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Research
My
research efforts with focus on understanding fundamental properties
of biological molecules contribute to the research program carried
out in the Bowers group. Using methods typically used in the field
of Physical Chemistry we examine properties of biomolecules such
as their three-dimensional structure (folding), their interaction
with solvent molecules, and their propensity to form aggregates.
My
physical chemist's approach to understanding the complex world of
biochemistry is to start with small model systems and progressively
increase the complexity of the systems studied. For example, we
studied in depth the conformation of small biopolymers (e.g. diglycine
through hexaglycine [1]) and in some cases isomerization between
different conformers [2] (e.g. dinucleotides); we examined systematically
various factors contributing to the stability of amino acid zwitterions;[3]
and we carefully studied hydration effects by adding individual
water molecules one by one to small peptides, nucleotides, and similar
systems.[4] Insights gained from these simple systems are essential
for attempting to understand results of our projects involving biologically
relevant systems such as the hormone oxytocin,[5] the calcium-binding
protein calmodulin,[6] and proteins involved in misfolding and aggregation
phenomena that underlie many diseases including Alzheimer's, Parkinson's,
and Mad Cow Disease.[7]
As
nearly all of the experiments carried out in our group require custom-built
instrumentation, I am also interested in instrument design and construction.[8]
The machines we build, specially designed mass spectrometers equipped
with a drift cell, are used to probe the naked, hydrated, or clustered
biomolecules by measuring their masses and/or cross sections at
room temperature and often as a function of temperature from 80
K to 600 K. Careful analysis of the experimental results yield,
depending on the type of study, information about the molecule shape,
about the biomolecule-water interaction, or the extent of biomolecule
aggregation.[9]
When
ever possible, experimental results are compared to theoretical
calculations we carry out on large computer systems available to
our group. Computations ranging from executing our own code [10]
to running standard molecular mechanics/dynamics and high-level
ab-initio calculations are designed to theoretically evaluate molecule
structures based on their energies and to deduce the experimentally
observed quantities (collision cross section, water binding energy
etc.) for those structures.
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More specific information regarding
the following topics can be found here:
or
on the Bowers Group web pages:
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research
projects
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metal-biomolecule
systems
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- hydration
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| References |
[1]
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(a)
Salt Bridge Structures in the Absence of Solvent? The Case
for the Oligoglycines
Thomas Wyttenbach, John E. Bushnell, and Michael T. Bowers
J.
Am. Chem. Soc. 1998, 120, 5098
(b) Bowers Group
web page: .../oligoglycines/
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| [2] |
(a)
Folding Energetics and Dynamics of Macromolecules in the Gas
Phase: Alkali Ion-Cationized Poly(ethylene terephthalate) Oligomers
Jennifer Gidden, Thomas Wyttenbach, Joseph J. Batka, Patrick
Weis, Anthony T. Jackson, James H. Scrivens, and Michael T.
Bowers
J.
Am. Chem. Soc. 1999, 121, 1421
(b) Bowers Group
web page: .../dinucleotides/isomerization/
(c) Bowers Group web page:
.../synthetic_polymers/pet/ |
[3]
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(a)
On the Stability of Amino Acid Zwitterions in the Gas Phase:
The Influence of Derivatization, Proton Affinity, and Alkali
Ion Addition
Thomas Wyttenbach, Matthias Witt, and Michael T. Bowers
J.
Am. Chem. Soc. 2000, 122, 3458
(b) Bowers Group
web page: .../zwitterions/
(c) Bowers Group
web page:
.../zwitterions/effects/
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[4]
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(a)
Hydration of Biomolecules
Thomas Wyttenbach and Michael T. Bowers
Chem.
Phys. Lett. 2009, 480, 1-16
(b) Bowers Group
web page: .../hydration/
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[5]
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Interactions
of the Hormone Oxytocin with Divalent Metal Ions
Thomas
Wyttenbach, Dengfeng Liu, and Michael T. Bowers
J.
Am. Chem. Soc. 2008, 130, 5993
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[6]
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The
Effect of Calcium Ions and Peptide Ligands on the Relative
Stabilities of the Calmodulin Dumbbell and Compact Structures
Thomas Wyttenbach, Megan Grabenauer, Konstantinos Thalassinos,
James H. Scrivens, and Michael T. Bowers
J.
Phys. Chem. B 2010, 114, 437–447
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[7]
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(a)
Amyloid b-Protein: Monomer Structure
and Early Aggregation States of Ab42
and its Pro19 Alloform
Summer L. Bernstein, Thomas Wyttenbach, Andrij Baumketner,
Joan-Emma Shea, Gal Bitan, David B. Teplow, and Michael T.
Bowers
J.
Am. Chem. Soc. 2005, 127, 2075
(b) my Alzheimer's
page:
.../Alzheimers/
(c)
Bowers Group web page: .../proteins/
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[8]
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(a)
Design of a New Electrospray Ion Mobility Mass Spectrometer
Thomas Wyttenbach, Paul R. Kemper, and Michael T. Bowers
Int.
J. Mass Spectrom. 2001, 212, 13
(b) Bowers Group
page: .../instrument/esi/
(c) Bowers Group
web page:
.../instrument/esi/details/
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(d)
A New Instrument with High Mass and High Ion Mobility Resolution
Thomas Wyttenbach, Paul R. Kemper, Goekhan Baykut, Melvin A.
Park, and Michael T. Bowers
Int.
J. Mass Spectrom.2018, 434,108
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| [9] |
Gas-Phase
Conformations: The Ion Mobility/Ion Chromatography Method
Thomas Wyttenbach and Michael T. Bowers
Top.
Curr. Chem. 2003, 225, 207 |
| [10] |
(a)
Effect of the Long-Range Potential on Ion Mobility Measurements
Thomas Wyttenbach, Gert von Helden, Joseph J. Batka, Jr.,
Douglas Carlat, and Michael T. Bowers
J.Am.Soc.Mass
Spectrom.1997,8,275
(b)
.../research/cross-sections
(c) Bowers Group web page:
.../cross-sections/sigma
(d) Online cross
section calculator:.../WebPSA
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(e)
Factors Contributing to the Collision Cross Section of Polyatomic
Ions in the Kilodalton to Gigadalton Range
Thomas Wyttenbach, Christian Bleiholder, and Michael T. Bowers
Anal.
Chem. 2013, 85, 2191-2199
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