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[ PhD Program: Structural Biology Keyword: ]

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NameEmailPhd ProgramResearch InterestsPublications
Asokan, Aravind email , , , , , publications

Our research group is focused on combining the tools and principles of molecular biology and genetics with chemistry to generate a synthetic viral toolkit. The lab-derived synthetic viral entities are utilized to dissect mechanisms of viral tissue tropism, as new reagents for applications in genomics and proteomics and as new vectors for human gene therapy applications.

Berkowitz, Max email , , , , publications

We use computational techniques (multiscale molecular dynamics computer simulations) to study interactions of proteins and peptides with membranes and to study interactions of shock waves with membranes of neural cells. Specifically, we study the interaction of antimicrobial peptides with bacterial membranes to understand how they destroy such membranes.  In our study of shock wave interacting with brain tissue we investigate the importance of cavitation effect (collapse of bubbles) created by shock waves. Detailed molecular level knowledge of the processes we investigate using computational methodology is very helpful in understanding processes such as TBI (traumatic brain injury).  The computational methodology we use is also playing now an important role in the filed of drug design.  Member of the Molecular & Cellular Biophysics Training Program.

Bourret, Bob email , , , , publications

Our long-term goal is to define the molecular mechanisms of two-component regulatory systems, which are utilized for signal transduction by bacteria, archaea, eukaryotic microorganisms, and plants.  Our current focus is to identify and understand the features that control the rates of several different types of protein phosphorylation and dephosphorylation reactions.  The kinetics of phosphotransfer reactions can vary dramatically between different pathways and reflect the need to synchronize biological responses (e.g. behavior, development, physiology, virulence) to environmental stimuli.  Member of the Molecular & Cellular Biophysics Training Program.

Brennwald, Patrick email , , , , , publications

We are interested in the mechanism by which eukaryotic cells are polarized and the role of vesicle transport plays in the determination and regulation of cell polarity and tumorigenesis.

Brustad, Eric M email , , , publications

The Brustad group is interested in applying chemical principles to expand biological systems beyond Nature’s design. We make use of developing technologies such as unnatural amino acid mutagenesis and non-natural cofactor design to increase the chemical functionality available to proteins. Current efforts are directed towards the genetic incorporation of organocofactor mimics as well as heme protein engineering through the incorporation of orthogonal metalloporphyrin scaffolds. We combine methods in synthetic chemistry, molecular biology, X-ray crystallography, and directed evolution to optimize the function of our protein engineering efforts.

Campbell, Sharon email , , , , publications

Current research projects in the Campbell laboratory include structural, biophysical and biochemical studies of wild type and variant Ras and Rho family GTPase proteins, as well as the identification, characterization and structural elucidation of factors that act on these GTPases.  Ras and Rho proteins are members of a large superfamily of related guanine nucleotide binding proteins.  They are key regulators of signal transduction pathways that control cell growth. Rho GTPases regulate signaling pathways that also modulate cell morphology and actin cytoskeletal organization.  Mutated Ras proteins are found in 30% of human cancers and promote uncontrolled cell growth, invasion, and metastasis. Another focus of the lab is in biochemical and biophysical characterization of the cell adhesion proteins, focal adhesion kinase, vinculin, paxillin and palladin.  These proteins are involved in actin cytoskeletal rearrangements and cell motility, amongst other functions. Most of our studies are conducted in collaboration with laboratories that focus on molecular and cellular biological aspects of these problems. This allows us to direct cell-based signaling, motility and transformation analyses. Member of the Molecular & Cellular Biophysics Training Program.

Carter, Charles email , , , , , , publications

Molecular evolution and mechanistic enzymology find powerful synergy in our study of aminoacyl-tRNA synthetases, which translate the genetic code. Class I Tryptophanyl-tRNA Synthetase stores free energy as conformational strain imposed by long-range, interactions on the minimal catalytic domain (MCD) when it binds ATP.  We study how this allostery works using X-ray crystallography, bioinformatics, molecular dynamics, enzyme kinetics, and thermodynamics. As coding sequences for class I and II MCDs have significant complementarity, we also pursuing their sense/antisense ancestry.  Member of the Molecular & Cellular Biophysics Training Program.

Clemmons, David R email , , , , , , publications

Cross-talk between insulin like growth factor -1 and cell adhesion receptors in the regulation of cardiovascular diseases and complications associated with diabetes.

Costello, Joe email , , , , , publications

The main research project is to determine the role of intercellular junctions in normal development, cell aging and cataract formation in human and animal lenses.

Dokholyan, Nikolay email , , , , , publications

The mission of my laboratory is to develop and apply integrated computational and experimental strategies to understand, sense, and control misfolded proteins, and uncover the etiologies of human diseases. UNDERSTAND: We are working toward understanding of the protein misfolding diseases, such as Lou Gehrig’s disease and cystic fibrosis.. Other areas of interest include HIV, Graft versus Host disease (fatal autoimmune response to bone marrow transplant), and understanding and developing new drugs for pain. SENSE: We are working toward developing genetically-encoded proteins that bind and report rare/intermediate conformations of target molecules (proteins and RNA). CONTROL: We are working toward developing genetically-encoded proteins that control target proteins with light and/or drugs. We have developed novel approach for drug activation/deactivation of kinases, and light-activatable protein to manipulate protein function with light. We are working toward extending these approaches to other classes of proteins and on multiplexing, whereby we selectively activate/control several distinct cellular pathways via targeting several proteins simultaneously.

Erie, Dorothy email , , , , publications

The research in my lab is divided into two main areas – 1) Atomic force microscopy and fluorescence studies of protein-protein and protein-nucleic acid interactions, and 2) Mechanistic studies of transcription elongation. My research spans the biochemical, biophysical, and analytical regimes.

Griffith, Jack email , , , , , , publications

We are interested in basic DNA-protein interactions as related to – DNA replication, DNA repair and telomere function.  We utilize a combination of state of the art molecular and biochemical methods together with high resolution electron microscopes.

Harden, Kendall email , , , , , publications

We focus on mechanistic/structural aspects of regulatory proteins (heterotrimeric and Ras family GTPases, RGS proteins, and PLC isozymes) involved in inositol lipid signaling, and on G protein-coupled receptors for extracellular nucleotides.

Jarstfer, Michael email , , , , publications

The Jarstfer lab uses an interdisciplinary approach to solve biological problems that are germane to human health.   Currently we are investigating the structure of the enzyme telomerase, we are developing small-molecules that target the telomere for drug discovery and chemical biology purposes, and we are investigating the signals that communicate the telomere state to the cell in order to control cellular immortality. We are also engaged in a drug/chemical tool discovery project to identify small molecules that control complex social behavior in mammals.  Techniques include standard molecular biology and biochemistry of DNA, RNA, and proteins, occasional organic synthesis, and high throughput screening.

Johnson, Gary L. email , , , , publications

Spatio-temporal regulation of signal relay systems in cells using live cell fluorescence imaging and targeted gene disruption of signaling proteins to define their role in development, physiology and pathophysiology.

Ke, Hengming email , , , , publications

Our research focuses on the structure and function of medically important proteins from the crystallographic approach.  The current topics include cycolphilin, calcineurin, heat shock protein 90 (hsp90), and cyclic nucleotide phosphodiesterase.

Ko, Ching-Chang email , , , , publications

Ko’s laboratory has focused on bone regeneration using biomaterials and biomechanical approaches. The on-going project is to develop a new synthetic process for biomimetic bone nanocomposites. The new biomaterial and its scaffolds are under development for stem cell-mediated bone regeneration. Biomechanical principles that regulate mineral crystallization are incorporated with the biomaterial approach to translate research outcomes to clinical usage (e.g., immediately loaded dental implants). My lab is also interested in understanding reverse engineering principles of bio-mienralization.

Krupenko, Sergey email , , , , publications

Dr. Krupenko’s research is focused on the role of folate metabolism in cellular homeostasis and cancer disease. He is especially interested in the function of a major folate enzyme and a putative tumor suppressor ALDH1L1 as metabolic regulator and a guardian of non-malignant phenotype. At present he studies function of this enzyme and related proteins using mouse knockout models. Recently his research team has also demonstrated that dietary folate regulates cancer metastasis. He now pursues studies of specific signaling pathways involved in metastatic response to dietary folate status.

Kuhlman, Brian email , , , , publications

We use a combination of experimental and computational methods to redesign protein-protein interactions.  The potential applications for this technology include enhancing protein therapeutic and creating new tools to study signaling pathways.

LeCluyse, Edward L email , , , , publications

Dr. Edward (Ed) LeCluyse is currently a Senior Research Investigator in the Institute for Chemical Safety Sciences at The Hamner Institutes of Health Sciences.  Dr. LeCluyse leads a program initiative to identify and develop novel in vitro hepatic model systems to examine cellular responses to drugs and environmental chemicals that target known toxicity pathways. The focus of his research efforts has been to create more organotypic, physiologically-relevant in vitro models that integrate the architectural, cellular and hemodynamic complexities of the liver in vivo.

Lee, Andrew email , , , , publications

We study protein structure and dynamics as they relate to protein function and energetics. We are currently using NMR spectroscopy (e.g. spin relaxation), computation, and a variety of other biophysical techniques to gain a deeper understanding of proteins at atomic level resolution.  Of specific interest is the general phenomenon of long-range communication within protein structures, such as observed in allostery and conformational change.  A. Lee is a member of the Molecular & Cellular Biophysics Training Program.

Lentz, Barry email , , , , publications

The regulatory role of platelet membrane phosphatidylserine in blood coagulation; mechanism of protein-mediated membrane fusion in secretory processes and virus infection.  Director of the Molecular & Cellular Biophysics Training Program.

Liu, Jian email , , , publications

The overall goal of our research is to develop an enzyme-based approach to synthesize heparin- and heparan sulfate-like therapeutics.  The lab is currently focusing on improving the anticoagulant efficacy of heparin drug as well as synthesizing heparin-like compounds that inhibit herpes simplex virus infections.  We are also interested in using protein and metabolic engineering approaches for preparing polysaccharides with unique biological functions.

Lockett, Matthew Ryen email , , , publications

Research in the Lockett group focuses on the development of analytical model systems to: i) chemically modify the surface of thin films, and study chemical and biochemical reactions occurring on those surfaces; ii) study drug metabolism in an environment that closely mimics the human liver; iii) measure tumor invasion in an environment that closely mimics human tissue. /  / While these problems require techniques found in analytical chemistry, biochemistry, molecular biology, bioengineering, and surface science we are particularly interested in the technologies that allow us to quantitatively measure reactions and analytes.

McGinty, Robert email , , , , , publications

The McGinty lab uses structural biology, protein chemistry, biochemistry, and proteomics to study epigenetic signaling through chromatin in health and disease.  Chromatin displays an extraordinary diversity of chemical modifications that choreograph gene expression, DNA replication, and DNA repair – misregeulation of which leads to human diseases, especially cancer. We prepare designer chromatin containing specific combinations of histone post-translational modifications. When paired with X-ray crystallography and cryo-electron microscopy, this allows us to interrogate mechanisms underlying epigenetic signaling at atomic resolution.

Neher, Saskia email , , , , , publications

Our lab seeks to better understand the maturation and regulation of a group of human lipases.  We aim to uncover how these lipases properly fold and exit the ER, and how their activity is subsequently regulated.  We study the membrane-bound and secreted proteins that play a role in lipase regulation.  Our research can potentially impact human health as biochemical deficiencies in lipase activity can cause hypertriglyceridemia and associated disorders, such as diabetes and atherosclerosis.  We are an interdisciplinary lab and aim to address these questions using a variety of techniques, including membrane protein biochemistry, enzymology, and structural and molecular biology.

Parise, Leslie email , , , , , , , , publications

The overall goal of our laboratory is to understand the molecular interface between cell signaling and adhesion receptors in blood diseases and cancer in order to develop novel therapeutic targets and approaches. One area of study is platelets because they become activated by cellular signals and adhere to each other and the blood vessel wall via specific adhesion receptors. These events can block blood flow, causing heart attacks and stroke, the leading causes of death in the US. Another area of research is sickle cell disease, since red blood cells in these patients are abnormally adhesive and also cause blood vessel blockages. A third area is cancer since cancer cells use similar cellular signals and adhesion receptors in tumorigenesis and metastasis. Our work involves a wide array  of technologies that include molecular, structural and cellular approaches as well as clinical/translational studies with human patients.

Pielak, Gary J. email , , , , , publications

My graduate students and I use the formalism of equilibrium thermodynamics and the tools of molecular biology and biophysics to understand how nature designs proteins.

Prins, Jan F. email , , , , publications

Our group develops computational methods for the analysis of high throughput sequence data.  Our focus is on transcriptome analysis and its applications.

Redinbo, Matt email , , , , , , , publications

The Redinbo Laboratory examines dynamic cellular processes using structural, chemical, molecular and cell biology. Our goals are to discover new drugs and to elucidate molecular pathways essential to human disease.  Current projects include developing the first drugs that target the human microbiome, unraveling the nature of innate immunity in the human lung, and discovering how microbial systems exchange genes, including those that encode antibiotic resistance.

Riordan, John email , , publications

The primary research focus is the structure, function and biosynthetic processing of membrane proteins which provide permeability pathways through the membranes of cells. Much of the current work is concentrated on the ion channel protein, CFTR (cystic fibrosis transmembrane conductance regulator) which is absent or dysfunctional in patients with cystic fibrosis. To elucidate the molecular mechanisms of CFTR function, we study single channel properties by electrophysiological techniques, enzymatic activity and physical interaction with other cellular molecules. A major objective of studies with the purified molecule is to obtain 3-dimensional structure information so that small molecules capable of recognizing features of its surface shape can be synthesized and used to modulate its folding and activity.

Shih, Yen-Yu Ian email , , , , publications

Dr. Shih is the Director of Small Animal Magnetic Resonance Imaging (MRI) at the Biomedical Research Imaging Center. His lab has implemented multi-model MRI techniques at high magnetic field to measure cerebral blood oxygenation, blood flow, blood volume, and oxygen metabolism changes in preclinical animal models. Dr. Shih’s lab is also developing simultaneous functional MRI (fMRI) and electrophysiology recording techniques at high spatial resolution to elucidate the pathophysiological mechanisms of neurovascular diseases. They will apply these techniques to (i) explore/validate functional connectivity network and neurovascular coupling in the rodent brain, (ii) study tissue characteristics after stroke, and (iii) investigate deep brain electrical stimulation, optogenetic stimulation, and pharmacogenetic stimulation in normal and Parkinsonian animal models.

Slep, Kevin email , , , , , , , publications

Our lab examines cytoskeletal dynamics, the molecules that regulate it and the biological processes it is involved in using live cell imaging, in vitro reconstitution and x-ray crystallography.  Of particular interest are the microtubule +TIP proteins that dynamically localize to microtubule plus ends, communicate with the actin network, regulate microtubule dynamics, capture kinetochores and engage the cell cortex under polarity-based cues.

Snoeyink, Jack email , publications

My primary research area is computational geometry, in which one studies the design and analysis of algorithms for geometric computation. Computational geometry finds application in problems from solid modeling, CAD/CAM, computer graphics, molecular biology, data structuring, and robotics, as well as problems from discrete geometry and topology.  Most of my work involves identifying, representing, and exploiting geometric and topological information that permit efficient computation.  My current focus is on applications of computational geometry in Molecular Biology and Geographic Information Systems (GIS). Examples of the former include docking and folding problems, and scoring protein structures using Delaunay tetrahedralization.

Sondek, John email , , , , , , publications

Our laboratory studies signal transduction systems controlled by heterotrimeric G proteins as well as Ras-related GTPases using a variety of biophysical, biochemical and cellular techniques. Member of the Molecular & Cellular Biophysics Training Program.

Tropsha, Alexander email , , , , , , , publications

The major area of our research is Biomolecular Informatics, which implies understanding relationships between molecular structures (organic or macromolecular) and their properties (activity or function). We are interested in building validated and predictive quantitative models that relate molecular structure and its biological function using statistical and machine learning approaches. We exploit these models to make verifiable predictions about putative function of untested molecules.

Weeks, Kevin email , , , , , , publications

The Weeks group invents novel chemical microscopes for understanding the structure and function of RNA and then applies these technologies to leading, and previously intractable, problems in biology. Most projects in the laboratory span fundamental chemistry or technology development and ultimately lead to practical applications in virology (especially HIV), next-generation structure analysis, drug design, and understanding RNA structure in living cells.  Collectively, this work has led to extensive recognition of graduate student colleagues in the laboratory.

Weinberg, Richard email , , , publications

I’m a neurobiologist who uses immunocytochemistry and electron microscopy to address functional questions. I am trying to elucidate the molecular organization of synaptic signaling in the rodent neocortex, hippocampus, and striatum. I’m also interested in the actin cytoskeleton of dendritic spines, and how spines may remodel during LTP.

Williams, David C. Jr. email , , , , publications

The overall objective of our research is to understand the connection between structure of protein-DNA complexes, protein dynamics and function.  We currently focus on the methyl-cytosine binding domain (MBD) family of DNA binding proteins.  The MBD proteins selectively recognize methylated CpG dinucleotides and regulate gene expression critical for both normal development and carcinogenesis.  We use a combination of NMR spectroscopy and biophysical analyses to study protein-DNA and protein-protein complexes involving the MBD proteins.  Building on these studies, we are developing inhibitors of complex formation as potential molecular therapeutics for b-hemoglobinopathies and cancer.