| Presenter |
Abstract/Interest |
Dustin Bleile
Grad student
Chemistry
SFU |
UDP-galactopyranose mutase (UGM) is
the key enzyme involved in the biosynthesis of the cell wall of
tuberculosis. A protocol that combines the use of STD-NMR spectroscopy,
molecular modeling, and CORCEMA-ST calculations was applied to the
investigation of the binding of UDP-Galf and its C3-fluorinated analogue
to UGM from Klebsiella pneumoniae. Combined MD simulations and STD-NMR
experiments were used to create models of UGM with UDP-Galf and
UDP-[3-F]Galf as bound ligands. Calculated values of saturation-transfer
effects with CORCEMA-ST (complete relaxation and conformational exchange
matrix analysis of saturation transfer) were compared to the experimental
STD effects. Taken together, these results are used to rationalize the
different rates of catalytic turnover of UDP-Galf and UDP-[3-F]Galf , and
shed light on the mechanism of action of UGM.
|
Peter Borowski
Postdoc
Mathematics
UBC |
A polymer model for the oscillations
of the Min proteins in E.coli: possible patterns in both wildtype cells
and filamentous mutants
A group of proteins that is important for reliable cell division in
E.coli - the Min proteins - show spatiotemporal oscillatory patterns
along the long axis of the rod-shaped cell. Experiments both in vivo and
in vitro suggest that these proteins organise in polymers and a recent
model explains many of the wildtype patterns as well as mutants in terms
of growing and shrinking polymers. Here, we analyse the possible patterns
and dynamics that are a result of this polymer model. The focus is on the
filamentous cell mutant, a bacterium that grows to very long tubes and
shows a spatial pattern in experiments.
|
Kerry Chan
Grad student
Molecular biology and biochemistry
SFU |
Bimodal agonism is a form of
time-independent receptor desensitization observed in the homomeric
catfish olfactory cyclic nucleotide-gated (CNG) A2 channel. At low
concentrations, cGMP binding increases the channel open probability but
at high concentrations, cGMP binding decreases the channel open
probability. The CNGA2 binding domain (BD) is responsible for bimodal
agonism; however, what structural features underlie bimodal agonism is
still unclear. Through making regional substitutions between the normal
and bimodal BD we have concluded that there is no single residue that is
critical in producing bimodal agonism. Rather, multiple residues in the
CNGA2 BD, or residues from neighboring CNGA2 BDs in a tetramer might be
cooperating to produce bimodal agonism.
|
Yuchun Chen
Grad student
Chemistry
SFU |
During chemotherapy, multidrug resistance (MDR) pump can prevent the accumulation of anti-cancer drugs
in the drug-resistant cancer cells, and make it impossible to kill the
cancer cells.
Using the single cell chip, we were able to trap a single leukemia cell
and monitor the real-time cellular drug concentration. We found that the
fluorescence intensity decreased as the drug (Daunorubicin) was pumped
out of the cell. However, in the presence of sodium vanadate as an
inhibitor compound, the cellular daunorubicin concentration remained
high, which implies vanadate may be a potential modulator to reverse MDR,
thus improve the effectiveness of cancer therapy.
|
John Cheng
Grad student
Chemistry
UBC |
Our research involves the study of
aurein peptides (primarily active aurein 2.2-CONH2/aurein 2.3-CONH2 and
inactive aurein 2.3-COOH), a class of amphibian cationic antimicrobial
peptides active against Staphylococcus aureus. To date, our
solution-state CD and 1H NMR studies have shown that the three aurein
peptides adopt a continuous alpha-helical structure in the presence of
trifluoroethanol and phospholipid(s). Our solid-state oriented CD and
31P NMR studies have demonstrated that aurein 2.2-CONH2 and aurein
2.3-CONH2 effectively perturb the DMPC/DMPG bilayers (bacterial
membranes), while displaying minor effects on the DMPC bilayers
(mammalian membranes). These aurein peptides are thus potential future
antibiotics against resistant bacteria.
|
Michael Dahabieh
Undergrad student
Molecular biology and biochemistry
SFU |
Untranslated RNA is often termed “junk” RNA, but is it truly useless? An example of “junk” RNA discovered relatively recently is the riboswitch, which is composed of an aptamer/ ligand-binding domain, and a platform/communication domain. For the purine riboswitches (guanine and adenine), when their ligands (guanine and adenine respectively) are bound, a conformational change is induced, regulating downstream genes. Riboswitches are of interest to us because unlike proteins, the ligand-induced conformational changes leading to a tertiary structure govern the regulatory activity. It is essential to understand the dynamics of riboswitch conformers, as such properties likely control riboswitch function.
|
Michael Damiani
Grad student
Chemistry
SFU |
A potentiometric comparison of flavoproteins Cryptochrome and Photolyase in their employment of FAD
cofactors for mediating electron transfer.
|
Benjamin Downing
Grad student
Physics
SFU |
Collagen is a triple helical protein
which plays a vital structural role in human connective tissues. I
describe how we intend to study collagen’s mechanical properties, using
an optical tweezers apparatus to stretch individual molecules and measure
their response to the applied force.
|
Didier Falconnet
Post-doc
Physics and Michael Smith Labs
UBC |
High-Throughput Microfluidic Technologies for Systems Studies of
Protein Signaling in Yeast
James Taylor, Didier Falconnet, Antti Niemistö, Stephen Ramsey,
Tim Galitski, and Carl Hansen
Elucidating complex biological networks is of central interest for
understanding cellular function and the mechanisms of disease. Current
experimental techniques generally lack the ability for precise modulation
of environmental stimuli and are limited to averaged measurements of large
populations of cells.
Our microfluidic technology allows for the temporal control of the
microenvironment, enabling the study of complex biomolecular circuits
under time varying stimuli in 256 different experiments (chambers) running
simultaneously. We are currently using our platform to interrogate the
dynamics of MAPK signaling pathways in yeast.
|
Michel Gauthier
Post-doc
Physics
SFU |
Most of the theoretical models describing the translocation of a polymer chain through a nanopore assume
that the polymer is always relaxed during the process. We use Molecular
Dynamics simulations to directly test this hypothesis by looking at the
escape time of unbiased polymer chains. We find that the translocation
process is not quite in equilibrium for the systems studied, even though
the translocation time is about 10 times larger than the relaxation time.
Our most striking result is the observation that the last half of the
chain escapes in less than 12% of the total escape time.
|
Will Guest
Grad student
Experimental Medicine
UBC |
Normally folded prion protein (PrPc)
can undergo template directed misfolding to adopt a pathogenic
conformation (PrPsc) responsible for a range of animal and human
diseases. The short PrPc beta sheet is relatively unstable compared to
the rest of the PrPc globular domain tertiary structure. Recent evidence
suggests that dissociation of the PrPc beta sheet may be an early event in prion misfolding. The Gibbs free
energy of PrPc beta sheet dissociation was estimated to indicate
the likelihood of dissociation by calculating separately the effects of
increased configurational freedom, increased solvation, and hydrogen bond
and salt bridge breakage arising from dissociation.
|
Kamila Gwiazda
Grad student
Cellular and Physiological Sciences
UBC |
Kamila Gwiazda, Ting Yang, James D. Johnson
The link between obesity, characterized by high free fatty acids, and diabetes is emerging. Chronic exposure to the fatty acid palmitate causes beta-cell apoptosis, a critical event in diabetes pathophysiology. Palmitate’s mechanism of action is not fully understood. Palmitate was shown to transiently increase cytosolic calcium levels in MIN6 cells and human beta-cells. Here we show that palmitate treatment results in reversible calcium depletion from the ER, contributing to the increase in cytosolic calcium. Further, we show that the cytosolic calcium signal is generated by flux from both intracellular stores and the extra-cellular space.
|
Shirin Hadizadeh
Grad student
Physics
UBC |
Proteins are chains of amino acids that have been evolutionary designed
to perform a specific biological function. To this end, it is necessary for the protein to adapt a welldefined conformational structure, under specific biological conditions. The
problem of protein folding is that how the onedimensional sequence of amino acids in protein chain determines its native unique
threedimensional structure in space. The information processing is a nonlocal, collective process rather than a trivial translation of message. Proposed Topics:
(1) Protein folding in a confined area; (2) Crowding agents and excluded volume; (3) Protein folding in the presence of a thermal ratchet
|
Mani Hamidi
Undergrad student
Physics
UBC |
Community Structure and Biological Network Organization
Networks (or graphs) provide an analytical method for the representation and systems-level analysis of complex processes such as biological protein-protein and genetic regulatory interactions. The topological and dynamical properties of these networks provide meaningful biological information which may be of value. The modularity in the topology of a network is one of these properties, and its relationship with the dynamical properties a network and
biological measures such as essentiality of individual genes in the network are explored here.
|
Astrid van der Horst
Post-doc
Physics
SFU |
The picoNewton forces that can be
exerted and measured using optical tweezers lie in the force range of
many biomolecular properties and events. However, when probing systems
such as cells or protein networks, the 3D character of such materials
calls for more flexibility in manipulating trapped particles. Holographic
optical tweezers, enabling interactive control over multiple trapped
particles in 3D, supply this flexibility.
In the setup presented here, holographic tweezers are combined with
high-speed (>kHz) camera imaging to perform quantitative force
measurements on biomaterials. Our initial experiments include
investigating the stiffness dependence of a trap on the position of other
traps.
|
Alexandra Jilkine
Grad student
Mathematics
UBC |
Wave-pinning and cell polarity from a bistable reaction-diffusion system
Cell polarization is a process in which various proteins are recruited
to the plasma membrane and segregate at an emergent front or back of the
cell in response to external signals. Many such proteins cycle between
active membrane-bound forms and inactive cytosolic forms. We show that a
biochemical “circuit” of a simple system with a single active/inactive
protein pair with positive feedback to its own activation has an
inherent capability for polarizability that crucially depends on
exchange between active and inactive forms of the chemicals with unequal
rates of diffusion, and overall conservation. We explain the
mathematical basis of this phenomenon, and show how it can account for
spatial amplification, maintenance of polarity, as well as sensitivity
to new stimuli typical in polarization of eukaryotic cells.
|
James Johnson
Faculty
Cellular and Physiological Sciences
UBC |
Regulation of the beta-cell life cycle
by insulin
Beta-cell apoptosis is a critical event in the pathogenesis of type 1
diabetes, but endogenous regulators of the beta-cell life cycle are not
well understood. Our data demonstrate that insulin itself can prevent
apoptosis in human and mouse islets at sub-nanomolar concentrations and
that this involves a previously unexplored calcium signaling pathway.
Surprisingly, higher insulin concentrations often failed to protect
islets. This correlates well with our observations that insulin signaling
in human beta-cells follows a bell-shaped dose-response profile. Thus
insulin has complex autocrine feedback effects on beta-cell survival and
proliferation. Selectively exploiting the pro-survival actions of insulin
or its downstream signaling targets could unlock the potential of
clinical islet transplantation and lead to new therapeutic strategies
aimed at preventing or delaying diabetes. |
Eric Lin
Grad student
Kinesology
SFU |
In adult cardiac cells the established
mechanism of excitation-contraction coupling is by
calcium-induced-calcium-release (CICR) mediated by Cav1.2. However
neonatal cardiomyocytes induce CICR primarily through reverse-mode
Na+-Ca2+ exchanger (NCX) activity. We investigated the spatial
arrangements of NCX and caveolin-3 (cav-3) in developing rabbit
ventricular myocytes with traditional and novel image processing and
analysis techniques. NCX and cav-3 on the peripheral membrane are not
highly colocalized and are distributed in mutually exclusive clusters.
3-D distance analysis revealed that NCX and cav-3 are separated by ~0.5
µm and that this distance is not developmentally regulated.
|
Edwin Moore
Faculty
Cellular and Physiological Sciences
UBC |
Ryanodine receptors (RyR) regulate the
calcium concentration, and therefore the force of contraction, of cardiac
muscle cells. Current models of excitation-contraction coupling, based on
local control theory, assume that all ryanodine receptors are equivalent
and are distributed at dyads; our evidence indicates that this is false.
Using immunofluorescence microscopy, transmission EM, immunoEM and
electron tomography, we find RyR are distributed at dyads, but also in
sarcoplasmic reticulum that is adjacent to caveolae and longitudinal
t-tubules. We describe an algorithm for determining the 3D distances
between RyR clusters; a necessary prerequisite to mathematical modeling
of the calcium transient.
|
Jinhe Pan
Grad
Chemistry
UBC |
The fusion peptide of TBEV is known to
be the only portion of the envelope protein that inserts deeply into
membranes of infected cells to facilitate the viral and host cell
membrane fusion. Previous studies have demonstrated that the minimal
oligomerization state of envelope proteins is trimeric at post-fusion
stage. In the present study, four types of mimic fusion peptides were
designed and chemically synthesized. With the data of secondary
structure, fusogenicity of the peptides and peptide penetration, we
conclude that within the four designed peptides, TFPtr (a trimer mimic)
by itself is able to serve as the best fusion model.
|
Oksana Prychyna
Undergrad student
Chemistry
SFU |
Untranslated RNA is often termed “junk” RNA, but is it truly useless? An example of “junk” RNA discovered relatively recently is the riboswitch, which is composed of an aptamer/ ligand-binding domain, and a platform/communication domain. For the purine riboswitches (guanine and adenine), when their ligands (guanine and adenine respectively) are bound, a conformational change is induced, regulating downstream genes. Riboswitches are of interest to us because unlike proteins, the ligand-induced conformational changes leading to a tertiary structure govern the regulatory activity. It is essential to understand the dynamics of riboswitch conformers, as such properties likely control riboswitch function.
|
David Scriven
Staff
Cellular and Physiological Sciences
SFU |
I am interested in biophysics, excitation-contraction coupling in cardiac muscle and cellular structure. I am a co-presenter with Dr. Edwin Moore.
|
Monica Szczepina
Graduate
Chemistry
SFU |
Investigating the Binding of a Carbohydrate-mimetic Peptide to an Anti-carbohydrate Antibody by STD-NMR Intensity-restrained CORCEMA Optimization (SICO)
Monica G. Szczepina and B. Mario Pinto
Saturation transfer difference (STD) NMR spectroscopy probes the
bioactive solution conformation of MDWNMHAA 1 when bound to mAb SYA/J6.
The ligand topology, or epitope, can be mapped via the CORCEMA-ST
(Complete relaxation and conformational exchange matrix analysis of
saturation transfer) program which performs a total matrix analysis of
relaxation and exchange effects to generate predicted STD-NMR
intensities. Predicted STD-NMR intensities are compared to experimental
data in an effort to identify the global minimum of the bioactive, bound
conformation. The bound conformation is further refined with a simulated
annealing protocol (SICO) to validate the preferred ligand binding mode.
|
Vincent Tabard-Cossa
Post-doc
Physics
UBC |
Solid-State Nanopore Force Spectroscopy
Vincent Tabard-Cossa, Matthew Wiggin, Dhruti Trivedi, Nahid Jetha and Andre Marziali
Nanometer-sized pores in insulating membranes, (nanopores), are emerging
as important tools for the detection and analysis of biomolecules.
Recently, nanopore force spectroscopy has been successfully applied to
the study of DNA-DNA interactions using alpha-Hemolysin pores.
Single molecule force spectroscopy (FS) techniques can observe
biomolecular structure, dynamics, and interactions by exerting forces
directly on an individual molecule and tracking its response as a
function of time. Nanopore FS, employs an electric field inside the pore
to apply controlled forces to a charged molecule.
I will present the work accomplish thus far to expand this nanopore FS
technique to the SiNx solid-state platform, which is more amenable to
technology development. The measurements consist in determining the
dissociation time of the DNA duplex under force which provides knowledge
of the dissociation energy and in turns depends on the nucleotide
sequence of the DNA molecule. To realize what can become a rapid clinical
genotyping assay for personalized health care, work towards the following
specific aims has been pursued: i) Understand and control
DNA/silicon-based nanopore interaction, to extract reliable kinetics from
FS experiments, ii) Optimize electrical noise characteristics of ionic
current through solid-state nanopores, to improve SNR iii) Design and
test DNA probe properties (e.g. length, bead type) best suited to perform
solid-state nanopore FS.
|
Andrew Tait
Grad student
Chemistry
UBC |
The bottlenecks in studying the structure and function of biologically-significant membrane proteins have
been the lack of high yields of pure membrane protein in their
native-state, and subsequent inability to study said protein by
techniques that produce high-resolution structural data. Here, we
describe methods that provide high yields of U24, a membrane protein from
Human Herpesvirus Type-6 (HHV-6), and experimental procedures that offer
a wealth of information about the secondary, tertiary and overall
structure and function of this protein. Based on the available data, we
can hypothesize about possible mechanisms for U24’s involvement in
multiple sclerosis.
|
Xiaohui Yao
Grad student
Chemistry
SFU |
Many biological events, such as
enzyme-substrate recognition, require coordinated interaction at critical
subsites. For UDP-galactopyranose mutase, this recognition is assisted by
sampling of distinct protein conformers, specifically, a dynamic
equilibrium between “open” and ”closed” states of the “recognition loop”.
We show that the substrate-enzyme interactions at the cofactor (FAD)
subsite and the Trp160 subsite coordinate each other so that protein
dynamics are utilized in substrate recognition.
|
