Vol 31, Part I - forums.sou.edu • Index page - Southern Oregon ...

ABSTRACTS – Symposia
Biophysical Insights from Experimental
Approaches to Computational Simulations
Wednesday, 8:30 a.m. in WILLOWS 1 & 2
94 Discovery of a Nanoscale Clamp for Protein and Chromatin
Binding, RICCARDO BARON (Department of Medicinal
Chemistry, College of Pharmacy, The Henry Eyring Center
for Theoretical Chemistry, University of Utah, 30 S 200
E Room 201, Salt Lake City, UT 84112; nidia.martinez@
gmail.com).
LSD1 associated with its corepressor protein CoREST
is an exceptionally relevant target for epigenetic drugs.
Hypotheses for the role of LSD1/ CoREST as a multidocking
site for chromatin and protein binding would require
significant molecular flexibility, and LSD1/CoREST largeamplitude
conformational dynamics is currently unknown.
Our molecular dynamics simulations reveals that the LSD1/
CoREST complex in solution functions as a reversible
nanoscale binding clamp. We show that the H3 histone tail
binding pocket is an allosteric site for regulation of the rotation
of SWIRM/ SANT2 domains around the Tower domain.
Thus, targeting this site and including receptor flexibility are
crucial strategies for future drug discovery.
95 Deconstructing and Reconstructing a Protein Capsid,
KENNETH WOYCECHOWSKY (Department of Chemistry,
Universtiy of Utah, 315 S 1400 E Room 2020, Salt
Lake City, UT 84112; kwoycech@chem.utah.edu).
Icosahedral protein capsids are often used in Nature for
the storage, transport, or regulation of encapsulated cargo
molecules. These structures are attractive for various applications
in bionanotechnology, such as drug delivery and
catalysis. Towards these ends, the usefulness of protein capsids
will depend upon an understanding of their supramolecular
chemistry. Lumazine synthase from Aquifex aeolicus
(AaLS) self-assembles into a 60-subunit dodecahedral capsid
and provides an appealing scaffold for engineering novel
encapsulation systems. However, an inability to control
AaLS capsid assembly has presented a major obstacle for
cargo loading in vitro. Here, we use structure-guided design
to identify a set of three amino acids that act as important
determinants of capsid assembly. Simultaneous mutagenesis
of these three residues prevents capsid formation, halting
self-assembly at the pentameric stage. This pentameric AaLS
variant provides the basis for engineering a redox switch to
build 60-subunit capsids in vitro. The capsid assembly process
involves the formation of a covalent adduct between a
unique cysteine in the variant (C37A/R40S/H41S/I125C-
AaLS) and thiophenol. This modification adds non-polar
surface area at position 125, presumably recapitulating a key
feature of the isoleucine present at this position in the wildtype
protein. The spontaneous, non-covalent assembly of the
thiophenol-modified pentamers yields capsids that resemble
those of wild-type AaLS, as assessed by size-exclusion
chromatography and electron microscopy. Further, we have
used this assembly switch to encapsulate the enzyme horseradish
peroxidase, which remains active inside the capsid.
By understanding the structural determinants for AaLS capsid
assembly, we are able to deconstruct this capsid into its
constituent pentamers by mutagenesis and reconstruct the
capsid by chemical modification. Control of capsid assembly
enables the encapsulation of enzymes and other molecules in
vitro, which should prove useful in the construction of novel
drug delivery and catalytic systems.
96 Determining Realistic Structural Ensembles for Intrinsically
Disordered Proteins, F MARTY YTREBERG
(Department of Physics, University of Idaho, Moscow, ID
83844; ytreberg@uidaho.edu).
Intrinsically disordered proteins (IDPs) are common in
humans and their dysfunction is associated with many human
diseases. IDPs are highly dynamic, contain varying amounts
of transient secondary structure, and rarely have tertiary
interactions. Given these structural features, most experimental
and computational methods in structural biology are
not suitable for IDPs. I will describe our new approach that
combines experiment and simulation to generate structures
for IDPs using the transactivation domain of tumor suppressor
protein p53 as a model system; one of the most commonly
mutated genes found in human tumors. Results from
our study show that, while independent IDP ensembles do
not appear to be structurally similar, one can calculate features
that are consistent between ensembles. These findings
suggest that the consistent features have biological significance,
and that one should gauge the quality of the ensembles
based on the ability to reproduce these features.
97 Chromatographic Stationary Phase Development for
the Analysis of Solute Interactions with Phospholipid Membranes,
ERIC E ROSS (Department of Chemistry and Biochemistry,
Gonzaga University 502 East Boone Avenue,
Spokane, WA 99258-0102; rosse@gonzaga.edu).
The retention time of a solute in chromatography is
related to its partition or binding behavior between stationary
and mobile phases. The specific research utility of a
chromatographic system designed to probe biomembrane
interactions is a factor of the replicated membrane attributes,
the chromatographic efficiency of the materials, and
the system’s compatibility with various chromatographic
formats. The most realistic membrane models used to date
for chromatography, such as gel-supported liposomes, are
compatible with the least efficient and most performancelimited
supports, while higher performing materials based
on covalently derivatized solids replicate fewer membrane
attributes. This research describes the development of new
materials composed of dynamic lipid bilayers supported
within porous particles that are fabricated from Stöber silica
colloids. Preliminary results obtained in a high performance
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