Structural Biology
Macromolecules underlie all biological processes and play either dynamic roles in catalysis or signaling or static roles in scaffolding or information storage. Knowing the structure of the proteins and nucleic acids involved in a particular biological process is key to understanding their biochemical function as well as their specificity and mechanism of action.
Research conducted by the investigators in the Structural Biology program is aimed at elucidating the structural basis for a variety of important biological processes, including signal transduction, membrane transport, microbial pathogenesis, neural development, intercellular interactions, and the regulation of gene expression. Among the methods being used to examine macromolecular structure are x-ray crystallography, electron microscopy, mass spectrometry, biochemical and genetic analysis, and computer-assisted structural modeling. In addition, high resolution ultrasound and magnetic resonance imaging methods are being developed to visualize mammalian organs in utero and after birth.
Administrative Assistants:
Rebecca Hawkins, Anne Ng
My laboratory is interested in the molecular mechanisms by which the
insulin receptor and other receptor tyrosine kinases (RTKs) are activated
upon ligand binding, and the structural basis for recruitment of
downstream signaling proteins to activated receptors. The main
experimental technique we employ for three-dimensional structure
determination is x-ray crystallography. Members of the RTK family
include, among others, the insulin and insulin-like growth factor-1 (IGF1)
receptors, fibroblast growth factor receptor, platelet-derived growth
factor receptor, and epidermal growth factor receptor. RTKs play critical
roles in signal transduction pathways that mediate cell proliferation,
differentiation, migration and metabolism, both in organismal development
and in adult homeostasis. RTKs have also been implicated in the onset or
progression of numerous cancers.
Our group aims to understand the molecular mechanisms of secondary
membrane transporter proteins using X-ray crystallography and
cryo-electron microscopy. Secondary active transporters use a solute
gradient to drive the translocation of ions, sugars, drugs, nucleosides,
amino acids, or neurotransmitters, across the membrane. Many of such
proteins are involved in the pathogenesis of diseases, and some are also
drug targets. For example, both Prozac and cocaine exercise their
effects by binding to secondary membrane transporters. Crystal
structures of such proteins will directly reveal the substrate-binding
site and the substrate-translocation pathway, and can suggest the
conformational changes required for the substrate translocation.
In the eukaryotic nucleus genomic DNA is hierarchically packaged by histone proteins into chromatin. The fundamental repeating unit of chromatin is the nucleosome, which is comprised of ~146 base pairs of DNA wrapped around an octamer of histones. Gene silencing factors such as Polycomb Repressive Complexes (PRC), the Silent Information Regulator (SIR) complex or Heterochromatin Protein 1 (HP1) specifically bind and organize nucleosomes to form higher-order, compacted chromatin structure. Epigenetic modifications of histones are known to regulate binding of these factors. Compaction of chromatin has been proposed to cause gene repression by creating a block to transcription processes. This compaction is crucial for establishment, maintenance and propagation of distinct patterns of gene expression. In higher eukaryotes, defective gene silencing can result in developmental defects, cellular transformation and malignant outgrowth.
Understanding how chromatin structure and genome architecture regulate gene expression is one of the most important, unexplained frontiers in biology. The goal of our laboratory is to understand the organization and dynamics of chromatin complexes important for the regulation of gene expression both at the genetic and epigenetic levels. We use a combination of structural approaches, including x-ray crystallography and electron microscopy, coupled with biophysical and biochemical experimentation to study mechanisms by which gene silencing complexes impact chromatin structure and repress transcription.
Molecular details of these complexes will be pivotal to understanding their biological function in both normal and disease states and will be central to the development of novel epigenetics-based therapeutics.
Post-transcriptional processes play a crucial role in controlling gene expression in all organisms. Our research is aimed at elucidating the molecular mechanisms by which such control is imposed. We are particularly interested in two important means by which genes are regulated post-transcriptionally: messenger RNA degradation and repression by microRNAs and siRNAs. The goal of our investigations is to identify and characterize the proteins, RNA elements, and molecular mechanisms that govern these key regulatory processes in bacterial and mammalian cells.
The main focus of our lab is the study of proteins and their roles in cellular signaling events. While great strides in understanding
intracellular signal transduction have been made in recent years by using molecular biological techniques, we feel that a more complete
understanding of the dynamics of intracellular decision-making processes can be gained only by studying the proteins directly. We use mass
spectrometry as the main tool for our studies because of the wide variety of information about protein structure it can provide while requiring
only small amounts of protein for analysis.
Our lab focuses on membrane transport by ATP-dependent ion pumps and
intercellular adhesion by cell-cell junctions. We use electron microscopy
to determine 3D structures of proteins involed in these processes. For
membrane transport, we use electron crystallography to study helical
assemblies of Ca-ATPase and its relatives in the family of P-type ATPases.
For intercellular adhesion, we use electron tomography to map the
molecular architecture of desmosomes and adherens junctions in
situ.
Extensive genetic information and new techniques to manipulate the
genome of the mouse have led to its widespread use for studying
development and modeling human diseases. In this rapid proliferation of
methods to genetically engineer mice, in vivo technologies to analyze
anatomical structure and function in the mouse have not kept pace. The
results of transgenic and gene targeting experiments are usually
analyzed using histological methods, which are static and
two-dimensional, making it difficult to understand the underlying
developmental and disease processes, which are dynamic and
three-dimensional. We are developing both ultrasound and magnetic
resonance micro-imaging approaches to provide noninvasive, dynamic
structural and functional data on developmental and disease processes in
mice.
