Walter Chazin, Ph.D.
Dr. Chazin received a B.Sc. in chemistry from McGill University in 1975 and a Ph.D. in chemistry from Concordia University in Montreal in 1983. He was a postdoctoral fellow in the lab of Kurt Wüthrich at the E.T.H. in Switzerland (2002 Nobel laureate in Chemistry). After 13 years on faculty in the Department of Molecular Biology at the Scripps Research Institute, he moved to Vanderbilt in 1999 where he holds the Chancellor’s Chair in Medicine as Professor in the Departments of Biochemistry and Chemistry, and serves as Director of the Center for Structural Biology and the Molecular Biophysics Training Program. He has mentored ~100 graduate students and postdocs and ~30 undergraduate students in his 29 years as an independent investigator. He has published over 200 peer reviewed papers and 50 book chapters and reviews, and serves on a number of advisory committees and editorial boards. His honors include American Cancer Society Junior Faculty and Faculty Research Awards, serving as a National Academy of Science International Travel Fellow and NAS Teaching Fellow, Regents Visiting Professor at the University of Naples in Italy, and appointments as a Fellow of the American Association for the Advancement of Science and Fellow of the Biophysical Society.
My background in NMR and chemistry frames the way I think, but the deciding factor for choosing problems is not the approach, but rather the biology and biochemistry. This requires a “whatever it takes” attitude in terms of approaches and generates the many collaborations (technical, biological, medical) that is a hallmark of our research. While trained in protein NMR, I have evolved into having a broad-based vision of structural biology/molecular biophysics that involves the complementary application of structural approaches, including spectroscopy, scattering, crystallography and microscopy. This means that although we focus on the medicine and biology, our problems sometimes require developing unique solutions. NMR remains the core approach, used mostly as a tool for characterization of structural interfaces and dynamics. X-ray crystallography is the method of choice for structure determination. Scattering provides the unique ability to study complex proteins and protein complexes, and we are rapidly adapting to the ‘electron microscopy revolution’ for these systems. With powerful structural information in hand, we are equipped to tackle in vitro and cell-based biochemistry and provide critical insights into the fundamental biology and medicine that drives our research.
As the lab manager, I develop laboratory guidelines, manage the day-to-day operations of the lab, and generate protein for various projects.
RAGE and calprotectin are proteins that have been identified as key components of cellular signaling and bacterial pathogenesis, respectively. I generate these proteins and others for structural and functional analysis by our lab and the labs of our collaborators.
Intracellular trafficking of the HIV-1 virus, a potential target for therapeutic treatment, is still poorly understood. In collaboration with the lab of Xinhong Dong at Meharry Medical College, we are investigating the role of filamin, an actin cross-linking protein, in the transport and organization of the HIV capsid. To do so, I am using a variety of structural and biochemical techniques to probe the specific interactions of this protein.
Remy Le Meur, Ph.D.
DNA replication and repair are fundamental biological mechanisms requiring the concerted action of a variety of proteins regulated in time and space. Replication Protein A (RPA) is the major single-stranded DNA binding protein, which both protects the sensitive single-stranded DNA and recruits replication and repair factors to the DNA. My current research in the Chazin lab focuses on understanding how RPA can regulate replication-associated Base Excision Repair (BER), especially through its interaction with NEIL1. I am also interested in studying the structure and function of RADX, a newly discovered RPA-related protein that is involved in genome stability.
Agnieszka Topolska-Wos, Ph.D.
Nucleotide-excision repair (NER), a biological mechanism for repairing DNA damage, is a potential target for developing more effective anticancer combination therapies. This incredibly complex process involves co-operation of more than 30 different proteins bound to a DNA damage site and maintains the integrity of our genome. Unfortunately, NER and its components are still not fully understood. My project is focused on unravelling the role of the XPA and RPA proteins in NER. To define the structural and molecular details of the XPA-RPA interaction, I am using an array of structural biology techniques in combination with molecular biology tools, such as confocal microscopy on patient-derived cell lines. This analysis will eventually be extended to other proteins in the NER machinery.
Natalia (Natasha) Kozlyuk, Ph.D.
The receptor for advanced glycation end products (RAGE) is a pattern recognition receptor associated with the inflammatory response via signaling through the NF-κB pathway. Surplus of RAGE activation has been shown to induce symptoms associated with chronic inflammation in diseases such as diabetes, arthritis and Alzheimer’s
disease. My research project consists of using SAR by NMR and a fragment-based drug design approach to generate small molecule inhibitors that block RAGE-ligand interactions. This will allow us to further dissect the mechanism of RAGE activation-induced inflammation.
Swati Balakrishnan, Ph.D.
The mammalian protein calprotectin, a calcium binding protein, is one of the ligands recognized by the pattern recognition receptor RAGE. This interaction leads to an up-regulation of several inflammation-inducing pathways and is linked to diseases including arthritis, cardiovascular disease and diabetes. My current focus is on studying the structural aspects of this interaction and its component proteins by integrating multiple structure elucidation techniques. I hope to gain a deeper understanding of RAGE-ligand interactions and insight into the design of potential RAGE inhibitors.
Certain pathogens have evolved to bypass the host defense mechanism, stealing the transition metals from calprotectin (CP) by either secreting small ultra-high affinity chelators or directly binding CP. To further investigate this mechanism and understand the host-pathogen struggle, I am working to create two powerful CP variants: one that has higher affinity for Zn (II) than the native protein and the other that binds Mn (II) but not Zn (II). These two reagents will enable us to define the molecular mechanism of zinc piracy and the characterization of the specific metal requirements of key human pathogens. To achieve this goal, I will use a protein engineering approach.
Pre-mRNA processing protein 40 (Prp40) is a modular protein that has an essential role in the initiation step of pre-mRNA splicing. This splicing factor is composed of two WW domains and six FF domains. Prp40 interacts with the calcium-binding protein centrin2 (Cen2). In addition, Prp40 has been reported to interact with calmodulin (CaM), another calcium-binding protein. Thus, the focus of my research project is to characterize calcium-dependent regulation of the activity of Prp40. The first goal of my project is to obtain a high-resolution structure of Cen2 in complex with the third FF domain of Prp40. The second goal is to validate the interaction between CaM and Prp40 and obtain a high-resolution structure of the complex. This may contribute to a better understanding of the mechanisms of action of calcium sensing proteins in modulating cellular protein machinery.
Somatic mutation of DNA damage repair genes is observed in approximately one-third of all human cancers, as surveyed by The Cancer Genome Atlas. These cancer-associated mutations can lead to DNA damage repair pathway dysfunction that ultimately contributes to genomic instability, tumor progression, and poor patient survival. Of interest to our laboratory, the nucleotide excision repair (NER) pathway repairs bulky DNA adducts formed by platinum-based chemotherapies. NER activity correlates with tumor response to platinum based chemotherapies and is a promising biomarker for the appropriate use of chemotherapeutic strategies. I use a combination of computational, in vivo, and structural techniques to investigate the mechanisms by which cancer-associated NER pathway mutations contribute to NER dysfunction in cancer. Ultimately, these studies will contribute to a broader understanding of NER functions as well as how cancer-associated mutations in NER disrupt normal activity and affect response to therapy.
The polymerase α-primase complex initiates synthesis of a new DNA strand during replication. The primase enzyme begins synthesis by polymerizing 7-12 ribonucleotides before pausing. This product is then transferred to the active site of polymerase α. I am using a variety of biophysical, structural, biochemical, and electrochemical techniques to probe the basis for this intramolecular transfer. This will provide a basis for understanding polymerase handoff during replication.
Calprotectin (CP) is an S100 protein that plays a role in the inflammatory response by acting as a ligand for the receptor for advanced glycation end-products (RAGE) and Toll-like receptor 4 (TLR-4). Activation of these receptors leads to upregulation of inflammatory cytokines, chemokines, and CP through the NF-κB pathway. As CP is secreted from the cell it serves as a ligand for these receptors creating a positive feedback loop. In the case of people with irritable bowel disease (IBD) these pathways are stimulated which leads to damage of the gastrointestinal tract and disease symptoms. The goal of my work is to block the interaction of CP with these inflammatory receptors by developing high affinity inhibitors of CP.
John (Johnny) Cordoba
The coordinated interaction of many proteins is required to faithfully replicate DNA. The synthesis of new DNA is initiated on unwound DNA by the polymerase α-primase complex, an enzyme complex unique in its ability to synthesize nucleotides de novo on a bare template. However, it is unclear how exactly pol α-primase gains access to single-stranded DNA that is tightly bound by RPA. I aim to elucidate the interaction of RPA and primase using biochemical and biophysical techniques in order to more fully understand how hand-off of the single-stranded template from RPA to primase occurs in the context of the greater replisome.
The receptor for advanced glycation end products (RAGE) is a multi-ligand pattern recognition receptor associated with the inflammatory response via signaling through the NF-κB pathway. The interactions between RAGE and its various ligands have been known to play a major role in the inflammation-related pathologies of many different chronic diseases. My project aims to develop a virtual screening approach to find small molecules that can bind at the interface between RAGE and its ligands in order to better study the mechanisms through which RAGE potentiates these chronic disease pathologies and to evaluate RAGE as a potential therapeutic target.
Arun Kumar Alphonse Ignatius
Christopher G. Bunick
Yue (Ryan) Gao
Nicholas P. George
Randal R Ketchem
Jens Chr. Madsen
Craig Vander Kooi