32 research outputs found
What is the Real Nature of Ferrous Soybean Lipoxygenase-1? A New Two-Conformation Model Based on Combined ONIOM(DFT:MM) and Multireference Configuration Interaction Characterization
The geometric and spectral features of the ferrous resting state of soybean lipoxygenase-1 (SLO-1) have remained puzzling. We have theoretically characterized ferrous SLO-1 by means of the ONIOM(DFT:MM), TDDFT, and CASSCF/SORCI methods, taking explicitly into account the effect of the protein environment. Two conformations found theoretically in this study, Conf-A and Conf-B, have almost equal stability but have quite different geometries, with short and long FeâO<sub>694</sub> distances, respectively. While neither of the geometries agreed well with the crystal structure of the enzyme, an averaged geometry showed excellent agreement. Therefore, we propose that the crystal structure reflects a mixture of these two conformations. The calculated circular dichroism (CD) spectra for Conf-A and Conf-B were found to agree well with the two experimental spectra obtained previously for âsix-coordinateâ and âfive-coordinateâ forms of ferrous SLO-1, respectively
ONIOM (DFT:MM) Study of the Catalytic Mechanism of <i>myo</i>-Inositol Monophosphatase: Essential Role of Water in Enzyme Catalysis in the Two-Metal Mechanism
<i>myo</i>-Inositol monophosphatase (IMPase),
a putative
target of lithium therapy for bipolar disorder, is an enzyme that
catalyzes the hydrolysis of <i>myo</i>-inositol-1-phosphate
(InsÂ(1)ÂP) into <i>myo</i>-inositol (MI) and inorganic phosphate.
It is known that either two or three Mg<sup>2+</sup> ions are used
as cofactors in IMPase catalysis; however, the detailed catalytic
mechanism and the specific number of Mg<sup>2+</sup> ions required
have long remained obscure. To obtain a clearer view of the IMPase
reaction, we undertook extensive ONIOM hybrid quantum mechanics and
molecular mechanics (QM/MM) calculations, to evaluate the reaction
with either three or two Mg<sup>2+</sup> ions. Our calculations show
that the three-metal mechanism is energetically unfavorable; the initial
inline attack of a hydroxide ion on the Ins(1)P substrate markedly
destabilized the system without producing any stable transition state
or intermediate. By contrast, for the two-metal mechanism, a favorable
pathway was obtained from QM/MM calculations. In our proposed two-metal
mechanism, the phosphoryl oxygen of the substrate acts as an acidâbase
catalyst, activating a water molecule in the first step, and the resultant
hydroxide ion attacks the substrate in an inline fashion. A second
water molecule, bound to a Mg<sup>2+</sup> ion, was found to play
an essential role in the final proton-transfer step that leads to
the formation of an MI product; this is achieved by lowering the energy
barrier by 2.5 kcal/mol compared with the barrier for the mechanism
that does not use this water molecule. Our results should advance
our understanding of the IMPase mechanism, and this could have profound
implications for the treatment of disease in the central nervous system
Effect of Protein Environment within Cytochrome P450cam Evaluated Using a Polarizable-Embedding QM/MM Method
Metalloenzymes accommodate cofactors
and substrates in their active
sites, thereby exerting powerful catalytic effects. Understanding
the key elements of the mechanism via which such binding is accomplished
using a number of atoms in a protein is a fundamental challenge. To
address this issue computationally, here we used mechanical-embedding
(ME), electronic-embedding (EE), and polarizable-embedding (PE) hybrid
quantum mechanics and molecular mechanics (QM/MM) methods and performed
an energy decomposition analysis (EDA) of the nonbonding protein environmental
effect in the âcompound Iâ intermediate state of cytochrome
P450cam. The B3LYP and AMBER99/QP302 methods were used to deal with
the QM and MM subsystems, respectively, and the nonbonding interaction
energy between these subsystems was decomposed into electrostatic,
van der Waals, and polarization contributions. The PE-QM/MM calculation
was performed using polarizable force fields that were capable of
describing induced dipoles within the MM subsystem, which arose in
response to the electric field generated by QM electron density, QM
nuclei, and MM point charges. The present QM/MM EDA revealed that
the electrostatic term constituted the largest stabilizing interaction
between the QM and MM subsystems. When proper adjustment was made
for the point charges of the MM atoms located at the QMâMM
boundary, EE-QM/MM and PE-QM/MM calculations yielded similar QM electron
density distributions, indicating that the MM polarization effect
does not have a significant influence on the extent of QM polarization
in this particular enzyme system
Estrogen Formation via HâAbstraction from the OâH Bond of <i>gem</i>-Diol by Compound I in the Reaction of CYP19A1: Mechanistic Scenario Derived from Multiscale QM/MM Calculations
Recent experiments suggested that,
contrary to traditional belief,
the third step of aromatase-catalyzed estrogen formation should be
effected by compound I (Cpd I), rather than by ferric peroxide. We
performed QM/MM calculations to address the question of how Cpd I
drives the aromatization process. Surprisingly, the calculations show
that the reaction begins with hydrogen abstraction from the OâH
bond of a <i>gem</i>-diol substrate, which is followed by
barrierless homolytic CâC bond cleavage and then 1ÎČ-H-abstraction.
Proton-coupled electron transfer enables the cleavage of the strong
OâH bond. Another product, carboxylic acid, can be formed from
either the <i>gem</i>-diol or aldehyde
Pivotal Role of Water in Terminating Enzymatic Function: A Density Functional Theory Study of the Mechanism-Based Inactivation of Cytochromes P450
The importance of the mechanism-based inactivation (MBI)
of enzymes,
which has a variety of physiological effects and therapeutic implications,
has been garnering appreciation. Density functional theory calculations
were undertaken to gain a clear understanding of the MBI of a cytochrome
P450 enzyme (CYP2B4) by <i>tert</i>-butylphenylacetylene
(tBPA). The results of calculations suggest that, in accordance with
previous proposals, the reaction proceeds via a ketene-type metabolic
intermediate. Once an oxoironÂ(IV) porphyryn Ï-cation radical
intermediate (compound I) of P450 is generated at the heme reaction
site, ketene formation is facile, as the terminal acetylene of tBPA
can form a CâO bond with the oxo unit of compound I with a relatively
low reaction barrier (14.1 kcal/mol). Unexpectedly, it was found that
the ketene-type intermediate was not very reactive. Its reaction with
the hydroxyl group of a threonine (Thr302) to form an ester bond required
a substantial barrier (38.2 kcal/mol). The high barrier disfavored
the mechanism by which these species react directly. However, the
introduction of a water molecule in the reaction center led to its
active participation in the reaction. The water was capable of donating
its proton to the tBPA molecule, while accepting the proton of threonine.
This water-mediated mechanism lowered the reaction barrier for the
formation of an ester bond by about 20 kcal/mol. Therefore, our study
suggests that a water molecule, which can easily gain access to the
threonine residue through the proton-relay channel, plays a critical
role in enhancing the covalent modification of threonine by terminal
acetylene compounds. Another type of MBI by acetylenes, <i>N</i>-alkylation of the heme prosthetic group, was less favorable than
the threonine modification pathway
Electrochemical Properties of Phenols and Quinones in Organic Solvents are Strongly Influenced by Hydrogen-Bonding with Water
The electrochemical behavior of several phenols, quinones
and hydroquinone
in acetonitrile (CH<sub>3</sub>CN) with varying amounts of water were
investigated to understand the effect of hydrogen-bonding on their
voltammetric responses. Karl Fischer coulometric titrations were performed
to obtain an accurate reading of the water concentrations. The solvent/electrolyte
mixture was carefully dried using 3 Ă
molecular sieves to obtain
an initial water content that was close to the substrate concentration
(âŒ1 Ă 10<sup>â3</sup> M), and higher water contents
were then achieved via the addition from microliter syringes. It was
found that small changes in what is often considered âtraceâ
amounts of water were sufficient to substantially change the potential
and in some cases the appearance of the voltammetric waves observed
during the oxidation of the phenols/hydroquinones and reduction of
the quinones. Density functional theory calculations were performed
on the reduced/oxidized species in the presence of varying numbers
of water molecules to better understand the hydrogen-bonding interactions
at the molecular level. The results highlight the importance of accurately
knowing the trace water content of organic solvents when used for
voltammetric experiments
Pd-Catalyzed Conversion of Alkynylâλ<sup>3</sup>âiodanes to Alkenylâλ<sup>3</sup>âiodanes via Stereoselective 1,2-Iodine(III) Shift/1,1-Hydrocarboxylation
Alkynyl-λ<sup>3</sup>-iodanes have been established as alkynyl
cation equivalents for the alkynylation of carbon- and heteroatom-based
nucleophiles. Herein, we report an unprecedented reaction mode of
this compound class, which features a PdÂ(II)-assisted 1,2-IÂ(III) shift
of an alkynylbenziodoxole. A PdÂ(II) catalyst mediates this shift and
the subsequent interception of the transient vinylidene species with
carboxylic acid (1,1-hydroÂcarboxylation). The product of this
stereoselective rearrangementâaddition reaction, ÎČ-oxyalkenylÂbenziodoxole,
represents a novel and useful building block for further synthetic
transformations
Co<sup>2+</sup>/Co<sup>+</sup> Redox Tuning in Methyltransferases Induced by a Conformational Change at the Axial Ligand
Density functional theory and quantum mechanics/molecular
mechanics
computations predict cobÂ(I)Âalamin (Co<sup>+</sup>Cbx), a universal
B<sub>12</sub> intermediate state, to be a pentacoordinated square
pyramidal complex, which is different from the most widely accepted
viewpoint of its tetracoordinated square planar geometry. The square
pyramidality of Co<sup>+</sup>Cbx is inspired by the fact that a Co<sup>+</sup> ion, which has a dominant d<sup>8</sup> electronic configuration,
forms a distinctive Co<sup>+</sup>--H interaction because of
the availability of appropriately oriented filled d orbitals. This
uniquely H-bonded Co<sup>+</sup>Cbx may have catalytic relevance in
the context of thermodynamically uphill Co<sup>2+</sup>/Co<sup>+</sup> reduction that constitutes an essential component in a large variety
of methyltransferases
Pd-Catalyzed Conversion of Alkynylâλ<sup>3</sup>âiodanes to Alkenylâλ<sup>3</sup>âiodanes via Stereoselective 1,2-Iodine(III) Shift/1,1-Hydrocarboxylation
Alkynyl-λ<sup>3</sup>-iodanes have been established as alkynyl
cation equivalents for the alkynylation of carbon- and heteroatom-based
nucleophiles. Herein, we report an unprecedented reaction mode of
this compound class, which features a PdÂ(II)-assisted 1,2-IÂ(III) shift
of an alkynylbenziodoxole. A PdÂ(II) catalyst mediates this shift and
the subsequent interception of the transient vinylidene species with
carboxylic acid (1,1-hydroÂcarboxylation). The product of this
stereoselective rearrangementâaddition reaction, ÎČ-oxyalkenylÂbenziodoxole,
represents a novel and useful building block for further synthetic
transformations
Gold(I)/Gold(III)-Catalyzed Selective Synthesis of <i>N</i>âSulfonyl Enaminone Isomers from Sulfonamides and Ynones via Two Distinct Reaction Pathways
Au-catalyzed chemoselective
methods for synthesizing <i>N</i>-sulfonyl enaminones are
developed. Two different isomers are obtained
in a chemocontrolled manner by employing the different properties
of AuÂ(I) and AuÂ(III) catalysts. Hydroamidation and proton-assisted
carbonyl activation followed by MeyerâSchuster rearrangement
are proposed as the working mechanisms for the reactions. A wide range
of substrates afforded moderate to excellent yields and selectivities.
These reactions represent the first examples of transition-metal-catalyzed
enamine synthesis from sulfonamides and alkynes