Structural
Mechanistic Biochemistry. Enzymes play a key role in all metabolic
and cell-signaling processes. Characterization of an enzyme’s
biological function must include the description of its
mechanisms at an atomic level. Our laboratory is deciphering
the catalytic mechanism of several enzyme families, using
a combination of molecular biology, biochemistry and structural
Biology. Systems
under study fall into two classes: 1) Enzymes that recognize
or process phosphates and 2) redox enzymes. These systems
include: ATP-synthase, pyrophosphate hydrolases, farnesyl
pyrophosphate synthases, PI3K, flavoenzymes, copper hydroxylases,
and non-heme iron oxygenases. All experiments necessary
to address mechanistic questions are carried out in the
laboratory. Cloning and expression, ultrapurification,
kinetic characterization, mutational analysis, mass spectrometry,
crystallization, and structure determination by x-ray diffraction
are some of the techniques we bring to bear to characterize
the mechanisms of these enzymes. In addition to being intrinsically
interesting some of these systems are being developed as
targets for drug design.
Structural
Thermodynamics. Most biological processes rely
upon recognition and binding among macromolecules. We have
developed several systems, such as anti-peptide antibodies
and lectins, that we are using to study protein-ligand
interactions. As part of this research, we are developing
computational methods to calculate the changes in the thermodynamic
variables (ΔG, ΔH, ΔS) that take place when
a protein recognized another macromolecule or a small ligand.
Techniques used in this work involve monoclonal antibody
development, x-ray diffraction and calorimetry, followed
by empirical parameterization, and molecular mechanics/dynamics
and statistical mechanics calculations. Results of these
studies have a major impact on our understanding of binding
energetics, including the estimation of binding affinities
for structure-based drug
design.
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Structures: deposited coordinates
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