|Ruben Abagyan (Professor of Pharmacy, Division of Pharmaceutical Chemistry)
The Abagyan laboratory is interested in the further development of new powerful approaches for computational structural biology that will help with building develop predictive models of biomolecular systems and assemblies for all known proteome. It will include modeling of complex dynamic processes that that depend on flexible rearrangements of loops and termini, ligand binding and/or post-translational modification using all available crystallographic information. We developed and are maintaing the Pocketome database that is used to identify targets of drags. We will apply of the internal coordinate mechanics, that we invented and were first to apply to fold a small protein and dock protein and a peptide ab initio as a the lower energy state.
|Rommie Amaro (Professor of Chemistry and Biochemistry, Director, National Biomedical Computation Resource (NBCR); co-director, Drug Design Data Resource)
The Amaro Lab is broadly concerned with the development and application of state-of-the-art computational and theoretical techniques to investigate the structure, function, and dynamics of complex biological systems. At the interface of chemistry, biology, physics, and pharmacology, our research integrates both applied and basic science components, with goals to bridge the interface between basic and clinical research. We are particularly interested integrating new structural and dynamical knowledge gained from molecular dynamics simulations in drug discovery programs, and in expanding the range and complexity of molecular constituents represented in such simulations. We are also actively developing novel multiscale methods for elucidating the time dependent dynamics of complex biological and chemical systems at the molecular level.
|Michael Burkart (Professor of Chemistry and Biochemistry)
Inspired by the breathtaking structure and activity of molecules found in Nature, our research addresses the critical need for new medicines by capturing the power of biosynthesis. We have focused upon modular fatty acid, polyketide, and non-ribosomal peptide biosynthetic pathways that hold enormous promise as metabolic factories to produce novel therapeutics, fine chemicals, and biomaterials. While the basic mechanisms of these pathways have been understood for decades, efforts to control them have largely failed, primarily due to a fundamental knowledge gap in the molecular events within these complex enzyme systems. We address these problems by combining the design of small molecules to the evaluation of activity and structure within biological systems. For instance, over the last decade we have developed a novel toolbox of methods to probe the functional and structural roles of carrier proteins (CPs) within modular synthases, initially focusing on acyl-CPs in bacterial lipid biosynthesis. We have applied these tools to determine the exact residues mediating protein•protein and protein•substrate interactions that regulate reactivity. Here our tools unite modern structural biology with mechanism-guided probes to unveil the fundamental details of this central metabolic pathway. We have since seen that this approach can be applied to a wide array of modular biosynthetic systems, reaching pathways that produce antibiotic, anticancer, and anti-inflammatory leads.
|Kevin Corbett (Associate Professor, Ludwig Institute, Cell and Molecular Medicine)
The Corbett laboratory, established in 2011, is focused on understanding the molecular mechanisms of chromosome organization and recombination in eukaryotic meiosis, from the level of individual recombination proteins up to entire chromosomes. Our work to date has focused on the chromosome axis, a meiosis-specific structure responsible for organizing chromosomes as a linear array of chromatin loops, which aids the recognition and alignment of homologous chromosomes. The chromosome axis additionally recruits and controls factors that generate DNA breaks along chromosomes, then repair these breaks as inter-homolog crossovers. We have identified the molecular mechanisms of chromosome axis self-assembly, and shown that these mechanisms are conserved from yeast to man. Our current efforts are focused on how the chromosome axis interacts with recombination proteins; a major future effort will involve the chromosome-scale regulation of meiotic recombination. We are also using complementary methods such as Hi-C chromosome conformation capture to explore the architecture of meiotic chromosomes and plan to use cryo-electron tomography to study the protein scaffolds that impose and control this architecture. Our ability to use these disparate methods to gain a comprehensive picture of meiotic chromosome organization and recombination is helped immensely by the highly-collaborative and multi-disciplinary environment at UCSD.
|Galia Debelouchina (Assistant Professor of Chemistry and Biochemistry)
The goal of the Debelouchina lab is to develop chemical and spectroscopic tools for structural biology in cells. In particular, we are working on sensitivity-enhanced NMR methodologies (solution and solid-state), that allow us to obtain multidimensional NMR spectra from much smaller amounts of biological samples (ng to ug). In parallel, we are devising chemical biology tools to specifically label and select individual protein targets in the cellular environment. We are applying these approaches to study the molecular basis of biological phase transitions, a curious phenomenon responsible for the formation of membraneless cellular compartments and implicated in many biological processes including the stress response, DNA damage repair, gene and chromatin regulation. This highly dynamic biological process concentrates proteins and nucleic acids in space and time, and may involve the formation of liquid-liquid droplets, gel or amyloid states. Sensitivity-enhanced NMR spectroscopy is ideally suited to describe the molecular basis of these states in the cellular environment, and our ultimate goal is to understand how they contribute to biological function and disease.
|Edward Dennis (Professor of Chemistry and Biochemistry and Professor of Pharmacology)
The phospholipase A2 (PLA2) superfamily consists of sixteen groups and many subgroups, and constitutes a diverse set of enzymes that have a common catalytic activity due to convergent evolution. These enzymes exhibit a large array of functions, but of special interest is the inflammatory cascade of eicosanoids which is initiated by the release of free arachidonic acid by some types of phospholipase A2, all of which interact with membrane phospholipids. However, different PLA2 types have unique three-dimensional structures and unique catalytic residues as well as specific tissue localization, distinct biological functions, and with which membrane phospholipids have unique allosteric interactions. Understanding how the different PLA2s associate with phospholipid membranes, specific phospholipid substrate molecules, and inhibitors on a structural and molecular basis has advanced in recent years due to our introduction of hydrogen/deuterium exchange mass spectrometry (HD/MS) approaches. We now integrate HD/MS approaches with molecular dynamics to define the specific interactions of the PLA2 with lipid substrates, inhibitors and membranes for all of the major types of PLA2, including secretory s-PLA2, cytosolic c-PLA2, lipoprotein-associated LpPLA2, and calcium-independent iPLA2 For example, we have synthesized and defined the precise binding interactions of very potent and highly specific fluoroketone inhibitors of i-PLA2 and oxoamide inhibitors of c-PLA2 including defining important details of the binding pocket association and sites for each polar group and each acyl chain in the phospholipid substrate and inhibitor. We can now define the precise nature and molecular dynamics of the interaction of these enzymes with specific substrate phospholipids pulled into the catalytic site from membranes and how new potent specific inhibitors block substrate phospholipid binding. Recent work has led us to propose the important hypothesis that “Membranes are allosteric activators of phospholipase A2 enabling it to extract, bind, and hydrolyze phospholipid substrates”. We are currently expanding on the molecular and structural details and generalizing the hypothesis to other membrane associating enzymes. Defining the molecular details and consequences of the association of water-soluble proteins with membranes is fundamental to understanding protein–lipid interactions and membrane functioning. We determined the catalytic cycle of each type of human PLA2. We introduced computational techniques guided by DX/MS for studying membrane interactions. This was used to create structural complexes of each enzyme with a single phospholipid substrate molecule. The substrate extraction process was studied using steered molecular dynamics. Simulations of the enzyme–substrate–membrane system has revealed important information about the mechanisms by which these enzymes associate with the membrane and then extract and bind their phospholipid substrate We further demonstrated that the membrane acts as an allosteric ligand that binds the enzyme’s interfacial surface, shifting its conformation from a closed (inactive) state in water to an open (active) state at the membrane interface; this provides the first detailed picture of how these enzymes work. We continue to define these interactions at greater and greater molecular detail.
|Neal Devaraj (Associate Professor of Chemistry and Biochemistry)
Natural cells have a number of mechanisms to organize biochemical pathways, one of the most prominent being membrane compartmentalization. All living cells utilize membranes to define physical boundaries, control transport, and perform signal transduction. We are developing and exploring novel reactions that can trigger de novo membrane formation and reproduction. We believe such studies could reveal some of the fundamental chemical principles that led to the origin of life and reveal the organizational principles that govern modern membranes. Furthermore, we are studying how such reactions could improve our ability to study membrane localized structures (membrane proteins) and signaling. Our bottom up studies will help build dynamic models for living cell behavior.
|Olga Dudko (Associate Professor of Physics)
We search for general principles that unify seemingly very different and often formidably complex biological systems. We try to capture these principles in the form of physical theories that are reasonably simple and abstract, yet are capable of generating concrete, experimentally testable predictions.
|Gourisankar Ghosh (Professor of Chemistry and Biochemistry)
Our research focuses primarily on the detailed mechanisms of signaling pathways that lead to the regulation of gene expression by nuclear factor κB(NF-κB). We have recently initiated a second project that aims to understand mRNA processing and transport. The foundation of our research rests upon high resolution x-ray structures of proteins and protein complexes. Hypotheses derived from these three-dimensional structures are tested through biochemical and biological experiments to provide greater functional understanding of these important regulatory processes. In most cells NF-κB dimers are retained in the cytoplasm due to their association with a family of inhibitor proteins called the IκBs. Various stimuli trigger a series of phosphorylation reactions that ultimately activate specific Iº B kinase complexes (IKKs). Phospho-IκB is degraded by the ubiquitin-linked proteasome pathway, resulting in free Rel/NF-κB dimers. These dimers then translocate to the nucleus and bind to specific DNA targets to induce transcription. Involvement of multiple family members of NF-κB, IκB and IKK in a differential manner adds complexity to this signaling pathway. We are interested in determining the mechanism of a) NF-κB dimer formation, b) regulation of NF-κB by IκBs, c) IKK regulation, d) ubiquitination of IκBs and e) transcriptional regulation by NF-κB. The lab also works on serine/arginine rich proteins (SR proteins) are essential for pre-messenger RNA processing and possibly for mRNA transport from the nucleus to the cytoplasm. SR proteins are modular in nature, containing an N-terminal RNA binding domain and C-terminal domain rich in SR/RS dipeptides. Phosphorylation of the serines of the RS dipeptides is essential for splicing and transport activities of the SR proteins. A novel class of kinases known as SR protein kinases (SRPKs) specifically phosphorylate these serines. We are interested in structure/function studies of the SR proteins and SRPKs in both yeast and mammalian systems.
|Michael Gilson (Professor of Pharmacy, Division of Pharmaceutical Chemistry)
We use theory, computation and experiment to study how biomolecules perform their many functions and to advance methods for molecular modeling and design. Computer-aided drug design and molecular motors are areas of particular interest, and we make use of a number of approaches and methods, including statistical mechanics, molecular simulations, numerical modeling, NMR, calorimetry and organic synthesis.
|Kamil Godula (Assistant Professor of Chemistry and Biochemistry)
The research in the Godula lab focuses on glycans at the cell-matrix interface. Glycans are one of the four main building blocks of life and, as such, are linked to virtually all aspects of human endeavor. However, due to the lack of a direct link between the glycome and the genome, glycans have been largely excluded from the biomedical and technological revolution sparked by the discovery of the structure of DNA and the beginning of the modern era of molecular biology. Current efforts in the Godula lab focus on the design of materials that mimic cell surface glycoconjugates and chemical strategies to introduce these materials to control glycan presentation at the cellular boundary. The two main areas under investigation are the use of cell surface glycan engineering to 1) control growth factor activity in stem cell differentiation into therapeutically useful cell types and 2) to study host glycan-pathogen interactions in early stages of infection.
|Tracy Handel (Professor of Pharmacy, Chair Division of Pharmaceutical Sciences, Cancer Center Liason)
The Handel lab is focused on a class of G protein-coupled receptors (GPCRs) called chemokine receptors. These 7-transmembrane receptors are best known for their role in the migration of many cell types in the context of development, immune surveillance and inflammation. However, they are also involved in numerous diseases including inflammatory and metabolic diseases, cancer, and diseases caused by pathogens such as HIV and malaria. We study these receptors at a basic level to understand how they work and at a more translational level to aid in the development of chemokine receptor-targeted therapeutics. Specifically, we dissect their function through cell signaling and sometimes in vivo experiments, to structure determination by crystallography and Cryo-EM. Our goal is to gradually visualize larger multi-protein complexes involving the ligands as well as downstream signaling effectors such as G proteins and -arrestins in different functional states. Static structures are then complemented with dynamic studies through MD simulations and experiments that specifically address protein dynamics (single molecule fluorescence and radiolytic footprinting). Finally, we work with medicinal chemists at UCSD and pharmaceutical companies to optimize small molecule antagonists with the intention of identifying compounds worthy of clinical trials. As membrane complexes that involve heterogeneous protein-protein interactions, our research program relies on state of the art biophysical and computational methods and equipment/infrastructure and collaboration across numerous disciplines (structure, computation, chemistry, cell and in vivo biology). Our program is characterized as trans-scale because we address the structure of complexes centered on these receptors in the context of signaling in the cell and in the context of drug discovery that involves the entire organism.
|Thomas Hermann (Associate Professor of Chemistry and Biochemistry, Co-Director, UCSD Center for Drug Discovery Innovation)
We are exploring the structure, function and molecular recognition of ribonucleic acid (RNA). RNA molecules participate as key players in many biological processes and adopt complex architectures that are required for function. The development of ligands that bind specifically to RNA targets opens exciting new ways to expand the existing repertoire of protein-directed therapeutics. Our research employs diverse techniques, including molecular biology, biochemistry, X-ray crystallography as well as synthetic organic chemistry.
|Mike Holst (Professor of Mathematics)
My research group continues to work at the intersection of mathematics, computational science, and physics/chemistry, and I think we would add breadth and strength to CTSBB in these areas. I can provide more detailed descriptions of my current research projects whenever you might need those.
|Enfu Hui (Assistant Professor Molecular Biology)
My lab works on the biochemical mechanisms of T cell signaling, with a focus on a group of co-inhibitory receptors that are key cancer immunotherapy targets. Despite the huge therapeutic potential, these receptors are very poorly understood at a biochemical and cell biological level. We aim to fill this gap with a combination of reconstitution, imaging and proteomic approaches. The complex cellular environment makes it difficult to understand the precise mechanism of signaling events. To this end, we reconstitute purified receptors, enzymes and adaptor proteins onto model membranes that mimic the plasma membrane of T cells. This bottom up approach provides the membrane geometry that traditional biochemistry lacks, and the biophysical precision that conventional cell biology lacks. The ability to manipulate each component, to measure reaction rates, and to visualize recruitment and clustering events, will allow us to dissect the biochemical basis and emergency properties of T cell signaling networks. In addition, we are also using total internal reflection microscopy to visualize the spatiotemporal dynamics of signaling molecules in live T cells. Our goal is to push the field towards an in-depth, quantitative understanding of T cell signaling. The themes and approaches of my lab align well with the overall goal of CTSBB.
|Patricia Jennings (Professor of Chemistry and Biochemistry)
Cellular processes and life are ultimately regulated by the actions of biomolecules. Molecular biophysics techniques allow the quantitative examination of atomic and molecular motions in specific biomolecules and their interactions in macromolecular complexes. Our particular research interests are focused on investigating how protein folding and assembly impacts important signaling processes and on understanding the basic biophysical rules that govern those processes. Towards this goal we have developed combined experimental/theoretical tools to investigate the energy landscape that controls the folding/misfolding of proteins. Proteins, however, do not have one landscape for folding and another for function. The real challenge we are undertaking is to generalize these ideas to accommodate both folding and function. Ultimately, we are working towards understanding the molecular basis for specific signaling molecule binding and organelle/cellular response. For this reason, we test ideas generated from our continued investigations of the folding and function of cytokine Interleukin-1b (IL-1b) on diverse structural systems such as protein kinases, green fluorescent protein and the mitoNEET family of proteins. We are continuing to develop methodologies to investigate how folding is linked to function and are applying and further developing approaches to investigate how the native energy landscape of signaling enzymes control recognition, allosteric modulation, substrate binding and activity in vitro, in vivo and in silico.
|Simpson Joseph (Professor of Chemistry and Biochemistry)
Our lab is interested in understanding the molecular mechanism of translational control by ncRNAs and proteins. We are currently studying translation control mechanisms in Fragile X syndrome, influenza A virus life cycle, and a ncRNA that is critical for the recovery of the heart after a heart-attack. We use biochemical, biophysical and structural approaches to dissect the mechanism of translational control.
|Judy Kim (Associate Professor of Chemistry and Biochemistry)
The Kim group investigates the role of protein dynamics and structure on function. The motivating questions center on the role of protein environment on long-range, biological electron transfer reactions, and identification of lipid-protein interactions that guide membrane protein folding. A combination of optical methods are utilized, including time-resolved electronic and vibrational spectroscopic techniques, as well as measurements of energy transfer and quenching. Collectively, these efforts complement other biochemical and computational efforts in biophysics, and lead to highly interdisciplinary approaches to probe complex biological problems.
|Elizabeth Komives (Professor of Chemistry and Biochemistry, Program Director Molecular Biophysics Training Grant)
Research in the Komives lab focuses on the role of dynamics in protein-protein interactions studied using solution biophysics and proteomics approaches. Biological systems of interest include blood coagulation, transcription factor signaling, and ubiquitin degradation pathways. The Komives lab uses a broad range of experimental approaches including solution biophysical measurements of binding kinetics and thermodynamics and is particularly interested in the role of protein dynamics in molecular interactions. Komives pioneered the use of amide H/D exchange mass spectrometry for identifying protein-protein interfaces and characterization of intrinsically disordered regions. Through effective collaborations, her lab integrates theory and experiment to provide insights into the ways in which protein dynamics control function particularly changes in function that occur during macromolecular interactions. By measuring NMR relaxation dispersion in thrombin, the Komives lab demonstrated how surprisingly dynamic serine proteases are, and she recently found a dynamic allosteric pathway connecting the exosite 1 allosteric effector binding site with the active site. Her work on the IκBα has impact far beyond that system leading to a deeper understanding of the role of frustration in the energy landscapes of proteins that bind to other partners and the nature of cooperativity in repeat proteins. Recent work includes integrating biophysics of IκB/NFκB interactions, one of the most important cell regulatory systems, with theoretical and cell biological studies demonstrating how biological function critically depends on biophysical control. She showed that IκB folds on binding to NFκB. Her work helped to elucidate that folding of IκBα defines its degradation rate in vivo, and that degradation of IκBα controls NFκB signaling. Most recently she demonstrated that IκBα enhances the kinetics of dissociation of NFκB from transcription sites. This work represents a paradigm shift for understanding transcription control mechanisms. A new project in the lab aims to understand the dynamics involved in E3 ubiquitin ligase function.
|Elena Koslover (Assistant Professor of Physics)
Research in the Koslover group is centered on the multi-scale physics of intracellular soft matter, from biopolymers, to membranes, to fluids. We develop and implement analytical and computational techniques grounded in statistical physics, continuum mechanics, and fluid dynamics, to understand how collective physical phenomena arise from biomolecular constituents and how they are harnessed for cellular function. In particular, we are exploring the dynamics of multimodal transport within eukaryotic cells, studying (with the aid of in vivo data from experimental collaborators) how active motor-driven motion couples together with passive diffusion and advective fluid flow to deliver and disperse organelles within the cytoplasm. We are also studying the self-assembly and mechanical behavior of active polymer networks, such as the actomyosin networks in the cytoskeleton and fibrin networks in coagulating blood.
|Bo Li (Professor of Mathematics)
We develop modern mathematical theories, biophysical models, and computational tools to investigate biomolecular interactions, both chemical and mechanical, and their consequences in biological cellular functions. Specifically, we construct new-generation biomolecular solvation theories, and hybrid and multiscale computational models for protein dynamics, protein-protein interactions, and drug-protein bindning. We also study how biomolecular interactions determine mesoscopic chemical and physical properties of individual cells, such as cell motility, membrane mechanical functions, and growth of bacterial cellular colonies. One of our current research objectives is to understand how molecular structural properties can determine the macroscopic activities of protein kinases that are directly related to cancer. We hope to bring in modern mathematics and scientific computing to explain experimental findings and to predict quantitatively biological cellular functions.
|Andres Leschziner (Professor of Cell and Molecular Medicine and Biology, Molecular Biology Section, Co-director UCSD cryo-EM facility)
The Leschziner group is interested in understanding how large macromolecular machines couple energy, in the form of nucleotide hydrolysis, to conformational changes and in the functional roles played by these structural rearrangements. We approach this question with a combination of cell biological, biochemical, biophysical and structural approaches with a particular focus on cryo-electron microscopy (cryo-EM).
|J. Andrew McCammon (Distinguished Professor of Chemistry and Biochemistry and Pharmacology)
The McCammon group uses computer models and formal techniques to examine how proteins, nucleic acids, and biological membranes function. These studies show, for example, how a substrate may be attracted to the active site of an enzyme by electrostatic interactions, and how the atoms within an enzyme move to participate in the catalytic transformation of a bound substrate. On the supramolecular scale, we study protein-protein interactions and the channeling of intermediates among different proteins. These methods are of practical importance in the design of new enzymes that can be synthesized by genetic engineering techniques, and in the design of new drugs that bind strongly to their receptors. Our simulation studies benefit from the excellent computing facilities to which we have access. These facilities include parallel supercomputers and sophisticated computer graphics systems that allow for the visualization of the atomic dynamics in solutions or protein molecules by virtual reality methods.
|Andrew McCulloch (Distinguished Professor of Bioengineering, Program Director Training Program in Multi-scale Analysis of Biological Structure and Function)
Andrew McCulloch, Distinguished Professor of Bioengineering and Medicine, develops multi-scale computational models of cardiac cells and the heart in health and heart diseases including heart failure and arrhythmia. His lab also conducts in-vitro and structural biology studies to obtain the data required to formulate these models and in-vivo studies to validate the models. The focus of cardiac myocyte models developed by Dr. McCulloch’s lab include biophysical and biochemical systems models of cardiac myocyte ionic currents and action potential propagation, calcium cycling and excitation contraction coupling, myofilament interactions and sarcomere mechanics, mechanoenergetics and energy metabolism, cell signaling and mechanotransduction. Dr. McCulloch has been a core PI of the NIH-funded National Biomedical Computation Resource directed by Dr. Amaro and involving Drs. Ellisman and McCammon. He also co-directs with Drs Ellisman, Sejnowski and Taylor the Interfaces Graduate Training Program, an NIBIB T32 on Multi-Scale Biology. And he teaches with Drs. McCammon and Sejnowski a lab course on Numerical Analysis for Multi-Scale Biology (BENG/CHEM/PHARM/MATH 276) as part of the interdisciplinary PhD Specialization in Multi-Scale Biology, a PhD specialization with students from 10 participating graduate program that Dr. McCulloch directs. A large fraction of the faculty named in this proposal are investigators of the NIBIB T32 and faculty members opf the multi-scale biology specialization.
|Uli Muller (Associate Professor of Chemistry and Biochemistry)
The Muller lab studies the distribution of catalytic function in sequence space of RNA. The scientific question is focused on how life could have originated in an RNA world scenario, where catalytic RNAs originated from a prebiotic environment. To do this, new RNAs catalyzing specific reactions are identified from large, random sequence pools (typically 10^14 different sequences) and characterized for their biochemical characteristics. These studies elucidate how life could have emerged, and provide a ‘biologically unbiased’ look at the origin of biochemical activity.
|Cornelius Murre (Professor of Molecular Biology)
In essence, the chromatin fiber is a polymer, and its physical properties can be examined in statistical-mechanical terms of polymer physics. The development of new imaging approaches has made it possible to address to describe the trajectories adopted by the chromatin fiber in physical terms. Specifically, during the past two years, we have adopted and modified these approaches to enable tracking the motion of multiple regulatory DNA elements in live B-lineage cells. Using fractional Langevin dynamics modeling we found that DNA elements within the immunoglobulin locus have a high probability of reaching each other in minutes and that geometric confinement, in large part, controls the first-passage times for genomic encounters. Currently our studies are aimed to describe gene regulation and antigen receptor assembly in physical terms by combining experimental and theoretical approaches.
|Larissa Podust (Associate Professor, SSPPS)
My laboratory provides research training for health professions graduate and undergraduate students to develop research careers at the interface of structural biology and infectious tropical diseases. We closely collaborate with the Center for Discovery and Innovation in Parasitic Diseases (CDIPD), James Mckerrow, Director, to facilitate structure-based drug design targeting neglected tropical diseases. In collaboration with members of CDIPD we set up a shared crystallography facility in the Pharmaceutical Sciences Building at the University of California, San Diego, where students learn to operate the state-of-the-art instruments required to express and purify protein targets, optimize crystallization conditions, monitor target growth in crystallization drops, and finally, harvest and test crystals for X-ray diffraction. During their training, students are exposed to the principles underlying modern drug development, from compound screening in vitro and in vivo to validation of structure-based design and optimization using medicinal chemistry, all via interactions with CDIPD faculty and staff.
|Samara Reck-Peterson (Professor of Cell and Molecular Medicine and Biology, Cell and Developmental Biology Section, HHMI, Director Nikon Imaging Center)
The Reck-Peterson lab uses quantitative approaches including single-molecule imaging, cryo-electron microscopy (in collaboration with the lab of Andres Leschziner), proteomics, and live-cell imaging to analyze the cellular interstate system of microtubule tracks on which of dynein and kinesins traffic their cargo. Cytoplasmic dynein-1 is the only motor used for long-distance minus-end-directed microtubule-based trafficking in eukaryotic cells ranging from human neurons to the hyphae of filamentous fungi. Yet, it transports dozens, if not hundreds of different cargos. One of our lab’s goals is to understand how this large, multi-subunit, motor is regulated. Dynein has two regulators that are conserved and required for most (perhaps all) of its functions: the dynactin complex and Lis1/ Nudel. Current experiments in the lab are focused on determining how these regulators work In addition to cytoplasmic dynein-1, at least 15 kinesin motors (in humans) are responsible for moving cargo in the opposite direction as dynein. This small subset of motors is responsible for nearly all long distance transport in eukaryotic cells. What is the full list of dynein and kinesin cargos? What links the motors to different cargos? How is specificity achieved? Do all cargos have a distinct mechanism for recruiting motors? We are addressing these questions using two different discovery-based approaches.
|Doug Smith (Associate Professor of Physics)
Our group applies and develops techniques for single DNA molecule manipulation with optical tweezers to study the physical properties of DNA and biological processes involving DNA, including molecular-motor driven viral DNA packaging, protein-mediated DNA looping, chromatin structure and assembly, and protein-mediated DNA unzipping/rezipping. In these studies we collaborate with microbiologists, biochemists, molecular biologists, and computational biophysicists. Our biophysical studies of viral DNA packaging are aimed at understanding the mechanism of the ATP-powered molecular motor and understanding how the physical behavior of tightly confined DNA affects DNA packaging and ejection. To gain insights on the mechanism of the molecular motor we are combining our single-molecule techniques for measuring the motor function with site-directed mutagenesis and molecular modeling.
|Palmer Taylor (Distinguished Professor of Pharmacy and Pharmacology)
Dr. Palmer Taylor’s research centers around molecular recognition and drug design in the cholinergic nervous system. In particular, he studies inhibitors and reactivators of acetylcholinesterase as well as agonists, antagonists and allosteric modifiers of the nicotinic acetylcholine receptor. His approach has involved the structural elucidation of these two protein products, mechanistic analyses of their function and the design of nicotinic receptor, subtype-selective agonists and antagonists and cholinesterase reactivator that enable passage across the blood- brain barrier. Characterization of targets and drug leads involve involves spectroscopy, magnetic resonance, crystallography and fast-reaction, kinetic techniques. The receptor active drugs carry potential use in disorders of development of the nervous system, as found in schizophrenia, and in ageing-related neurodegeneration, as seen with Alzheimer’s and Parkinson’s diseases. Development of antidotes useful in organophosphate pesticide and nerve agent toxicities requires both site direction to the acetylcholinesterase active center, but also tissue disposition and pharmacokinetic considerations.
|Susan Taylor (Distinguished Professor of Chemistry and Biochemistry and Pharmacology)
The Taylor laboratory uses interdisciplinary approaches, coupling rigorous biochemistry, biophysics, and computation with cell biology and structural biology, to understand the structure, function, dynamics, and localization of cAMP-dependent protein kinase (PKA) and its associated proteins. Our comprehensive and multi-scale work has established PKA as the prototype for the large and biological extremely important protein kinase superfamily. A primary strategy is to couple crystallographic studies with biochemical and biophysical characterizations that include solution studies such as small angle Xray and neutron scattering (SAXS/SANS), fluorescence polarization, H/D exchange mass spectrometry (H/DMS), and NMR. Most recently we are adding cryo EM to our toolbox of approaches that we use to solve structure and dynamics. Our structure of the PKA catalytic subunit, the first protein kinase structure to be solved, represents a fully active kinase bound to an inhibitor peptide and ATP while subsequent structures of holoenzyme complexes and various AKAP complexes provide a solid foundation for mapping the unique properties of any protein associated with PKA signaling. The quaternary structures of each of the four functionally non-redundant holoenzymes reflect unique quaternary structures and distinct pathways for allosteric signaling. These complexes are anchored to scaffod proteins referred to as A Kinase Anchoring Proteins and these anchored complexes are major structural challenges where we are requiring both crystallography and cryo EM. We are also poised to map the properties of any disease associated proteins such as the C fusion protein that drives fibrolamellar hepatocellular cancer (FLHCC), point mutants in C that drive Cushing’s Disease, and point mutations in RI that drive Carney Complex Disease and Acrodysostosis. A final recent project, carried out in collaboration with A. Leschziner and E. Villa is the large multi domain protein that is associated with Parkinson’s Disease. This project, funded by the Michael J. Fox Foundation is merging biochemistry, biophysics and cell biology with crystallography, cryo EM and cryo electron tomography. Familial mutants of LRRK2 wrap around microtubules, and the structures of these LRRK2 decorated microtubules in cells are are now being elucidated by Villa using cryo ET.
|Navtej Toor (Associate Professor of Chemistry and Biochemistry)
The projects in our lab focus on the structure and function of non-coding RNAs found in prokaryotic and eukaryotic genomes. Two genetic elements particularly abundant in these organisms are introns and retroelements. For example, ~70% of the human genome consists of spliceosomal introns and non-LTR retroelements. Both of these are considered to have evolved from a class of introns which originated in bacteria billions of years ago called the group II introns. Group II introns share many structural and/or biochemical features with spliceosomal introns and non-LTR retroelements. We are also interested in studying the untranslated regions (UTRs) from viruses, which play a major role in regulating infectivity.
|Elizabeth Villa (Assistant Professor of Biology, Molecular Biology Section, Co-director UCSD cryo-EM facility)
Macromolecules rarely operate in isolation inside cells. At any given time, the average protein is part of a complex of over 10 macromolecules, and these supramolecular complexes are in turn embedded in intricate networks inside cells. We are broadly interested in revealing the structure and function of macromolecular complexes in their natural environment at the highest possible resolution in order to reveal their structural dynamics and interactions. We call it bringing structure to cellular biology.We have a strong focus on building tools for quantitative cell biology, using cryo-electron microscopy and tomography, cell biophysics, computational analysis, and integrative modeling. This potent combination allows us to look at macromolecular complexes in their native environment and derive their structure, context, and interaction partners.Our biological focus is on the study of the nuclear periphery, as nuclear biology remains one of the most exciting challenges in the cell, and it is uncharted territory structurally. Our thrust in this area includes projects such as: the structural dynamics of the yeast nuclear pore complex, the mechanical communication between the cytoskeleton and the nucleus, and the molecular architecture of the genome and its association to the nuclear envelope. We also collaborate with different laboratories to open windows into various cellular events. These projects tend to have a translational component, and include studying the inner life of bacteria and studying the effects of LRRK2 in Parkinson’s disease, among others.
|Dong Wang (Associate Professor of Pharmacy)
Our research interests focus on the interfaces between Chemistry and Biology. In particular, we are interested in understanding the fundamental mechanisms of transcription process and its functional interplay with epigenetic and chromatin regulation, as well as DNA lesion recognition and repair during transcription. My group takes a multidisciplinary approach, combining structural biology, chemical biology, computational biology, biochemical, and genetic methods, to study key protein complexes involved in these processing pathways. The results will have implications for transcription regulation, DNA damage recognition and DNA repair. Moreover, understanding how cells process these DNA lesions during transcription will help us to decipher the mechanisms of drug action and resistance and pave the way for rational improvement of novel anticancer drugs.
|Wei Wang (Professor of Chemistry and Biochemistry)
The Wang group is interested in understanding the function-structure relationship of macromolecules. The current projects include characterization and engineering chromatin reader proteins to develop new probes for monitoring chromatin dynamics, and deciphering the association between chromatin interactions and epigenomic modifications.
|Jin Zhang (Professor of Pharmacology, Live Cell Imaging Center)
The research focus of my laboratory is to understand the spatiotemporal regulation of signal transduction in living systems. Current projects include development of new molecular tools and imaging technologies, and study of spatiotemporal regulation of cAMP/PKA, Ca2+/calcineurin, PI3K/Akt/mTOR, MAPK and AMPK pathways, in the context of energy metabolism, cell differentiation or insulin secretion by β cells.