At least 15 research groups in the UCLA Department of Chemistry & Biochemistry carry out research in the area of Systems Biology and Biological Regulation.
This discipline combines efforts to characterize the structural, biochemical, and in vivo functional properties of individual biomolecules and pathways with the cutting-edge approaches of modern genomics, proteomics, and metabolomics. It combines both experimental and computational approaches to model biological systems and tests the predictions of the models.
Investigators in this focus area are addressing questions concerning such topics as gene regulation at both transcriptional and post-transcriptional levels, metabolic regulation and homeostasis, regulation of cell shape and motility, intracellular transport and compartmentation, phylogenomics, and molecular evolution.
Faculty Research Summaries
Professor Soumitra Athavale
The Athavale group has broad interest in synthetic organic chemistry, (bio)molecular evolution and chemical biology, with research encompassing four main themes: (1) synthetic methodology and biocatalysis, (2) design principles of synthetic evolutionary systems, (3) fundamental relationships in enzyme structure and function, and (4) engineering enzymes as next-generation therapeutics.
Professor Keriann M. Backus
In the area of chemical biology, the Backus Group combines chemical probe synthesis with activity based protein profiling and chemical proteomics to develop chemical tools to manipulate the human immune system. Research within the group spans chemical biology, organic synthesis, pharmacology, immunology, biochemistry and systems biology.
Professor James U. Bowie
Professor James Bowie and his group are fascinated by protein structure, folding and stabilization. This interest has led them into three main areas: (1) learning how membrane proteins fold and how they can be stabilized; (2) the structures and biological functions of a biological polymer they discovered, that is formed by a very common protein module called a SAM domain; (3) developing and stabilizing enzyme pathways for the production of biofuels.
Professor Guillaume F. Chanfreau
Professor Guillaume Chanfreau’s laboratory is interested in gene expression regulation in eukaryotic cells, with a particular emphasis on post-transcriptional steps. Within this large field, they are focusing on understanding how cells degrade RNAs that arise from malfunctions in gene expression pathways (“RNA surveillance”). In particular, they are analyzing the functions of the double-stranded RNA endonuclease RNase III and of the nonsense-mediated decay pathway in RNA surveillance, and how these enzymes regulate gene expression.
Professor Irene Chen
The Irene Chen Research Lab studies life-like biochemical systems to understand their fundamental properties and address emerging challenges in biotechnology and infectious disease. Our focus is biomolecular design and evolution in two nanoscale systems: simple synthetic cells and bacteriophages (phages).
Professor Catherine F. Clarke
Professor Catherine Clarke and the Clarke lab study the biosynthesis and functional roles of coenzyme Q (ubiquinone or Q). Q functions in mitochondrial respiratory electron transport and as a lipid soluble antioxidant. The group is using the yeast Saccharomyces cerevisiae (bakers yeast) to elucidate the biosynthetic metabolism of Q. Their experimental approach employs a combination of molecular genetics, lipid chemistry and biochemistry to delineate the steps responsible for Q biosynthesis.
Professor Steven G. Clarke
A major interest of Professor Steven Clarke’s Laboratory is understanding the biochemistry of the aging process. The group is particularly interested in the generation of age-damaged proteins by spontaneous chemical reactions and the physiological role of cellular enzymes that can reverse at least some portion of the damage. They have focused their efforts on the degradation of aspartic acid and asparagine residues and the subsequent metabolism of their racemized and isomerized derivatives. The group is presently determining the biological role of protein methyltransferases that can initiate the conversion of D-aspartyl residues to the L-configuration as well as the conversion of isopeptide linkages to normal peptide bonds. Such “repair” reactions may greatly increase the useful lifetime of cellular proteins and may help insure organismal survival. View Professor Clarke’s YouTube Lecture
Professor Robert T. Clubb
Professor Robert Clubb investigates the molecular basis of bacterial pathogenesis. In particular, they study how microbes display and assemble cell wall attached surface proteins, and how they acquire essential nutrients from their host during infections. The group’s study could lead to creating new inhibitors of bacterial infections.
Professor Stuart Conway
The Conway Group uses organic chemistry to develop biologically active small molecules for medicinal chemistry and chemical biology studies in living systems. They have a strong interest in developing probes that modulate epigenetics processes, which are relevant for cancer and neglected tropical diseases. They also have expertise in developing pro-drugs that are activated in hypoxia, and imaging tools that enable the study of the tumor microenvironment..
Professor Albert J. Courey
Professor Albert Courey and his group study the molecular basis of cell development. During embryogenesis, a cluster of apparently undifferentiated cells is transformed into an ordered array of differentiated tissues. Using Drosophila as a model system, his research group combines biochemical and genetic approaches to study the molecular basis of this amazing transformation. Essentially all the regulatory circuits they study are conserved throughout the animal kingdom. Therefore, their studies have important implications for human health and development.
Professor Juli Feigon
Professor Juli Feigon and her research group study nucleic acid structure and specific recognition of nucleic acids by proteins. Her group focuses on determining the three-dimensional structures of DNA and RNA, and on investigating their interactions with various proteins and ligands, and to study nucleic acid folding.
Professor Carla M. Koehler
Professor Carla Koehler and her research group encompass two major areas: Understanding the mechanism of protein import into mitochondria and determining the process by which defects in mitochondrial protein translocation lead to disease.
Professor Sriram Kosuri
The Kosuri laboratory develops methods to vastly increase our ability to empirically explore relationships between DNA sequence and biological function. This is being acheived by developing and combining three related technologies: DNA synthesis, DNA sequencing, and genome engineering. The ability to synthesize thousands to millions of designed DNA sequences and to link those sequences to phenotypes or readouts of various cellular functions makes it possible to probe the sequence-function relationships underlying diverse biological phenomena on unprecedented scales. This is allowing new discoveries on broad ranging systems from bacteria to humans.
Professor Joseph A. Loo
The research interests of Professor Loo’s group include the development and application of bioanalytical methods for the structural characterization of proteins and post-translational modifications, proteomics-based research, and the elucidation of disease. The composition and structure of noncovalently-bound protein-protein and protein-ligand interactions are studied by electrospray ionization mass spectrometry and ion mobility.
Professor Margot E. Quinlan
Professor Margot Quinlan and her group use biochemistry, microscopy and genetic approaches to study regulation of the actin cytoskeleton. The group is currently focused on Spire (Spir) and Cappuccino (Capu), two proteins that collaborate to build an actin network essential for early body axis development. Combining an in vitro understanding of the mechanism of Spir and Capu with in vivo studies of polar cells will provide insight into how the actin cytoskeleton is regulated and a broader understanding of cell polarity.
Professor Michael Robert Lawson
Normal and problematic mRNAs are translated differently by ribosomes, with the former being released for translation again and the latter targeted for decay. The Lawson lab aims to understand the interactions between ribosomes, mRNA sequence and structure, and specialized decay factors that drive these decisions, using a range of biochemical and structural techniques. Ultimately, a better understanding of these mechanisms could lead to new treatments for the 11% of heritable human diseases associated with premature stop codons.
Professor Emil Reisler
Professor Emil Reisler’s group investigate cell motility and force generation mechanism of actin, tubulin, and a family of motor proteins. The aim of these studies is to obtain a structural description of the mechanism of motion and force generation. At the cellular level, the group studies the function, interactions, and structural transitions of the assembled protein systems.
Professor Jose Rodriguez
Professor Jose Rodriguez studies the complex architecture of biological systems – from single biomolecules to cellular assemblies – at high resolution. His work is largely based on diffraction phenomena and combines computational, biochemical and biophysical experiments. The development of new methods is central to this work, particularly using emerging technologies in cryo-electron microscopy, nano and coherent x-ray diffraction, and macromolecular design. Combined, these tools can reveal undiscovered structures that broadly influence chemistry, biology, and medicine.
Professor Danielle L. Schmitt
The Schmitt Lab studies how cells regulate metabolism and cellular signaling in both space and time. Their approach is to develop genetically encoded biosensors for small metabolites and kinases for quantitative live cell imaging applications to observe metabolic regulation with high spatiotemporal regulation in single cells. The ultimate goal of this work is to understand how metabolism is spatiotemporally regulated in normal, healthy cells, and how metabolic diseases perturb this compartmentalized regulation.
Professor Jorge Z. Torres
Professor Jorge Torres’ research group is interested in understanding the mechanisms of cell division. Currently they are discovering and characterizing novel enzymatic activities that are critical for cell division (cancer targets) and discovering or designing small molecules that can inhibit their function (anti-cancer agents). To do this, they are taking multidisciplinary approaches that utilize human cancer cell lines and high throughput proteomic and small molecule screening with a combination of disciplines, including biochemistry, cell biology, chemoinformatics, chemical biology and microscopy.
Professor Roy Wollman
Professor Roy Wollman’s Lab studies information processing in intracellular and intercellular signaling networks in the presence of a high degree of single-cell variability.