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Faculty and Senior Scientists

Bill DeGrado  Please click here for more information.

Paul Billings  Platelet adhesion to collagen in vessel walls is the initial event in thromus (blood clot) formation. My research focuses on the role that integrin α2β1, a major collagen receptor on the platelet surface, plays in platelet adhesion. We have developed a series of small molecule antagonists that block integrin activation and ligand binding. The goal of this work is to develop anti-thrombotic agents, which will reduce platelet adhesion and subsequent heart attacks and stroke.

Postdocs

	Shalom Goldberg (C.V.) I am working on the E. coli Tar protein – a membrane-spanning aspartate receptor involved in chemotaxis. Tar is part of a 2-component system that allows E. coli to swim toward higher concentrations of aspartate. I am using de novo protein design to alter the activity of the receptor. I am also characterizing both native and mutant forms of Tar structurally and biophysically. This work is in collaboration with Mark Goulian’s lab. I am also involved in using computational design to generate proteins with novel enzymatic activities.
	Bryan Berger (C.V.) Our work is directed at understanding factors that influence homo- and heterooligomerization of transmembrane helices, with particular emphasis on integrins, and how these processes influence cell signaling. Integrins are a diverse family of heterodimeric, single-pass transmembrane (TM) proteins consisting of an α and β-chain that are involved in cell-cell and cell-matrix interactions such as tissue migration, adhesion and cancer metastasis. Our group has developed a “push-pull” model for regulating integrin function based on integrin αIIbβ3, in which the TM portions of the heterodimer remain associated in the inactive state, then dissociate upon activation. We are extending this model to a wide range of other integrins. Additionally, we are developing novel genetic approaches that can be used to examine specificity of TM homo- and heterooligomers. Using these approaches, we have identified novel sequences that can target a given TM helix, particularly integrins such as αIIb.
	Ilan Samish  The function of many transmembrane (TM) proteins depends upon specific dynamic interactions between TM helices. To better understand these important and yet enigmatic interactions, hierarchical clustering and biophysical characterization of TM proteins will be conducted. The knowledge gained from these studies will be applied to study integrins, a medically important class of TM proteins. The dynamic binding between integrin subunits, which is mediated via TM helices, controls integrin function. Although their TM sequences are very similar, different integrins interact in a specific and highly regulated manner and are therefore an ideal model system to test functional interprotein recognition within the membrane environment. Molecular dynamics will be used to study specific integrins. The gained insight will be integrated into computational protein design methods with the aim of designing de novo TM helices that bind specifically to integrin TM helices. The designed proteins will be synthesized and experimentally characterized.
	Amanda Reig (C.V.) Di-iron carboxylate enzymes are utilized by nature to catalyze a wide variety of oxidation reactions, including the conversion of methane to methanol, the formation of desaturated fatty acids, and the generation of a tyrosyl radical that facilitates the biosynthesis of deoxyribonucleotides. Their divergent reactivities, however, belie their structural similarities. We seek to comprehend the metal-protein interactions that govern the reactivities of the di-iron carboxylate enzymes at a molecular level by developing a model system which accurately mimics the geometric, electronic, and catalytic properties of the natural enzymes. Advances in computational protein design have led to the development of a self-assembling four-helix bundle that contains a di-iron carboxylate active site (DFsc). This scaffold is well-suited for systematic investigations of the structure/function relationships found in the natural di-iron carboxylate enzymes as it is easily modifiable via point mutations and it mimics not only the first, but also the second and third, coordination spheres of the natural di-iron cluster. Structural characterization of DFsc and variants is being undertaken utilizing X-ray crystallography. In addition, we are investigating the redox potentials and catalytic abilities of these proteins as a function of their structural variations. Finally, as a test of our understanding of the structure/function relationships present in the natural di-iron carboxylates, we are computationally redesigning DFsc to enhance its catalytic efficiency via stabilization of postulated catalytic intermediates.
	Cinque Soto (C.V.) My overall goal is to develop a suite of computational methods that can be used in de novo protein design and structure prediction. Currently, I am focusing on extending homology modeling methods so that they can be applied to computational protein design. As a first step toward this goal, I have begun developing a local backbone sampling algorithm that can incorporate external restraints. This sampling algorithm will be useful in providing backbone flexibility in de novo protein design.
	Rudresh Acharya (C.V.) I am interested in crystallographic work on membrane proteins. In the DeGrado lab I am working on the crystal structure determination of transmembrane domain (TM) of avian influenza proton channels; AM2 and BM2. The function of the channel is essential for viral replication. Recently, we have determined the crystal structures of apo and drug (Amantadine) bound forms of AM2TM protein at high and low resolution respectively.
	Ivan Korendovych (C.V.) I’m working on characterization of de novo porphyrin binding membrane peptides and protein crystal engineering.
	Jade Qiu  Library selection and rational design are complementary strategies for ligand discovery. Both have been employed extensively to generate ligands for soluble proteins. While our group has shown that computationally designed peptides specifically recognize the trans-membrane helices of integrins, it is not clear yet whether peptide ligands to specific trans-membrane targets can be selected from on-bead libraries. I am currently exploring such possibilities with a peptide library designed to target integrins. With this project we aim to (1) optimize selection conditions for membrane peptides; (2) generate peptide ligands with specific activities in lipid bilayer; and (3) elucidate the biological functions of selected membrane peptides.
	Jason Donald (C.V.) Personal Page I am interested in the modeling and design of membrane protein interactions, particularly those that use ionizable groups (arginine, lysine, aspartic acid, and glutamic acid) to make stable interfaces. Such interactions play an important role in immune response and coagulation. To have a better understanding of these interactions, we are computationally modeling several proteins, such as gpVI and the T-cell receptor, that interact using ionizable residues in the membrane. When the models have been validated experimentally, we will design peptides that specifically bind natural proteins using ionizable groups in the membrane. Such peptides could allow the manipulation of several important health-related protein systems, including those related to heart and infectious diseases.
	Jon Rudick (C.V.) I am developing specific, potent inhibitors of 1) integrin α2β1 and 2) glycoprotein 120 (gp120) as tools for validating the role these biological targets play in thrombosis and HIV entry, respectively. Integrin α2β1 is a major receptor for collagen, which is a strong platelet agonist and a component of the extracellular matrix. We aim to demonstrate that that inhibition of integrin α2β1 with small molecule antagonists will result in biologically significant inhibition of adhesion and platelet activation. HIV entry into cells involves interaction between the viral envelope protein gp120 and at least two membrane proteins on the target cell, CD4 and a co receptor (e.g., CCR5). We hypothesize that a sulfotyrosine binding site of the envelope gp120 (Science 2007, 317, 1930) can be exploited to prevent binding to CCR5. These goals are being pursued using chemical synthesis to develop structure activity relationships (SAR).
	Anjali Ganjiwale  My project involves structural characterization of transmembrane proteins using NMR. I am currently working on M2 protein, proton-selective ion channel, integral in the viral envelope of the influenza A virus and is a potent therapeutic drug target. However M2 protein is susceptible to mutations leading to drug resistance. The objective of the project is to address basic questions about (1) Mechanism of opening and closing of the proton channel (2) Mechanism of inhibition of channel by Amanadine/Rimantadine, common antiviral drugs (3) Studying interaction of new anti viral drugs.
	Gevorg Grigoryan (C.V.) Understanding how transmembrane (TM) helices recognize each other is an important and challenging problem. Despite their tremendous importance in biology, membrane proteins have not received their fair share of investigation, partly due to difficulties with experimental characterization. The lack of experimental data has also hampered theoretical developments, although, in principle, membrane proteins should not be more difficult to treat computationally than soluble proteins. Since the α-helix is the most common secondary structure in known TM regions, understanding the principles of TM helix interaction is critical. I plan to utilize the integrin system to study structural and sequence determinants of TM helix interaction preferences. I plan to approach this by establishing a cycle between computational design and experimental characterization of TM helical peptides that interfere with the TM dimerization of integrins. Further, I will take advantage of the diversity within the integrin family to study the specificity of TM helix recognition. This work should further the understanding of the importance of TM association in integrins, which is crucial given their involvement in human disease. Insight gained from the study will also likely contribute to the fields of membrane protein folding and de novo design. More information can be found here.

Graduate Students

	Doug Metcalf (C.V.) I am interested in determining the structure of membrane proteins through molecular modeling and experiment. I have developed software to model interactions between membrane helices. Additionally I use NMR experiments to solve solution structures. My favorite model system is integrin αIIbβ3. Integrin αIIbβ3 is the platelet fibrinogen receptor which causes blood to clot when it is activated.
	Scott Shandler (C.V.) My research involves the computational design and experimental characterization of molecules containing β-amino acids. A new software platform (TIGER) has been developed to aid in the design process, and microwave peptide chemistry is being used to synthesize the designed molecules.
	Alexei Polishchuk (C.V.) Influenza virus infection is a major public health concern, causing significant morbidity, mortality, and economic losses worldwide. Currently available influenza vaccines are limited in efficacy, and resistance is mounting to the two classes of antiviral drugs licensed to treat influenza infection. One such class of therapeutics, the aminoadamantyl derivatives amantadine and rimantadine, block the M2 proton channel of influenza A virus. We are undertaking structural studies to understand the mechanism of amantadine inhibition of M2, and the mechanism by which common mutations impart resistance to the drug. Aside from its important role as a drug target, M2 is also of interest both as a model integral membrane protein and a very compact ion channel that nevertheless is regulated by pH and rectifies the proton current. We are engineering subtle variants of the transmembrane core of M2 that will help us better understand its function as an ion channel. We are also pursuing structural and functional studies on a homologous ion channel, BM2, that is found in the influenza B strains.
	Dave Moore (C.V.) I am studying the role of transmembrane (TM) domains in the regulation of growth factor receptor and integrin signaling. My research can be broken into three categories: 1) The study of TM oligomerization in bacterial model systems; 2) The structural characterization of TM oligomerization using biophysical techniques such as NMR and AUC; and 3) The use of exogenous designed peptides to probe receptor oligomerization and the activation of downstream signaling cascades.
	Dan Kulp (C.V.) The goal in the de novo design of protein complexes is to both describe sidechain-ligand interaction and specify coordinates of a backbone from first-principles. My work has been to develop technology to enable this type of approach, specifically working on a novel fragment-based method to describe sidechain-ligand interactions and geometric hashing algorithm to search for backbone scaffolds. This work has enabled exciting side projects: classification and identification of interactions involving transmembrane dimers and trimers, de novo design of Extradiol-Cleaving Catechol Dioxygenase in a foreign active site, protein-protein inhibition by beta peptides and redesign of a nucleotide binding protein to preferentially bind GDP over ADP.
	Yong Ho Kim (C.V.) My research interests lay at the interface of Inorganic/Nanochemistry and biology based on peptide design. The main focus of my research is directed toward understanding how living systems form nano-structures by a variety of processes as well as how mimic systems artificially reflect natural system in terms of binding and growing metals or metal ions. My research project involves the design and synthesis of peptides for bio-mineralization of a metal nanocluster, specifically provided within a central cavity of a hexameric helical bundle. Our group has developed De novo protein design providing an attractive approach to probe the features required for the folding and function of proteins. In my work, the Domain Swapped Dimer (DSD) protein that forms tubular structures by self assembly is introduced as a template of nanoclusters or nanorods.
	Meredith Miller (C.V.) Cardiovascular disease remains the single greatest killer of Americans, accounting for 1 out of every 2.6 deaths from all causes in this country. Platelets play a critical role in cardiovascular disease both in the development of atherosclerosis and in acute thrombotic events such as myocardial infarctions and stroke. Current anti-platelet therapeutics demonstrate significant failings in terms of both safety and efficacy. Advances in understanding in platelet biology have provided new targets for antithrombotic drug development including glycoprotein VI (GPVI) and the integrin α2β1 in order to improve safety and efficacy. My project consists of using high-throughput screening technology to identify inhibitors of glycoprotein VI for optimization as pharmaceuticals, as well as improvement of inhibitors of integrin α2β1 on the “right-hand” side of the molecule to achieve physiologically relevant inhibition.
	Lisa Span  I am studying the interaction of the transmembrane domains of different integrin alpha and beta chains and the factors that effect their association. I am also involved in developing new biological assays to study transmembrane association.
	Yao Zhang (C.V.) MS1 was derived from the water soluble GCN4-P1 coiled coil, which is a widely used peptide in the study of soluble protein folding. Previous research showed that MS1 exhibits a reversible monomer-dimer-trimer association in detergent micelles. It suggested that a single Asn side chain in a transmembrane segment can mediate the oligomerization of hydrophobic helices. My current project is developing a high-through put assay for examing the energetics of different amino acid interaction during helix association, using MS1 as a model membrane peptide . The assay is based on crosslinking equilibrium that can be detected with high sensitivity using HPLC.
	Jun Wang (C.V.) The first project I am working on is M2 inhibition. M2 is a proton channel which plays an important role in influenza virus decoating process in the endosome. With the most recent solved M2 structure by our group as well as others, our efforts now focus on design and synthesis new compounds to fit in the newly discovered larger cavity adjacent to His-Trp tetrad. The second project aims at identifying inhibitors targeting PhoQ-PhoP two component signaling (TCS) pathway. PhoP-PhoQ is a master regulon found in many bacteria species which regulates bacteria sensing of [Mg2+], pH, as well as antimicrobial peptides. From the drug discovery point of view, it would be interesting to find small molecule drugs to block this signaling pathway, such that the bacteria has less chance to become resistant.
	Geronda Montalvo  Protein folding is a critical problem in chemistry, biochemistry, biophysics, and molecular biology. By elucidating the mechanisms of protein folding, unfolding, and stabilization, we gain significant insight into the links between folding dynamics and disease, and lay the groundwork for the design of new nano-structured materials. As our understanding of protein folding has expanded, scientists have designed synthetic “foldamers” including β-peptides, which are non-biological sequence-specific oligomers that fold into three-dimensional structures. β-peptides form stably folded helices similar to those formed by α-peptides; however, they are generally more stable than α-helices, a fact that has been corroborated by computer simulations. Additionally the thermodynamic and proteolytic stability of β-peptides offers advantages over α-peptides for pharmacological and nanotechnological applications. Still, despite considerable interest in this topic, there have been no kinetic studies on the folding of β-peptides. Recent developments in instrumentation for kinetic T-jump studies have enabled us to take major steps forward in comprehending the dynamics and kinetics of proteins. The folding of large and complex molecules is still technically difficult, because of the complexity of the folding kinetics and the frequent requirement for chaperones. Thus, small peptides provide attractive model systems; their structural simplicity and rapid reversible folding rates are beneficial for both experimental and computational studies of folding. My project entails studying the folding and unfolding kinetics of a variety of β-peptide structures using rapid kinetic methods.
	Graham Clinthorne

Staff

	Jessica Incmikoski  DeGrado Lab Administrative Assistant
	Bruk Mensa
	Emma Magavern

(29 total)