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Scientific Report 2005
Molecular Biology
Quantum Chemistry for Intermediates,
Reaction Pathways, and Spectroscopy
L.
Noodleman, D.A. Case, W.-G. Han, F. Himo,* T. Lovell,** T. Liu,*** M.J. Thompson,****
R.A. Torres
*
Royal Institute of Technology, Stockholm, Sweden
** AstraZeneca R&D, Mölndal,
Sweden
*** University of Maryland, College Park, Maryland
**** Boston University,
Boston, Massachusetts
We use a combination of modern quantum chemistry (density functional theory) and classical
electrostatics to describe the energetics, reaction pathways, and spectroscopic
properties of enzymes and to analyze systems with novel catalytic, photochemical,
or photophysical properties.
Critical biosynthetic and regulatory processes may involve catalytic transformations of fairly small molecules
or groups by transition-metal centers. The iron-molybdenum cofactor center of nitrogenase
catalyzes the multielectron reduction of molecular nitrogen to 2 ammonia molecules
plus molecular hydrogen. We are continuing our work on the catalytic cycle of this
enzyme, following up on our earlier research on the structure of the MoFe7S9X
prismane active site, where the central ligand X most likely is nitride.
Class I ribonucleotide
reductases are aerobic enzymes that catalyze the reduction of ribonucleotides to
deoxyribonucleotides, providing the required building blocks for DNA replication
and repair. These ribonucleotide-to-deoxyribonucleotide reactions occur via a long-range
radical (or proton-coupled electron transfer) propagation mechanism initiated by
a fairly stable tyrosine radical, “the pilot light.” When this pilot light
goes out, the tyrosine radical is regenerated by a high-oxidation-state iron(III)-iron(IV)-oxo
enzyme intermediate, called intermediate X. We are using density functional and
electrostatics calculations in combination with analysis of Mössbauer, electron
nuclear double resonance, and magnetic circular dichroism spectroscopic findings
to search for a proper structural and electronic model for intermediate X. On the
basis of these studies, we propose that intermediate X contains a di-oxo that bridges
the iron(III)-iron(IV) in an asymmetric diamond structure (Fig. 1).
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| Fig. 1. Proposed model for the active site of class I ribonucleotide reductase intermediate X. |
In studies
with E. Getzoff and M.J. Thompson, Department of Molecular Biology, and D. Bashford,
St. Jude Children’s Hospital, Memphis, Tennessee, we are examining the basis
for the spectral tuning of the chromophore at the active site of photoactive yellow
protein as an example of a light-activated signal transducing protein.
In collaborations
with K. Hahn, A. Toutchkine, and D. Gremiachinsky, University of North Carolina,
Chapel Hill, North Carolina; F. Himo, Royal Institute of Technology, Stockholm,
Sweden; and M. Ullmann, University of Bayreuth, Bayreuth, Germany, we examined the
optical properties of solvent-dependent fluorescent dyes as prototypes for fluorescent
tags that could act as reporters of protein conformational change due to ligand
binding. These detailed calculations will be used to improve design strategies for
stable and optically useful dyes.
Also, with
Dr. Bashford’s group, we are studying reaction pathways for the catalytic dephosphorylation
of a tyrosine side chain by a low molecular weight protein tyrosine phosphatase.
The reaction occurs in 2 distinct steps: first, formation and then hydrolysis of
a phosphocysteine intermediate.
In a collaboration
with K. Janda and T. Dickerson, Department of Chemistry, we used quantum chemical
density functional theory methods to examine the mechanism of nornicotine-catalyzed
aldol reactions in aqueous solution. Nornicotine is a long-lived nicotine metabolite
generated under physiologic conditions in cigarette smokers. This reaction leads
to abnormal protein glycation and to covalent modification of steroid drugs, including
the prescription corticosteroid prednisone.
We are continuing
our collaboration with K.B. Sharpless, V.V. Fokin, R. Hilgraf, and V. Rostovtsev,
Department of Chemistry, on the catalytic mechanisms used by transition-metal ions
in click chemistry, in which metal centers catalyze ring formation from multiply bonded precursors. Our current focus is the mechanism of copper(I) reactions, because copper(I)
in water shows great versatility in ligating organic azides and alkynes to form
5-membered heterocycles (triazoles) with wide molecular diversity. On the basis
of density function theory calculations, we predict that an unusual 6-membered copper(III)
metallocycle intermediate is formed, with only a low barrier to the triazole-copper(I)
derivative, leading to the triazole product after proteolysis.
Publications
Asthagiri,
D., Liu, T., Noodleman, L., Van Etten, R.L., Bashford, D.
On the role of the conserved aspartate in the hydrolysis of the phosphocysteine
intermediate of the low molecular weight tyrosine phosphatase. J. Am. Chem. Soc.
126:12677, 2004.
Dickerson,
T.J., Lovell, T., Meijler, M.M., Noodleman, L., Janda, K.D.
Nornicotine aqueous aldol reactions: synthetic and theoretical investigations into
the origins of catalysis. J. Org. Chem. 69:6603, 2004.
Himo,
F., Lovell, T., Hilgraf, R., Rostovtsev, V.V., Noodleman, L., Sharpless, K.B., Fokin,
V.V. Copper(I)-catalyzed
synthesis of azoles: DFT study predicts unprecedented reactivity and intermediates.
J. Am. Chem. Soc. 127:210, 2005.
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