Biomembranes can be defined loosely as structures bounding all cells and cell organelles; they are typically composed of lipids, proteins, steroids, sugars etc. Roughly 30% of all human proteins are membrane proteins. Vital to health, they control the flow of information and materials between cells and mediate critical activities such as nerve impulses and hormone action. Membrane proteins are the targets of more than half of all drugs on the market today, thus understanding their structures and mechanisms of function will provide valuable contributions to the discovery and improvement of pharmaceuticals. Membrane proteins are also key components in the formulation of vaccines against bacterial, viral and fungal human pathogens.
The importance of studying biomembranes and membrane proteins has been recognized by the National Institutes of Health (NIH) whose webpages feature a specific call for increased research in this area: http://grants.nih.gov/grants/guide/pa-files/PA-02-060.html, which states: "Despite the importance of membrane proteins, the knowledge of their high resolution structures and mechanisms of action has lagged far behind the knowledge of these properties of proteins in general."
"Membrane proteins are the most challenging - but arguably the most important - proteins for structural biologists to tackle," says Peter Preusch, program director at the National Institute of General Medical Sciences. "By lowering the barriers to solving their structures, these projects could lead to new scientific and medical insights that hinge on understanding membrane proteins."
Disciplines that currently collaborate only on an ad hoc basis are experiencing increasing demand for continuous and structured collaborations, including teaching and graduate training. Collaborative interdisciplinary work in the biomembrane area now results in increasing opportunities for funding by state and federal agencies, and commercialization by industry.
Carrying out true interdisciplinary research at the intersection of life sciences and technology is not without challenges. The biomembrane theme overlaps traditionally distinct disciplines, which means that not only must researchers learn how to work in worlds alien to their training, but they also must learn how to work with people from culturally different educational backgrounds. In most universities, engineers and physical scientists are separated from biologists and life scientists during freshman year.
The Center brings together researchers from biological and physical disciplines. The Center provides an organizational structure to coordinate existing strengths into a more formal, coherent and effective unit, with a greater capacity to direct its energies toward specific goals.
The research interests of the faculty members and existing collaborations are discussed below. However, it is useful to list several of the general research directions that are being pursued at the Center:
Participants of the Center are faculty from eleven department in five different Schools at UCI and have a long history of already existing collaborations. Some of the groups that have worked and published together for several years:
The Center currently has 36 members from eleven UCI departments distributed in four Schools. Below is a list of all current participants with a brief description of their research interests, ordered by department. This information along with contact information will also be placed on the webpage of the Center. The participating faculty (i) study structure, dynamics of membrane and membrane systems, (ii) carry out theoretical modeling of these systems, (iii) ask fundamental questions how these systems are related to human diseases, (iv) prepare biomimetic systems, and (v) apply biological and synthetic systems in the area of surface chemistry and biotechnology.
Department of Molecular Biology & Biochemistry
David Camerini: Dr. Camerini's group is interested in several membrane related aspects of HIV-1 replication and immunity. In particular, they are studying cell signaling and pathogenesis associated with entry of HIV-1 into cells via CD4 and CCR5 in contrast to entry mediated by CD4 and CXCR4. They are also studying mechanisms of defensin mediated inhibition of HIV-1 replication including virion inactivation, which likely involves viral membrane disruption.
Melanie Cocco: The Cocco lab uses NMR spectroscopy to characterize the structure of membrane proteins interacting with membrane mimetics. The lab is interested in both the structures of peripherally associated proteins (defensins) and integral membrane proteins (transmembrane helices). NMR allows them to characterize the specific interactions of proteins with lipids.
Paul Gershon: Dr. Gershon's expertise is mass spectrometry of proteins and protein mixtures, including membrane proteins. This includes the identification of proteins, their protein partners, post-translational modifications and the sites thereof, and investigation of ligand-binding sites and polypeptide main-chain and side chain solvent exposure.
Celia Goulding: The principal research of Dr. Goulding focuses on utilizing proteomic and crystallographic techniques to elucidate and characterize new systems of protein complexes in Mycobacterium tuberculosis, in the hope of finding novel anti-TB drug targets. Her overall goal is to create a systems approach, shifting the focus of structural biology from a single protein to molecular assemblies. Initially her efforts will concentrate on a mycobacterial iron up-take system that scavenges iron from humans in the form of heme, and then uptakes this heme to be broken down for iron usage either within the bacterial membrane or cytosol. The other systems of immediate interest also contain potential protein drug targets and protein membrane components.
Chris Hughes: The Hughes laboratory is investigating mechanisms of blood vessel formation. There are two recognized mechanisms for formation of new blood vessels: vasculogenesis (the formation of vessels de novo through aggregation of cells derived from endothelial precursors) and angiogenesis (the growth of new vessels from pre-existing vessels). Vasculogenesis is particularly critical during development of the embryo. Angiogenesis, while important in development, also occurs in the adult during, for example, wound healing and ovulation. New blood vessel growth is also a critical phase of solid tumor growth; without a new blood supply tumors cannot grow more than about 1-2mm in diameter. We have used differential cDNA screening to identify genes involved in tube formation, a critical process in the development of a blood vessel.
Hudel Luecke: Dr. Luecke is a protein crystallographer with an emphasis on integral membrane proteins. He focuses on structure-function studies and structure-based drug discovery. Targets include G protein-coupled receptors (GPCRs, the target of more than half of all drugs on the market today) and photoreceptors. Recently, Dr. Luecke's laboratory has solved the atomic resolution structure of the light-driven ion pump bacteriorhodopsin (BR) in the resting state at very high (1.55 Å) resolution. Together with the structures of several photocycle intermediates "frozen in mid-stroke" his lab has been able to develop a detailed atomic mechanism of light-driven ion pumping. In addition, the structures of a related membrane protein that serves as the primary receptor in archaeal phototaxis (sensory rhodopsin) and that of a photoreceptor from Anabaena, the first eubacterial rhodopsin structure, have been determined. His laboratory also studies annexins, a family of proteins which interact with phospholipid bilayers in a Ca2+-dependent manner.
Ray Luo: The Luo research group uses computational and theoretical approaches to study molecular biophysical problems. Currently his group is working on continuum solvent models that can be used for molecular dynamics simulations and structural analysis of membrane proteins.
Department of Neurobiology & Behavior
Ricardo Miledi: The main aim of the Miledi laboratory is to understand, at the molecular level, the transmission of signals across nerve cells, a process which underlies all brain functions. Proper understanding of the mechanisms of synaptic transmission requires detailed knowledge of the receptors, i.e., the proteins on which neurotransmitters act. The laboratory aims at obtaining this knowledge by combined biochemical and electrophysiological approaches.
Ian Parker: Interests of the Parker group lie in the area of cell signaling, i.e., the ways in which excitable cells in the nervous system communicate with each other as well as within themselves. Specific topics include the mechanisms of neurotransmitter release, the interaction of neurotransmitters with their receptors, and the role of intracellular messengers in linking receptor binding to the final cellular response.
Department of Developmental & Cell Biology
Tau-Mu Yi: The Yi lab is a systems biology lab interested in the quantitative description of G-protein signaling, and the analysis of the robustness of biological networks. The approach is to use a combination of quantitative experiments and mathematical modeling. One of the projects is to perform structure-function analysis on the yeast G-protein coupled receptor, Ste2p, and to correlate changes in function caused by mutations to defects in gradient-sensing and mating.
Department of Physiology & Biophysics
Michael D. Cahalan: The Cahalan laboratory has pursued a research program designed to understand the molecular mechanisms and physiological role of ion channels in the immune system. In addition, they seek to image the dynamics of cell motility and interactions in lymphoid organs.
George K. Chandy: Dr. Chandy's laboratory is developing therapeutic agents for human disease by targeting potassium channels. They focus on autoimmune diseases (multiple sclerosis, rheumatoid arthritis, type-1 diabetes mellitus, psoriasis), organ and bone marrow transplantation, atherosclerosis, vascular restenosis following angioplasty, and neurological diseases. The lab has cloned the relevant potassium channel genes, developed specific inhibitors of these channels, demonstrated the functional role of the channels in normal and diseased cells, and demonstrated therapeutic efficacy of our inhibitors in animal models of human disease. Pre-clinical toxicity studies are underway for the most promising compounds. They intend to evaluate these compounds in patients in the next few years with the hope that someday they will ameliorate human disease.
Harry Haigler: The long-term goal of the Haigler lab is to understand the molecular and cellular mechanisms by which the hormone epidermal growth factor (EGF) controls growth and differentiation of eukaryotic cells. The EGF mitogenic pathway is activated by phosphorylation of certain regulatory proteins. Annexin I, which is a high-affinity substrate for the EGF-stimulated kinase, is a major focus of the Haigler lab. Recent research has been directed toward determining the biological function of annexin I, how this function is modulated by phosphorylation, and the role it plays in transduction of the EGF-induced mitogenic signals
James E. Hall: Dr. Hall's laboratory has two current projects: investigation of the properties of aquaporin in the lens and the mechanism of toxicity of amyloid oligomers. The goal of the aquaporin project is an understanding of the role of water permeability regulation in the development and homeostasis of the lens. The amyloid project seeks to define the toxic forms of amyloids and to formulate a biophysical theory of their action on lipid membranes.
Hamid Said: The water-soluble vitamins (folic acid, biotin, riboflavin, thiamin, pyridoxine) are essential micro-nutrients for normal cellular functions, growth and development. Studies in the Said laboratory over the past twenty years have characterized many aspects of the cellular/molecular mechanism and regulation of the absorption processes of these micronutrients. Their studies have ranged from the whole tissue level to the molecular level. They are currently interested in characterizing transcriptional regulation of the genes that code the membrane transporters of these vitamins, examining the cell biology of the transport proteins with regards to membrane targeting and intracellular trafficking, and working toward crystallizing the proteins for further investigations.
Stephen White: Dr. White's laboratory is devoted to understanding the folding and stability of membrane proteins with the goal of developing physical- and biology-based methods for predicting three-dimensional structure from amino acid sequence. The physical methods involve studies of the interactions of designed membrane-active peptides with lipid bilayers, x-ray and neutron diffraction structural studies of fluid lipid bilayers containing peptides and proteins, and molecular dynamics studies of peptides and proteins in lipid bilayers. The central thrust of this work is the development of physical hydrophobicity scales for describing the energetics of peptide-bilayer interactions in the context of atomic-level descriptions provided by the concerted use of diffraction and MD simulations. The biological methods, carried out in collaboration with Gunnar von Heijne at Stockholm University, involve studies of the code used by the SecY/Sec61 translocon apparatus to select transmembrane helices for insertion into membranes. These studies are also augmented by molecular dynamics simulations.
Department of Pathology & Laboratory Medicine
Luis M. de la Maza: Throughout the world Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen. In areas with poor sanitary conditions C. trachomatis causes trachoma, the most common cause of preventable blindness in the world. The only practical approach to prevent and eradicate these diseases is vaccinating the population at risk. De la Maza's lab has recently shown that a vaccine formulated with the native C. trachomatis major outer membrane protein (MOMP) can protect female mice against genital and respiratory challenge. Protection appears to be dependent on conformational epitopes present in the MOMP. The la'Ős intent is to initiate the structural and functional characterization of the native MOMP with the ultimate goal of formulating a vaccine using a recombinant preparation of MOMP. The structural and functional characterization of the native MOMP is going to require a team effort that includes protein chemists, bio physicists, crystallographers, etc. Therefore, the formation of a Center that will integrate the expertise of researchers working on membrane proteins will greatly facilitate and expedite the characterization of the native MOMP.
Andre Ouellette: Of relevance to this proposal, Dr. Ouellette's lab studies mechanisms of action and structure-activity relationships in alpha-defensins from mouse and rhesus macaques. The native peptides have a characteristic disulfide array and are selectively disruptive for electronegative model membranes that mimic the bacterial cell envelope and do not disrupt membranes consisting of more neutral phospholipids. Peptide microbicidal activity corresponds directly to the ability to disrupt membrane vesicles. The alpha-defensins derive from longer, inactive precursors that are not membrane disruptive and must be converted by specific proteinases to their mature membrane disruptive forms. The lab has many recombinant variants of two differing alpha-defensin primary structures that have mutations at canonical residue positions and vary in bactericidal activity and the ability to disrupt membrane.
Michael E. Selsted: Dr. Selsted and his collaborators have discovered and characterized several families of antimicrobial peptides which are produced by immune cells of higher mammals. Termed alpha-, beta-, and theta-defensins, these peptides provide the host with the ability to fend off potentially invasive pathogens. The recently characterized theta-defensins are cyclic molecules, and represent the first example of this molecular motif in animals. Defensins possess potent antimicrobial activities against bacteria, fungi, certain viruses, protozoa, and they also have cytotoxic activity against tumor cells.
Department of Biomedical Engineering
Steve George: Dr. George's work focuses on understanding the biology and physiology of the human lung as an integrated, whole organ. Within this context, he is pursuing two overarching areas of research, both of which combine cellular and whole organ studies, and experimental as well as theoretical techniques: 1) nitric oxide metabolism and 2) wound healing and tissue remodeling. Dr. George and his group are working toward an understanding of what changes in the local biochemical environment affect exchange dynamics at the cellular and whole-organ level. The project involves an understanding of the fluid mechanics of the bifurcating tubes, mass transfer coefficients and lung mechanics. Current research projects include a characterization of endogenous and exogenous nitric oxide exchange in the lungs; wound healing and extracellular matrix remodeling in the lungs; and cytokine-induced production of nitric oxide in the lungs.
Enrico Gratton: Expertise of the Gratton lab is in the area of fast relaxation in enzymes, fluorescence properties, hydration of proteins, IR spectroscopy of biological substances, nucleic acid-fluorescent probe interactions.
Department of Pharmacology
Olivier Civelli: The Civelli lab studies G protein-coupled receptors (GPCRs) and their natural ligands. Activation of these receptors is responsible for many physiological responses. Dr. Civelli focuses on responses that are related to brain function and to metabolism. The lab uses GPCRs which lack endogenous ligands as targets to identify these ligands and thus discover novel neurotransmitters. They then search for the functional significance of these novel neurotransmitter systems by studying aspects of their biology from the molecular to the behavioral levels, by developing mouse strains devoid of the ligand or of the receptor and by screening compound libraries to identify small molecule antagonists. GPCRs form the largest family of membrane proteins; they therefore represent an important subject of study for the Center for Biomembrane Systems.
Daniele Piomelli: Research in Dr. Piomelli's lab is focused on the function of lipid-derived messengers, with particular emphasis on the endogenous cannabinoids anandamide and 2-arachidonoylglycerol. Current research efforts converge on three areas: formation and inactivation of anandamide and 2-arachidonylglycerol; physiological roles of the endogenous cannabinoid system; development of therapeutic agents that target anandamide and 2-arachidonylglycerol metabolism.
Department of Microbiology & Molecular Genetics
Alan Goldin: The Goldin lab is studying two aspects concerning the role of voltage-gated sodium channels in normal and abnormal physiology in the central nervous system. First, they are examining the effects of mutations in sodium channels to determine how specific alterations in channel function result in disease in the CNS. They are using three approaches. First, they are studying the effects of spontaneous mutations in mice. For example, jolting results from a single amino acid change in a sodium channel expressed in the cerebellum, causing ataxia and involuntary movements. The second approach is to construct transgenic mice expressing sodium channels with well-defined mutations. They have expressed a channel with incomplete inactivation in the CNS of mice, which resulted in epilepsy and early mortality. The third approach is to identify candidate mutations in humans, and then examine the effects of those mutations by constructing transgenic mice. They are currently studying mutations that cause epilepsy in humans. The second area of research is to examine the roles of different sodium channel isoforms in the CNS. There are multiple different sodium channel isoforms, including at least four that are expressed in the CNS. These subtypes are localized in different regions of the CNS, and in different intracellular locations. The Goldin lab is studying the functional significance of those differences and the molecular mechanisms responsible for differential localization of the isoforms.
Department of Physics & Astronomy
Michael Dennin: Professor Dennin's interest is focused on the fundamental physics of driven systems. Many biological processes involve systems that are out of equilibrium, and this is a common feature of membrane-associated behavior in which active motion of molecules is necessary. Because of the focus on fundamental physics issues, Prof. Dennin works mostly with model membrane systems and their interactions with various proteins. As a model membrane, he uses Langmuir monolayers, a single layer of molecules at the air-water interface. His current research involves the interaction of annexins with spatial inhomogeneities in the monolayer and with the mechanical properties of monolayer-actin networks. By its very nature, this work is multidisciplinary, and the creation of a Center will greatly enhance the interactions across disciplines necessary for the continuation of this work.
Thorsten Ritz: Dr. Ritz's expertise is molecular dynamics modeling of ionic and water transport through biological channels and pores.
Zuzanna Siwy: Dr. Siwy focuses on studying fundamental physical and chemical processes that underlie functioning of biological channels with a special emphasize on calcium channels' selectivity. The lab prepares synthetic nanopores with tailored geometry and surface chemistry.
Department of Chemistry
Richard Chamberlin: Chemical synthesis is the central tool in the Chamberlin's lab general objective of controlling the biological activities of important target proteins, especially membrane receptors and phosphatases that modulate their activity, with new small molecule ligands. Current targets include ionotropic neurotransmitter (glutamate) receptors (iGluRs) and the serine-threonine phosphatases PP1 and PP2A. Employing ligand design in conjunction with combinatorial library synthesis, one goal is to develop sub-type selective ligands that will control the distinct functions of each iGluR sub-type. These studies may not only lead to a better understanding of such important processes as learning and memory, but also provide new details on mechanisms of brain damage in disorders such as stroke, epilepsy, and Alzheimer's disease. A second area of interest is the design and synthesis of small molecules that modulate the activity of the important serine-threonine protein phosphatases PP1 and PP2A, based on inhibitors such as the naturally occurring toxins okadaic acid, microcystin, and tautomycin.
Robert Corn: The Corn group research covers three main areas: surface chemistry, surface spectroscopy, and surface biochemistry as applied to biological surfaces and interfaces. Surface chemistry includes the development of robust attachment chemistries and microarray fabrication strategies for the formation of bioactive oligonucleotide (both DNA and RNA), polypeptide, protein, carbohydrate and phospholipid monolayers on metal, oxide and semiconductor surfaces. Surface spectroscopy includes the development and application of a variety of surface-sensitive spectroscopies to characterize condensed phase interfaces; for example, the lab routinely uses polarization modulation FTIR reflection-absorption spectroscopy (PM-FTIRRAS) to obtain the infrared vibrational spectra of monolayers at metal surfaces. Most recently, they have been using surface plasmon resonance imaging (SPR imaging) measurements to optically detect bioaffinity binding events onto chemically modified gold surfaces. Finally, their efforts in surface biochemistry center on the study of surface bioaffinity events and their coupling to surface enzymatic reactions and gold nanoparticles.
Craig Martens: The Martens group performs molecular dynamics simulation of water and aqueous solutions in nanoscale environments, and investigates non-equilibrium transport of water and ionic solutions through synthetic nanopores. The Martens group applies simulation and theory to exploiting biological principles in the design of nanotechnological devices for separation and rectified transport.
Rachel Martin: The Martin lab develops and uses solid-state NMR techniques to study locally ordered protein networks, including membrane proteins. In a solid-state NMR sample, samples of lipid and protein can be very close to native conditions, allowing control of factors such as lipid composition, ionic conditions, and hydration, without the additional constraints imposed on the sample by the requirements of X-ray crystallography or solution state NMR. One example of a system the Martin group is investigating is a novel class of defensin-like peptides (DLPs) from platypus venom whose biological function is currently unknown despite structural similarity in solution to known antimicrobial defensins. Many known defensins operate by pore formation or disruption of membranes. Determining structural information about defensins and related peptide toxins in membrane environments is a step toward understanding how subtle changes in amino acid sequence can produce very specific biological activities and may lead to the design of new antibacterial peptides.
Ken Shea: Dr. Shea's expertise is chemical organic synthesis and preparation of biomimetic structures and nanopores.
Doug Tobias: Dr. Tobias' expertise is molecular dynamics modeling of biological channels and protein-membrane complexes.
Christopher D. Vanderwal: Dr. Vanderwal's group is developing chemistry that will allow them to synthesize significant quantities of some naturally occurring polychlorinated sulfolipids, which make up a significant fraction of the membrane lipids of certain microalgae. These unusual lipids contain up to eleven chlorine atoms distributed along the length of an alkane chain of acetate origin. It is presumed that the capacity for certain species of algae to synthesize these membrane lipids has evolved to confer unique properties to their membrane structures. As these are only available from natural sources in minute quantities, a laboratory synthesis will allow for a full study of their solution conformations, as well as their membrane properties. These studies will be carried out in collaboration with our resident experts in NMR spectroscopy, as well as other groups associated with the UCI Center for Biomembrane Systems.
Department of Chemical Engineering & Materials Science
Regina Ragan: Dr. Ragan's research involves the exploration and development of novel material systems for nanoscale electronic and optoelectronic devices. One of the key issues in incorporating diverse materials in electronic and optoelectronic devices is to understand the material interfaces and how these affect electronic and/or optical properties. The effect of material interfaces is particularly important as we scale down to nanometer dimensions where the surface to volume ratio is high. Moreover, since the dimensions of devices will reach the dimensions of molecules, we strive to understand these interfaces at the atomic and molecular level. Dr. Ragan's research group uses self-assembly to fabricate one-dimensional and zero-dimensional organic/inorganic nanostructure arrays. The correlation of material interfaces with electron transport along the lateral axis of nanowires and transport through a molecule/metal nanowire junction is being studied to understand how these components will behave in nanoscale devices.
Szu Wang: Biology has been enormously successful in assembling very complex nanoscale systems, and the general strategy in Wang's laboratory leverages this ability by coupling nature-inspired macromolecular scaffolds with the tools of molecular biology and chemistry. Wang's group is currently investigating several areas that have technological relevance in pharmaceutics, tissue engineering, biosensors, and electronic and optical devices.
Department of Computer Science
Pierre Baldi: The Baldi research group develops and uses computational methods in chemoinformatics, bioinformatics, and systems biology to address problems in genomics, proteomics, and drug discovery. Examples of current projects include databases and expert systems for organic chemistry and drug discovery, for predicting protein structural properties, for mapping gene regulatory motifs on a genome-wide scale, and for large-scale molecular docking.