MBTP Students



	Andrew Markley Advisor: J. Dixon Chemistry & Biochemistry Year: 4	Jeff Noel Advisor: J. Onuchic Physics Year: 4
	David Erickson Advisor: T. Hwa Physics Year: 3	Andro Rios Advisor: Y. Tor Chemistry & Biochemistry Year: 3
	Brian Fugelstadt Advisor: E. Komives Year:	Eric Salgado Advisor: A. Tezcan Chemistry & Biochemistry Year: 4
	Michael Jamros Advisor: P. Jennings Chemistry & Biochemistry Year: 3	Diana Schlamadinger Advisor: J. Kim Chemistry & Biochemistry Year: 4
	Janina Moretti Advisor: Muller Year: 3	Yan Wang Advisor: S. Opella Chemistry & Biochemistry Year: 3

	Ingrid Devries Advisor: E. Komives Chemistry & Biochemistry	Ariane Jansma Advisor: T. Handel Chemistry & Biochemistry
	Carla Cervantes Advisor: E. Komives Chemistry & Biochemistry	Greg Hannum Advisor: T. Ideker
	Benjamin Andrews Advisor: P. Jennings Chemistry & Biochemistry	Byron Hetrick Advisor: S. Joseph Chemistry & Biochemistry
	Cecilia Cheng Advisor: S. Taylor Chemistry & Biochemistry	Stanley Howell Advisor: S. Opella Chemistry & Biochemistry
	Audrey Fischer Advisor: M. Montal Biology	Jeffrey Kearns Advisor: A. Hoffman Chemistry & Biochemistry
	Derek Fuller Advisor: D. Smith Physics	Anna-Clare Milazzo Advisor: Xuong Physics
	Ilya Gertsman Advisor: J. Johnson Chemistry & Biochemistry	Paul Whitford Advisor: J. Onuchic Physics
	Amy Davenport Advisor: E. Komives Chemistry & Biochemistry	Cathrina Salanga Advisor: T. Handel Chemistry & Biochemistry

	Melissa Wong Advisor: Chemistry & Biochemistry	Mikolai Fajer Advisor: J.A. McCammon Chemistry & Biochemistry
	Nick Treuheit Advisor: Chemistry & Biochemistry


Benjamin Andrews bandrews@ucsd.edu Department: Chemistry & Biochemistry Advisor: Pat Jennings
The protein folding problem is an issue that has gained attention since the sequencing of the human genome. How can a protein fold into a unique 3-Dstructure from the amino acid sequence; can we predict protein structure from an amino acid (and thus, DNA) sequence? Currently I am working on the folding of GFP, a widely used molecular marker. Using both computational modeling techniques as well as experimental stability and folding determinations, we hope to improve on the folding rate of GFP and related variants in its use as a protein folding & stability reporter.

Cecilia Cheng C2cheng@ucsd.edu Department: Chemistry & Biochemistry Advisor: Susan Taylor


Ingrid Devries idevries@ucsd.edu Department: Chemistry & Biochemistry Advisor: Elizabeth Komives
I am studying the folding and stability of the ankyrin repeat protein IkBa, which undergoes two folding transitions. The first folding transition occurs when IkBa is free, the second appears to be coupled to binding to NF-kB. Based on simulations, we have identified a number of mutation that should affect the first or second folding transitions. I will characterize the folding behavior of these mutants by determining the folding phi values to help determine the physical characteristics of ankyrin repeat proteins that causes them to fold.

Mikolai Fajer mfajer@gmail.com Department: Chemistry & Biochemistry Advisor: J.A. McCammon


Audrey Fischer Audreyf@ucsd.edu Department: Biology Advisor: Maurice Montal
I am studying the ion channel properties of the botulinum neurotoxin (BoNT), the most potent toxin known. BoNT is a dichain peptide: the heavy chain (100kD) forms an ion channel under endosomal conditions to 'chaperone' the light chain (50kD) protease and release it to the cytoplasm where it can cleave its substrate SNARE protein. One of the most intriguing properties of the BoNT is its conformational change triggered by a pH change. At pH 7.0 the holotoxin is inert and harmless; however lowering to endosomal pH 5.5 changes the heavy chain conformation into an active ion channel and partially unfolds the light chain. The heavy chain channel facilitates the translocation of the light chain across the membrane where it is released. A major goal of this project is to understand the novel modality of BoNT chaperone activity: protein conducting/translocating channels. We have developed a neuronal system to characterize the channel and chaperone activities of BoNT under conditions which closely emulate those prevalent at the endosome, and which are relevant to the neurotropism and neuroparalytic effects of BoNTs. We have also developed an in-vitro fluorescence assay to monitor BoNT enzymatic activity resulting from translocation of the light chain by the heavy chain channel.

Derek Fuller dfuller@physics.ucsd.edu Department: Physics Advisor: Doug Smith
I will be using optical tweezers to study packaging of the viral genome in the capsid of Phi29 and possibly other bacteriophages. Publications: D. N. Fuller, G. J. Gemmen, J. P. Rickgauer, A. Dupont, R. Millin, P. Recouvreux and D. E. Smith. A general method for manipulating DNA sequences from any organism with optical tweezers. Nucleic Acids Research, 2006, Vol. 34, No. 2 e15.

Ilya Gertsman gertsman@ucsd.edu Department: Chemistry & Biochemistry Advisor: J. Johnson
A number of bacteriophage and viruses (including lambda and Herpes) assemble into a precursor capsid that undergoes a maturation upon nucleotide packaging. We are studying the structure and expansion mechanism of HK97, a lambda like phage. The structure of the Procapsid is being studied using x-ray crystallography while intermediates of the expansion pathway are being probed with Hydrogen/Deuterium exchange coupled with mass spectrometry. The goal is to understand the properties of the HK97 fold and protein-protein interactions that facilitate the massive capsid reorganization and expansion the phage undergoes.

Greg Hannum ghannum@ucsd.edu Department: Advisor: T. Ideker


Byron Hetrick bhetrick@chem.ucsd.edu Department: Chemistry & Biochemistry Advisor: Simpson Joseph
Our lab studies the mechanism of translation in the eubacterial ribosome. The ribosome is the most common target for antibacterial drugs so, understanding the mechanism of protein synthesis is essential in understanding how many current drugs work and will aid in the design of future antibiotics. The focus of my research is understanding how the ribosome selects the correct tRNA based upon the interaction of the codon of the mRNA with the anticodon of the tRNA in the A-site of the ribosome. I an studying the kinetic mechanism of A-site selection using pre-steady state kinetics and fluorescence-based techniques.

Stanley Howell schowell@ucsd.edu Department: Chemistry & Biochemistry Advisor: S. Opella
The ability to obtain high-resolution structural information on integral membrane proteins associated with a bilayer environment continues to represent a bottleneck by conventional structure determination methodology. These lipo-protein mixtures have proven difficult to crystallize and the size of the ensemble creates long correlation times, drastically reduces the effectiveness of solution-state NMR techniques for NOE based structure determination. The current focus of research is the development of NMR techniques for the observation and utilization of anisotropic interactions for structure determination of membrane proteins. The integral membrane proteins of the mer operon: MerF (81 residues), MerT (116 residues), and MerC (153 residues), are being applied as test systems for developing the necessary methodology for expanding current techniques toward polytopic proteins of increasing complexity as well as the elucidation of the mechanistic details of the bacterial mercury detoxification system.

Michael Jamros mjamros@ucsd.edu Department: Chemistry & Biochemistry Advisor: Pat Jennings
Protein kinases play a prominent role in cell growth and therefore are promising targets for drug design for combating various cancers. The Src family of tyrosine kinases are an important group of enzymes that are up-regulated in many cancers, notably breast and colon cancer. These enzymes present an attractive chemotherapeutic target. Due to the abundance of kinases, finding unique binding surfaces is necessary in the design of selective inhibitors. To find these binding surfaces it is important to understand how the Src enzymes are naturally regulated and how they use molecular cross-talk to engage large substrate proteins. Two functionally distinct enzymes, Csk (C-terminal Src kinase) and Chk (Csk homologous kinase), down-regulate the Src kinases. While both Csk and Chk down-regulate Src and have a high homology (55% identity), the two differ in expression pattern, subcellular localization, and substrate selectivity. I am characterizing the interaction observed between Chk and Src by investigating the molecular factors that control this interaction and impact the mechanism of Src down-regulation. Additionally, I am working to further elucidate how Csk operates in regulating Src.

Ariane Jansma ajansma@ucsd.edu Department: Chemistry & Biochemistry Advisor: T. Handel
My Current research project is focused in several areas. The first part involves the expression and structural characterization of the chemokine Mec using 3- and 4-dimensional heteronuclear NMR experiments as well as X-ray crystallography if the protein is amenable. The second part involves the expression and biophysical analysis of the 7-transmembrane chemokine receptors D6 and Duffy. Techniques for biophysical analysis will include mass spectrometry to characterize the presence and homogeneity of post-translational modifications, 19F NMR to examine structural homogeneity, and EPR analysis. Our lab is also initiating a concerted effort in the EPR analysis of the chemokine receptor CCR1. Finally, I am interested in studying the two specific receptors for MEC, CCR10 and CCR3, in terms of ligand/receptor interactions using techniques such as NOE experiments to examine distance/contact information. Overall, I am hoping to combine my previous experience in NMR spectroscopy of small molecules with these new techniques in order to gain a thorough knowledge of the structure and function of these complex chemokine/receptor systems.

Jeffrey Kearns jkearns@chem.ucsd.edu Department: Chemistry & Biochemistry Advisor: Alex Hoffman
The NFkB family of transcription factors is comprised of dimeric associations of five NFkB protein monomers. These dimers are held in a latent form in the cytoplasm by IkB inhibitor proteins and translocate to the nucleus upon inducible degradation of the IkBs. Each NFkB dimer activates overlapping but distinct gene expression programs that include the genes for NFkB monomers and IkB inhibitors. Complexity in this signaling network arises from the temporal, stimulus, and cell-type specific activation of individual dimers as well as both negative and positive feedback mechanisms. My research project involves tightly integrated computational and biochemical studies to explore network complexity and the mechanisms through which stimuli elicit specific network responses. Three projects I am currently exploring include the interplays between cellular localization and inducible IkB degradation, negative feedbacks provided by individual IkBs, and positive feedbacks provided by inducible NFkB monomers. Kearns, J. D., S. Basak, et al. (2006). "IkBe provides negative feedback to control NFkB oscillations, signaling dynamics, and inflammatory gene expression." J. Cell Biol. 173(5): 659-664

Andrew Markley markley@ucsd.edu Department: Chemistry & Biochemistry Advisor: Jack Dixon
Almost every species of bacteria use some form of antimicrobial defense to establish a niche in their respective environments. Working with colleagues in the Dixon, Nizet, and Dorrestein labs, I have discovered a new, widely distributed class of antibiotic biosynthetic gene clusters. We have determined that enzymes within these operons post-translationally modify small, ribosomally encoded prepropeptides into antimicrobially active molecules. It is my goal to characterize the enzymatic activity of these biosynthetic enzymes and determine the final structure of the antibiotic peptides.

Anna-Clare Milazzo amilazzo@physics.ucsd.edu Department: Physics Advisor: Xuong


Jeff Noel jknoel@ucsd.edu Department: Physics Advisor: Jose Onuchic
Coarse-grained structure-based models of protein folding have been shown to correctly reproduce folding mechanisms. These models allow for a tremendous amount of sampling. I have developed a structure-based model that includes a closer approximation to the real protein geometry by including all the heavy atoms, as opposed to only having beads at the positions of the alpha-carbons. I am applying this model in two directions. First, this model is currently investigating the information contained in the packing of side-chains during folding. Second, I am looking at native state dynamics. The folding landscape is the same landscape on which the dynamic fluctuations the protein's function depends on take place. Since structure-based models describe folding well, I am able to look beyond folding into conformational motions of the folded state. Several groups have attempted to use short time scale molecular dynamics with empirical forcefields to connect with long time scale motions captured with experiments. With the longer time scales available to structure-based models I will explore the connection between short time scales and long time scales in protein dynamics. [1] Whitford, P.W., Noel, J.K., Gosavi, S., Schug, A., Onuchic, J.N., An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with Empirical Forcefields. Proteins: Structure, Function, Bioinformatics, Volume 75 (2), 1 May 2009, Pages 430-441. [2] Suzuki, Y., Noel, J.K., Onuchic, J., An analytical study of the interplay between geometrical and energetic effects in protein folding. Journal of Chemical Physics, Volume 128, 8 January 2008, Pages 025101-(1-6).

Andro Rios acrios@ucsd.edu Department: Chemistry & Biochemistry Advisor: Yitzhak Tor
The structural diversity and catalytic ability of RNA continues to inspire and motivate scientists to obtain a better understanding of this molecule. With a desire to be part of this intriguing field of study, I am designing and synthesizing fluorescent nucleosides that closely resemble the natural RNA nucleosides in terms of size, shape and hydrogen-bonding capabilities. With these newly developed fluorescent nucleosides I can exploit their photophysical characteristics to serve as probes for my studies relating to RNA tertiary structure and for specific mechanistic investigations involving ribozymes.

Eric Salgado esalgado@chem.ucsd.edu Department: Chemistry & Biochemistry Advisor: A. Tezcan
Metal coordination is an essential structural element in many systems, such as the zinc-finger proteins and calcium-binding EF hand motifs. In many instances, metals are also central to mediating protein-protein interactions, as observed during cellular metal transport. My research is aimed towards the goal of designing and constructing novel metal-binding motifs on protein surfaces that will serve to guide protein-protein interactions under the control of metal coordination. By rationally designing protein-protein interfaces that can be controlled as such, one could potentially gain the ability to manipulate cellular processes while, at the same time, forming functional protein complexes and crystal lattices.

Diana Schlamadinger dschlama@chem.ucsd.edu Department: Chemistry & Biochemistry Advisor: J. Kim
Antimicrobial peptides (AMPs) play an essential role in the innate immunity of multicellular organisms and serve as a defense against bacterial infection. Some AMPs, such as human neutrophil peptides (HNPs), may function by forming oligomeric structures within the membrane of bacteria allowing for leakage of cell contents. Elucidating the mechanism by which HNPs insert into model membranes advances current understanding of the activity of AMPs. We aim to probe molecular mechanisms of HNP-membrane interactions by measuring the evolution of secondary structure, hydrogen bonding states, and local solvent environments of the backbone and aromatic amino acids using various spectroscopic methods such as absorbance, fluorescence, circular dichroism (CD), and UV resonance Raman spectroscopy (UVRR). Effects of Tryptophan Microenvironment, Soluble Domain, and Vesicle Size on the Thermodynamics of Membrane Protein Folding: Lessons from the Transmembrane Protein OmpA K.M. Sanchez, J. E. Gable, D. E. Schlamadinger, and J.E. Kim. Biochemistry, 2008, in press. Foster Resonance Energy Transfer and Conformational Stability of Proteins: An Advanced Biophysical Module for Physical Chemistry Students K.M. Sanchez, D. E. Schlamadinger, J. E. Gable and J.E. Kim. J. Chem. Educ, 2008, 85, 1253.

Yan Wang yaw004@ucsd.edu Department: Chemistry & Biochemistry Advisor: S. Opella
The focus of my current research is to determine the structure of virus protein "u" (Vpu) from HIV-1 and its interaction with the CD-4 receptor using both solution- and solid-state NMR techniques.

Paul Whitford pwhitfor@physics.ucsd.edu Department: Physics Advisor: J. Onuchic
I am developing simplified models to describe allosteric conformational changes in proteins. Using these models I am studying the relationship between protein structure and protein function and am exploring the energetic landscapes of conformational changes.

Amy Davenport adavenpo@ucsd.edu Department: Chemistry & Biochemistry Advisor: E. Komives
The repeating, almost slinky-like, structure of IκBα; allows for interesting studies of the dynamical properties, most of which have been bulk/ensemble average experiments that have given much insight into the folding and binding actions. However, these studies tell us little about what a single protein is doing at any given time. To study this, I will be using an optical method, FRET, as a sort of molecular ruler to look at single molecule dynamics. I hope to bridge computer-based molecular dynamics simulations with my bench work to come out with a more complete picture of what IκBα; does as a "kicking and screaming stochastic model" in real time.

Cathrina Salanga csalanga@ucsd.edu Department: Chemistry & Biochemistry Advisor: T. Handel
Chemokines are involved in leukocyte migration associated with routine immune surveillance, as well as induced migration in response to events such as injury or infection; however, inappropriate expression or utilization of chemokines and their receptors has been shown to result in numerous inflammatory diseases. Therefore my research aims to elucidate the molecular mechanisms of chemokine:receptor binding and receptor activation. Currently, I am using H/D exchange with Mass Spectrometry to identify the respective binding epitopes on a chemokine receptor and ligand, though the results may also reveal dynamic and conformational changes associated with activation or antagonism of the chemokine receptor. Information gleaned from these studies will guide more directed studies of the receptor-ligand interactions and complement other ongoing studies chemokine receptor-ligand interactions in the Handel lab.

Melissa Wong Department: Chemistry & Biochemistry Advisor:
It is well established that the transcriptional master circuit, the Major Immediate Early (MIE) circuit, of human cytomegalovirus (CMV) drives CMVs transcriptional cascade and all downstream viral gene expression. However, the mechanisms governing CMVs diverse viral lifecycle choices, especially latency, remain unknown. Using a coupled computational-experimental approach, I am studying the feedback mechanisms that may contribute to the MIE circuits control of its lytic and latent states.

David Erickson Department: Physics Advisor: Terry Hwa
The lack of a nuclear membrane in prokaryotes allows translation and messenger RNA degradation to start before transcription has completed. The simultaneity of the processes results in a coupling that has vast implications for the regulation of protein expression. While transcription is expected to affect translation, translation also affects transcription and both processes affect mRNA degradation. Although the couplings are unavoidable in prokaryotes and apply to the expression of every prokaryotic gene, this level of genetic regulation is widely overlooked relative to the large amount of work on transcriptional regulation. I study the molecular mechanisms responsible for the couplings and plan to integrate them into a comprehensive computational model of transcription-translation-degradation coupling. I will explore the implications of this model and verify predictions experimentally.

Janina Moretti Department: Chemistry & Biochemistry Advisor: Muller
Our aim is to understand on a structural level how amino acid/peptide cofactors can help RNA function. As a model system, we are using a catalytic RNA (ribozyme) that is able to polymerize RNA in a template-dependent fashion. This RNA is small enough for structural studies but large enough to display sophisticated functions such as binding and aligning two substrates and catalyzing a multi-turnover reaction that can be quantified very reproducibly. Our first results show that an arginine cofactor positioned near the active site improves ribozyme polymerization. This effect is weak, probably because the ribozyme was never adapted to the presence of cofactors. To adapt the ribozyme to these cofactors we are performing an in vitro selection in the presence of the cofactors. After this selection, we will study the interplay between ribozyme and cofactors, to understand why RNA needs proteins.

Carla Cervantes Department: Chemistry & Biochemistry Advisor: E. Komives
One of the reasons why functional proteins might be unfolded or partly folded in vivo is the relative ease and rapidity by which they can be degraded when not in complex with their biological target. Preliminary data indicate that the ankyrin repeat domain of IkBa may be incompletely folded in the absence of NF-kB. The overall goal of this project is to test this hypothesis by comparing the structure and dynamics of the IkBa protein free in solution and in complex with NF-kB. The project consists of two major specific aims, one concerned with NMR characterization of free IkBa[67-287] and the other with the complex between IkBa and NF-kB. This should give important information on the extent to which the flexibility of IkBa observed in the free protein is preserved in the complex. Since the function of IkBa is so intimately related to its folded state, the experiments described herein should provide not only a detailed characterization of the free form of IkBa, but also important insights into its function in vivo through characterization of its complex with NF-kB.