridge nucleates considerable inter-monomer
interactions, characterized by an S-shaped C-terminus
[35,39], which is absent in the Plasmodium sequences
Arg308 from rat arginase I aligns with Ile in
Plasmodium (408: P falciparum; 368: P knowlesi;
436: P vivax; 353: P berghei; 376: P yoelii) The
P falciparum Arg404y salt-bridge partner to Glu295x
aligns with small and⁄ or hydrophilic residues in
other organisms (e.g Ser, Thr, Cys, Ala and Glu)
In the bacterial structure, the Asp199x cognate forms
an inter-monomer bridge with Glu256y that is
medi-ated either by urea or by free arginine, depending
on the crystallization conditions [36]
To determine other possible interactions, the salt-bridge analysis tool of vmd [52] was employed to search for all possible salt-bridges in the protein, using co-ordinates prior to sampling All salt-bridges with a hydrogen bond donor⁄ acceptor distance less than 3.2 A˚ were identified Only one other interaction between adjacent monomers was found between Glu400x and Lys340y However, this interaction was not stable during molecular dynamics This instability was observed both with and without the active-site metal, Mg2+ Thus, this interaction is likely to be only
of secondary importance in maintaining quaternary structure, and attention was focused on the Glu295x– Arg404yinteraction instead
Protein stability Before proceeding with detailed analysis, it was sary to ensure that gross changes to the protein neces-sitated by the modelling dificulties would not compromise the interpretation of the results The omis-sion of parts of the protein is potentially problematic
in that it introduces an unnatural chain break and therefore potential instability The deletion of insert 1 creates a protein fragment on the outer edge of the tri-mer complex that does not interact extensively with any neighbouring monomers, and largely makes intra-monomer contacts This fragment was stable for at least 50 ns of simulation and, apart from the loss of some secondary structures in this region (described below), remained in contact with the rest of the protein
The protein stability of PfArg was monitored by the change in Ca rmsd during equilibration and sampling compared to the starting co-ordinates In both cases, with and without Mg2+, there is an increase in rmsd, which typically equilibrates after approximately 20 ns (Fig 4) However, without Mg2+, the Ca rmsd equili-brates at approximately 1 A˚ more than in the presence
of Mg2+, which was usually observed by 20 ns in both the constant number of atoms and constant pressure (NP) and constant number of atoms, constant pressure and temperature (NPT) ensembles and persisted up to
50 ns in the NPT simulations
The effect of removing the metal on conservation of secondary structure during sampling was also moni-tored In general, a greater loss of secondary structural integrity was observed for nonmetal systems in both the NP and NPT ensembles In the absence of Mg2+,
a complete loss of secondary structure is observed for certain elements Combining both NP and NPT ensembles gives a total of six simulations of the mono-mer, which can be used to observe any general loss of
Arg308/327
Asp204/223
Fig 3 Salt-bridges in PfArg Template residue numbers are shown
in italics (rat ⁄ human) The conserved interaction between Arg346 x
and Glu347y(P falciparum) is indicated Glu295xaligns with acidic
residues in the template structures (Asp204 ⁄ Asp223) but forms a
novel interaction with Arg404 y compared to the template residues
that interact with Arg308 ⁄ Arg327 in the C-terminus Monomers are
shown in green, light blue and mauve Template backbones are
transparent, and template salt-bridge residues are depicted
in lighter shades of red (acidic) and blue (basic) The image was
generated using VMD.
Trang 5secondary structure However, these data are not
suffi-cient to determine possible co-operative effects between
monomers The monomers⁄ chains are arbitrarily
desig-nated A, B and C In chain B of the NP simulation,
the first and second b-strands are both lost, whereas
the second half of the first a-helix is lost in chain C of
the NPT simulation The first half of the third a-helix
is also lost in chains B and A of the NP and NPT
sim-ulations, respectively All of these secondary structural
elements align with cognate elements in all of the
tem-plates The sixth helix (310) of the model is lost in
some chains of both the metal and metal-free
simula-tions Whether this element is a helix is uncertain
because it only aligns with a 310-helix in the bacterial
template In both P falciparum and the bacteria, the
N-terminal residue is a proline, which often forms the
N-terminal cap of both a-helices and 310-helices, and is
also over-represented as the helix capping residue when
followed by a b-strand [53] The absence of helical
structure in the mammalian templates indicates the
possibility of another conformation in the P falcipa-rum structure
During sampling, insert 2 moves considerably and does not retain its interaction as predicted by the origi-nal homology model prior to molecular dynamics Furthermore, there are some noticeable differences between the metal and nonmetal simulations In both the NP and NPT ensembles, insert 2 partially occupies the interface between two adjacent monomers, which is more pronounced, however, when Mg2+ is included (results not shown)
Similar effects on protein stability were observed for simulations of five mutants (Glu295 Ala, Glu295 Arg, Arg404 Ala, Glu295x Ala⁄ Arg404y Ala, Glu347 Gln)
of the PfArg model For all mutations, there is also a greater increase in rmsd (described above) compared
to the wild-type model with Mg2+ The largest increase is observed for Glu347 Gln, which is approxi-mately double that of wild-type enzyme without
Mg2+ The mutations Glu295 Ala, Glu295 Arg, Glu295x Ala⁄ Arg404y Ala show a similar increase to wild-type enzyme without Mg2+ The smallest effect is observed for Arg404 Ala, which is similar to the wild-type enzyme without Mg2+ for part of the 50 ns run (results not shown)
Stability of inter-monomer salt-bridges
In all arginases studied to date, there is a conserved inter-monomer salt-bridge represented in P falciparum
by Arg346x–Glu347y (Fig 3) The cognate salt-bridge
in the templates used is between Arg255⁄ 274 ⁄ 249x– Glu256⁄ 275 ⁄ 250y (rat, human and bacterial templates, respectively) These residues align unambiguously and the salt-bridge forms reliably during modelling Considering the established importance of this inter-action, its integrity was monitored during modelling and simulation
In the sampling runs, the Arg346x–Glu347y interac-tion was generally stable and intact for both the Mg2+ and Mg2+ -absent cases One inter-monomer bridge did break in the presence of Mg2+ in the NP ensem-ble In the NPT ensembles, the interactions remain intact with and without Mg2+ but there is an increase
in the average standard deviation of the salt-bridge dis-tance in the absence of Mg2+ (Fig 5) This suggests that the Arg346x–Glu347y interaction is susceptible to removal of Mg2+, even though the interaction remained intact
As described above, visual inspection of the homol-ogy models suggested a further interaction between Glu295x and Arg404y Although not fully formed in the homology models, the salt-bridge distance did
0 2 4 6 8 10 12 14 16 18 20
Time (ns)
0
1
2
3
4
5
6
7
8
C α deviation
(NP ensemble)
Time (ns)
0
1
2
3
4
5
6
(NPT ensemble)
Fig 4 Effect of removing Mg 2+ on backbone C a rmsd A running
average was calculated using a window of 500 frames (250 fs per
frame) With Mg 2+ , removed ( ), a greater increase is observed
than with Mg 2+ (+) included, implicating Mg 2+ in the structural
stabilization of the enzyme.
Trang 6adopt standard values (± 4 A˚) during minimization
and heating of the systems The integrity of this
inter-action was found to be more susceptible to removal of
Mg2+ than the Arg346x–Glu347y interaction Between
the NP and NPT ensembles, there are six Glu295x–
Arg404y salt-bridges In the Mg2+ -free systems, the
salt-bridge was broken in half of these (Fig 6) In the
NP ensemble, two interactions are broken between
chain A and B, and chain B and C by the end of
20 ns The third interaction was transiently broken
(chain C and A) In the NPT ensemble, only one of
these interactions (chain A and B) was broken by the
end of 50 ns
The alignment used to model insert 2 also affected
the Arg346x–Glu347y interaction In models where
insert 2 was predicted to interact at the trimer
inter-face, the interaction was broken during in vacuo
simu-lations in charmm [54] It was also observed during
simulation with charmm that models built without the
imposition of symmetry on the internal co-ordinates
tended to disturb the Arg346x–Glu347y interaction
The stability of this interaction was improved by using
models built with symmetry imposed on internal
co-ordinates (i.e with perfectly super-imposable
monomers) (results not shown)
During the simulation of the mutant enzymes, there was no effect on the integrity of Arg346x–Glu347y interaction for mutations directed at Glu295x and⁄ or Arg404y For the simulation of Glu347 Gln, however,
an interesting result was obtained: two out of three of the Glu295x–Arg404y interactions were broken during the sampling run This indicates that Glu347 Gln may also effect trimer destabilization through disturbing Glu295x–Arg404y as well by the loss of the Arg346x– Glu347y interaction Conversely, the results do not indicate that disturbing the Glu295x–Arg404y interac-tion affects the Arg346x–Glu347ysalt-bridge
Coordination geometry of Mn2+/Mg2+
Highly conserved residues are involved in a specific co-ordination pattern by donation of free electron pairs for the binuclear Mn2+ cluster in existing crys-tal structures In rat I arginase, the more deeply bur-ied ion (Mn2+A) is co-ordinated by His101, Asp124, Asp128, Asp232 and the bridging solvent in a square pyramidal geometry The respective residues in
P falciparum are His193, Asp216, Asp220 and Asp323 The second metal, Mn2+
B is co-ordinated
by His126, Asp124, Asp232, Asp234 and the bridg-ing solvent in a distorted octahedral geometry in rat I arginase (His218, Asp216, Asp323, Asp325 in
P falciparum)
0 10 20 30 40 50
Time (ns) 0.1
0.2
Arg346–Glu347 salt bridge
0
1
2
3
4
5
6
7
8
9
Fig 5 Effect of removing Mg 2+ on backbone Arg346x–Glu347y
salt-bridge A running average was calculated using a window of
500 frames (250 fs per frame) Distances for all interactions from
the NP and NPT ensembles are plotted against the right y-axis In
the NP ensemble, including Mg 2+ , one of the salt-bridges is broken
between chains A and B (d) All other salt-bridges remain intact for
both the NP and NPT ensembles with (black) and without (purple)
Mg 2+ The average standard deviation for the NPT ensemble is
plotted against the left y-axis with (black) and without (red) Mg2+.
Solid lines indicate the average sum for all three chains, and the
mean over the entire run is indicated by the dashed lines With
Mg2+removed, there is an increase in the standard deviation.
Time (ns)
0
5
10
15
20
Glu295–Arg404 salt bridge
Fig 6 Effect of removing Mg2+on backbone Glu295 x –Arg404 y salt-bridge A running average for the interaction between each chain-pair combination was calculated using a sliding window of 500 frames (250 fs per frame) The NP simulation was terminated after 20 ns In the absence of Mg 2+ (purple) in the NP ensemble, all three interac-tions were broken (chains: d, AB; r, BC; , CA), albeit that between chains CA only transiently In the NPT ensemble, only the bridge between chains A and B ( ) was broken in the absence of Mg2+ The interactions remained intact with Mg 2+ present (black).
Trang 7During modelling, the conformations adopted by the
co-ordinating residues did not entirely conform to
known crystal structures from homologues The most
notable difference is Asp323, which is expected to form
a monodentate bridging interaction between the two
ions During the simulations, it formed a bidentate
bridge instead All other expected co-ordinating atoms
were oriented close enough to interact with the ions
The only other missing interaction was that of the
bridging OH– because no attempt was made to
intro-duce the bridging solvent molecule The Mg2+–Mg2+
distance was also approximately 0.6 A˚ greater than the
known Mn2+–Mn2+ distance The Mg2+ ions
remained in the active site during the simulations and
restricted the movement of the interacting ligands
When Mg2+ is removed, considerable movement is
observed in the co-ordinating residues in both the
NPT and NP simulation
Site-directed mutagenesis of Glu295xand
Arg404y
Modelling predicts that Glu295x–Arg404y is necessary
for trimer formation The existence of a
structural-metal dependency between trimer formation and
activ-ity in P falciparum arginase supports the involvement
of the Glu295x–Arg404y interaction The effects of
mutating Glu295x and Arg404y were therefore
deter-mined in the recombinantly expressed enzyme and are
summarized in Table 1 PfArg was found to be more
susceptible to mutations introduced at Glu295xthan at
Arg404y Mutating Glu295 to Ala or Arg considerably
reduces enzyme activity (by 96% and 73%,
respec-tively) under standard assay conditions, which is also the case for the double mutant Glu295 Ala⁄ Arg404 Ala (95%) However, single mutations of Glu295 to Arg and Arg404 to Ala leads to altered Km values of
146 mm and 45 mm for l-Arg, respectively, which is
up to 11-fold higher compared to the wild-type argi-nase The catalytic activity (as kcat) of these mutants were 7 and 11 s)1, respectively, and were thus 27% and 46% of that for the wild-type enzyme The result-ing efficiencies expressed as kcat⁄ kmvalues are reduced
in both mutants to 1.6% and 46%, respectively, com-pared to the wild-type The elution profile of all mutants analysed by gel filtration revealed monomeric forms, except for Glu295 Ala, which is partially tri-meric (Fig 7) By contrast, trimer formation is more susceptible to mutation of Arg404 The partial activity
of Arg404 Ala is the first clear evidence of active monomers for PfArg
Discussion
From the multiple sequence alignment used for model-ling, two parasite-specific inserts were identified in the
P falciparum sequence Proteins from Plasmodium fre-quently have large inserts relative to sequences from homologues in other organisms [55] These inserts are often characterized by low complexity [56,57] and⁄ or have a strong amino acid bias towards small and hydrophilic residues Apart from possible global func-tions [55–57], it has been demonstrated that inserts may have local functions relative to their enzymes [22,58,59] Plasmodium-specific inserts can be difficult
to delineate in sequences of low homology Thus,
Table 1 Comparison of kinetic parameters for wild-type (WT) and
mutant arginases The results are derived from at least three
inde-pendent assays with standard deviations ND, not detectable.
V max
(lmolÆmin)1Æmg)1)
K m (mM)
k cata,b (s)1)
k cat ⁄ K ma,b (mM)1Æs)1)
(100%)
1.9 (100%) Glu295 Ala 1.3 ± 0.3 d ND 1.0 ± 0.2 d
(4%)
ND Glu295 Arg 8.4 ± 0.9 146 ± 6 6.7 ± 0.7
(27%)
0.03 (1.6%) Arg404 Ala 14.3 ± 0.9 45 ± 3 11.4 ± 0.7
(46%)
0.25 (13%) Glu295 Ala ⁄
Arg404 Ala
(5%)
ND
a Percentage of WT value is shown in parentheses b Calculated
from 48 kDa per monomer c Values, without standard deviation,
are taken from Mu¨ller et al [24].d£ 5% of WT activity in standard
assay.
Fig 7 Effect of Glu295 x –Arg404 y salt-bridge mutations on trimer formation Recombinant proteins were separated on a Superdex S-200 gel sizing column (1 · 30 cm) using a buffer containing
50 mM Tris–HCl, pH 8, 1 mM dithiothreitol and 1 mM MnCl 2 Aliquots of 100 lL of the elution fractions (0.5 mL) were analysed
by western dot-blotting using monoclonal anti-Strep-tag serum (Institut fu¨r Bioanalytik) at a dilution of 1 : 5000 The corresponding molecular masses are given above the dots.
Trang 8where possible, other Plasmodium sequences were
included to assist with the insert delineation Because
of its length, most of insert 1 was left unmodelled
(resi-dues 81–147 removed; Fig 1) Insert 2 is considerably
shorter and more conserved and was therefore retained
for ab initio modelling The choice of alignment was
found to have a considerable effect on the
conforma-tion of insert 2 Because a small change in alignment
had a substantial effect on insert 2, it is important to
justify the choice of reference alignment used In the
fugue[60] derived alignment (see Experimental
proce-dures), insert 2 was predicted to fold away from the
trimer interface, compared to the clustalw derived
alignment The fugue alignment was favoured,
however, because the fugue software makes use of
environment-specific substitution tables and
structure-dependent gap penalties, and is thus generally expected
to give a more accurate starting alignment for
model-ling purposes The function of the inserts in PfArg has
yet to be established
Comparing the active site of the model with the
templates revealed only a small number of
substitu-tions The high conservation of the active site suggests
that inhibitors specific to the P falciparum active site
will be difficult to find Thus, an alternative means of
inhibition may be necessary if PfArg is to be of
poten-tial therapeutic value Therefore, attention was
direc-ted at the monomer interactions A novel
inter-monomer salt-bridge forms between Glu295x and
Arg404y Although Glu295 aligns with conserved
acidic residues in the templates, its interacting partner
does not align In mammalian structures, the acidic
equivalent nucleates considerable monomer
inter-actions by means of an S-shaped C-terminus by
form-ing a salt-bridge with Arg308 The importance of the
S-shaped tail is still in doubt because products
trun-cated after Arg308 can still form active trimers [61] In
bacterial structures, an interaction is formed with
another acidic residue (Glu256) that is mediated by
either urea or free arginine Finally, in the P
falcipa-rum model, Glu295 is predicted to interact with
Arg404, which does not align with mammalian Arg308
or bacterial Glu256 Thus, there appears to have been
evolutionary pressure to establish a strong
inter-mono-mer interaction in this region of the monointer-mono-mer-mono-
monomer-mono-mer interface The differences between the
P falciparum model and templates suggest this
salt-bridge as a possibly unique interaction and was
therefore subjected to scrutiny using molecular
dynam-ics and site-directed mutagenesis
The deletion of insert 1 for modelling did not
adversely affect the stability of the model Although
potential problems with respect to introducing a chain
break could have been avoided by ligating the ends of the gap, this would also be unnatural Because the fragment was apparently stable and closing the gap unligated is less parsimonious, the break was left in The equilibration of Ca rmsd during molecular dynamics at a larger distance for the Mg2+ -free systems suggests that removing the active site metals has a detrimental effect on protein stability It was previously reported that removing Mn2+, either by dialysis and chelation with EDTA, or by mutagenesis
of Mn2+ co-ordinating residues in the active site, of PfArg not only abolished enzyme activity, but also promoted dissociation of the trimer, which could be reversed by addition of Mn2+[24] The general loss of secondary structure further mirrors the increase in rmsd upon removing the metal and confirms the necessity of the active site metals for protein stability Removing the active site metals also affected the conformation of insert 2 during molecular dynamics, which generally remained more solvent exposed and made less inter-monomer contacts This suggests that insert 2 may also be involved in maintaining the trimer and thus part of the structural metal dependency The temperature of the NP ensemble was allowed
to increase (310 to 332K) by not coupling it to a temperature bath Although it is usual to apply some means of keeping temperature constant (isothermal ensemble), sampling at higher temperatures allows the system to overcome energy barriers faster In the present study, the increase in temperature accelerates the effects of removing Mg2+ In the NPT ensemble, only one Glu295x–Arg404y interaction is broken after
20 ns, whereas, in the NP ensemble with increasing temperature, all three have been broken before 20 ns The effect of the increasing temperature is also reflected in the rmsd, which is more pronounced and more rapid in the NP ensemble The increasing temperature may be detrimental, however, as reflected by breaking an Arg346x–Glu347y interaction
in the NP ensemble with Mg2+ For this reason, subsequent simulations were carried out in the NPT ensemble
Because most simulations based on classical mechanics do not model metal co-ordination, the conformations adopted by the co-ordinating residues did not entirely conform to known crystal structures from homologues The larger distance between the
Mg2+ atoms compared to Mn2+ in known structures
is partly a result of the inability of the software to recognize co-ordination chemistry natively as well as the larger van der Waals radius of Mg2+compared to
Mn2+ Because of the stability of the Mg2+cluster, it was considered unnecessary to introduce artificial
Trang 9restraints to replicate metal-co-ordination Because the
presence of Mg2+ was able to stabilize the
co-ordina-ting residues by electrostatic interactions alone, this
approach appears to be viable for investigating the
structural metal dependency These results also suggest
that structural metal dependency involves free
move-ment of the metal co-ordinating residues
The existence of the inter-monomer salt-bridge
between Glu295x and Arg404y was corroborated by
site-directed mutagenesis of the recombinant enzyme
All mutants tested promoted trimer dissociation, with
incomplete dissociation for Glu295 Ala but contrasts
with Glu295 Arg, which led to complete dissociation
Mutating Glu295 to Arg is expected to be more drastic
compared to Ala because this would introduce a
positive charge and thus an electrostatic repulsion in
the vicinity of the Glu295x–Arg404y interaction
Inter-estingly, this mutation leads to active but less efficient
monomers with a 11-fold increased Km value of
146 mm for l-arginine, indicating altered substrate
binding By contrast, mutating Glu295 to Ala reduced
the activity to 4% of the wild-type enzyme but with its
trimeric conformation partially retained The Kmvalue
for the Glu295 Ala mutant was not measurable
because it was not saturated up to 200 mm arginine
Mutating Arg404 to Ala abolished trimer formation
However, this mutant enzyme shows 46% activity (as
kcat) and 13% efficiency (as kcat⁄ Km) and its Kmvalue
is approximately three-fold increased compared to the
wild-type enzyme This result is similar to the
previ-ously reported behaviour of the rat liver arginase
Arg308 mutants, which, as monomers, still had a
resid-ual activity of 41% and an efficiency in the range
13–17% [44] Size-exclusion chromatography therefore
suggests that certain mutations abolish trimerization,
although the enzymatic data suggests that
trimeriza-tion is not absolutely necessary for activity However,
the possibility that a weakened trimer can form under
enzyme assay conditions cannot be excluded Such a
possibility is suggested by rat arginase, where the
Arg308 Lys mutant is apparently active as a monomer,
but nonetheless crystallizes as a trimer [44] Although
it has been demonstrated that disturbing the oligomer
via the conserved interaction between Arg346x and
Glu347y largely inactivates the enzyme, it still has 10%
residual activity [24] The results of the Arg404 Ala
mutation indicates that it is possible to produce active
monomers and, furthermore, that certain mutations
can partially compensate for induced structural
insta-bility of monomerization by long range allosteric
effects Although there is a dependency between trimer
formation and enzyme activity, these results indicate
that it is not complete This incompleteness was
sug-gested by previous results where mutating His193 in the active site also results in an inactive trimer [24] as was also found for the Glu295 Ala mutation in the present study Mutations that disturb the Arg346x– Glu347y and Glu295x–Arg404y interactions both result
in decreased activity Furthermore, during simulations
of the Glu347 Gln mutant, the Glu295x–Arg404y inter-action is also disturbed These observations suggest that disruption of both interactions may provide a novel means of inhibiting PfArg These results suggest that formation of the Glu295x–Arg404y salt-bridge is necessary for trimer formation, and that the hypothesis that the enzyme can be inhibited via disturbing the trimer warrants further investigation
It is expected that disturbing the interactions involved in trimer formation mediate their effects via the co-ordination of Mn2+ in the active site, which is required for the arginase chemistry This is reflected by the increased equilibrium rmsd during molecular dynamics, which should ultimately translate into lost co-ordination of Mn2+ in the active site The loss of
Mn2+ under such conditions, however, has yet to be observed directly Nonetheless, the decreased activity
of monomeric mutants and the increased equilibrium rmsd of modelled mutants suggests that this may be the case
It has been demonstrated that rat arginase I loses some activity (33–41% of kcat) when the trimerization
is disturbed by mutagenesis [44] This has not been observed for human arginase I, where fully functional monomers have been obtained [45,48,62] Despite the high sequence similarity (87%) between arginase I from rat and human [63], they differ in their kinetic properties Human arginase I has a substantially lower
Km for arginine compared to rat arginase I Further-more, the Kd values for the inhibitors S-(2-borono-ethyl)-l-cysteine and 2-amino-6-boronohexanoic acid are one order of magnitude less than for the rat coun-ter part [38,46,64] This suggests that it may be possi-ble to inhibit PfArg via disturbing oligomerization without affecting the human counterpart
Arginine levels in in vitro cultures of P falciparum are depleted by PfArg, although the relevance of arginase as a malaria drug target remains to be dem-onstrated [65] Hypoargininaemia has been linked to the progression of severe malaria and may be related
to the requirement of arginine for NO biosynthesis [66] It has been speculated that low host NO bene-fits the parasite by causing increased expression of host intracellular adhesion molecule-1, which is used
by parasatized red blood cells to adhere to the vas-cular endothelium and thus avoid spleen clearance Arginase knockouts of the rodent malaria parasite,
Trang 10P berghei (ANKA strain), are viable and show
simi-lar growth behaviour ex vivo and in infected mice
[65], although this has yet to be established for the
human parasite
Experimental procedures
Sequence alignments
Reference multiple alignments were generated using
align-ment included eukaryotic arginases types I and II, and
bacterial arginases The sequences used for the clustalw
alignment (Entrez accession number are given in brackets
for non-Plasmodium species, PlasmoDB reference numbers
are used for Plasmodium sequences) were: A thaliana
(P46637, Q9ZPF5), Schizosaccharomyces pombe (P37818,
P30759), Homo sapiens (P78540, P05089), Mus musculus
(O08691, Q61176), Rattus norvegicus (O08701, P07824),
(Q59174), Coccidioides immitis (P40906), Emericella
070380), P vivax (Pv098770), P falciparum (PFI0320w),
Seq-uences for P knowlesi, P vivax, P yoelii and P berghei
were obtained using blast (available at: http://plasmodb
Although the reference alignments were often highly
redun-dant, all sequences were retained to offset the bias of
including five Plasmodium sequences
Homology modelling
models Trimeric models were constructed on the rat
argi-nase I (PDB code: 1RLA[abc]), human argiargi-nase II (PDB
code: 1PQ3[abc]) and B caldovelox (PDB code: 1CEV[abc])
templates Superimposable monomers were constructed by
imposing symmetry restraints on the internal coordinates of
all atoms during the model building process The effect of
various sequence alignments was determined by generating
multiple models with different random number seeds and
monitoring the effect on the number of residues in
dis-allowed regions of the Ramachandran plot and on the
overall G-factor score from procheck [69] Problem areas
were identified as residues that frequently fell in disallowed
values and maximized the G-factor were used for molecular
dynamics In the final run, one model was chosen from a
total of 33 for molecular dynamics
Molecular dynamics
Hydrogen atoms were added automatically using charmm 32b1 [54,70] All residue positions are given relative to their own sequence The histidine protonation scheme adopted was based on the requirements for co-ordination of metal atoms in the active site in known structures Thus, His193 and His218 (which align with His101 and His126 in rat
was protonated on both nitrogen atoms His233 aligns with His141 in human arginase I The double protonation of His233 was based on the high resolution (1.29 A˚) crystal structure of human arginase I [38], for which hydrogen positions were also determined, as well as previous specula-tion concerning activity [35] All remaining histidines were
lysine residues were charged Because the current common protein forcefields (charmm, amber, gromos) were not
It was thus assumed that any effects of the metal on trimer formation were largely electrostatic in nature
Although charmm was initially used for molecular dynam-ics, it was found to perform too slowly on the available hard-ware (Pentium IV Beowulf cluster with GigaBit Ethernet)
was also used for analysis of molecular dynamics trajectories [52] stride software, as provided with vmd, was used to assign secondary structure The multiseq plugin [73] was used
to visualize secondary structure alignments Salt-bridges between arginine and glutamate residues were measured
these atoms of 4 A˚ corresponds to the typical distance of
The system was explicitly solvated (transferable inter-molecular potential water model) using the solvate plugin
of vmd The protein was padded with solvent for 12 A˚ in the x- and y-axis (xy being coplanar with the trimer) and
10 A˚ in the z-axis NaCl counter ions were added with the
with charge balancing to create a net system charge of zero
Nonbonded interactions were shifted to zero from 10 A˚
to a cut-off of 12 A˚ All nonbonded interactions connected
by more than four covalent bonds were included Prior to solvation, the trimer complex was minimized in namd
system with solvent and ions were simulated with periodic boundary conditions using particle mesh Ewald Sums for the electrostatic calculations A typical cell size was