Chemical and Structural Biology|
Quality control of protein folding in the cell by molecular chaperones |
Professor of Pathology & Laboratory Medicine; Chief, Division of Cell Pathology 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. |
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Biophysical studies of molecular recognition and rational drug design |
Professor of Pharmacology, Biochemistry & Biophysics, and Medicine Research Themes - Infectious disease (antibiotics, antimicrobial peptides, antibiotic resistance, vancomycin); Neurodegeneration (amyloidogenesis, Alzheimer's disease); Cardiovascular disease (lipoprotein structure and function) |
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Biomembrane function: thermodynamics, dynamics and mechanics |
Associate Professor of Chemistry 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. |
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Chromosome segregation; chromatin structure; epigenetic centromere specification; hydrogen/deuterium exchange |
Associate Professor of Biochemistry & Biophysics Dr. Black's laboratory is interested in how particular proteins direct accurate chromosome segregation at mitosis. |
Kathleen Boesze-Battagalia, Ph.D. Tetraspanin protein structure and role in degenerative disease processes
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Associate Professor, Department of Biochemistry, School of Dental Medicine 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. In a 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. A new area of research is focused on mechanisms of microbial pathogenesis and immunotoxicity in collaboration with Dr. B.J. Shenker, SDM. Over the past several years, significant progress has been made in our understanding of the etiology and pathogenesis of oral infectious diseases. However, the nature and contribution of the immune system to these disorders remain unclear. We propose that the immune system plays a primary role in minimizing and/or preventing infection and immunoregulatory abnormalities contribute to the pathogenesis of and susceptibility to oral infectious disorders such as periodontal disease. Previous studies in the Shenker lab have demonstrated that the A.actinomycetemcomitans immunoinhibitory protein is a member of the family of cytolethal distending toxins; this toxin induces G2 arrest in lymphocytes and eventually leads to activation of the apoptotic cascade. The cytolethal distending toxins (Cdts) are a family of heat-labile protein cytotoxins produced by several different bacterial species including diarrheal disease-causing enteropathogens such as some Escherichia coli isolates, Campylobacter jejuni, Shigella species, Haemophilus ducreyi and Actinobacillus actinomycetemcomitan. Regardless of the microbial source of Cdt, the heterotrimeric holotoxin functions as an AB2 toxin where CdtB is the active (A) unit and the complex of CdtA and CdtC comprise the binding (B) unit. CdtA and CdtC are required for the toxin to associate with lipid microdomains within lymphocyte membranes and Cdt-mediated toxicity is dependent upon the integrity of these lipid domains. The active (A) unit, CdtB, exhibits sequence homology with inositol polyphosphate 5-phosphatases specifically within highly conserved regions corresponding to the active site. Analysis of CdtB indicates that its structure can be superimposed on inositol polyphosphate 5-phosphatase with an rmsd of 3.5Å over 183 Cx atoms. In our most recent work we report that CdtB exhibits phosphatidylinositol-3,4,5-triphosphate phosphatase (PI-3,4,5-P3) phosphatase activity similar to that of the tumor suppressor phosphatases, PTEN and SHIP1. Mutation analysis indicates that Cdt toxicity correlates with phosphatase activity; furthermore, lymphocytes treated with toxin exhibit reduced PI-3,4,5-P3 levels. Finally, lymphocyte sensitivity to Cdt-induced G2 arrest correlates with intracellular levels of PI-3,4,5-P3. Our observations suggest that CdtB, like SHIP1 and PTEN, mediates its regulatory effects by dephosphorylating PI-3,4,5-P3 and thereby modulating the activity of pleckstrin homology proteins such as Akt. Future studies are underway to assess the role of membrane association in toxin entry as well as to determine the mechanism of Cdt-B mediated toxicity. |
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Actin cytoskeleton, structural biology |
Professor of Physiology Structure Biology of the Actin Cytoskeleton 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. |
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Methods and applications of protein structure prediction |
Adjunct Professor of Biochemistry & Biophysics 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. |
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Oxido-reductase engineering; design and chemical synthesis of redox proteins |
Eldridge Reeves Johnson Professor of Biochemistry & Biophysics 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. |
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Protein folding; structure, structure change, and dynamics; H-exchange; NMR |
Professor of Biochemistry & Biophysics 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. |
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Regulation of chromatin structure and its impact on human diseases |
Assistant Professor of Biochemistry & Biophysics 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. Structural biology, growth factor receptor signaling, molecular mechanisms of protein-protein interactions |
Associate Professor of Physiology 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. |
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Spectroscopic study of protein folding/misfolding |
Professor of Chemistry 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. |
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Motor proteins studied by photochemistry and spectroscopy |
Professor of Physiology, and Biochemistry & Biophysics 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. |
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Protease function, chemical biology, proteomics, biochemistry, cell biology, malaria |
Assistant Professor of Pharmacology My laboratory focuses on developing and exploiting new technologies at the interface between biology and chemistry to study protease function. We use a variety of techniques including the synthesis of small molecule inhibitors, quantitative proteomics, genomics, recombinant protein expression, and molecular genetics in order to better understand proteolytic systems. Although these tools are useful to study any biological system, much of our biological efforts are aimed at understanding proteases in the parasite P. falciparum, the causative agent of malaria. The completed genomes of many pathogens including P. falciparum are a rich resource in the search for novel therapies and allow the possibility of more systematic approaches to therapeutic discovery and design. In particular, I believe chemical strategies for global proteome analysis will become increasingly more important to enable functional characterization and profiling of enzyme activity. Therefore we develop universal chemical-based proteomics tools to functionally analyze the role of proteases in a variety of biological systems. We can use these chemical tools for enzyme discovery, for screening of small molecule and for investigating biological pathways |
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Biological chemistry of nitric oxide; oxidative processes, protein aggregation and neurodegeneration. |
Gisela and Dennis Alter Research Professor of Pediatrics, and Pharmacology The research efforts of my laboratory are focused on three areas: |
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Pathobiology of Alzheimer's and Parkinson's disease |
Professor of Pathology & Laboratory Medicine 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. |
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Biochemistry/biophysics of intermolecular interactions of growth factor receptor signaling |
George W. Raiziss Professor of Biochemistry & Biophysics Research Interests of the Lemmon Lab: |
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Gene regulation; protein crystallography; structural basis of recognition |
Professor of Biochemistry & Biophysics 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. |
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G-protein-receptor-arrestin mechanisms; visual signal transduction |
Professor of Biochemistry & Biophysics Research Interests of the Liebman Lab:
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Structural biology; transcription; protein-DNA interactions; heat shock response |
Associate Professor of Biochemistry & Biophysics |
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Biochemistry of contractile proteins, biophysics of cell motility, and characterization of unconventional myosins |
Professor of Physiology 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. |
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Structure-function of aldo-keto reductases; role in steroid hormone action and chemical carcinogenesis |
Professor of Pharmacology, and Biochemistry & Biophysics 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. |
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Semi-synthesis of labeled proteins to probe and control conformation
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Assistant Professor of Chemistry 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. |
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Computational structural biology and systems biology; cell membrane mediated trafficking; targeted drug delivery; cancer signaling
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Associate Professor of Bioengineering, and Biochemistry & Biophysics 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. |
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NMR; protein folding mechanism; protein structure, dynamics and function |
Adjunct Professor of Biochemistry & Biophysics 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. |
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Pathogenesis of dormancy in mycobacterium tuberculosis; biomolecular computation and enzymology and cell biology of serine proteases and serine protease inhibitors |
Professor of Medicine 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. |
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Protein engineering; synthetic biology; cell-fate decisions |
Associate Professor of Bioengineering The Sarkar laboratory utilizes both experimental and computational methods to quantitatively understand fundamental biomolecular (e.g., binding, catalysis) and cellular (e.g., signaling, trafficking, gene regulation) processes. We seek to understand and manipulate the operation of biomolecular networks, and consequently cellular behavior, by integrating novel molecular design strategies into a cell engineering framework. Current applications range from controlling cell fate decisions to engineering novel therapeutic ligands, receptors, and signaling networks to generating molecular devices for use in synthetic biology. |
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Theory, simulation and design of proteins and folding molecules |
Associate Professor of Chemistry 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. |
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Theory of protein and nucleic acid structure and function |
Associate Professor of Biochemistry & Biophysics 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. |
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Regulation of beneficial or neuropathogenic prions and amyloids by protein-remodeling factors, molecular chaperones, and small molecules |
Assistant Professor of Biochemistry & Biophysics 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. |
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Protein radicals and electrochemistry; cation-x interactions; protein forced folding |
Research Assistant Professor of Biochemistry & Biophysics Our work involves two quite different projects: |
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Structural biology; protein-protein interactions; x-ray crystallography |
Jacob Gershon-Cohen Professor of Medical Science 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. |
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Protein structure and dynamics; molecular recognition and signal transduction; NMR spectroscopy |
Benjamin Rush Professor of Biochemistry & Biophysics 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. |
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Structural studies of molecular/cellular mechanisms in blood clotting and fibrinolysis |
Professor of Cell & Developmental Biology 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. |
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ADAMTS13 metalloprotease and microvascular thrombosis |
Associate Professor of Pathology & Laboratory Medicine 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. |
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