STBB students may rotate with and join the lab of faculty who have appointments in the STBB Graduate Program. Explore our faculty and their research below.
|Many essential cellular processes are carried out by "macromolecular machines", large assemblies that often include tens of different proteins, each making a specific contribution to the function of the machine. Characterization of these large macromolecular complexes using a combination of techniques constitutes the next frontier in structural biology. Interestingly, despite including many different proteins, macromolecular complexes often display minimal enzymatic activity. This suggests that they truly function as macromolecular machines, in which function is related to "mechanical" changes that affect interactions and activity. Characterizing different states and conformations of a macromolecule, and correlating these findings to biochemical and functional information, can be essential to establish the mechanism of these remarkable cellular machines.|
|David Bain, PhD||The long-term goal of our research is to determine the molecular principles and logic that underlie transcriptional regulation in humans. As a model system, we studying the human steroid receptors, how they assemble at complex promoter sequences, and the relationship between these interactions and cellular outcomes. Our group uses thermodynamic approaches to experimentally dissect receptor- promoter binding energetics and statistical thermodynamics to synthesize overall behavior; we collaborate closely with Dr. James Lambert¹s lab (UCDenver Pathology) to link these findings to in vivo behavior.|
John Bankston, PhD
Ion channels are basic molecular elements responsible for the generation of cellular electricity. The opening and closing (gating) of these transmembrane proteins give rise to ionic fluxes that generate electrical signals in tissues all across the body. The generation of these signals is critical for phenomena as diverse as nerve action potentials, sensory transduction, pain sensing, muscle contraction, hearing, vision, and hormone secretion. Ion channels gate in response to external stimuli such as binding of ligands (ligand-gated ion channels) or changes in transmembrane electric field (voltage-gate ion channels). Our research is focused on understanding fundamental molecular mechanisms of ion channel function. This includes studying the basic structural elements involved in coupling a stimulus to a change in state (from close to open for instance) as well as studying how ion channels function as larger macromolecular complexes. To attack these questions, we use a combination of electrophysiology, biochemistry, fluorescence imaging, electron paramagnetic resonance spectroscopy, and structural biology. Trainees in the lab would be encouraged to take projects that would provide expertise in more than one of these approaches.
|Brad Bendiak, PhD||Structural analysis of protein glycosylation using NMR and mass spectrometry.|
|Carlos Catalano, PharmD, PhD||Research in the Catalano lab focuses on molecular mechanisms of virus assembly in the double-stranded DNA viruses. We couple detailed enzyme kinetic analyses with biophysical and structural interrogation of the molecular motor that "packages" the viral genome into a capsid shell. Maturation of the nucleoprotein particle into an infectious virus is examined in defined reaction mixtures. The lambda capsid system is further harnessed for the construction of "designer" nanoparticles for use as therapeutic and diagnostic agents.|
|Uwe Christians, MD, PhD||We are committed to advancing individual medicine by examining the unique biology of an individual to assess truly personalized treatments. Our state of the art facility provides integrated solutions to systems biology and is located at Colorado's Fitzsimons Bioscience Park.|
Mair Churchill, PhD
|My lab is interested in understanding the molecular basis of essential processes that regulate gene expression. We use biophysical, biochemical methods, and structural methods, including X-ray crystallography. Our insights into these fundamental mechanisms will contribute to a better understanding and ability to regulate gene expression processes involved in human diseases from cancer and heart disease to bacterial infections and will assist in drug development efforts.|
Churchill Lab Website
|Angelo D’Alessandro, PhD||Omics technologies, especially metabolomics and proteomics, have helped us revealing emerging patterns in systemic responses to acute or chronic hypoxia. By focusing on cancer metabolism and (red) blood cell biology, we are increasingly appreciating shared molecular mechanisms driving systemic responses to trauma/ hemorrhagic shock, I/R injury, sickle cell disease, aging and inflammation, mammalian hibernation and pulmonary hypertension.|
Shaodong Dai, PhD
Metal ions are essential nutrients in all forms of life. Despite their important roles, metals can be toxic and elicit different kinds of immune responses, causing diseases. Chronic beryllium disease is a fibrotic lung disorder caused by beryllium exposure, while nickel ion is the dominant allergen for contact dermatitis. Our major goal is to understand the mechanisms of the metal containing ligands for alpha/beta TCRs from metal reactive human T cells. Using structural biology we will be able to discern the respective rule for metal binding and find potent compounds to inhibit metal binding, thus abrogating T cell responses. We are also interested in the molecular basis of metal induced autoimmunity.
Elan Eisenmesser, PhD
The Eisenmesser lab takes a unique approach to understand protein function, and particularly enzyme function, by utilizing molecular engineering methods to control both structural interactions and the underlying movements that underlie their conformational changes.
|Kirk Hansen, PhD|
We are focused on developing and utilizing strategies for the detection and characterization of proteins in health and disease. Our goal is to understand underlying mechanisms of disease at the molecular level using mass spectrometry as our primary analytical tool.
Using cell culture models we are performing studies to identify ECM components and modifications that influence metastatic potential of breast epithelial cells. We are also developing quantification methods to identify mediators of multiple organ failure in shock models and patients.
|Robert Hodges, PhD||Synthetic peptide and antipeptide approaches play major roles in understanding protein structure and function.|
|Michael Holers, PhD||The basic and translational research focus of my laboratory is on two areas. The first is the roles of complement receptors and membrane regulatory proteins in the immune response, with a special emphasis on B lymphocytes and autoimmune diseases. The second is the role of autoantibodies and the evolution of autoimmunity in RA from the pre-symptomatic autoantibody-positive period through the onset of clinically active disease.|
|Lawrence Hunter, PhD||Development and application of advanced computational techniques for biomedicine, particularly the application of statistical and knowledge-based techniques to the analysis of high-throughput data and of biomedical texts. Also, neurobiologically and evolutionarily informed computational models of cognition, and ethical issues related to computational bioscience. My laboratory is currently focused on knowledge-driven extraction of information from the primary biomedical literature, the semantic integration of knowledge resources in molecular biology, and the use of knowledge in the analysis of high-throughput data. |
Aaron Johnson, PhD
|Our work focuses on the formation and regulation of chromatin domains and their ultimate roles in the nucleus. We are particularly interested in the mechanisms of heterochromatin establishment and function. Heterochromatin operates in organisms from yeast to humans to determine cell identity and maintain genome stability by silencing genes. Because heterochromatin functions in such central processes, misregulation of this genomic structure can have dire consequences such as cancer or abnormal development. Our work investigates the mechanisms by which silencing is carried out. We use a combination of in vitro assembly of chromatin domains, mechanistic biochemistry, proteomic analysis, and genome-wide chromatin profiling to understand the complex superstructural “neighborhoods” of chromosomes.|
Johnson Lab Website
David Jones, PhD
|The action of small molecules at receptors and other proteins in signalling cascades leads to major changes in behavior. These small molecules act by producing a change in protein structure and dynamics that ultimate leads to changes in nueronal signalling. Our research focuses on two different classes of modulators of neuronal signal transduction, namely alcohols and pheromones. Alcohols act on a variety of receptors and other neuronal proteins, and lead to pharmacological changes that can result in alcohol intoxication and alcohol dependency. |
Jones Lab Website
John Kappler, PhD
|Atopic Dermatitis, Autoimmunity/Rheumatology, Basic Immunology, Cancer, Chronic Beryllium Disease, Genetics, Immunobiology, Molecular Immunology, Type-1 Diabetes, Structural Biology |
Kappler Faculty Profile
Jeffrey Kieft, PhD
|How does RNA form complex and dynamic 3-D structures that drive diverse biological functions? We are particularly interested in viral RNA, which is at the tip of the evolutionary spear. Our work has implications for human health and for understanding the greater “RNA World.|
Kieft Lab Website
Tatiana Kutateladze, PhD
|Research in my group focuses on the molecular mechanisms of epigenetic regulation and phosphoinositide signaling. We apply high field NMR spectroscopy, X-ray crystallography and a wide array of biochemical and molecular biology approaches to characterize the atomic-resolution structures and functions of chromatin- and lipid-binding proteins implicated in cancer and other human diseases.|
Kutateladze Lab Website
|Daniel LaBarbera, PhD||The LaBarbera laboratory is focused on drug discovery and development targeting cancer and diabetes. To accomplish this we utilize a multidisciplinary approach encompassing assay development for high-throughput screening (HTS) and confocal image based high-content screening (HCS), natural products small molecule library development, mechanism of action studies, and drug design and medicinal chemistry. The LaBarbera lab has pioneered techniques in validating and implementing 3D-tissue culture models of human disease for HCS/HTS,including: human lens epithelial spheroids (lentoids) for diabetic eye disease research and the multicellular tumor spheroid (MCTS) model for cancer research. We couple these models with surrogate biomarker reporters for phenotypic screening to identify small molecule bioactive modulators of human disease. Once we identify lead compounds we determine and validate their molecular target(s) and characterizethe mechanism(s) of action using in silico, in vitro, cell based, and in vivo models to design more potent “druglike” lead compounds with a long-term goal of clinical translation.|
Maggie Lam, PhD
Our lab is interested in developing mass spectrometry and computational methods to understand protein dynamics in health and disease. Current projects include developing multi-omics strategies to quantify protein alternative isoforms; investigating the role of ER stress and protein glycosylation in cellular stress responses; and identifying the trends and focuses of research topics in the biomedical literature.\
|Krishna Mallela, PhD||Muscular dystrophy (MD) refers to a group of degenerative muscle diseases that cause progressive muscle weakness. MD affects all types of muscles. For example, decreased function of heart muscles causes heart diseases that include cardiomyopathy and congestive heart failure. At present there is no cure available for MD, although certain palliative treatments are available to ease the pain associated with MD. Duchenne MD (DMD) and Becker MD (BMD) are two prominent types of MD, which are caused by the deficiency of a vital muscle protein known as dystrophin.|
Mallela Lab Website
Michael McMurray, PhD
Our research focuses on identifying molecular mechanisms underlying the assembly of macromolecular complexes, with a focus on multisubunit complexes formed by septin proteins.
|Catherine Musselman, PhD|
The Musselman laboratory is interested in the structural basis of chromatin signaling. We use NMR spectroscopy to investigate histone tail conformations in the context of the nucleosome, regulation of these conformations by histone PTMs, and mechanisms of histone tail binding.
David Pollock, PhD
|Protein, RNA, and other functional molecules that exist in living organisms are the product of millions of years of evolution. The substitutions that have occurred over the years had to have been compatible with the constraints of structure and function, and thus the evolutionary record provides critical data for understanding macromolecular structure/function/sequence relationships.|
Pollock Lab Website
Srinivas Ramachandran, PhD
Regulation of genome access underlies growth, development, and disease states. We uncover fundamental mechanisms that shape genome access by mapping chromatin structure at high temporal and spatial resolution using leading-edge experimental and computational methods.
Nichole Reisdorph, PhD
Dr. Reisdorph's research is designed to integrate clinical proteomics, metabolomics, and bioinformatics in order to develop and customize clinically relevant methodologies to diagnose or monitor disease states. Results from these studies will also significantly enhance the knowledge of the biochemical mechanisms of diseases. In addition, Dr’s Reisdorph’s facility will specialize in post-translational modification analysis as well as the identification of differentially regulated proteins from a variety of sources including cell extracts, biofluids, and tissue samples. Dr. Reisdorph uses a variety of techniques in her work, including two-dimensional gel electrophoresis, DiGE, tandem mass spectrometry, and quantitative labeling and non-labeling strategies. Dr. Reisdorph organizes proteomics hands-on workshops and web-based courses through National Jewish and the University of Colorado Denver. Since 2005, Dr. Reisdorph and her team have instructed almost a dozen 3-4 day workshops, for a total of over 120 individuals, who come from a variety of backgrounds. Dr. Reisdorph is currently expanding her training program to include additional hands on courses, such as quantitative proteomics, and distance-learning courses, such as database searching.
Ming-Feng Tsai, PhD
We study molecular mechanisms and physiological functions of transporters and ion channels. Our current research focuses on the mitochondrial calcium uniporter, which controls cell ATP production and apoptosis. We used a wide range of tools, including membrane biochemistry, electrophysiology, cryo-EM, genome editing, and imaging.
Chandra Tucker, PhD
Research in the Tucker Lab focuses on development of technologies for manipulation and probing of protein interactions and pathways. In particular, we are focusing on the emerging area of cellular optogenetics, developing pioneering new engineered protein tools to precisely regulate cell function with light.
Beat Vogeli, PhD
We develop NMR methods and apply them together with other biophysical methods to study biologically relevant systems at atomic resolution: Diverse dynein motor adaptors and their cargos, allostery in key cell regulator Pin1, Olduvai domains involved in brain function and disease, and various RNA and DNA segments.
|Gongyi Zhang, PhD|
RNA Polymerase II (Pol II) pausing is a unique transcription regulation mechanism in higher eukaryotes. We found that release of paused Pol II, phosphorylation of CTD-Pol II by CDK9, and cleavage of arginine methylated histone tails on + 1 nucleosome by JMJD5, are intrinsically coupled. We are trying to elucidate the underlying mechanism.
Rui Zhao, PhD
Our first research focus is to understand the mechanism of pre-mRNA splicing using a combination of cryo-EM, crystallography, biochemistry and molecular biology approaches. Our second focus is to target the Six1/Eya transcriptional complex for anti-cancer drug design.
Hongjin Zheng, PhD
We are interested in the broad field of structure and function relationship of membrane proteins and membrane protein complexes. Right now, our focus is on the mechanism of protein translocation between cytosol and mitochondria. We use primarily X-ray crystallography and Cry-Electron Microscopy to explore the structural characteristics of the corresponding membrane proteins, so to understand their biological roles in the cell.
|Morkos Henen, PhD||My research interest focuses on applying state-of-the-art NMR techniques to study protein structure, dynamics, and drug-discovery. I'm studying variable systems that have therapeutic interests such as dynein machinery as a target for neurodegenerative diseases and PHD2 as a target for gastrointestinal diseases. We collaborate with various groups on campus and in Europe. |
|Robert Murphy, PhD (Emeritus)||Research in this laboratory focuses on the basic biochemistry and pharmacological control of lipid mediators derived from both enzymatic and nonenzymatic pathways largely employing techniques of sophisticated mass spectrometry to address critical issues. The term lipid mediators is used here in the context that many of the compounds under investigation have potent and diverse biological activities that permit cells to intercommunicate with each other. |
|Natalie Serkova, PhD||Our research interests are in developing physiologically-based imaging end-points for cancer detection and response to novel anti-cancer therapies. We are also interested in developing novel molecular probes and protocols for non-invasive imaging of inflammation proteins, oncoproteins and endogenous metabolites (so-called "molecular imaging").|
|Quentin Vicens, PhD|
My research as a semi-independent investigator in Jeff Kieft's lab touches upon the characterization of exonuclease-resistant RNAs in unexpected places, as well as the role of ADAR1, which protects against auto-immune disorders by editing cellular RNAs.