Chemistry

Chemistry
Room:
Session
E
19 Baxter
Searching for Anomalies in the Lengths of Transmembrane Alpha Helices
Amarise Little
Mentors: William Clemons and Axel Müller
Proteins in the transmembrane region coil into alpha helices, and cross the cell membrane in a perpendicular
manner. Identifying anomalies, such as re-entrant loops or helices that cross the membrane diagonally, can be
helpful in determining the topology of a certain protein. The objective was to find, among transmembrane proteins,
these helices of anomalous lengths. Using a database of proteins with transmembrane regions, lengths of all
transmembrane alpha helices were calculated. This was done by using the coordinates of the predicted membrane
region in conjunction with the transformed coordinates of the atoms associated with a certain protein. This helped
differentiate the transmembrane atoms from the atoms outside of the membrane. Lengths of chains inside of the
membrane were obtained by counting the number of residues in a contiguous chain of atoms. After calculating the
lengths of chains, it is seen that the lengths, from about 1800 proteins, results in a normalized distribution, with
lengths above the 95th percentile showing anomalies in their transmembrane structures.
MySQL Bioinformatics Database Construction
Nauman Javed
Mentors: William Clemons Jr. and Axel Müller
Bioinformatics databases such as GenBank and Uniprot have become key tools in modern proteomic and genomic
analysis. However, the utility of these databases is often limited by inconsistencies in accession numbers, sequence
annotations, and genomic locations, which creates redundancies and difficulties in advanced queries and interdatabase mappings. In this project we seek to consolidate several gene and protein databases into a centralized
MySQL database with non-redundant gene to protein mappings, sequence annotations, and source information.
The database will also pre-calculate common bioinformatics features including computationally heavy parameters
such as transmembrane domain locations and mRNA secondary structure. Such a database will allow for the
efficient processing of advanced queries that are otherwise difficult with the currently available databases.
Effect of Mismatches on Spin Selectivity of Electron Transmission Through Double-Stranded DNA
Sylvia Hürlimann
Mentors: Jacqueline K. Barton and Theodore Zwang
In recent years, double stranded DNA (dsDNA) has been shown to have a large spin polarization in electron
transmission that is several orders of magnitude larger than what the current theory predicts. A study of how
mismatches affect the spin polarization of dsDNA could shed light to the biological implications of the effect and
help improve the theory. Alkyne labeled dsDNA was attached to a self-assembled monolayer of 12-azidododecane1-thiol on nickel surfaces using a Cu(I) catalyzed azide-alkyne cycloaddition in order to inject a current in the
dsDNA and vary its spin polarization. Progress has been made towards attaching the dsDNA to nickel and
investigating the effect that mismatches in dsDNA has on spin selectivity. Further measurements need to be made
using chronoamperometry and chronocoulometry to quantify the effect that mismatches have on spin polarization
of dsDNA.
Oligosaccharide and Glycopeptide Glycan Analysis Utilizing Gas-Phase Free Radical and Acid-Catalyzed
Reactions
Lily Chen
Mentors: Jesse L. Beauchamp and Daniel Thomas
While the significance of glycans in organic processes has been increasingly demonstrated, the structural
complexity of glycans inhibits effective analysis. Consequently, there has been a continued search for improved
methods of examining glycans. We sought to determine the effectiveness of biomimetic reagents PRAGS, FRAGS, I
and FRAGS II (Figure 1) and develop a protocol for studying glycoprotein glycans. Though not every glycan was
subjected to all variations, model oligosaccharide samples containing Man5GlcNAc2, lewis-B-tetrasaccharide, lewisY-tetrasaccharide, lacto-N-fucopentaose V, LNDFH I, lacto-N-tetraose, maltoheptose, NA2 and M3N2 have been
used to test derivatization levels under different reaction conditions. Furthermore, model glycan samples were
subjected to LTQ mass spectrometry, reverse phase liquid chromatography mass spectrometry (RP-LC-MS), and
hydrophilic interaction liquid chromatography mass spectrometry (HILIC-ESI-MS) in order to identify the best
equipment for examining sample contents. In addition, the purification process of glycans from glycopeptides is
being refined using fetuin, IgG, RNase B, and ovalbumin. Thus far, MeFRAGS has been shown to derivatized Nlinked glycans poorly. In addition, HILIC-ESI-MS has been shown to produce the clearest amount of accurate
signals in spectra, so upon successful development of optimal purification and derivatization protocol, results will
indicate the effectiveness of PRAGS and FRAGS towards glycans from glycopeptides.
Figure 1. Biomimetic reagents for mass spectrometric sequencing of glycans. Blue box shows functional group for
coupling to glycans; red oval shows free radical precursor. Bond highlighted in red undergoes homolytic cleavage
to generate radical.
Development of a Dielectric Barrier Discharge Ionization Imaging Mass Spectrometer (DBDI-IMS)
Andrew Lucas
Mentors: J. L. Beauchamp, Josh Wiley, Daniel Thomas, and Kevin Barraza
Imaging mass spectrometry uses mass spectrometric techniques to map the spatial distribution and abundance of
specific chemicals on a surface such as a tissue sample. Our approach employs a dielectric barrier discharge
ionization (DBDI) source to implement plasma-based ionization of surface analytes at atmospheric pressure for
mass spectrometric analysis. Chemical analysis is performed using a Thermo Scientific LTQ-XL mass spectrometer
equipped with an atmospheric pressure inlet for ion sampling. When combined with an x-y translation stage, this
experimental methodology can be used to scan a surface and develop a two-dimensional image showing the spatial
distribution and abundance of analytes on the surface. A key goal in our effort has been to achieve high spatial
resolution (small pixel size) while maintaining reasonable sensitivity for detection of targeted analytes. Several
designs for the ionization sources and ion sampling interface to the mass spectrometer were tested to determine
spatial resolution and detection sensitivity. The implementation of a system for DBDI-IMS, the factors that
determine spatial resolution, and initial results are presented. Spatial resolution of 2 mm has been achieved, with
the potential for significantly smaller pixel size employing an improved source and collector design.
Development of a Scalable and Efficient Computational Framework for the Structure Prediction of
G Protein-Coupled Receptors
Christina Lin
Mentor: Ravinder Abrol
G protein-coupled receptors (GPCRs) are a family of membrane proteins that control cellular response. Each GPCR
exists in multiple conformations, differing in helix tilts and rotations. Identification and analysis of the lowestenergy conformations of GPCRs are essential to understanding the proteins’ function. The BiHelix and SuperBiHelix
methods are able to completely sample the conformational space available to GPCRs in the lipid bilayer
environment, which spans from 35 million to 10 trillion possible conformations per starting structure. The existing
program runs on a fixed number of 12 processors by assigning each helix pair’s conformational sampling to one
processor, as the first attempt at this parallel sampling problem. The program will be rewritten using two different
parallelization strategies to be able to utilize any number of available processors, based on conformations rather
than helix pairs. One strategy implements a Python language library called Jug, and the other is written from
scratch. The better parallelization strategy will be chosen for the final implementation to facilitate an efficient
conformational sampling of GPCRs, reducing the time needed for structure prediction by at least half.
Structure Determination of Free Fatty Acid Receptors
Stefan J. Grampp
Mentor: Ravinder Abrol
This project aimed to determine accurate structures of the human free fatty acid receptors FFA1, 2, 3, and 4.
These proteins were modeled with GEnSeMBLE structure prediction methodology, combining homology-based and
ab initio methods.
The extent of the transmembrane helices was determined by a consensus of secondary structure prediction
algorithms. The shapes of these helices were determined by assuming homology with the transmembrane helices
of three similar human proteins, CXCR1, PAR1, and HT2BR. Another set of helical shapes was determined ab initio
via extensive molecular dynamics modeling starting from a straight helix. The helices were then placed in a bundle
based on a template GPCR, and bi-helical interaction energies were evaluated to determine the most stable
rotation angle for each helix.
The structures produced via the homology methods and those produced ab initio were then energetically compared
to find the most stable structures overall. Helical interaction energies were then re-evaluated for the best
structures using helix rotation and helix tilt angles to produce final structures. These structures will be used to
model ligand binding sites and then to screen for novel molecules that could serve as therapeutics targeting free
fatty acid receptors.
Rotational Spectra and Structure of Valproic Acid
AbhijitKrishna V. Puranam
Mentors: Geoffrey Blake and Brandon Carroll
This work examined the spectra of valproic acid in the microwave region to determine its rotational spectra and its
structure. This compound is used in the pharmaceutical industry in the treatment of epilepsy and bipolar disorder,
but the mechanism by which the compound treats these disorders is not fully understood. The spectra will allow the
exact structure of valproic acid to be determined which will be useful to clinical research regarding this compound.
To obtain this spectra a chirped pulse, microwave, Fourier transform spectrometer was used from 8 to 17 GHz.
Improvements in this technique in ultra-cold environments (2 K) allow relatively easy elucidation of rotational
spectra and molecular structure. These spectra were then fitted to theoretically generated spectra which were
based ab initio calculations of the structure of valproic acid. Thus, the final rotational constants and molecular
structure of Valproic Acid were determined.
Phosphine Catalyzed Asymmetric Intermolecular Oxygen γ-Addition
William Reichard
Mentors: Gregory C. Fu and Daniel Ziegler
There exist many methods which can be used to introduce stereocenters into the alpha and beta positions of
carbonyl compounds, however there are few known methods which can be used to introduce stereocenters in the
gamma position. A phosphine catalyzed process for the asymmetric gamma addition of oxygen nucleophiles to
carbonyl compounds is under development. Conditions which currently offer the best yield (85%) and high
enantiometric excess (96%) are shown below.
tBuO2C
OMe
OMe
PMB-OH
2.0 equiv
10% (R)-SP
toluene, r.t.
0.25 M, 24 h
tBuO2C
85 % yield
OPMB 96% ee
Mechanistic Studies of Nickel-Catalyzed Negishi Couplings of Unactivated Alkyl Halides
Saaket Agrawal
Mentors: Gregory C. Fu and Nathan D. Schley
Cross-coupling chemistry with unactivated alkyl halides can potentially be a powerful and general method for C-C
bond formation. Though significant improvements have been made to catalytic conditions, mechanistic
understanding remains limited. Herein, we describe progress towards mechanism elucidation of nickel-catalyzed
Negishi couplings of unactivated alkyl halides. EPR studies of our system have shown the presence of a Ni(I) alkyl
intermediate in the catalytic mixture, a departure from the Ni(II) resting state recently shown to exist in the nickelcatalyzed Negishi arylation of propargylic halides. This suggests that the mechanism of catalysis may be a function
of nucleophile and electrophile identity. Further studies are aimed at a deeper understanding of the mechanism.

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