Transcript Study on Binding Small Molecules on GC Stationary Phase with

Linear scaling semiempirical molecular orbital calculations
on the complexation of zinc ions by the Alzheimer’s b-amyloid peptide
Zoltán A. Fekete1, Eufrozina A. Hoffmann2, Tamás Körtvélyesi1,2, Botond Penke3
1HPC
Group, University of Szeged, Hungary
2Department of Physical Chemistry, University of Szeged, Hungary
3SZTE-MTA Research Group on Supramolecular and Nanostructured Materials, Szeged , Hungary
< http://HPC.inf.hu/>
Asp-Ala-Glu-Phe-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-Leu-Val-Phe-Phe-Ala-Glu-Asp-Val-Gly-Ser-Asn-Lys-Gly-Ala-Ile-Ile-Gly-Leu-Met-Val-Gly-Gly-Val-Val-Ile-Ala
Asp-Ala-Glu-Phe-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-Leu-Val-Phe-Phe-Ala-Glu-Asp-Val-Gly-Ser-Asn-Lys-Gly-Ala-Ile-Ile-Gly-Leu-Met-Val-Gly-Gly-Val-Val-Ile-Ala
Asp
Ala
Glu
Phe
Arg
Abstract
The Alzheimer’s β-amyloid peptide, Aβ, found as aggregated species in Alzheimer’s disease
brain, is linked to the onset of dementia. The toxic properties of Aβ depend on oligomerization and
aggregation. In addition, Aβ toxicity is aggrevated by the presence of zinc ions, which affect the
secondary structure of the peptide. We report the modeling of possible interactions of zinc ions with
Aβ(1-42), one of the most amyloidogenic species known.
The aim of the current study was twofold. First, in order to theoretically handle several Aβ(1-42)
monomers together, a quantum chemical method was sought that is capable of handling peptide systems
Asp
Ala
Glu
Asp
PM3&ZnB/SCRF
optimized aqueous
structure with 2
explicit waters
4) Building up the quasistructural water network within
the His6-Asp7-His14 pocket: a
second explicit H2O is put in.
The hydrogen-bonding solvent
interactions may facilitate the
arrangement favorable for
metal binding.
Phe
Arg
comprised of several hundreds residues. Our tests validated the semiempirical parameterization of zinc
His
termed ZnB, developed by Merz et al. originally for treating zinc metalloenzymes, as capable of
His
Asp
Ser
The second part of our project considered several possible structures along feasible pathways of
Aβ(1-42) oligomers and their zinc complexes is possible, requiring only modest computer resources.
forming proto-aggregate monomers upon complexing zinc with the apo-peptide. DivCon/ZnB
Gly
calculations probed putative intermediate conformations, which may play role in the eventual
Tyr
which are the only ones confirmed unequivocally by experiments. Exploring the potential energy
Glu
Val
His
pathological mis-folding event. Likely participating ligand residues are suggested, besides the histidines
landscape at this novel level of theory provides new structural clues for the process.
Asp-Ala-Glu-Phe-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-Leu-Val-Phe-Phe-Ala-Glu-Asp-Val-Gly-Ser-Asn-Lys-Gly-Ala-Ile-Ile-Gly-Leu-Met-Val-Gly-Gly-Val-Val-Ile-Ala
1)
Glu
Phe
Arg
His
4)
describing complexation of zinc by Aβ(1-42). Used in conjunction with the linear scaling semiempirical
program DivCon („Divide and Conquer”), also by Merz et al., fully quantum chemical treatment of
Ala
Asp
Asp
Ser
Ser
Gly
Gly
Tyr
Glu
Val
His
Zinc complexing @
ASP7–HIS14
PM3&ZnB/SCRF optimized
aqueous structure
5) This is one possible arrangement for
the initial embedding of a Zn2+ ion
within the His6-Asp7-His14 pocket (for
simplicity, explicit H2O molecules are
not yet inserted here). The complexing
ion can stabilize a rearranged structure
developing subsequently, with a twist
of the backbone moving the His13
residue into the vicinity of this region.
Tyr
Glu
Val
His
5)
His
His
Gln
Gln
Gln
Lys
Lys
Lys
Leu
Database structure + calculated protonation
Leu
Val
Val
Phe
Phe
Phe
Ala
1) Starting structure is taken from the PDB. An initial guess for
the protonation state is made with a simple Poisson-Boltzmann
calculation. This indicated a possibly unusual charge for His14,
sensitive to the ionic strenght and permittivity of the medium…
Zinc complexing @
ASP7–HIS13–HIS14
PM3&ZnB/SCRF optimized
aqueous structure
6) In this optimized structure a
possible binding motif for Zn2+
ion is depicted. The
arrangement of His13 and
His14 coupled by the zinc is
often considered a
precondition of aggregating
Aß. It is interesting to note the
unusually active role of Asp7
in the forming of this complex
(while His6 is merely a
spectator in this instance).
Phe
Ala
Asp-Ala-Glu-Phe-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-Leu-Val-Phe-Phe-Ala-Glu-Asp-Val-Gly-Ser-Asn-Lys-Gly-Ala-Ile-Ile-Gly-Leu-Met-Val-Gly-Gly-Val-Val-Ile-Ala
Glu
Glu
Asp
Asp
Val
Gly
Detail of structure, PM3&ZnB optimized
2)
His
Leu
Val
Phe
Phe
6)
Ala
Glu
Asp
Val
Val
Gly
Gly
Ser
Ser
Asn
Asn
Lys
Lys
Lys
Gly
Gly
Gly
Ala
Ala
Ala
Ile
Ile
2) The initial crude coordinates are refined by the DivCon routine
(implemented in AMBER9), using the ‘ZnB’ reparametrization of
the PM3 Hamiltonian. No dielectric is considered at this stage…
Asp-Ala-Glu-Phe-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-Leu-Val-Phe-Phe-Ala-Glu-Asp-Val-Gly-Ser-Asn-Lys-Gly-Ala-Ile-Ile-Gly-Leu-Met-Val-Gly-Gly-Val-Val-Ile-Ala
Gly
Leu
Met
Val
3)
Ile
Gly
Leu
Met
Val
Val
Gly
Gly
Val
Val
Val
Val
Ala
7) A more densely packed structure is formed, with His6 turned
to complete a tetrahedral coordination around the Zn2+ ion.
Asp7 is still bound to the metal in this instance.
Met
Gly
Ile
Ile
Ile
Leu
Gly
3) Exploring the micro-hydratation of a putative metal binding
region: this is a snapshot of a pocket being formed by His6Asp7-His14. The structure is optimized in implicit aqueous media
(SCRF solvent model), with one explicit H2O added…
Asn
7)
Ile
Gly
PM3&ZnB/SCRF optimized aqueous
structure with 1 explicit water
Ser
Zinc complexing @
ASP7–HIS13–HIS14–HIS6
PM3&ZnB/SCRF optimized
aqueous structure
Ile
Ala
Conclusions and outlook
• We have validated the use of linear scaling ‘DivCon/ZnB’ method of Merz et al. for handling zinc metallopeptides.
• The current investigation revealed a novel multi-functional role played by Asp7 in the process of zinc binding by Aβ.
• It was demonstrated that this protocol makes feasible a quantum chemical treatment of systems containing hundreds
of amino acid residues: on our commodity cluster, typical CPU times for one SCF cycle are well under 1 minute/residue!
• This performance will enable studying Aβ aggregates with several monomer units by ‘DivCon/ZnB’;
a further development of the protocol (incorporating extended General AMBER FF augmented with metallo-protein
parameters from Hoops and Merz) can also handle dynamics with QM/MD.
• We made, and are releasing, user tools for molecular coordinate processing to streamline work with DivCon format:
<http://Zoli.alturl.com/moletools/>
Partial funding was provided by the Hungarian Scientific Research Fund (OTKA/61577),
and by the Hungarian National Office for Research and Technology (grants RET 08/2004, ALAP4-00092/2005).
Asp-Ala-Glu-Phe-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-Leu-Val-Phe-Phe-Ala-Glu-Asp-Val-Gly-Ser-Asn-Lys-Gly-Ala-Ile-Ile-Gly-Leu-Met-Val-Gly-Gly-Val-Val-Ile-Ala
Gly
Gly
Val
Val
Ile
Ala