Biochemistry and Molecular Biophysics Graduate Group

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Yair Argon, Ph.D.

Quality control of protein folding in the cell by molecular chaperones

Professor of Pathology & Laboratory Medicine; Chief, Division of Cell Pathology
Children's Hospital of Philadelphia, 816B Abramson Research Center
Tel: 267-426-5131 (office) / 267-426-5130,29,28 (lab) / 267-426-5346 (administrator)
Fax: 267-426-5165
Email: yargon@mail.med.upenn.edu
Email: ARGONY@email.chop.edu
Argon CHOP website

Orchestrating protein folding in the cell is a key process underlying the expression of membrane receptors and secreted proteins. Inefficient folding leads to inappropriate protein-protein interactions, inability to transport proteins from the ER to the Golgi complex, and is the molecular basis of many diseases. The molecular chaperones in the ER govern proper folding and assembly, recognize misfolded proteins and either improve folding or direct them to degradation. Our work focuses on two molecular chaperones, BiP and GRP94.

 

Paul H. Axelsen, M.D.

Biophysical studies of molecular recognition and rational drug design

Professor of Pharmacology, Biochemistry & Biophysics, and Medicine
105 Johnson Pavilion
Tel: (215) 898-9238
Email: axe@upenn.edu
Axelsen Lab Page

Research Themes - Infectious disease (antibiotics, antimicrobial peptides, antibiotic resistance, vancomycin); Neurodegeneration (amyloidogenesis, Alzheimer's disease); Cardiovascular disease (lipoprotein structure and function)
Focus Areas - Rational drug design and molecular recognition; Protein-lipid interactions (involved in protein folding, misfolding, and amyloidogenesis); Mechanisms and consequences of oxidative lipid membrane damage

 

Tobias Baumgart, Ph.D.

Biomembrane function: thermodynamics, dynamics and mechanics

Associate Professor of Chemistry
250N Chemistry 1973 Wing
Tel: 215-573-7539 / Fax: 215-898-6242
Email: baumgart@sas.upenn.edu
Baumgart lab page

Among the most fascinating biological structures found in nature are biomembranes that surround cellular systems and intracellular organelles. These membranes function as barriers between cellular compartments, as transport vehicles and regulators, and contain machineries important for biological functioning. Cell biology has traditionally focused on examining protein / protein interactions. However, the physical chemistry and mechanical properties of the lipid bilayer matrix are tightly coupled to the functioning of membrane associated proteins in ways that are largely unknown. This provides rich opportunities for exciting and important new insights.

We examine lipid / protein interactions in biological and model membranes by laser scanning confocal microscopy techniques. Membrane domain formation is studied in a temperature-dependent fashion. We are particularly interested in establishing the molecular details that determine how membrane proteins redistribute between lipid domains to understand how lipid / protein interactions influence membrane functioning. Furthermore, we use mechanical methods to deform membranes and examine membrane curvature-dependent lipid / protein interactions that include redistribution in membrane curvature gradients, curvature-dependent binding of peripheral membrane proteins, and we study protein geometries dependent on lipid membrane curvature.

 

Ben E. Black, Ph.D.

Chromosome segregation; chromatin structure; epigenetic centromere specification; hydrogen/deuterium exchange

Associate Professor of Biochemistry & Biophysics
913A Stellar-Chance Labs
Tel: 215-898-5039 (office) / Fax: 215-573-7058
Lab: 912 Stellar Chance Labs
Tel: 215-898-4476 (lab)
Email: blackbe@mail.med.upenn.edu
Black Department of Bichemistry & Biophysics webpage

Dr. Black's laboratory is interested in how particular proteins direct accurate chromosome segregation at mitosis. In humans, the chromosomal element—the centromere—that directs this process is not defined by a particular DNA sequence. Rather, the location of the centromere is dictated by an epigenetic mark generated by one or more resident proteins. These centromeric proteins interact directly with the DNA to create a specialized chromatin compartment that is distinct from any other part of the chromosome. By taking biophysical, biochemical, and cell biological approaches, our work is to define the composition and physical characteristics of the protein and protein/DNA complexes that epigenetically mark the location of the centromere on the chromosome. This work involves building centromeric chromatin from its component parts for analysis of its physical characteristics, developing biochemical assays to reconstitute steps in the process of establishing and maintaining the epigenetic mark, and using cell-based approaches to study the behavior of proteins involved in centromere inheritance and other essential aspects related to chromosome segregation at cell division.

 

Kathleen Boesze-Battaglia, Ph.D.

Tetraspanin protein structure and role in degenerative disease processes

 

Associate Professor, Department of Biochemistry, School of Dental Medicine
520 Leon Levy Building
Tel: 215-898-9167 / Fax: 215-898-3695
Email: battagli@biochem.dental.upenn.edu
Boesze-Battaglia Dental School webpage

Tetraspanin membrane proteins encompass a functionally diverse group of proteins involved in cell adhesion, cell recognition and membrane fusion events. These proteins are characterized by a highly conserved extra-cellular domain, known as the EC-2 domain that is involeid in formation of disulfide linked oligomers and functionally diverse C-termini. We are interested in understanding the role of two retinal specific tetraspanins, peripherin-2, the product of the rds gene, and it’s non-glycosylated homologue rom-1, in the development and progression of degenerative diseases. A murine model of retinitis pigmentosa (RP) in which a 10 kb insertion of exogeneous DNA results in an rds null allele as well as a rom-1 knockout mouse suggest that although peripherin-2 and rom-1 cooperate to generate healthy photoreceptors, they are not functionally equivalent and rom-1 likely plays a subsidiary role. Peripherin-2 and rom-1 form both homo and hetero-tetramers with peripherin-2 shown to oligomerize further to form octamers. Our studies focus on the regulatory and functional role played by the C-terminus of peripherin-2 in the formation of photoreceptor cells and in the maintenance of cell stability through the organization of intra-membraneous sacs known as disks. The C-terminal domain is required in the formation of newly developing membrane evaginations destined to become disks as well as their alignment along the outer segment portion of the cell. Domains within this region are postulated to be necessary for protein and vesicle targeting, calcium dependent calmodulin binding, membrane fusion, and the regulation of this fusion through the binding of a newly identified protein, melanoregulin. Using a combination of pull-down, immuno-precipitation, proteomic, confocal and live cell imaging techniques and as well as solution NMR, we have begun to define the regulatory surface of peripehirn-2. An understanding of how this region aids in disk membrane monogenesis and in maintaining photoreceptor viability is essential for the development of viable therapeutic approaches to slow the progression of these degenerations.

A second series of studies is designed to address the role of cholesterol in photoreceptor function and dysfunction during degeneration. Using a combination of membrane micro-domain isolation techniques, fluorescence anisotropy studies and functional readouts we have shown that membrane cholesterol is heterogeneously distributed within disks as a function of age and spatial distribution. Moreover this distribution results in compromised GPCR function due to changes in the membrane micro-environment and membrane fusion process.

Lastly, in a newly developing project, we have expanded our interest in cholesterol to address the role of this lipid in mineralizing tissue. Mutations within various cholesterol biosynthetic enzymes results in chondrodysplasia puntacta; punctate calcification of cartilage, leading in its’ more severe forms to mental retardation and in milder forms to skeletal abnormities including craniofacial defects. Using a combination of RNA interference techniques, membrane lipid asymmetry measurements and confocal microscopy we have focused our effort on understanding how enzymes involved in the maintenance of lipid asymmetry when devoid of a cholesterol- rich membrane environment begin to dysfunction leading to alterations in the formation of the core mineralizing component, the matrix vesicle. Through a series of collaborations we are utilizing AFM and primary cell culture models to understand how depletion of cell membrane cholesterol alters mineral formation and deposition.

 

Roberto Dominguez, Ph.D.

Actin cytoskeleton, structural biology

Professor of Physiology
728 Clinical Research Building
Tel: 215-573-4559 / Fax: 215-573-5851
Email: droberto@mail.med.upenn.edu
Dominguez Lab Page

Structure Biology of the Actin Cytoskeleton
The actin cytoskeleton plays an essential role in multiple cellular functions, including cytokinesis, vesicular trafficking and the maintenance of cell shape and polarity. The driving force for these processes is the dynamic remodeling of the actin cytoskeleton into supramolecular functional networks. Remodeling of the cytoskeleton is a tightly regulated process, which involves hundreds of actin-binding and signaling proteins. The main focus of the research in our lab is to understand the molecular basis for how protein-protein interaction networks bring together cytoskeleton scaffolding, nucleation, elongation, and signaling proteins to accomplish specific cellular functions. Another area of significant interest is the study of large multi-domain proteins that connect the actin cytoskeleton to the cell membrane, and sense or induce membrane curvature.

Our primary research tool is protein X-ray crystallography. The atomic snapshots resulting from crystal structures provide a wealth of knowledge, but lack information about the dynamic aspects of protein-protein interaction. To obtain this kind of information we also use a host of other approaches, including mutagenesis, bio-informatics, and biophysical methods such as isothermal titration calorimetry (ITC), multi-angle light scattering (MALS), small and wide angle X-ray scattering (SAXS/WAXS). The lab collaborates with cell biologists and electron microscopists to study actin cytoskeletal proteins in the cellular environment.

 

Roland L. Dunbrack, Jr. Ph.D.

Methods and applications of protein structure prediction

Adjunct Professor of Biochemistry & Biophysics
Member, Institute for Cancer Research, Fox Chase Cancer Center
Tel: 215-728-2434 / Fax: 215-728-2412
Email: Roland.Dunbrack@fccc.edu
Dunbrack Fox Chase Cancer Center Webpage

The Dunbrack group concentrates on research in computational structural biology, including homology modeling, fold recognition, molecular dynamics simulations, statistical analysis of the PDB, and bioinformatics. In developing these methods, we use methods from various areas of mathematics and computer science, including Bayesian statistics and computational geometry. We place an emphasis on large-scale benchmarking of new methods and comparison with existing methods. We are interested in applying comparative modeling to important problems in various areas of biology. Areas of particular interest include DNA repair, proteases and other peptide-binding protein families, and membrane proteins.

 

P. Leslie Dutton, Ph.D.

Oxido-reductase engineering; design and chemical synthesis of redox proteins

Professor of Biochemistry & Biophysics
1005 Stellar-Chance Labs
Tel: 215-898-0991 / Fax: 215-573-2235
Email: dutton@mail.med.upenn.edu
Dutton Department of Biochemistry & Biophysics page / Dutton Lab

The Dutton lab is interested in determining factors governing electron tunneling through natural proteins engaged in electron transfer, energy conversion, signaling, regulation and enzyme redox catalysis. We are also involved in de novo design and synthesis of proteins engineered to perform natural functions such as electron transfer, proton translocation, charge driven conformational changes and redox catalysis in structured highly simplified settings.

 

S. Walter Englander, Ph.D.

Protein folding; structure, structure change, and dynamics; H-exchange; NMR

Professor of Biochemistry & Biophysics
1006-8 Stellar-Chance Labs
Tel: 215-898-4509 / Fax: 215-898-2415
Email: engl@mail.med.upenn.edu
Englander Department of Bichemistry & Biophysics page / Englander Lab

Dr. Englander's laboratory is interested in macromolecular structure, dynamics, and function and has developed the use of hydrogen exchange (HX) approaches in protein and nucleic acid studies.  Many hydrogens in proteins and nucleic acids are in continual exchange with the hydrogens in solvent water. These can provide literally hundreds of probe points that are sensitive to structure, structure change, internal dynamics, energy, and functional interactions at identifiable positions throughout a macromolecule. Work in this lab has explained the chemistry of protein and nucleic acid HX processes and has formulated the physical models that appear to explain the ways in which internal motions in proteins and nucleic acids determine the HX rates of their individual protons. The lab has developed and is using special hydrogen exchange methods that can measure the specific parts of any protein involved in any function, the protein folding process as it occurs on a sub-second time scale, the energetic stability of individual bonding interactions, structure change, etc.

Methods in use include the range of protein biophysical techniques including 2D NMR, mass spectrometry, fast reaction stopped-flow, spectroscopy, and mutational analysis. The lab has in recent years produced a coherent explanation for how proteins fold, and discovered the new foldon dimension of protein structure and behavior. Present work is directed at testing and enlarging the folding model and investigating the broader significant of the foldon paradigm.

 

Hua-Ying Fan, Ph.D.

Regulation of chromatin structure and its impact on human diseases

Assistant Professor of Biochemistry & Biophysics, and Genetics
9-133 Smilow Center for Translational Research
Tel: 215 573-5705
Email: hfan@mail.med.upenn.edu
Fan Department of Bichemistry & Biophysics Webpage

The Fan lab is interested in understanding the mechanisms of epigenetic regulation. Epigenetics describes the process by which a specific transcriptional program, induced by a signal, is maintained and inherited through cell divisions without the necessary presence of the original signal. Chromatin structure holds the secrets of epigenetic regulation. To dissect the mechanisms of epigenetic regulation, our research is focused in two main directions. First, we study how ATP-dependent chromatin remodelers regulate chromatin structure and how defects in these activities can lead to disease. Currently, we are using CSB (Cockayne Syndrome complementation group B) as a model protein to understand the function of ATP-dependent chromatin remodeling in DNA repair, aging and cancer. Second, we wish to understand how epigenetic regulatory mechanisms influence cancer cell self-renewal and differentiation, mechanisms that might impact the programming and reprogramming capacity of cancer cells. Results from our studies will, therefore, not only shed light on fundamental mechanism of epigenetic regulation, but will provide novel insights into the causes and mechanisms of disease.

 

Kathryn M. Ferguson, Ph.D.
Graduate Group Chair

Structural biology, growth factor receptor signaling, molecular mechanisms of protein-protein interactions

Associate Professor of Physiology
364 Clinical Research Building
Tel: 215-573-1207 / Fax: 215-573-5851
Email: ferguso2@mail.med.upenn.edu
Ferguson lab website

We are interested in the stereochemical details of molecular interactions in signal transduction pathways, in particular those emanating from the stimulation of cell surface receptors by growth factors. Recent work has led to the proposal of a novel mechanism for the growth factor activation of one of the receptors we study, the Epidermal Growth Factor (EGF) receptor. Using X-ray crystallography combined with a variety of biophysical and biochemical approaches, we are addressing the implications of this model on both the activation and inhibition of the EGF receptor.

Developing directions in the laboratory involve biophysical and structural studies of protein-protein interactions that control events in intracellular vesicle trafficking pathways and endocytosis, and in innate immune signaling.

 

Feng Gai, Ph.D.

Spectroscopic study of protein folding/misfolding

Professor of Chemistry
254 Chemistry Building
Tel: 215-573-6256 / Fax: 215-573-2112
Email: gai@sas.upenn.edu
Gai Lab Homepage

The focus of our research is to study how proteins fold from random or quasi-random coils to their biologically functional conformations. We are particularly interested in the kinetic aspects of the folding mechanisms. Novel laser spectroscopic methods are being used and developed to study the early folding events and folding intermediates. Recent works involve the study of the helix-coil transition, helix-helix interaction, and x-sheet formation. In addition, single molecule techniques, such as confocal fluorescence spectroscopy and microscopy, are being used to investigate the heterogeneity in folding kinetics as well as protein spontaneous fluctuation and polymerization.

 

Yale E. Goldman, M.D., Ph.D.

Motor proteins studied by photochemistry and spectroscopy

Professor of Physiology, and Biochemistry & Biophysics
611B Clinical Research Building
Tel: 215-898-4017 / Fax: 215-898-2653
Email: goldmany@mail.med.upenn.edu
Pennsylvania Muscle Institute

Actomyosin in muscle is an energy transducer that can be probed by biophysical, physiological, chemical and structural methods. Modified forms power many cell biological motions such as targeted vesicle transport and cell division. We are developing novel techniques, such as single molecule fluorescence polarization and laser photolysis of 'caged molecules', to map protein structural changes in real time and to relate them to the enzymology and mechanics of the mechanism.

The ribosome translates the genetic code into amino acid sequences with enormous fidelity and also constitutes a motor translocating along the mRNA exactly 3 bases per step. Energy from splitting GTP by G-protein elongation factors (EFs) is transformed into translational accuracy and maintenance of the reading frame. Powerful techniques developed for studies on motor proteins, including single molecule fluorescence and optical traps, are being applied to understand the structural biology, energetics and function of EFs and their interaction with the ribosome.

 

Harry Ischiropoulos, Ph.D.

Biological chemistry of nitric oxide; oxidative processes, protein aggregation and neurodegeneration.

Gisela and Dennis Alter Research Professor of Pediatrics, and Pharmacology
417 Abramson Research Center
Tel: 215-590-5320
Email: ischirop@mail.med.upenn.edu
Ischiropoulos lab page

The research efforts of my laboratory are focused on three areas:
1) Biological chemistry of nitric oxide in cardiovascular diseases and thrombosis. We employ proteomics to discover the complement of proteins modified post-transitionally by nitric oxide on cysteine and tyrosine residues.The functional consequences of these modifications on nitric oxide signaling in atherosclerosis and deep vein thrombosis are under investigation.
2) Oxidative processes in protein aggregation and neurodegeneration. We use cellular and mouse models to investigate the role of oxidative chemistry in the aggregation of α-synuclein and in neurodegeneration.
3) Functional proteomics to turn inventories of cellular secretomes to biological insights by defining secreted proteins that regulate neuron growth, differentiation and death

 

Virginia M.-Y. Lee, Ph.D.

Pathobiology of Alzheimer's and Parkinson's disease

Professor of Pathology & Laboratory Medicine
Director, Center for Neurodegenerative Disease Research
The John H. Ware 3rd Professor in Alzheimer’s Research
3 Maloney, Hospital of the University of Pennsylvania
Tel: 215-662-6427 / Fax: 215-349-5909
Email: vmylee@mail.med.upenn.edu
CNDR Webpage

Dr. Virginia M.-Y. Lee’s research interest focuses on tau, a-synuclein and amyloid beta precursor protein (APP), and their roles in the pathobiology of neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson’s disease (PD), and frontotemporal dementias (FTD). In particular, we wish to determine the pathogenesis of senile plaques, Lewy bodies and neurofibrillary tangles because these are major lesions found in the brains of AD patients and other neurodegenerative diseases. Information obtained from research program may shed light on how neurons degenerate in AD and PD and lead to a better understanding of the etiology of these diseases. A multi-disciplinary approach (including biochemical and molecular studies of neuronal culture systems, animal models and human tissues obtained at autopsy) is used in the laboratory to address these research issues in common with these neurodegenerative diseases. Our other research efforts focus on an increased understanding of the normal functions of tau, synucleins, and APP.

 

Mark A. Lemmon, Ph.D.

Biochemistry/biophysics of intermolecular interactions of growth factor receptor signaling

George W. Raiziss Professor of Biochemistry & Biophysics
322A Clinical Research Building
Tel: 215-898-3072 / Fax: 215-573-4764
Email: mlemmon@mail.med.upenn.edu
Lemmon Department of Biohemistry & Biophysics page / Lemmon Lab Page

Research Interests of the Lemmon Lab:
Signaling by receptor tyrosine kinases from the ErbB/HER family
EGF receptor signaling in Drosophila
Membrane recruitment by phosphoinositide-binding domains
Dynamin-family large GTPases in intracellular trafficking

 

Mitchell Lewis, D.Phil.

Gene regulation; protein crystallography; structural basis of recognition

John Morgan Professor of BIomedical Rsearch and Education
Department of Biochemistry & Biophysics
813B Stellar-Chance Labs
Tel.: 215-898-0711 (lab) 215-898-0949 (office) / Fax: 215-898-4217
Email: lewis@mail.med.upenn.edu
Lewis Department of Bichemistry & Biophysics Page

The major objective of our research is to understand how proteins respond to metabolites and regulate transcription. Our work has focused on the repressor of bacteriophage lambda and the lac operon of E. coli. For almost half a century, these two systems have served as the paradigm for understanding gene regulation. The primary focus of our lab has been to provide detailed structural information on these two systems.

 

Paul A. Liebman, M.D.

G-protein-receptor-arrestin mechanisms; visual signal transduction

Professor of Biochemistry & Biophysics
260 Anatomy-Chemistry Building
Tel.: 215-898-6917 / Fax: 215-573-8093
Email: liebmanp@mail.med.upenn.edu
Liebman Department of Bichemistry & Biophysics Page

Research Interests of the Liebman Lab:

  • Analysis of misfolding of signaling proteins upon loss of their obligatory small ligand. Role of misfolding in biological aging
  • Thermodynamics, kinetics and protein-protein contact mechanism of signal transduction proteins.
  • Computational modeling, complex systems analysis of simultaneous actions of GTPase activator protein, phosducin, arrestin and receptor phosphorylation in signal transduction.
  • Rich interplay of analytical math, biophysical instrumentation, reaction chemistry and physics, molecular graphics computing, dual wavelength kinetic spectroscopy, intrinsic tryptophan and tyrosine fluorescence dynamic and static light scattering, centrifugal and gel filtration polymer size analysis, microcalorimetry, CD, osmotic stress, hydrostatic pressure plus all the standard wet lab preparation techniques.

 

Ronen Marmorstein, Ph.D.

X-ray crystallography, chromatin regulation, tumor suppressors, oncoproteins, kinases, aging, structure-based inhibitor design

Wistar Professor of Biochemistry & Biophysics
Hilary Koprowski, M.D. Professor, The Wistar Institute
327 Wistar Institute
Tel: 215-898-5006 / Fax: 215-898-0381
Email: marmor@wistar.org
Marmorstein Department of Biochemistry & Biophysics page

The laboratory uses a broad range of molecular, biochemical and biophysical research tools centered on X-ray crystal structure determination to understand the mechanism of macromolecular recognition and post-translational histone and protein modifications in the regulation of gene expression, chromatin and epigenetics. The laboratory is particularly interested in gene regulatory proteins and kinases that are aberrantly regulated in cancer and age-related metabolic disorders such as type II diabetes and obesity, and the use of high-throughput small molecule screening and structure-based design strategies towards the develop protein-specific small-molecule compounds to treat such diseases.

 

Hillary C.M. Nelson, Ph.D.

Structural biology; transcription; protein-DNA interactions; heat shock response

Associate Professor of Biochemistry & Biophysics
813A Stellar-Chance Labs
Tel: 215-573-7473
Email: hnelson@mail.med.upenn.edu
Nelson Department of Biochemistry & Biophysics page

 

E. Michael Ostap, Ph.D.

Biochemistry of contractile proteins, biophysics of cell motility, and characterization of unconventional myosins

Professor of Physiology
Director, Pennsylvania Muscle Institute
700A Clinical Research Building
Tel: 215-573-9758 (office); 215-898-3685 (lab)
Email: ostap@mail.med.upenn.edu
Ostap Laboratory Page

The goal of our research is to understand the function, regulation, and molecular mechanism of the ubiquitously expressed molecular motors called myosins. The physiological roles and molecular mechanisms of many members of the myosin superfamily are not well understood. To better define the roles of myosin isoforms, we are using a rigorous interdisciplinary approach that combines chemistry, biophysics, cell, and molecular biology. We are obtaining a physical framework in which to discuss the cellular functions of myosins by investigating the enzymatic and structural properties of native and recombinant myosin isoforms, and we are investigating the in vivo localization, organization, dynamics, and physiology of myosin-I in fixed and live cells using high-resolution microscopy techniques.

 

Trevor M. Penning, Ph.D.

Structure-function of aldo-keto reductases; role in steroid hormone action and chemical carcinogenesis

Professor of Pharmacology, and Biochemistry & Biophysics
Director, Center of Excellence in Environmental Toxicology (CEET)
1315 Biomedical Research Building II/III
Tel: 215-898-9445
Fax: 215-573-0200
Email: penning@mail.med.upenn.edu
Penning Pharmacology website / AKR website / CEET website

The aldo-keto reductase (AKR) superfamily: roles in steroid hormone action and mechanisms of carcinogen activation. Structure-function studies are being performed on discrete AKR isoforms that regulate the occupancy and trans-activation of steroid hormone receptors. The goal is rational drug-design. Some AKRs are implicated in the metabolic activation of polycyclic aromatic hydrocarbons which are human carcinogens by forming reactive and redox-active o-quinones. The DNA-damaging events that result from quinone formation and the mutational consequences of these lesions are being studied.

 

E. James Petersson, Ph.D.

Semi-synthesis of labeled proteins to probe and control conformation

 

Assistant Professor of Chemistry
350N Chemistry Building
Tel: 215-898-0487
Email: ejpeterssonsasupennedu
Petersson lab website

Protein motion underlies both proper function and disease in biological systems. Many signaling and transport proteins require complex rearrangements for function, and some proteins, such as amyloids, misfold into toxic conformations. Studying these protein motions not only aids our understanding of diverse biological phenomena, it also contributes to an important fundamental problem in biochemistry: understanding how motions propagate from one end of a protein to another. The Petersson laboratory is developing tools to address questions of how dynamic proteins mediate communication and how the cellular environment catalyzes protein misfolding, from detailed in vitro folding studies to modeling protein motion in living cells. These tools include novel chromophores, which we synthesize and incorporate into proteins through unnatural amino acid mutagenesis and synthetic protein ligation.

 

Ravi Radhakrishnan, Ph.D.

Computational structural biology and systems biology; cell membrane mediated trafficking; targeted drug delivery; cancer signaling

 

Associate Professor of Bioengineering, and Biochemistry & Biophysics
540 Skirkanich Hall
Tel: 215-898-0487 / Fax: 215-573-2071
Email: rradhak@seas.upenn.edu
Radhakrishnan lab website

Radhakrishnan directs a computational research laboratory with research interests at the interface of chemical physics and molecular biology. The goal of the computational molecular systems biology laboratory is to provide atomic and molecular level characterization of complex biomolecular systems and formulate quantitatively accurate microscopic models for predicting the interactions of various therapeutic agents with innate biochemical signaling mechanisms. The lab specializes in several computational algorithms ranging from techniques to treat electronic structure, molecular dynamics, Monte Carlo simulations, stochastic kinetic equations, and complex systems analyses in conjunction with the theoretical formalisms of statistical and quantum mechanics, and high performance computing in massively parallel architectures.

 

Heinrich Roder, Ph.D.

NMR; protein folding mechanism; protein structure, dynamics and function

Adjunct Professor of Biochemistry & Biophysics
Senior Member, Institute for Cancer Research
Fox Chase Cancer Center,
Tel: (215) 728-3123 / Fax: (215) 728-3574
Email: Heinrich.Roder@fccc.edu
Roder Lab Page

To decipher the mechanism by which proteins acquire their precisely folded three dimensional structures remains one of the most important challenges of structural biology. We approach this complex problem by using optical and NMR methods for detailed structural, thermodynamic and kinetic studies on several small proteins with diverse structural characteristics. To monitor their folding or unfolding reactions, we rely on various optical probes coupled with rapid mixing techniques, including a new continuous-flow method with greatly improved time resolution (~50 microsec). Hydrogen exchange and NMR methods provide insight into the structural and dynamic properties of kinetic intermediates and partially folded equilibrium states. By combining these biophysical approaches with site-specific mutagenesis, we can elucidate the role of individual residues in stabilizing the various conformational states that participate in folding.

 

Harvey Rubin, M.D., Ph.D.

Pathogenesis of dormancy in mycobacterium tuberculosis; biomolecular computation and enzymology and cell biology of serine proteases and serine protease inhibitors

Professor of Medicine
522 Johnson Pavilion
Tel: 215-662-6475 / Fax: 215-662-7842
Email: rubinh@mail.med.upenn.edu
Rubin ISTAR page

The work in the lab is focused in three areas: elucidating the genetic and metabolic regulatory networks that allow tuberculosis to persist in the human host for years, determination of the molecular basis of serine protease inhibition and mathematical modeling of complex biomolecular systems.

 

Jeffery G. Saven, Ph.D.

Theory, simulation and design of proteins and folding molecules

Professor of Chemistry
266 Cret Wing of Chemistry
Tel: 215-573-6062 / Fax: 215-573-2112
Email: saven@sas.upenn.edu
Saven Chemistry Web page

The Saven group uses primarily theory and computation to study biomolecules, polymers, and condensed phase systems. A current thrust of the group involves developing computational tools for understanding the properties of protein sequences consistent with a chosen three-dimensional structure. The group works closely with experimental groups at Penn and at other universities; some group members are involved in joint theoretical/experimental projects. Recent projects involve the design of soluble and membrane bound proteins, discerning the origins of conservation in naturally occurring proteins, biomolecular simulation, design of nonbiological folding molecules, and developing "physically-based" search methods for sequence databases.

 

Kim A. Sharp, Ph.D. 

Theory of protein and nucleic acid structure and function

Associate Professor of Biochemistry & Biophysics
805A Stellar-Chance Labs
Tel.: 215-573-3506 / Fax: 215-898-4217
Email: sharpk@mail.med.upenn.edu
Sharp Department of Biochemistry & Biophysics page / Sharp Lab Page

The goal of the research is to gain a detailed understanding at the molecular and physical chemical level of how proteins bind and recognize other proteins, drugs, ligands and nucleic acids. Theoretical and computational methods used include Poisson-Boltzmann electrostatics, Molecular and Browian Dynamics, and Monte Carlo simulations.

 

James Shorter, Ph.D.

Regulation of beneficial or neuropathogenic prions and amyloids by protein-remodeling factors, molecular chaperones, and small molecules

Associate Professor of Biochemistry & Biophysics
805B Stellar-Chance Labs
Tel: 215-573-4256 (office) / 215-573-4257 (lab)
Email: jshorter@mail.med.upenn.edu
Shorter Lab website / Shorter Department of Biochemistry & Biophysics page
Read about Dr. Shorter's NIH Director's New Innovator Award (October 2007)

Life demands that proteins fold into elaborate structures to perform the overwhelming majority of biological functions. We investigate how cells achieve such successful protein folding. In particular, we seek to understand how cells prevent, reverse, or even promote the formation of prion and amyloid fibers.

 

Emmanuel Skordalakes, Ph.D.

X-ray crystallography; telomere biology; cancer and aging

Wistar Institute Associate Professor of Biochemistry & Biophysics
321 Wistar Institute
Tel: 215-495-6884 (Office); 215-898-2202 (Lab)
Email: skorda@wistar.org
Skordalakes website

In recent years several links have begun to emerge between the integrity of eukaryotic chromosome ends, known as telomeres, and both cancer and aging. Studies from several research laboratories have identified proteins involved in replicating and regulating telomere length and stability; however, the function of these telomere maintenance factors and their role in human disease are far from fully established. The long-term goal of the Skordalakes laboratory is to understand how telomeric complexes protect chromosome ends and mediate their replication and apply this information in pursuit of anticancer therapies.

 

David Speicher, Ph.D. 

Cancer proteomics; structure-function of membrane associated proteins: protein chemistry and mass spectrometry

Wistar Institute Professor of Biochemistry & Biophysics
151 Wistar Institute
Tel: 215-898-3972
Fax: 215-898-0664
Email: speicher@wistar.org
Speicher lab website

Our research group primarily focuses on proteomics of human diseases and structure-function of protein-protein interactions. We are currently pursuing two structure-function projects that primarily utilize biophysical methods, such as isothermal titration calorimetry and sedimentation equilibrium, and mass spectrometry to probe protein structures, protein-protein interactions and function. One project involves the giant membrane skeletal protein spectrin, a human actin crosslinking protein that plays a key role in stabilizing the plasma membrane in most cell types. Current studies focus on the proteotypical spectrin tetramers found in human red blood cells and their role in membrane purturbations caused by hereditary hemolytic anemia mutations. Another project involves structure-function analysis of peroxiredoxin 6, an antioxidant enzyme with glutathione peroxidase activity and phospholipase activity, which plays a critical role in protecting lung and other tissues from damage due to oxidative stress

 

Cecilia Tommos, Ph.D.

Protein radicals and electrochemistry; cation-x interactions; protein forced folding

Research Assistant Professor of Biochemistry & Biophysics
905 Stellar-Chance Labs
Tel: 215-746-2444
Email: tommos@mail.med.upenn.edu
Tommos Department of Biochemistry & Biophysics page

Our work involves two quite different projects:
1) Understanding the redox chemistry of protein radicals. Amino-acid radicals represent key components in biological processes ranging from energy transduction to carcinogenesis and, yet, virtually nothing is known about the thermodynamic properties of these species. This situation reflects the simple fact that the characteristically reactive and thermodynamically hot radical state is highly challenging to study in the natural systems. We have created a model protein system specifically made to facilitate structural, spectroscopic and electrochemical studies of amino-acid radicals. Using this system we aim to systematically characterize the thermodynamic properties of amino-acid radicals as a function of structural motifs in the protein environment.
2) Developing a "protein forced folding" method for the structural analysis of intrinsically unfolded proteins. Structural genomics studies have revealed that a surprising large fraction of the proteins from various genomes, including that of humans, are unfolded under in vitro conditions. Several factors may contribute as to why a protein is found unfolded in the test tube, e.g., it lacks an essential ligand. Another possibility is that the test-tube protein lacks the unique environment of the densely packed cell in which molecular crowding stabilizes the compact folded state of the protein relative to its structurally more extended unfolded states. We showed in a pilot study that a highly unstable model protein could be forced folded into a well-defined structure by placing the protein in a reverse micelle "bag". When the size of the "bag" was made sufficiently small, the protein was observed to adopt the structurally more compact form of the folded protein. We are now in the process of exploring the potential of this confined-space approach to force fold naturally unfolded proteins. This project is conducted in collaboration with Professor Wand.

 

Gregory D. Van Duyne, Ph.D.

Structural biology; protein-protein interactions; x-ray crystallography

Jacob Gershon-Cohen Professor of Medical Science
Professor of Biochemistry & Biophysics
809B Stellar-Chance Labs
Tel: 215-898-3058
Fax: 215-573-4764
Email: vanduyne@mail.med.upenn.edu
Van Duyne Department of Biochemistry & Biophysics page

We are interested in understanding on a structural and biochemical level how DNA and RNA molecules are maintained and processed by living cells. In addition to the mechanisms and regulation of genome replication and transcription, this includes processes such as DNA repair, site-specific and homologous recombination, transposition, condensation of chromosomes, chromosome pairing and segregation, and RNA trafficking and splicing. Our approach is to establish three-dimensional models of macromolecular assemblies relating to a particular biological question using X-ray diffraction methods and to then develop mechanistic and functional models that can be tested experimentally.

 

A. Joshua Wand, Ph.D.

Protein structure and dynamics; molecular recognition and signal transduction; NMR spectroscopy

Benjamin Rush Professor of Biochemistry & Biophysics
Office: 905 Stellar-Chance Labs
Main Laboratory: 902-904 Stellar-Chance Labs
NMR Laboratory: G6 Blockley Hall
Tel. 215-573-7288 (office); 215-573-7289 (main lab); 215-573-5969 (NMR lab) / Fax: 215-573-7290
Email: wand@mail.med.upenn.edu
Wand lab page
Wand Department of Biochemistry & Biophysics page

Dr. Wand's research focuses on exploring the relationships between static structure, structural dynamics and function in a range of protein systems. Current efforts are centered on calmodulin, a main player in calcium-mediated signal transduction, GP130, an somewhat promiscuous interleukin and antigen-antibody complexes. A key concept is the balance between changes in structure (enthalpy) and dynamics (entropy) in the setting of the free energy of association between proteins. They are also interested in similar issues in the context of interactions with small ligands such as drugs. Through these studies a remarkably rich manifold of fast dynamical modes have been revealed and a surprising functional role for them discovered.

The Wand lab is also committed to continuing improvement and development of novel NMR techniques. They have recently focused on high pressure NMR to probe the protein ensemble, sparse sampling methods for rapid and sensitivity-optimized data collection, NMR relaxation methods to measure conformational dynamics throughout the protein and a novel method to approach large soluble, unstable and membrane proteins by solution NMR methods. The latter approach involves the use of reverse micelle encapsulation to provide a protective environment for proteins to allow them to be dissolved in low viscosity fluids such as liquid ethane. The initial idea was to use the low viscosity of ethane to overcome the slow tumbling problem for solution NMR spectroscopy presented by large protein in water. Applications have since been expanded to studies of proteins of marginal stability by employing the confined space of the reverse micelle, suppression of protein aggregation to allow study of intermediates of aggregation such as occur in amyloid formation, and studies of both integral and peripherally anchored membrane proteins.

 

John W. Weisel, Ph.D.

Structural studies of molecular/cellular mechanisms in blood clotting and fibrinolysis

Professor of Cell & Developmental Biology
1054 Biomedical Research Building II/III
Tel.: 215-898-3573 / Fax: 215-898-9871
Email: weisel@mail.med.upenn.edu
Weisel Cell and Developmental Biology Web page

The research in this lab has focused on the molecular and cellular mechanisms of blood coagulation and fibrinolysis, as analyzed through the use of various biophysical and structural techniques, including visualization of molecules and supramolecular aggregates and measurements of mechanical properties of cellular and extracellular structures. Molecular mechanisms of the dissolution of the clot by the fibrinolytic system are under investigation. The interactions of integrins with various adhesive proteins and with the cytoskeleton is also a focus of research. The results of these studies have implications for basic mechanisms of protein-protein and protein-cell interactions as well as for clinical aspects of hemostasis, thrombosis and atherosclerosis.

 

Jeremy E. Wilusz, Ph.D.

Regulation of noncoding RNA biogenesis and function

Assistant Professor of Bichemistry & Biophysics
363 Clinical Research Building
Tel: 215-898-8862
E-mail: wilusz@mail.med.upenn.edu
Wilusz Department of Biochemstry & Biophysics page

The sequencing of the human genome provided quite a surprise to many when it was determined that there are only ~20,000 protein-coding genes, representing less than 2% of the total genomic sequence. Since other less complex eukaryotes like the nematode C. elegans have a very similar number of genes, it quickly became clear that the developmental and physiological complexity of humans probably can not be solely explained by proteins. We now know that most of the human genome is transcribed, yielding a complex repertoire of RNAs that includes tens of thousands of individual noncoding RNAs with little or no protein-coding capacity. Among these are well-studied small RNAs, such as microRNAs, as well as many other classes of small and long transcripts whose functions and mechanisms of biogenesis are less clear – but likely no less important. This is because many of these poorly characterized RNAs exhibit cell type-specific expression or are associated with human diseases, including cancer and neurological disorders. Our goal is to characterize the mechanisms by which noncoding RNAs are generated, regulated, and function, thereby revealing novel fundamental insights into RNA biology and developing new methods to treat diseases.

Much of our work has focused on the MALAT1 locus, which is over-expressed in many human cancers and produces a long nuclear-retained noncoding RNA as well as a tRNA-like cytoplasmic small RNA (known as mascRNA). Despite being an RNA polymerase II transcript, the 3’ end of MALAT1 is produced not by canonical cleavage/polyadenylation but instead by recognition and cleavage of the tRNA-like structure by RNase P. Mature MALAT1 thus lacks a poly(A) tail yet is expressed at a level higher than many protein-coding genes in vivo. We recently showed that the 3’ end of MALAT1 is protected from 3’-5’ exonucleases by a highly conserved triple helical structure. Surprisingly, when this structure is placed downstream from an open reading frame, the transcript is efficiently translated in vivo despite the lack of a poly(A) tail. This result challenges the common paradigm that long poly(A) tails are required for efficient protein synthesis and suggests that non-polyadenylated RNAs may produce functional peptides in vivo via mechanisms that are likely independent of poly(A) binding protein. To address these issues, we are currently elucidating the molecular mechanism by which a triple helix functions as a translational enhancer. In addition, we are developing approaches to identify additional triple helices that form across the transcriptome, thereby revealing new paradigms for how RNA structures regulate gene expression.

Besides MALAT1, only a handful of long RNA polymerase II transcripts (e.g. histone mRNAs) have been clearly shown to be processed at their 3’ ends via non-canonical mechanisms. This is likely because nearly all previous studies characterizing the transcriptome have focused only on polyadenylated RNAs, thereby missing RNAs that lack a poly(A) tail. Nevertheless, it is becoming increasingly clear that non-polyadenylated RNAs are much more common and play significantly greater regulatory roles in vivo than previously appreciated. For example, an abundant class of circular RNAs has recently been identified in human and mouse cells. Two of these circular RNAs clearly function as microRNA sponges, but it is largely unknown why all the other circular RNAs are produced or how the splicing machinery selects certain regions of the genome (and not others) to circularize. We aim to identify and characterize additional RNAs whose 3’ ends are generated via unexpected mechanisms, thereby revealing novel paradigms for how RNAs are processed and, most importantly, new classes of noncoding RNAs with important biological functions.

 

X. Long Zheng, M.D., Ph.D.

ADAMTS13 metalloprotease and microvascular thrombosis

Associate Professor of Pathology & Laboratory Medicine
816G Abramson Research Building
Tel: 215-590-3565 (Office); 215-590-3890 (Lab) / Fax: 267-426-5165
Email: zheng@email.chop.edu
Zheng website

ADAMTS13 (a disintegrin and metalloprotease with thrombospondin type 1 repeats) cleaves von Willebrand factor (VWF) at the Tyr1605-Met1606 bond. Inability to cleave VWF by ADAMTS13 due to hereditary or acquired deficiency of ADAMTS13 activity may result in an exaggerated VWF-mediated platelet aggregation and thrombus formation in small arteries, leading to a lethal syndrome, thrombotic thrombocytopenic purpura (TTP).

The Zheng laboratory is investigating the biological function of ADAMTS13 and particularly focusing on: 1) the domains of ADAMTS13 required for substrate recognition and cleavage in vitro and in vivo; 2) the biosynthesis and secretion of ADAMTS13 in polarized endothelial and epithelial cells; 3) the interaction between ADAMTS13 and autoantibody against ADAMTS13 in patients with TTP.

The technologies being used in the laboratory include but are not limited to recombinant DNA, protein expression and purification, protein-protein interaction, protein refolding and structural determination. In addition, cell culture, transfection, immunofluorescent and confocal microscopy, and various biochemical and biophysical assays will be employed in the laboratory.

The advancement in this area of research will not only provide more insight into understanding of the pathogenesis of TTP, but also provide better tools for diagnosis and cure of TTP as well as other blood clotting-related disorders.