Cryo Electron Microscopy (cryoEM) has emerged as a revolutionary method in structural biology, enabling the determination of the three-dimensional structures of biological macromolecules at near-atomic resolution without the need for crystallization. We utilize cryoEM and cryoET to understand the structural mechanisms underlaying various fundamental or disease-causing biological processes.
Shared Facility
Researchers
The Moiseenkova-Bell laboratory research is focused on structure-function analysis of Transient Receptor Potential (TRP) channels and their interaction with agonists/antagonists to enhance our understanding of their function at the molecular level. In addition, her laboratory research program seeks to understand how TRP channels regulate cellular functions and the role of their dysregulation in human disease.
CryoEM and CryoET cryoET cryoEM Mass Spectrometry
The Marmorstein laboratory studies the molecular mechanisms of (1) epigenetic regulation (2) protein post- and co-translational modification with a particular focus on protein acetylation, and (3) enzyme signaling in cancer and metabolism. The laboratory uses a broad range of biochemical, biophysical and structural research tools (X-ray crystallography and cryo-EM) to determine macromolecular structure and mechanism of action. The laboratory also uses high-throughput small molecule screening and structure-based design strategies to develop protein-specific small-molecule probes to interrogate protein function and for preclinical studies.
Chemical Biology X-ray Crystallography cryoEM
The Chang laboratory specializes in the utilization and advancement of cryo-electron tomography (cryo-ET) methods and related technologies for investigating molecular structures inside cellular context. His research group employs cryo-ET to investigate a wide spectrum of host-pathogen interactions, unraveling the structural mechanisms behind various diseases that can only be elucidated through such in situ structural biology methods.
CryoEM and CryoET cryoET cryoEM Mass Spectrometry
Eukaryotic gene expression by RNA polymerase II (pol II) requires the orchestration of a large number of factors during each stage of transcription. Proper gene regulation underlies organismal development, environmental responses and can be disrupted in disease. The goal of our lab is to determine the mechanisms of pol II transitions between initiation, elongation, and re-initiation, and its regulations in the context of chromatin, which we will accomplish through structural (cryo-EM and cross-linking mass spectrometry) and biochemical dissection of these macromolecular complexes.
The lab also aims to understand the mechanism of nucleotide excision repair (NER). The eukaryote genome is actively scanned for DNA damage through at least two independent mechanisms known as transcription-coupled nucleotide excision repair (TC-NER) and global genomic nucleotide excision repair (GG-NER). In particular, we focus on the mechanism of how a set of factors serve dual functions in NER and transcription and how they are regulated.
cryoET cryoEM Mass Spectrometry
The Black Lab is answering the most pressing questions in chromosome biology, such as:
- How does genetic inheritance actually work?
- How was epigenetic information transmitted to us from our parents?
- Can building new artificial chromosomes help us understand how natural chromosomes work?
- How are the key enzymes protecting the integrity of our genome specifically and potently activated by potential catastrophes like DNA breaks or chromosome misattachment to the mitotic spindle?
cryoET cryoEM Mass Spectrometry
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.
X-ray Crystallography cryoEM
The actin cytoskeleton plays an essential role in multiple cellular functions, including cytokinesis, vesicular trafficking, and the maintenance of cell shape and polarity. To accomplish these functions, the cytoskeleton undergoes constant remodeling into various forms of structural and functional networks, such as lamellipodia, filopodia, stress fibers and focal adhesions. Remodeling of the cytoskeleton of eukaryotic cells is a tightly regulated process, involving hundreds of actin-binding and signaling proteins. Additionally, many bacterial pathogens highjack the eukaryotic actin cytoskeleton during invasion. 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. We are also interested in understanding the function of BAR domain-containing proteins, which are emerging as a critical linkage between signaling, the cytoskeleton and cellular membranes. Our lab is finally deeply invested in understanding the role of cytoskeleton dynamics in muscle cells, particularly the differentiated vascular smooth muscle cell. Our primary research tool is structural biology, including cryo-EM and X-ray crystallography. The atomic snapshots resulting from these structural methods provide a wealth of knowledge, but lack information about the function, dynamics and energetic aspects of protein-protein recognition. To obtain this kind of information we use a host of other approaches, including bio-informatics, biophysical and biochemical methods and collaborative cellular studies.
X-ray Crystallography cryoEM
The Sgourakis lab sheds light on the dynamic molecular processes which determine immune recognition, signaling and the formation of long-term memory against viral, tumor and autoimmune targets. To address these questions, we integrate cutting-edge structural biology tools from (NMR) Nuclear Magnetic Resonance Spectroscopy, X-ray crystallography with complementary biophysical and biochemical techniques, computational modeling and functional assays.
NMR NMR cryoEM
Dr. Krishnaswamy studies molecular mechanisms underlying the reactions of blood coagulation. His laboratory investigates how the proteins of blood coagulation interact with each other and with membranes to yield a regulated clotting response to vascular injury or an unregulated response in thrombotic or bleeding disease.
X-ray Crystallography cryoEM
Protein folding and protein interactions underlie both proper function and disease in biological systems. Many receptor proteins signal through complex interactions and rearrangements, and some proteins, such as the Parkinson’s Disease protein α-synuclein, 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 proteins fold and change shape. The Petersson laboratory is developing tools to address questions of how peptides and proteins mediate cellular communication and how the cellular environment catalyzes protein misfolding, from detailed in vitrofolding studies to imaging in live animals. These tools include novel chromophores, which we synthesize and incorporate into proteins through unnatural amino acid mutagenesis and synthetic protein ligation. We apply these tools to several key disease areas through collaborations in the Perelman School of Medicine: preventing the acquisition of antibiotic resistance by bacteria, Parkinson’s Disease, and fluorescence-guided cancer surgery. In many cases, the balance between health and disease is governed by post-translational modifications, for which we study the enzymes that install them, both to understand their biological roles and to utilize them in synthetic protein modification. Finally, an area of particular interest in the Petersson laboratory is the introduction of thioamide modifications to the peptide backbone, which can serve as protein folding probes, or stabilizers for improved therapeutic peptides or in vivoimaging reagents.
NMR cryoEM
Kushol Gupta is a Research Assistant Professor in the Department of Biochemistry & Biophysics at the Perelman School of Medicine of The University of Pennsylvania, a member of the BMB graduate group, and directs the Johnson Foundation Structural Biology and Biophysics Core, a departmental resource that serves Penn and the greater region.
He is a structural biologist with expertise in both X-ray crystallography and solution biophysical methods, including small-angle X-ray and neutron scattering, light scattering, and analytical ultracentrifugation. His ongoing research focuses on retroviral integrases, their interaction with host factors, and a new class of drugs known as allosteric inhibitors of integrase (ALLINIs), which are potent antivirals against HIV. His research also includes other projects in the areas of phenylketonuria, RNA splicing, and site-specific recombination, highlighting the collaborative nature of research at Penn.
X-ray Crystallography X-ray Crystallography and Biophysics cryoEM
The Kulp Laboratory seeks to inspire innovative solutions to long standing problems in the development of efficacious vaccines through the fusion of artificial intelligence and protein structure engineering. New cutting-edge protein design and structure determination methods allow for exciting, rapid and iterative vaccine science. The lab focuses on creating immunogens for diseases that impose a significant health impact and without broadly effective vaccines, such as HIV, SARS-CoV-2, Influenza and Lassa, among others. Biophysical techniques, novel transgenic animal models, and advanced structural assessments are employed to study immune responses of next-generation vaccines. The lab posits that computational approaches can now be used to tackle previously insurmountable challenges ushering in a new era of precision structural vaccinology.
Computational Biology Computational Biology cryoEM
Circadian Clocks
Our laboratory is interested in circadian rhythms, which are daily cycles of physiology and behaviour that persist when organisms are isolated from the outside world. They represent a fundamental biological mechanism, and are present at all levels of life, from bacteria through to humans. We need them in order to anticipate and thus adapt to the solar cycle of night and day.
Although we now understand a great deal about some components of the clockwork, our recent work has implicated a significant contribution of non-transcriptional and post-translational processes to the time-keeping mechanism. In particular, we are interested in redox and metabolic oscillations that power the clockwork within single cells and tissues, such as those shown by peroxiredoxin proteins.
In humans, the sleep-wake cycle is the most obvious circadian rhythm but other, more subtle, endocrine rhythms coordinate our body's physiology. Disruption of our circadian programming through old age, neurological disease, and even shift-work, is a growing cause of significant ill health. Of note, disorders of metabolism, as well as cancer, have now been closely linked to circadian dysfunction.
We thus use a wide range of multi-disciplinary approaches, encompassing synthetic and systems biology, to deconstruct how clocks in the brain and in visceral tissues are able to control this vast array of physiological processes.
cryoEM Mass Spectrometry
The Tolbert lab research focuses on the biochemical mechanisms by which RNA viruses replicate within the cellular environment. Specifically, they use NMR spectroscopy and other biophysical methods to characterize complexes formed between host proteins and viral RNA elements. The group leverages their understanding of the foundational principles of these interactions to identify novel targets for therapeutic intervention.
NMR NMR cryoEM
Our work focuses on the structural and chemical biology of metal-requiring enzymes in human disease as well as biosynthetic enzymes that generate complex terpenoid natural products. Our research incorporates modern techniques of structural biology, such as X-ray crystallography, small-angle X-ray scattering, and cryo-EM, as well as techniques rooted in bioinorganic, bioorganic, and biophysical chemistry.
Our group, along with the entire Penn Chemistry community, is committed to providing an open and engaging environment in which all persons are welcome and respected. We are a diverse group of faculty, staff, and students, and our strength derives from our diversity. We value the highest ideals of respect and dignity in our daily interactions as we maintain an environment that is free from all forms of discrimination, harassment, and intimidation. Whoever you are and wherever you are on your journey of scholarship in the molecular sciences, you are welcome here.
X-ray Crystallography cryoEM
Our group is interested in chemical synthesis, synthetic methodology, chemical neuroscience, optogenetics, and photopharmacology. Natural products and photoswitches are always on our mind!
Chemical Biology cryoEM
The Foskett lab is interested, most generally, in membrane transport and cell signaling. The techniques we employ in the lab span the spectrum from biophysical to molecular. Biochemical and molecular tools are used within the context of physiological measurement, with the goal to understand how molecular behavior results in complex cell physiological processes in normal and disease states. We employ electrophysiology, including single ion channel patch clamping and two-electrode voltage clamping; digital low light-level fluorescence imaging microscopy of single living cells; micro-injection; yeast 2-hybrid system to examine and discover protein interactions; recombinant protein expression; molecular biology; and biochemistry.
cryoEM
The goal of our research is to understand the cellular machinery responsible for powering cell movements and shaping the architecture of cells, tissues, and organs. Our discovery-based research focuses on the role of the cytoskeleton, molecular motors, and signaling pathways in powering cell migration, muscle contraction, and the transport of internal cell compartments. The pathways investigated in our laboratory are crucial for several normal and pathological processes, including: cell and tissue development, endocytosis, wound healing, immune response, cardiomyopathies, and metastases of tumors.
Single Molecule Imaging cryoEM
While we conventionally think of genomic DNA as a simple polymer of A's, C's, G's, and T's, the chemistry of the genome is in fact far more interesting. Our laboratory focuses on the DNA modifying enzymes that provide an added layer of complexity to the genome. These enzymes can be involved in the purposeful introduction of mutations or in the chemical modification of nucleobases, making DNA a remarkably dynamic entity. Many of these processes are at the heart of the battle between the immune system and pathogens or are central to epigenetics.
Our work can be broadly classified in two areas:
Enzymatic deamination, oxidation and methylation of cytosine bases, with a focus on AID/APOBEC DNA deaminases and TET oxygenases
Targeting Pathogen Pathways that Promote Evolution and Antibiotic Resistance, with a focus on the LexA/RecA axis governing the bacterial SOS response.
We utilize a broad array of approaches, which include 1) biochemical characterization of enzyme mechanisms, 2) chemical synthesis of enzyme probes, and 3) biological assays spanning bacteriology, immunology, and virology to study DNA modifying enzymes and pro-mutagenic pathways.
Our research program aims to understand diversity generating enzymes and pathways in vitro, to perturb their function in physiological settings, and to harness the biotechnological potential of these diversity-generating pathways.
Chemical Biology cryoEM
More than 60% of current drug targets are membrane proteins, which come in the form of enzymes, receptors, channels, and transporters. This underlines the biomedical relevance of our research into the function of membrane proteins and lipids.
Our research is highly interdisciplinary and collaborative. Our group members typically have backgrounds in fields such as physical chemistry, chemical biology, biochemistry, physics, and various engineering disciplines, and we collaborate with multiple different groups in our department, elsewhere on campus, or at nearby research institutions.
Specifically, we are interested in the function of lipid transporters (flippases) and how these can be modulated through photopharmacology, the structure and function of proteins involved in endocytosis (using techniques such as Cryo Electron Tomography and various fluorescence labeling, microscopy, and spectroscopy approaches), the function of intrinsically disordered proteins on membranes (using 2D NMR spectroscopy and various fluorescence techniques), all complemented with micromanipulation techniques and interpretation with thermodynamic and statistical mechanical models and simulations. A recent development in our lab has been to ask to what extent and by what mechanisms protein-protein liquid phase separation, referred to as LLPS, contributes to some of these phenomena.
Single Molecule Imaging cryoEM
The Pallesen laboratory is interested in the function of receptors in the human immune system and how they interact with their surroundings, particularly in the context of infectious diseases and cancer. We are also interested in viral surface glycoprotein function and their mechanisms to evade immune responses.
CryoEM and CryoET cryoET cryoEM
The instruments in the Electron Microscopy Resource Laboratory represent a substantial investment and resource for the University of Pennsylvania research community. To ensure that these resources are available at the optimum performance level and a minimum of downtime, the Internal Cryo-Electron Microscopy Advisory Committee (CEMAC) oversees the services, policies, rules, and rates will be reviewed periodically by the committee and are subject to change.
cryoEM Staff
Our laboratory is focused on understanding the dynamics of intracellular motility. The active transport of membrane-bound organelles such as mitochondria along the cytoskeleton is essential in most eukaryotic cells, but is especially important in neurons. Neurons are highly polarized cells, with axons that can extend up to one meter, making them uniquely dependent on motor-driven transport. We explore the molecular mechanisms that lead to the coordinated activity of molecular motors during long-distance transport. Mutations in motors or required activators are sufficient to cause neuro-developmental and/or neurodegenerative disease; thus we study transport deficits in the context of human diseases including ALS, Huntington’s disease and Parkinson’s disease.
Organelle quality control is also essential to maintain healthy neurons. We explore the dynamics of autophagy, mitophagy, and lysophagy in neurons, examining biogenesis, cargo capture, trafficking, and cargo degradation. Mutations in key genes including PINK1, Parkin, OPTN, TBK1, and LRRK2 disrupt autophagy in neurons, strongly implicating defects in these pathways in neurodegenerative diseases including ALS and Parkinson's.
We focus on mechanistic cell biology, with approaches including: live cell imaging of cytoskeletal and organelle dynamics in primary neurons and human iPSC-derived neurons, in vitro reconstitution assays using TIRF microscopy to obtain single molecule resolution, and analysis of cellular and mouse models of neurodegenerative disease. Our lab takes an inclusive and collaborative approach to science, working with exceptional labs at Penn and worldwide, through the Pennsylvania Muscle Institute, the RM1 Mitochondrial Group, and the ASAP Collaborative Science Network.
Our success is built on our diversity; we are committed to mentoring scientists from a broad array of backgrounds and to supporting and enhancing opportunities for women and under-represented minorities in science.
Single Molecule Imaging cryoET
The curiosity-driven discovery of prokaryotic restriction-modification and CRISPR immune systems led to blockbuster molecular cloning, gene-editing, and diagnostic tools that have changed how we do science and medicine and have opened billion-dollar markets. Hundreds of new prokaryotic immune systems have been discovered in the past few years. However, the discovery of new immune systems outpaces our understanding of their roles in antiviral defense and therefore their development for novel transformative applications.
The Santiago-Frangos lab integrates bioinformatics, biochemistry, and structural biology to determine how fundamental biological processes including DNA integration and antiviral immunity have evolved and are regulated. We’ll also repurpose these mechanistic insights to develop new medical and biotech applications.
Computational Biology cryoET Research Areas